Updating workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4 from 0.3.5 to 0.3.6 #855

gxydevbot · 2025-05-19T04:23:41Z

Hello! This is an automated update of the following workflow: workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.5.1+galaxy2

The workflow release number has been updated from 0.3.5 to 0.3.6.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

…m 0.3.5 to 0.3.6

github-actions · 2025-05-19T04:33:36Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ Assembly-Hifi-HiC-phasing-VGP4.ga_0

Execution Problem:

Unexpected HTTP status code: 400: {"err_msg":"Workflow step has upgrade messages","err_code":0,"err_data":{"9":{"cols|xplot":"No value found for 'Column to plot on x-axis'.","cols|yplot":"No value found for 'Column to plot on y-axis'."}}}

github-actions · 2025-05-27T19:50:47Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Assembly-Hifi-HiC-phasing-VGP4.ga_0

Problems:

Output with path /tmp/tmp18rtvp8m/Nx Plot__154b94a9-db21-43c6-b72a-ff7c7b049cf8 different than expected
Expected file size of 65000+-10000 found 41415

Workflow invocation details

Invocation Messages

Steps

Step 1: Species Name:
- step_state: scheduled
Step 2: Assembly Name:
- step_state: scheduled
Step 11: Name for Haplotype 2:
- step_state: scheduled
Step 12: Bits for bloom filter:
- step_state: scheduled
Step 13: Homozygous Read Coverage:
- step_state: scheduled
Step 14: Genomescope Model Parameters:
- step_state: scheduled

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "Random Name", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 16: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "randName4", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 17: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmp9xnm653p/files/c/1/0/dataset_c10149ec-a666-4798-84da-abfc8436f54f.dat' 'yeast_reads_sub1_fastq_gz.fq.gz' &&  cutadapt  -j=${GALAXY_SLOTS:-4}   -b 'ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT'   -b 'ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT'    --error-rate=0.1 --times=1 --overlap=35    --action=trim --rc     --discard-trimmed   --minimum-length=1      --json=stats.json -o 'out1.fq.gz'  'yeast_reads_sub1_fastq_gz.fq.gz'  > report.txt

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
adapter_options	`{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "35", "revcomp": true, "times": "1"}`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"discard_casava": false, "discard_trimmed": true, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"}`
library	{"__current_case__": 0, "input_1": {"values": [{"id": 4, "src": "dce"}]}, "r1": {"adapters": [], "anywhere_adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}, {"__index__": 1, "adapter_source": {"__current_case__": 0, "adapter": "ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": false}], "front_adapters": []}, "type": "single"}
other_trimming_options	`{"cut": "0", "cut2": "0", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false}`
output_selector	`["report", "json_stats"]`
read_mod_options	`{"length_tag": "", "rename": "", "strip_suffix": "", "zero_cap": false}`

Step 18: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
adapter_options	`{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"}`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"}`
library	`{"__current_case__": 2, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired_collection"}`
other_trimming_options	`{"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false}`
output_selector	`None`
read_mod_options	`{"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false}`

Step 19: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -G -A 0 -B 0 --no-group-separator  -i -- 'Haploid' '/tmp/tmp9xnm653p/files/8/c/4/dataset_8c41cf92-7bf2-4a9c-a95f-f36cacd53762.dat' > '/tmp/tmp9xnm653p/job_working_directory/000/11/outputs/dataset_897f0d6a-1920-4556-a604-0a71ad24dbd2.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`""`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-G"`
url_paste	`"Haploid"`

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "vertebrata_odb10", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 3: Pacbio Reads:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 1, "default_value": "37", "param_type": "integer", "pick_from": [{"__index__": 0, "value": "32"}]}}`

Step 22: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types float,float,float,float,float,int  --file '/tmp/tmp9xnm653p/job_working_directory/000/14/configs/tmpqox8jtgc' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp9xnm653p/files/5/7/0/dataset_57057941-07df-4f8f-b765-07b4724c20bb.dat' '/tmp/tmp9xnm653p/job_working_directory/000/14/outputs/dataset_8b2f488a-d0ee-4d7d-abbf-92740a3946ba.dat'

Exit Code:

```
0
```

Standard Output:

c3*2
Computing 1 new columns with instructions ['c3*2;;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3*2"}], "header_lines_select": "no"}`

Step 23: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/cutadapt_0 &&     ln -s '/tmp/tmp9xnm653p/files/3/9/c/dataset_39cc3c1a-dae3-417f-89da-cba44a3d5bd0.dat' 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' && sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' && grep -q "This is cutadapt" 'multiqc_WDir/cutadapt_0/yeast_reads_sub1_fastq_gz.txt' || die "'This is cutadapt' or 'You are running cutadapt' not found in the file" &&    multiqc multiqc_WDir --filename 'report'       && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

Exit Code:

```
0
```

Standard Error:

/// MultiQC 🔍 v1.27

     version_check | MultiQC Version v1.29 now available!
       file_search | Search path: /tmp/tmp9xnm653p/job_working_directory/000/15/working/multiqc_WDir

          cutadapt | Found 1 reports

     write_results | Data        : report_data
     write_results | Report      : report.html
           multiqc | MultiQC complete

Standard Output:

total 80
-rw-r--r-- 1 1001 118    97 May 27 19:13 cutadapt_filtered_reads_plot.txt
-rw-r--r-- 1 1001 118    66 May 27 19:13 cutadapt_trimmed_sequences_plot_default_Counts.txt
-rw-r--r-- 1 1001 118    70 May 27 19:13 cutadapt_trimmed_sequences_plot_default_Obs_Exp.txt
-rw-r--r-- 1 1001 118   397 May 27 19:13 multiqc.log
-rw-r--r-- 1 1001 118   124 May 27 19:13 multiqc_citations.txt
-rw-r--r-- 1 1001 118   222 May 27 19:13 multiqc_cutadapt.txt
-rw-r--r-- 1 1001 118 44089 May 27 19:13 multiqc_data.json
-rw-r--r-- 1 1001 118    79 May 27 19:13 multiqc_general_stats.txt
-rw-r--r-- 1 1001 118    29 May 27 19:13 multiqc_software_versions.txt
-rw-r--r-- 1 1001 118   190 May 27 19:13 multiqc_sources.txt

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
comment	`""`
dbkey	`"?"`
export	`false`
flat	`false`
image_content_input	`None`
results	`[{"__index__": 0, "software_cond": {"__current_case__": 5, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "cutadapt"}}]`
title	`""`

Step 24: Pick forward 2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 9, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 2, "src": "dce"}]}}]}}`

Job 2:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 10, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 3, "src": "dce"}]}}]}}`

Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed -r --sandbox -e '' -e 's/bp//g' -e '' -e 's/,//g' -e '' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmp9xnm653p/files/8/9/7/dataset_897f0d6a-1920-4556-a604-0a71ad24dbd2.dat' > '/tmp/tmp9xnm653p/job_working_directory/000/18/outputs/dataset_51a53ace-40ed-4e3d-9237-a098ad20ccc4.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": "bp", "replace_pattern": "", "sed_options": null}, {"__index__": 1, "find_pattern": ",", "replace_pattern": "", "sed_options": null}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2", "sed_options": null}]`

Step 26: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp9xnm653p/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp9xnm653p/files/8/b/2/dataset_8b2f488a-d0ee-4d7d-abbf-92740a3946ba.dat' 'c7' T '/tmp/tmp9xnm653p/job_working_directory/000/19/outputs/dataset_b44e838b-6a3a-4705-bed1-94f5115c2ad1.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 27: __FILTER_EMPTY_DATASETS__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "6e3f44083b2e11f096ae7c1e52ec831e"
      
      input {"values": [{"id": 7, "src": "hdca"}]}

Step 28: Convert characters1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python /tmp/tmp9xnm653p/galaxy-dev/tools/filters/convert_characters.py --strip --condense /tmp/tmp9xnm653p/files/5/1/a/dataset_51a53ace-40ed-4e3d-9237-a098ad20ccc4.dat s /tmp/tmp9xnm653p/job_working_directory/000/20/outputs/dataset_c1516bf5-7eed-4daf-bbc8-ff4033e145e2.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
condense	`true`
convert_from	`"s"`
dbkey	`"?"`
strip	`true`

Step 29: Estimated homozygous read coverage:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 30: __UNZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "6e3f44083b2e11f096ae7c1e52ec831e"
      
      input {"values": [{"id": 16, "src": "dce"}]}
Step 4: Trim Hi-C reads?:
- step_state: scheduled

Step 31: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp9xnm653p/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp9xnm653p/files/c/1/5/dataset_c1516bf5-7eed-4daf-bbc8-ff4033e145e2.dat' 'c3' T '/tmp/tmp9xnm653p/job_working_directory/000/22/outputs/dataset_b087dcbf-0831-4a44-8d49-4d6d552e4e3a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 32: Homozygous read coverage for Hifiasm:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 1, "param_type": "integer", "pick_from": [{"__index__": 0, "value": null}, {"__index__": 1, "value": "21"}]}}`

Step 33: Collapse forward reads:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

(   cat "/tmp/tmp9xnm653p/files/5/1/c/dataset_51cd74fc-2f37-4f11-a73d-609ded019285.dat" ;   ) > /tmp/tmp9xnm653p/job_working_directory/000/26/outputs/dataset_c28ab94a-ef94-425d-adc3-b25d0a32c59c.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 34: Collapse reverse reads:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

(   cat "/tmp/tmp9xnm653p/files/5/f/8/dataset_5f8ed79c-9023-429e-a91b-84c7ab2a7c32.dat" ;   ) > /tmp/tmp9xnm653p/job_working_directory/000/27/outputs/dataset_cf8ee499-37c3-49d8-8b95-352e060ef4c5.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filename	`{"__current_case__": 1, "add_name": false}`
one_header	`false`

Step 35: Estimated genome size:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 36: Hifiasm:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp9xnm653p/files/6/c/0/dataset_6c0a90a8-6a63-4247-9194-e90129eaa64e.dat' input_0.fastq.gz &&  mkdir HiCF HiCR && ln -s '/tmp/tmp9xnm653p/files/c/2/8/dataset_c28ab94a-ef94-425d-adc3-b25d0a32c59c.dat' ./HiCF/input_0.fastqsanger.gz &&  ln -s '/tmp/tmp9xnm653p/files/c/f/8/dataset_cf8ee499-37c3-49d8-8b95-352e060ef4c5.dat' ./HiCR/input_0.fastqsanger.gz &&  hifiasm -t ${GALAXY_SLOTS:-1} -o output -f 32 -a 4 -z 0 -m 10000000 -p 100000 -n 3 -x 0.8 -y 0.2   --hom-cov 21  --h1 './HiCF/input_0.fastqsanger.gz' --h2 './HiCR/input_0.fastqsanger.gz' --l-msjoin 500000   --primary input_0.fastq.gz 2> output.log  && mkdir noseq_files && mv *.noseq.gfa noseq_files  && mkdir bin_files && mv *.bin bin_files

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastq.gz"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
advanced_options	`{"__current_case__": 0, "advanced_selector": "blank"}`
assembly_options	`{"__current_case__": 1, "adapter_length": "0", "assembly_selector": "set", "cleaning_rounds": "4", "disable_post_join": false, "hom_cov": "21", "ignore_error_corrected": false, "max_overlap": "0.8", "min_overlap": "0.2", "pop_contigs": "10000000", "pop_unitigs": "100000", "remove_tips": "3"}`
bins_out	`true`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_bits	`"32"`
hic_partition	`{"__current_case__": 1, "f_perturb": null, "h1": {"values": [{"id": 30, "src": "hda"}]}, "h2": {"values": [{"id": 31, "src": "hda"}]}, "hic_partition_selector": "set", "l_msjoin": "500000", "n_perturb": null, "n_weight": null, "seed": null}`
log_out	`true`
mode	`{"__current_case__": 0, "mode_selector": "standard", "reads": {"values": [{"id": 3, "src": "hdca"}]}}`
ont_integration	`{"__current_case__": 0, "ont_integration_selector": "blank"}`
purge_options	`{"__current_case__": 0, "purge_selector": "blank"}`
scaffolding_options	`{"__current_case__": 0, "scaffold_selector": "blank"}`

Step 37: Raw Unitig Image:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp9xnm653p/files/f/c/b/dataset_fcbc6382-99db-4993-847d-84381b4c410f.dat' input.gfa &&  export QT_QPA_PLATFORM='offscreen' && Bandage image input.gfa 'out.png' --height '2000' --nodewidth '25.0'

Exit Code:

```
0
```

Standard Error:

  File "/opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/threading.py", line 982, in run

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fontsize	`None`
height	`"2000"`
lengths	`false`
names	`false`
nodewidth	`"25.0"`
output_format	`"png"`
width	`None`

Step 38: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp9xnm653p/files/9/7/b/dataset_97b36e29-dbae-4f54-9126-463d0340a055.dat' 2288021 --nstar-report --locale en_US.UTF-8 --discover-paths --tabular > '/tmp/tmp9xnm653p/job_working_directory/000/31/outputs/dataset_aa788f52-6b76-4285-be44-46b0542c3668.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 39: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp9xnm653p/files/a/d/0/dataset_ad068132-0138-4e2a-b14e-bdb7c6b8df3b.dat' 2288021 --nstar-report --locale en_US.UTF-8 --discover-paths --tabular > '/tmp/tmp9xnm653p/job_working_directory/000/32/outputs/dataset_193fb03b-9102-460d-9dce-3fd8fdb09f5f.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": true, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 40: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp9xnm653p/files/9/7/b/dataset_97b36e29-dbae-4f54-9126-463d0340a055.dat' --out-size c  --discover-paths --tabular > '/tmp/tmp9xnm653p/job_working_directory/000/33/outputs/dataset_f969c7fd-93b5-4f82-a6aa-5b3a4b460625.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 5: Hi-C reads:
- step_state: scheduled

Step 41: gfastats gfa hap2 no sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp9xnm653p/files/9/7/b/dataset_97b36e29-dbae-4f54-9126-463d0340a055.dat' --discover-paths  -o dataset.gfa --no-sequence --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 51
Total scaffold length: 1351178
Average scaffold length: 26493.69
Scaffold N50: 23338
Scaffold auN: 40651.78
Scaffold L50: 16
Largest scaffold: 132684
Smallest scaffold: 16240
# contigs: 51
Total contig length: 1351178
Average contig length: 26493.69
Contig N50: 23338
Contig auN: 40651.78
Contig L50: 16
Largest contig: 132684
Smallest contig: 16240
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 409637:263447:265494:412600
GC content %: 39.15
# soft-masked bases: 0
# segments: 51
Total segment length: 1351178
Average segment length: 26493.69
# gaps: 0
# paths: 51

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "no_sequence": true, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 42: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp9xnm653p/files/a/d/0/dataset_ad068132-0138-4e2a-b14e-bdb7c6b8df3b.dat' --out-size c  --discover-paths --tabular > '/tmp/tmp9xnm653p/job_working_directory/000/35/outputs/dataset_6c94c97d-dfea-4b3a-bcd0-444bd4b227ea.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": true, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 43: gfastats gfa hap1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp9xnm653p/files/a/d/0/dataset_ad068132-0138-4e2a-b14e-bdb7c6b8df3b.dat' --discover-paths  -o dataset.gfa  --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 57
Total scaffold length: 1473565
Average scaffold length: 25852.02
Scaffold N50: 23819
Scaffold auN: 38682.45
Scaffold L50: 20
Largest scaffold: 132684
Smallest scaffold: 15406
# contigs: 57
Total contig length: 1473565
Average contig length: 25852.02
Contig N50: 23819
Contig auN: 38682.45
Contig L50: 20
Largest contig: 132684
Smallest contig: 15406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 448657:285670:288915:450323
GC content %: 38.99
# soft-masked bases: 0
# segments: 57
Total segment length: 1473565
Average segment length: 25852.02
# gaps: 0
# paths: 57
# edges: 4
Average degree: 0.07
# connected components: 1
Largest connected component length: 89366
# dead ends: 111
# disconnected components: 54
Total length disconnected components: 1384199
# separated components: 55
# bubbles: 0
# circular segments: 0
# circular paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "no_sequence": false, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 44: gfastats gfa hap2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp9xnm653p/files/9/7/b/dataset_97b36e29-dbae-4f54-9126-463d0340a055.dat' --discover-paths  -o dataset.gfa  --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 51
Total scaffold length: 1351178
Average scaffold length: 26493.69
Scaffold N50: 23338
Scaffold auN: 40651.78
Scaffold L50: 16
Largest scaffold: 132684
Smallest scaffold: 16240
# contigs: 51
Total contig length: 1351178
Average contig length: 26493.69
Contig N50: 23338
Contig auN: 40651.78
Contig L50: 16
Largest contig: 132684
Smallest contig: 16240
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 409637:263447:265494:412600
GC content %: 39.15
# soft-masked bases: 0
# segments: 51
Total segment length: 1351178
Average segment length: 26493.69
# gaps: 0
# paths: 51

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "no_sequence": false, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 45: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp9xnm653p/files/9/7/b/dataset_97b36e29-dbae-4f54-9126-463d0340a055.dat' --discover-paths  -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 51
Total scaffold length: 1351178
Average scaffold length: 26493.69
Scaffold N50: 23338
Scaffold auN: 40651.78
Scaffold L50: 16
Largest scaffold: 132684
Smallest scaffold: 16240
# contigs: 51
Total contig length: 1351178
Average contig length: 26493.69
Contig N50: 23338
Contig auN: 40651.78
Contig L50: 16
Largest contig: 132684
Smallest contig: 16240
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 409637:263447:265494:412600
GC content %: 39.15
# soft-masked bases: 0
# segments: 51
Total segment length: 1351178
Average segment length: 26493.69
# gaps: 0
# paths: 51

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 46: gfastats gfa hap1 no sequences:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp9xnm653p/files/a/d/0/dataset_ad068132-0138-4e2a-b14e-bdb7c6b8df3b.dat' --discover-paths  -o dataset.gfa --no-sequence --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 57
Total scaffold length: 1473565
Average scaffold length: 25852.02
Scaffold N50: 23819
Scaffold auN: 38682.45
Scaffold L50: 20
Largest scaffold: 132684
Smallest scaffold: 15406
# contigs: 57
Total contig length: 1473565
Average contig length: 25852.02
Contig N50: 23819
Contig auN: 38682.45
Contig L50: 20
Largest contig: 132684
Smallest contig: 15406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 448657:285670:288915:450323
GC content %: 38.99
# soft-masked bases: 0
# segments: 57
Total segment length: 1473565
Average segment length: 25852.02
# gaps: 0
# paths: 57
# edges: 4
Average degree: 0.07
# connected components: 1
Largest connected component length: 89366
# dead ends: 111
# disconnected components: 54
Total length disconnected components: 1384199
# separated components: 55
# bubbles: 0
# circular segments: 0
# circular paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "no_sequence": true, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 0, "terminal_overlaps_select": "no"}}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 47: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp9xnm653p/files/a/d/0/dataset_ad068132-0138-4e2a-b14e-bdb7c6b8df3b.dat' --discover-paths  -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 57
Total scaffold length: 1473565
Average scaffold length: 25852.02
Scaffold N50: 23819
Scaffold auN: 38682.45
Scaffold L50: 20
Largest scaffold: 132684
Smallest scaffold: 15406
# contigs: 57
Total contig length: 1473565
Average contig length: 25852.02
Contig N50: 23819
Contig auN: 38682.45
Contig L50: 20
Largest contig: 132684
Smallest contig: 15406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 448657:285670:288915:450323
GC content %: 38.99
# soft-masked bases: 0
# segments: 57
Total segment length: 1473565
Average segment length: 25852.02
# gaps: 0
# paths: 57
# edges: 4
Average degree: 0.07
# connected components: 1
Largest connected component length: 89366
# dead ends: 111
# disconnected components: 54
Total length disconnected components: 1384199
# separated components: 55
# bubbles: 0
# circular segments: 0
# circular paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": true, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 48: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp9xnm653p/job_working_directory/000/41/configs/tmpbgl4tz5e' '/tmp/tmp9xnm653p/files/a/a/7/dataset_aa788f52-6b76-4285-be44-46b0542c3668.dat' > '/tmp/tmp9xnm653p/job_working_directory/000/41/outputs/dataset_f7f21e7b-9b95-4c95-a3b2-28996720a4a2.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN{print \"Metric\\thap2\"}; {print}; "`
dbkey	`"?"`

Step 49: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp9xnm653p/job_working_directory/000/42/configs/tmpixz5qulq' '/tmp/tmp9xnm653p/files/1/9/3/dataset_193fb03b-9102-460d-9dce-3fd8fdb09f5f.dat' > '/tmp/tmp9xnm653p/job_working_directory/000/42/outputs/dataset_f275abde-4bd6-47dd-a90b-e4e2040c17c0.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN{print \"Metric\\thap1\"}; {print}; "`
dbkey	`"?"`

Step 50: Data Prep Hap2:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp9xnm653p/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmp9xnm653p/files/f/9/6/dataset_f969c7fd-93b5-4f82-a6aa-5b3a4b460625.dat' --output='/tmp/tmp9xnm653p/job_working_directory/000/43/outputs/dataset_9d489d42-a7d9-4215-8dbb-8a4d1b577d87.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6e3f44093b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp9xnm653p/job_working_directory/000/44/configs/tmpfzwpeyvm' '/tmp/tmp9xnm653p/files/9/d/4/dataset_9d489d42-a7d9-4215-8dbb-8a4d1b577d87.dat' > '/tmp/tmp9xnm653p/job_working_directory/000/44/outputs/dataset_331c5157-c9f1-40a9-acb8-cb829767225c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44093b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmp9xnm653p/files/3/3/1/dataset_331c5157-c9f1-40a9-acb8-cb829767225c.dat > '/tmp/tmp9xnm653p/job_working_directory/000/45/outputs/dataset_5a70c3bf-894e-4ad4-9cd1-bc866939596c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44093b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmp9xnm653p/files/3/3/1/dataset_331c5157-c9f1-40a9-acb8-cb829767225c.dat" "/tmp/tmp9xnm653p/job_working_directory/000/46/outputs/dataset_a20cd844-9dbd-4786-978b-92acfcec4a2e.dat" "1" "yes"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44093b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6e3f44093b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44093b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1351178", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmp9xnm653p/job_working_directory/000/71/configs/tmp7f066uf7' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp9xnm653p/files/a/2/0/dataset_a20cd844-9dbd-4786-978b-92acfcec4a2e.dat' '/tmp/tmp9xnm653p/job_working_directory/000/71/outputs/dataset_844b67c7-ee47-4483-80c3-215e62c362a0.dat'

Exit Code:

```
0
```

Standard Output:

c3/1351178
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1351178;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 51 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44093b2e11f096ae7c1e52ec831e"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1351178"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 6: Genomescope Summary:
- step_state: scheduled

Step 51: Data Prep Hap1:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp9xnm653p/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmp9xnm653p/files/6/c/9/dataset_6c94c97d-dfea-4b3a-bcd0-444bd4b227ea.dat' --output='/tmp/tmp9xnm653p/job_working_directory/000/48/outputs/dataset_d2f3587e-6125-4bfb-ab56-07b62508f07e.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6e3f440a3b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp9xnm653p/job_working_directory/000/49/configs/tmptw4dbvo9' '/tmp/tmp9xnm653p/files/d/2/f/dataset_d2f3587e-6125-4bfb-ab56-07b62508f07e.dat' > '/tmp/tmp9xnm653p/job_working_directory/000/49/outputs/dataset_84d55c46-e828-4455-a6bd-f514b8e475dc.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f440a3b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmp9xnm653p/files/8/4/d/dataset_84d55c46-e828-4455-a6bd-f514b8e475dc.dat > '/tmp/tmp9xnm653p/job_working_directory/000/50/outputs/dataset_6ca956f0-5e76-45a4-b87e-8ce86d9cbbb1.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f440a3b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmp9xnm653p/files/8/4/d/dataset_84d55c46-e828-4455-a6bd-f514b8e475dc.dat" "/tmp/tmp9xnm653p/job_working_directory/000/51/outputs/dataset_dc67364e-ebca-4ddf-9acb-b6df5cc0d2ec.dat" "1" "yes"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f440a3b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6e3f440a3b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f440a3b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1473565", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmp9xnm653p/job_working_directory/000/72/configs/tmpt0ljl2ix' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp9xnm653p/files/d/c/6/dataset_dc67364e-ebca-4ddf-9acb-b6df5cc0d2ec.dat' '/tmp/tmp9xnm653p/job_working_directory/000/72/outputs/dataset_f0859c88-231e-4445-b878-ec170e666a04.dat'

Exit Code:

```
0
```

Standard Output:

c3/1473565
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1473565;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 57 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f440a3b2e11f096ae7c1e52ec831e"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1473565"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 52: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed --sandbox -r -f '/tmp/tmp9xnm653p/job_working_directory/000/53/configs/tmp5b0t0yu2' '/tmp/tmp9xnm653p/files/3/0/c/dataset_30c197a4-f0ec-47b3-b6d8-6bcee6b82513.dat' > '/tmp/tmp9xnm653p/job_working_directory/000/53/outputs/dataset_1db011a6-91f8-4944-aa1d-2bcab65e1088.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/_path//g"`
dbkey	`"?"`

Step 53: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed --sandbox -r -f '/tmp/tmp9xnm653p/job_working_directory/000/54/configs/tmpdhl0imcm' '/tmp/tmp9xnm653p/files/9/c/f/dataset_9cfcf2e2-6e50-42d6-8b97-659580a2538e.dat' > '/tmp/tmp9xnm653p/job_working_directory/000/54/outputs/dataset_0a67bfca-e372-4499-9804-d46ccefa3c62.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/_path//g"`
dbkey	`"?"`

Step 54: join1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp9xnm653p/galaxy-dev/tools/filters/join.py' '/tmp/tmp9xnm653p/files/f/2/7/dataset_f275abde-4bd6-47dd-a90b-e4e2040c17c0.dat' '/tmp/tmp9xnm653p/files/f/7/f/dataset_f7f21e7b-9b95-4c95-a3b2-28996720a4a2.dat' 1 1 '/tmp/tmp9xnm653p/job_working_directory/000/55/outputs/dataset_e0301968-367d-40c7-853e-d96fdd1e6a1b.dat' -u -p --index_depth=3 --buffer=50000000 --fill_options_file=/tmp/tmp9xnm653p/job_working_directory/000/55/configs/tmphhgbmeuc

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
field1	`"1"`
field2	`"1"`
fill_empty_columns	`{"__current_case__": 1, "do_fill_empty_columns": {"__current_case__": 0, "column_fill_type": "single_fill_value", "fill_value": "."}, "fill_columns_by": "fill_unjoined_only", "fill_empty_columns_switch": "fill_empty"}`
header	`""`
partial	`"-p"`
unmatched	`"-u"`

Step 55: Plot Data:

step_state: scheduled

Subworkflow Steps

Step 1: Primary data:
- step_state: scheduled
Step 2: Alternate data:
- step_state: scheduled

Step 11: Size Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp9xnm653p/job_working_directory/000/79/configs/tmpqr3kwbxa' && Rscript '/tmp/tmp9xnm653p/job_working_directory/000/79/configs/tmpqr3kwbxa'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead. 
Warning message:
`aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp9xnm653p/files/9/d/9/dataset_9d968a67-81e3-4f11-a8b1-392a7d69fffd.dat', sep='\t')

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = aes(colour=factor(factor))

        gg_line = geom_line(size=1, alpha=1, gg_factor)

        color_scale = scale_color_brewer(palette='Set1', direction='1')

    names(input)[1] <- "factor"


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes_string(x=names(input)[1], y=names(input)[2])) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('Size Plot') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp9xnm653p/job_working_directory/000/79/outputs/dataset_0243b953-7ada-4720-90aa-306899cb7e37.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f440b3b2e11f096ae7c1e52ec831e"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cols	`{"__current_case__": 0, "header": "yes", "xplot": "1", "yplot": "2"}`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`"Size Plot"`
xlab	`"Scaffold number"`
ylab	`"Cumulative Size (Mb)"`

Step 3: Name of primary assembly:
- step_state: scheduled
Step 4: Name of alternate assembly:
- step_state: scheduled

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmp9xnm653p/files/f/0/8/dataset_f0859c88-231e-4445-b878-ec170e666a04.dat" "/tmp/tmp9xnm653p/job_working_directory/000/73/outputs/dataset_3f76cef9-bc4e-4fe2-9ffc-5d80e13e84f4.dat" "Hap1" "no"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f440b3b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Hap1"`
iterate	`"no"`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmp9xnm653p/files/8/4/4/dataset_844b67c7-ee47-4483-80c3-215e62c362a0.dat" "/tmp/tmp9xnm653p/job_working_directory/000/74/outputs/dataset_f166a1c3-5bb0-4fe6-b1aa-6701f11bc71b.dat" "Hap2" "no"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f440b3b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Hap2"`
iterate	`"no"`

Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp9xnm653p/files/3/f/7/dataset_3f76cef9-bc4e-4fe2-9ffc-5d80e13e84f4.dat' >> '/tmp/tmp9xnm653p/job_working_directory/000/75/outputs/dataset_58afff0d-316a-4b42-8741-371b2bb08b2f.dat' && cat '/tmp/tmp9xnm653p/files/f/1/6/dataset_f166a1c3-5bb0-4fe6-b1aa-6701f11bc71b.dat' >> '/tmp/tmp9xnm653p/job_working_directory/000/75/outputs/dataset_58afff0d-316a-4b42-8741-371b2bb08b2f.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f440b3b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 132, "src": "hda"}]}}]`

Step 8: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp9xnm653p/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp9xnm653p/files/5/8/a/dataset_58afff0d-316a-4b42-8741-371b2bb08b2f.dat' 'c8,c5,c6' T '/tmp/tmp9xnm653p/job_working_directory/000/76/outputs/dataset_484a16d4-69a7-408d-9330-dc59a63f5a5c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6e3f440b3b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8,c5,c6"`
dbkey	`"?"`
delimiter	`"T"`

Step 9: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp9xnm653p/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp9xnm653p/files/5/8/a/dataset_58afff0d-316a-4b42-8741-371b2bb08b2f.dat' 'c8,c4,c7' T '/tmp/tmp9xnm653p/job_working_directory/000/77/outputs/dataset_9d968a67-81e3-4f11-a8b1-392a7d69fffd.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6e3f440b3b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8,c4,c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 10: Nx Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp9xnm653p/job_working_directory/000/78/configs/tmpdygklbmn' && Rscript '/tmp/tmp9xnm653p/job_working_directory/000/78/configs/tmpdygklbmn'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead. 
Warning message:
`aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp9xnm653p/files/4/8/4/dataset_484a16d4-69a7-408d-9330-dc59a63f5a5c.dat', sep='\t')

names(input)[1] <- "xcol"
names(input)[2] <- "ycol"

    gg_facet = NULL
    gg_factor = aes(colour=factor(factor))

        gg_line = geom_line(size=1, alpha=1, gg_factor)

        color_scale = scale_color_brewer(palette='Set1', direction='1')

    names(input)[1] <- "factor"


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes_string(x=names(input)[1], y=names(input)[2])) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('Nx Plot') + xlab('x') + ylab('Nx (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp9xnm653p/job_working_directory/000/78/outputs/dataset_154b94a9-db21-43c6-b72a-ff7c7b049cf8.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f440b3b2e11f096ae7c1e52ec831e"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cols	`{"__current_case__": 0, "header": "yes", "xplot": "1", "yplot": "2"}`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`"Nx Plot"`
xlab	`"x"`
ylab	`"Nx (Mb)"`

Step 56: Busco Hap2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp9xnm653p/files/1/d/b/dataset_1db011a6-91f8-4944-aa1d-2bcab65e1088.dat' input.fa &&  busco --in 'input.fa' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --offline --download_path '/cvmfs/data.galaxyproject.org/byhand/busco/v5'  --lineage_dataset 'vertebrata_odb10'  --metaeuk  && mkdir BUSCO_summaries && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true)

Exit Code:

```
0
```

Standard Error:

2025-05-27 19:44:12 ERROR:	
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2025-05-27 19:19:49 INFO:	***** Start a BUSCO v5.8.0 analysis, current time: 05/27/2025 19:19:49 *****
2025-05-27 19:19:49 INFO:	Configuring BUSCO with local environment
2025-05-27 19:19:49 INFO:	Running genome mode
2025-05-27 19:19:49 INFO:	Input file is /tmp/tmp9xnm653p/job_working_directory/000/56/working/input.fa
2025-05-27 19:19:49 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_met
2025-05-27 19:19:49 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_met
2025-05-27 19:19:50 INFO:	Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2021-02-19)
2025-05-27 19:19:50 INFO:	Running 1 job(s) on bbtools, starting at 05/27/2025 19:19:50
2025-05-27 19:19:51 INFO:	[bbtools]	1 of 1 task(s) completed
2025-05-27 19:19:51 WARNING:	Unable to remove compressed refseq file in dataset download
2025-05-27 19:19:51 INFO:	Running 1 job(s) on metaeuk, starting at 05/27/2025 19:19:51
2025-05-27 19:26:51 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-05-27 19:26:51 INFO:	***** Run HMMER on gene sequences *****
2025-05-27 19:26:51 INFO:	Running 3354 job(s) on hmmsearch, starting at 05/27/2025 19:26:51
2025-05-27 19:27:13 INFO:	[hmmsearch]	336 of 3354 task(s) completed
2025-05-27 19:27:31 INFO:	[hmmsearch]	671 of 3354 task(s) completed
2025-05-27 19:27:47 INFO:	[hmmsearch]	1007 of 3354 task(s) completed
2025-05-27 19:28:04 INFO:	[hmmsearch]	1342 of 3354 task(s) completed
2025-05-27 19:28:19 INFO:	[hmmsearch]	1677 of 3354 task(s) completed
2025-05-27 19:28:31 INFO:	[hmmsearch]	2013 of 3354 task(s) completed
2025-05-27 19:28:42 INFO:	[hmmsearch]	2348 of 3354 task(s) completed
2025-05-27 19:28:53 INFO:	[hmmsearch]	2684 of 3354 task(s) completed
2025-05-27 19:29:06 INFO:	[hmmsearch]	3019 of 3354 task(s) completed
2025-05-27 19:29:22 INFO:	[hmmsearch]	3354 of 3354 task(s) completed
2025-05-27 19:29:23 INFO:	33 exons in total
2025-05-27 19:29:23 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2025-05-27 19:33:03 INFO:	Running 1 job(s) on metaeuk, starting at 05/27/2025 19:33:03
2025-05-27 19:42:50 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-05-27 19:42:50 INFO:	***** Run HMMER on gene sequences *****
2025-05-27 19:42:50 INFO:	Running 3332 job(s) on hmmsearch, starting at 05/27/2025 19:42:50
2025-05-27 19:43:00 INFO:	[hmmsearch]	334 of 3332 task(s) completed
2025-05-27 19:43:08 INFO:	[hmmsearch]	667 of 3332 task(s) completed
2025-05-27 19:43:15 INFO:	[hmmsearch]	1000 of 3332 task(s) completed
2025-05-27 19:43:22 INFO:	[hmmsearch]	1333 of 3332 task(s) completed
2025-05-27 19:43:29 INFO:	[hmmsearch]	1666 of 3332 task(s) completed
2025-05-27 19:43:37 INFO:	[hmmsearch]	2000 of 3332 task(s) completed
2025-05-27 19:43:44 INFO:	[hmmsearch]	2333 of 3332 task(s) completed
2025-05-27 19:43:51 INFO:	[hmmsearch]	2666 of 3332 task(s) completed
2025-05-27 19:43:59 INFO:	[hmmsearch]	2999 of 3332 task(s) completed
2025-05-27 19:44:05 INFO:	[hmmsearch]	3332 of 3332 task(s) completed
2025-05-27 19:44:06 INFO:	1 candidate overlapping regions found
2025-05-27 19:44:06 INFO:	34 exons in total
2025-05-27 19:44:06 INFO:	Results:	C:0.7%[S:0.6%,D:0.0%],F:0.3%,M:99.0%,n:3354	   

2025-05-27 19:44:07 INFO:	

    ---------------------------------------------------
    |Results from dataset vertebrata_odb10             |
    ---------------------------------------------------
    |C:0.7%[S:0.6%,D:0.0%],F:0.3%,M:99.0%,n:3354       |
    |22    Complete BUSCOs (C)                         |
    |21    Complete and single-copy BUSCOs (S)         |
    |1    Complete and duplicated BUSCOs (D)           |
    |10    Fragmented BUSCOs (F)                       |
    |3322    Missing BUSCOs (M)                        |
    |3354    Total BUSCO groups searched               |
    ---------------------------------------------------
2025-05-27 19:44:07 INFO:	BUSCO analysis done with WARNING(s). Total running time: 1457 seconds

***** Summary of warnings: *****
2025-05-27 19:19:49 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_genome_met
2025-05-27 19:19:49 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_genome_met
2025-05-27 19:19:51 WARNING:busco.busco_tools.base	Unable to remove compressed refseq file in dataset download

2025-05-27 19:44:07 INFO:	Results written in /tmp/tmp9xnm653p/job_working_directory/000/56/working/busco_galaxy
2025-05-27 19:44:07 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-05-27 19:44:07 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
2025-05-27 19:44:08 INFO:	****************** Start plot generation at 05/27/2025 19:44:08 ******************
2025-05-27 19:44:08 INFO:	Load data ...
2025-05-27 19:44:08 INFO:	Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully
2025-05-27 19:44:08 INFO:	Generate the R code ...
2025-05-27 19:44:08 INFO:	Run the R code ...
2025-05-27 19:44:12 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-05-27 19:44:12 INFO:	Plot generation done. Total running time: 4.129370450973511 seconds
2025-05-27 19:44:12 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "metaeuk"}}`
cached_db	`"v5"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}`
outputs	`["short_summary", "missing", "image", "gff"]`
test	`None`

Step 57: Busco Hap1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp9xnm653p/files/0/a/6/dataset_0a67bfca-e372-4499-9804-d46ccefa3c62.dat' input.fa &&  busco --in 'input.fa' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --offline --download_path '/cvmfs/data.galaxyproject.org/byhand/busco/v5'  --lineage_dataset 'vertebrata_odb10'  --metaeuk  && mkdir BUSCO_summaries && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true)

Exit Code:

```
0
```

Standard Error:

2025-05-27 19:44:22 ERROR:	
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2025-05-27 19:19:49 INFO:	***** Start a BUSCO v5.8.0 analysis, current time: 05/27/2025 19:19:49 *****
2025-05-27 19:19:49 INFO:	Configuring BUSCO with local environment
2025-05-27 19:19:49 INFO:	Running genome mode
2025-05-27 19:19:49 INFO:	Input file is /tmp/tmp9xnm653p/job_working_directory/000/57/working/input.fa
2025-05-27 19:19:49 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_met
2025-05-27 19:19:49 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_met
2025-05-27 19:19:50 INFO:	Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2021-02-19)
2025-05-27 19:19:50 INFO:	Running 1 job(s) on bbtools, starting at 05/27/2025 19:19:50
2025-05-27 19:19:51 INFO:	[bbtools]	1 of 1 task(s) completed
2025-05-27 19:19:51 WARNING:	Unable to remove compressed refseq file in dataset download
2025-05-27 19:19:51 INFO:	Running 1 job(s) on metaeuk, starting at 05/27/2025 19:19:51
2025-05-27 19:27:02 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-05-27 19:27:02 INFO:	***** Run HMMER on gene sequences *****
2025-05-27 19:27:02 INFO:	Running 3354 job(s) on hmmsearch, starting at 05/27/2025 19:27:02
2025-05-27 19:27:13 INFO:	[hmmsearch]	336 of 3354 task(s) completed
2025-05-27 19:27:31 INFO:	[hmmsearch]	671 of 3354 task(s) completed
2025-05-27 19:27:47 INFO:	[hmmsearch]	1007 of 3354 task(s) completed
2025-05-27 19:28:04 INFO:	[hmmsearch]	1342 of 3354 task(s) completed
2025-05-27 19:28:19 INFO:	[hmmsearch]	1677 of 3354 task(s) completed
2025-05-27 19:28:31 INFO:	[hmmsearch]	2013 of 3354 task(s) completed
2025-05-27 19:28:42 INFO:	[hmmsearch]	2348 of 3354 task(s) completed
2025-05-27 19:28:53 INFO:	[hmmsearch]	2684 of 3354 task(s) completed
2025-05-27 19:29:06 INFO:	[hmmsearch]	3019 of 3354 task(s) completed
2025-05-27 19:29:22 INFO:	[hmmsearch]	3354 of 3354 task(s) completed
2025-05-27 19:29:23 INFO:	42 exons in total
2025-05-27 19:29:23 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2025-05-27 19:33:02 INFO:	Running 1 job(s) on metaeuk, starting at 05/27/2025 19:33:02
2025-05-27 19:43:12 INFO:	[metaeuk]	1 of 1 task(s) completed
2025-05-27 19:43:12 INFO:	***** Run HMMER on gene sequences *****
2025-05-27 19:43:12 INFO:	Running 3326 job(s) on hmmsearch, starting at 05/27/2025 19:43:12
2025-05-27 19:43:19 INFO:	[hmmsearch]	333 of 3326 task(s) completed
2025-05-27 19:43:26 INFO:	[hmmsearch]	666 of 3326 task(s) completed
2025-05-27 19:43:32 INFO:	[hmmsearch]	998 of 3326 task(s) completed
2025-05-27 19:43:38 INFO:	[hmmsearch]	1331 of 3326 task(s) completed
2025-05-27 19:43:44 INFO:	[hmmsearch]	1664 of 3326 task(s) completed
2025-05-27 19:43:51 INFO:	[hmmsearch]	1996 of 3326 task(s) completed
2025-05-27 19:43:58 INFO:	[hmmsearch]	2329 of 3326 task(s) completed
2025-05-27 19:44:04 INFO:	[hmmsearch]	2661 of 3326 task(s) completed
2025-05-27 19:44:10 INFO:	[hmmsearch]	2994 of 3326 task(s) completed
2025-05-27 19:44:17 INFO:	[hmmsearch]	3326 of 3326 task(s) completed
2025-05-27 19:44:18 INFO:	4 candidate overlapping regions found
2025-05-27 19:44:18 INFO:	47 exons in total
2025-05-27 19:44:18 INFO:	Results:	C:0.8%[S:0.8%,D:0.0%],F:0.3%,M:98.9%,n:3354	   

2025-05-27 19:44:18 INFO:	

    ---------------------------------------------------
    |Results from dataset vertebrata_odb10             |
    ---------------------------------------------------
    |C:0.8%[S:0.8%,D:0.0%],F:0.3%,M:98.9%,n:3354       |
    |28    Complete BUSCOs (C)                         |
    |27    Complete and single-copy BUSCOs (S)         |
    |1    Complete and duplicated BUSCOs (D)           |
    |10    Fragmented BUSCOs (F)                       |
    |3316    Missing BUSCOs (M)                        |
    |3354    Total BUSCO groups searched               |
    ---------------------------------------------------
2025-05-27 19:44:18 INFO:	BUSCO analysis done with WARNING(s). Total running time: 1469 seconds

***** Summary of warnings: *****
2025-05-27 19:19:49 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_genome_met
2025-05-27 19:19:49 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_genome_met
2025-05-27 19:19:51 WARNING:busco.busco_tools.base	Unable to remove compressed refseq file in dataset download

2025-05-27 19:44:18 INFO:	Results written in /tmp/tmp9xnm653p/job_working_directory/000/57/working/busco_galaxy
2025-05-27 19:44:18 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2025-05-27 19:44:18 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
2025-05-27 19:44:19 INFO:	****************** Start plot generation at 05/27/2025 19:44:19 ******************
2025-05-27 19:44:19 INFO:	Load data ...
2025-05-27 19:44:19 INFO:	Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully
2025-05-27 19:44:19 INFO:	Generate the R code ...
2025-05-27 19:44:19 INFO:	Run the R code ...
2025-05-27 19:44:22 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2025-05-27 19:44:23 INFO:	Plot generation done. Total running time: 3.498497486114502 seconds
2025-05-27 19:44:23 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "metaeuk"}}`
cached_db	`"v5"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}`
outputs	`["short_summary", "missing", "image", "gff"]`
test	`None`

Step 58: Merqury:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p output_files && mkdir -p read-db.meryl && tar -zxf /tmp/tmp9xnm653p/files/b/a/8/dataset_ba83bf97-1f1a-4f72-b2da-8fd57168c9ca.dat -C read-db.meryl --strip-components=1 && ln -s '/tmp/tmp9xnm653p/files/0/a/6/dataset_0a67bfca-e372-4499-9804-d46ccefa3c62.dat' assembly_01.fasta && ln -s '/tmp/tmp9xnm653p/files/1/d/b/dataset_1db011a6-91f8-4944-aa1d-2bcab65e1088.dat' assembly_02.fasta && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta output_merqury &> /tmp/tmp9xnm653p/job_working_directory/000/58/outputs/dataset_57c87d6a-4aee-4fd8-acfe-3e990145c7cb.dat && mv output_merqury* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files  && sed -i '1s/^/assembly\tk-mer set\tsolid k-mers in assembly\tsolid k-mers in reads\tcompleteness %\n/' 'output_files/output_merqury.completeness.stats' && sed -i '1s/^/assembly\tunique k-mers\tcommon k-mers\tQV\terror rate\n/' 'output_files/output_merqury.qv'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
label	`"output_merqury"`
mode	`{"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 63, "src": "hda"}]}, "assembly_02": {"values": [{"id": 62, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 5, "src": "hda"}]}, "options": "default"}`
output_add_headers	`true`
output_selector	`["qv", "plots", "stats", "log", "hist"]`

Step 59: Compleasm Hap1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p 'galaxy_db/' && ln -s '/cvmfs/data.galaxyproject.org/byhand/busco/v5/lineages/vertebrata_odb10/' 'galaxy_db/vertebrata_odb10' && touch 'galaxy_db/vertebrata_odb10.done' &&  compleasm run -a '/tmp/tmp9xnm653p/files/0/a/6/dataset_0a67bfca-e372-4499-9804-d46ccefa3c62.dat' -o galaxy_output --mode busco -L 'galaxy_db' -l 'vertebrata_odb10' -t "${GALAXY_SLOTS:-1}"

Exit Code:

```
0
```

Standard Error:

[M::[email protected]*1.26] read 1473565 bases in 57 contigs
[M::[email protected]*1.14] 11572 blocks
[M::[email protected]*0.78] collected syncmers
[M::[email protected]*0.81] 677833 kmer-block pairs
[M::mp_mapopt_set_max_intron] set max intron size to 10000
[M::mp_idx_print_stat] 322886 distinct k-mers; mean occ of infrequent k-mers: 2.10; 0 frequent k-mers accounting for 0 occurrences
[M::worker_pipeline::5.848*0.90] mapped 3408 sequences
[M::worker_pipeline::10.465*0.94] mapped 3404 sequences
[M::worker_pipeline::14.923*0.95] mapped 3357 sequences
[M::worker_pipeline::19.501*0.96] mapped 3488 sequences
[M::worker_pipeline::23.926*0.97] mapped 3573 sequences
[M::worker_pipeline::28.436*0.97] mapped 3161 sequences
[M::worker_pipeline::32.939*0.98] mapped 3178 sequences
[M::worker_pipeline::36.954*0.98] mapped 3277 sequences
[M::worker_pipeline::40.882*0.98] mapped 3290 sequences
[M::worker_pipeline::44.835*0.98] mapped 3415 sequences
[M::worker_pipeline::48.656*0.98] mapped 3273 sequences
[M::worker_pipeline::52.879*0.98] mapped 3297 sequences
[M::worker_pipeline::58.286*0.98] mapped 3366 sequences
[M::worker_pipeline::64.455*0.97] mapped 3526 sequences
[M::worker_pipeline::71.370*0.95] mapped 3363 sequences
[M::worker_pipeline::77.825*0.94] mapped 3386 sequences
[M::worker_pipeline::83.786*0.94] mapped 3472 sequences
[M::worker_pipeline::89.946*0.93] mapped 3375 sequences
[M::worker_pipeline::96.577*0.92] mapped 3337 sequences
[M::worker_pipeline::102.709*0.92] mapped 3452 sequences
[M::worker_pipeline::108.736*0.91] mapped 3598 sequences
[M::worker_pipeline::115.175*0.91] mapped 3363 sequences
[M::worker_pipeline::122.036*0.91] mapped 3385 sequences
[M::worker_pipeline::129.128*0.90] mapped 3335 sequences
[M::worker_pipeline::135.421*0.90] mapped 3434 sequences
[M::worker_pipeline::142.083*0.90] mapped 3323 sequences
[M::worker_pipeline::148.242*0.90] mapped 3415 sequences
[M::worker_pipeline::155.168*0.89] mapped 3310 sequences
[M::worker_pipeline::161.896*0.89] mapped 3376 sequences
[M::worker_pipeline::168.576*0.89] mapped 3489 sequences
[M::worker_pipeline::175.324*0.89] mapped 3313 sequences
[M::worker_pipeline::182.210*0.88] mapped 3450 sequences
[M::worker_pipeline::188.427*0.88] mapped 3456 sequences
[M::worker_pipeline::194.892*0.88] mapped 3301 sequences
[M::worker_pipeline::201.365*0.88] mapped 3463 sequences
[M::worker_pipeline::206.922*0.88] mapped 3439 sequences
[M::worker_pipeline::213.049*0.88] mapped 3267 sequences
[M::worker_pipeline::219.076*0.87] mapped 3484 sequences
[M::worker_pipeline::225.305*0.87] mapped 3767 sequences
[M::worker_pipeline::231.629*0.87] mapped 3506 sequences
[M::worker_pipeline::237.645*0.87] mapped 3561 sequences
[M::worker_pipeline::244.547*0.87] mapped 3335 sequences
[M::worker_pipeline::250.088*0.87] mapped 3436 sequences
[M::worker_pipeline::255.869*0.87] mapped 3410 sequences
[M::worker_pipeline::262.133*0.87] mapped 3504 sequences
[M::worker_pipeline::267.966*0.87] mapped 3821 sequences
[M::worker_pipeline::274.587*0.86] mapped 3426 sequences
[M::worker_pipeline::280.575*0.86] mapped 3341 sequences
[M::worker_pipeline::287.270*0.86] mapped 3484 sequences
[M::worker_pipeline::293.870*0.86] mapped 3276 sequences
[M::worker_pipeline::300.380*0.86] mapped 3314 sequences
[M::worker_pipeline::306.653*0.86] mapped 3277 sequences
[M::worker_pipeline::312.775*0.86] mapped 3697 sequences
[M::worker_pipeline::319.509*0.86] mapped 3334 sequences
[M::worker_pipeline::325.959*0.86] mapped 3323 sequences
[M::worker_pipeline::331.879*0.86] mapped 3927 sequences
[M::worker_pipeline::338.449*0.86] mapped 3655 sequences
[M::worker_pipeline::345.216*0.86] mapped 3385 sequences
[M::worker_pipeline::351.687*0.86] mapped 3395 sequences
[M::worker_pipeline::357.687*0.86] mapped 3382 sequences
[M::worker_pipeline::363.844*0.86] mapped 3341 sequences
[M::worker_pipeline::369.755*0.86] mapped 3366 sequences
[M::worker_pipeline::375.718*0.86] mapped 3334 sequences
[M::worker_pipeline::382.544*0.86] mapped 3281 sequences
[M::worker_pipeline::389.063*0.86] mapped 3362 sequences
[M::worker_pipeline::395.011*0.86] mapped 3686 sequences
[M::worker_pipeline::401.227*0.86] mapped 3406 sequences
[M::worker_pipeline::407.525*0.86] mapped 3262 sequences
[M::worker_pipeline::413.964*0.86] mapped 3312 sequences
[M::worker_pipeline::420.370*0.86] mapped 3308 sequences
[M::worker_pipeline::427.039*0.86] mapped 3392 sequences
[M::worker_pipeline::433.242*0.86] mapped 3346 sequences
[M::worker_pipeline::438.922*0.86] mapped 3408 sequences
[M::worker_pipeline::443.722*0.86] mapped 3200 sequences
[M::worker_pipeline::448.855*0.86] mapped 3425 sequences
[M::worker_pipeline::453.297*0.87] mapped 3425 sequences
[M::worker_pipeline::458.105*0.87] mapped 3367 sequences
[M::worker_pipeline::462.946*0.87] mapped 3464 sequences
[M::worker_pipeline::467.526*0.87] mapped 3250 sequences
[M::worker_pipeline::472.146*0.87] mapped 3312 sequences
[M::worker_pipeline::477.076*0.87] mapped 3806 sequences
[M::worker_pipeline::482.173*0.87] mapped 3475 sequences
[M::worker_pipeline::486.997*0.87] mapped 3685 sequences
[M::worker_pipeline::492.111*0.87] mapped 3335 sequences
[M::worker_pipeline::497.387*0.88] mapped 3353 sequences
[M::worker_pipeline::502.425*0.88] mapped 3356 sequences
[M::worker_pipeline::507.348*0.88] mapped 3291 sequences
[M::worker_pipeline::512.265*0.88] mapped 3309 sequences
[M::worker_pipeline::517.613*0.88] mapped 3204 sequences
[M::worker_pipeline::522.325*0.88] mapped 3319 sequences
[M::worker_pipeline::526.972*0.88] mapped 3381 sequences
[M::worker_pipeline::532.029*0.88] mapped 3312 sequences
[M::worker_pipeline::536.807*0.88] mapped 3247 sequences
[M::worker_pipeline::541.621*0.88] mapped 3342 sequences
[M::worker_pipeline::546.975*0.88] mapped 3305 sequences
[M::worker_pipeline::552.041*0.89] mapped 3425 sequences
[M::worker_pipeline::557.243*0.89] mapped 3646 sequences
[M::worker_pipeline::562.745*0.89] mapped 3250 sequences
[M::worker_pipeline::567.866*0.89] mapped 3404 sequences
[M::worker_pipeline::573.422*0.89] mapped 3324 sequences
[M::worker_pipeline::579.755*0.89] mapped 3530 sequences
[M::worker_pipeline::586.450*0.89] mapped 3330 sequences
[M::worker_pipeline::593.579*0.89] mapped 3432 sequences
[M::worker_pipeline::599.658*0.89] mapped 3830 sequences
[M::worker_pipeline::606.316*0.89] mapped 3937 sequences
[M::worker_pipeline::612.944*0.89] mapped 3391 sequences
[M::worker_pipeline::620.459*0.88] mapped 3562 sequences
[M::worker_pipeline::627.167*0.88] mapped 3605 sequences
[M::worker_pipeline::633.640*0.88] mapped 3897 sequences
[M::worker_pipeline::639.705*0.88] mapped 4068 sequences
[M::worker_pipeline::645.974*0.88] mapped 3511 sequences
[M::worker_pipeline::652.680*0.88] mapped 3324 sequences
[M::worker_pipeline::658.424*0.88] mapped 3395 sequences
[M::worker_pipeline::664.700*0.88] mapped 3394 sequences
[M::worker_pipeline::671.159*0.88] mapped 3273 sequences
[M::worker_pipeline::677.630*0.88] mapped 3211 sequences
[M::worker_pipeline::683.530*0.88] mapped 3338 sequences
[M::worker_pipeline::689.742*0.88] mapped 3208 sequences
[M::worker_pipeline::695.843*0.88] mapped 3294 sequences
[M::worker_pipeline::701.877*0.88] mapped 3415 sequences
[M::worker_pipeline::708.515*0.88] mapped 3446 sequences
[M::worker_pipeline::714.881*0.88] mapped 3498 sequences
[M::worker_pipeline::721.686*0.88] mapped 3417 sequences
[M::worker_pipeline::728.721*0.88] mapped 3417 sequences
[M::worker_pipeline::734.985*0.88] mapped 3328 sequences
[M::worker_pipeline::741.765*0.88] mapped 3448 sequences
[M::worker_pipeline::748.576*0.88] mapped 3569 sequences
[M::worker_pipeline::754.175*0.88] mapped 4045 sequences
[M::worker_pipeline::760.784*0.88] mapped 3258 sequences
[M::worker_pipeline::767.552*0.88] mapped 3320 sequences
[M::worker_pipeline::774.321*0.88] mapped 3321 sequences
[M::worker_pipeline::780.745*0.88] mapped 3223 sequences
[M::worker_pipeline::787.681*0.88] mapped 3193 sequences
[M::worker_pipeline::794.484*0.88] mapped 3310 sequences
[M::worker_pipeline::800.522*0.88] mapped 3206 sequences
[M::worker_pipeline::807.140*0.88] mapped 3287 sequences
[M::worker_pipeline::813.760*0.88] mapped 3460 sequences
[M::worker_pipeline::820.411*0.88] mapped 3243 sequences
[M::worker_pipeline::827.100*0.88] mapped 3284 sequences
[M::worker_pipeline::833.377*0.88] mapped 3268 sequences
[M::worker_pipeline::840.515*0.87] mapped 3430 sequences
[M::worker_pipeline::848.385*0.87] mapped 3283 sequences
[M::worker_pipeline::855.944*0.87] mapped 3136 sequences
[M::worker_pipeline::862.757*0.87] mapped 3340 sequences
[M::worker_pipeline::869.141*0.87] mapped 4104 sequences
[M::worker_pipeline::875.555*0.87] mapped 3490 sequences
[M::worker_pipeline::882.477*0.87] mapped 3360 sequences
[M::worker_pipeline::889.453*0.87] mapped 3363 sequences
[M::worker_pipeline::896.105*0.87] mapped 3384 sequences
[M::worker_pipeline::903.053*0.87] mapped 3202 sequences
[M::worker_pipeline::909.425*0.87] mapped 3294 sequences
[M::worker_pipeline::916.136*0.87] mapped 3435 sequences
[M::worker_pipeline::922.160*0.87] mapped 3481 sequences
[M::worker_pipeline::927.959*0.87] mapped 3337 sequences
[M::worker_pipeline::934.979*0.87] mapped 3380 sequences
[M::worker_pipeline::941.311*0.87] mapped 3308 sequences
[M::worker_pipeline::947.014*0.87] mapped 3347 sequences
[M::worker_pipeline::953.295*0.87] mapped 3455 sequences
[M::worker_pipeline::959.567*0.87] mapped 3245 sequences
[M::worker_pipeline::965.388*0.87] mapped 3481 sequences
[M::worker_pipeline::971.068*0.87] mapped 3502 sequences
[M::worker_pipeline::977.987*0.87] mapped 3248 sequences
[M::worker_pipeline::983.715*0.87] mapped 3540 sequences
[M::worker_pipeline::989.511*0.87] mapped 3491 sequences
[M::worker_pipeline::995.426*0.87] mapped 3322 sequences
[M::worker_pipeline::1001.293*0.87] mapped 3485 sequences
[M::worker_pipeline::1007.193*0.87] mapped 3884 sequences
[M::worker_pipeline::1013.606*0.87] mapped 3447 sequences
[M::worker_pipeline::1019.881*0.87] mapped 3294 sequences
[M::worker_pipeline::1025.761*0.87] mapped 3422 sequences
[M::worker_pipeline::1032.163*0.87] mapped 3318 sequences
[M::worker_pipeline::1038.256*0.87] mapped 3210 sequences
[M::worker_pipeline::1044.337*0.87] mapped 3264 sequences
[M::worker_pipeline::1050.360*0.87] mapped 3572 sequences
[M::worker_pipeline::1056.716*0.87] mapped 3309 sequences
[M::worker_pipeline::1063.083*0.87] mapped 3235 sequences
[M::worker_pipeline::1069.358*0.87] mapped 3246 sequences
[M::worker_pipeline::1075.319*0.87] mapped 3349 sequences
[M::worker_pipeline::1081.810*0.87] mapped 3240 sequences
[M::worker_pipeline::1088.284*0.87] mapped 3161 sequences
[M::worker_pipeline::1094.606*0.86] mapped 3259 sequences
[M::worker_pipeline::1100.601*0.86] mapped 3252 sequences
[M::worker_pipeline::1106.837*0.86] mapped 3149 sequences
[M::worker_pipeline::1113.494*0.86] mapped 3595 sequences
[M::worker_pipeline::1119.805*0.86] mapped 3485 sequences
[M::worker_pipeline::1125.369*0.86] mapped 3287 sequences
[M::worker_pipeline::1131.506*0.86] mapped 3200 sequences
[M::worker_pipeline::1137.442*0.86] mapped 3249 sequences
[M::worker_pipeline::1143.795*0.86] mapped 3273 sequences
[M::worker_pipeline::1149.874*0.86] mapped 3329 sequences
[M::worker_pipeline::1156.330*0.86] mapped 3150 sequences
[M::worker_pipeline::1162.861*0.86] mapped 3282 sequences
[M::worker_pipeline::1168.608*0.86] mapped 3128 sequences
[M::worker_pipeline::1174.363*0.86] mapped 3144 sequences
[M::worker_pipeline::1180.225*0.86] mapped 3451 sequences
[M::worker_pipeline::1185.896*0.86] mapped 3466 sequences
[M::worker_pipeline::1192.030*0.86] mapped 3277 sequences
[M::worker_pipeline::1196.927*0.86] mapped 2560 sequences
[M::main] Version: 0.13-r248
[M::main] CMD: /usr/local/bin/miniprot --trans -u -I --outs=0.95 -t 1 --gff /tmp/tmp9xnm653p/files/0/a/6/dataset_0a67bfca-e372-4499-9804-d46ccefa3c62.dat galaxy_db/vertebrata_odb10/refseq_db.faa.gz
[M::main] Real time: 1196.928 sec; CPU: 1032.689 sec; Peak RSS: 0.209 GB

Standard Output:

Searching for miniprot in the path where compleasm.py is located
Searching for miniprot in the current execution path
Searching for miniprot in $PATH
Searching for hmmsearch in the path where compleasm.py is located
Searching for hmmsearch in the current execution path
Searching for hmmsearch in $PATH
miniprot execute command:
 /usr/local/bin/miniprot
Success download from https://busco-data.ezlab.org/v5/data/file_versions.tsv
Success download from https://busco-data.ezlab.org/v5/data/placement_files/list_of_reference_markers.eukaryota_odb10.2019-12-16.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/list_of_reference_markers.eukaryota_odb10.2019-12-16.txt
Success download from https://busco-data.ezlab.org/v5/data/placement_files/list_of_reference_markers.eukaryota_odb12.2025-01-15.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/list_of_reference_markers.eukaryota_odb12.2025-01-15.txt
Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt
Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxid-lineage.eukaryota_odb12.2025-01-15.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/mapping_taxid-lineage.eukaryota_odb12.2025-01-15.txt
Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt
Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb12.2025-01-15.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb12.2025-01-15.txt
Success download from https://busco-data.ezlab.org/v5/data/placement_files/supermatrix.aln.eukaryota_odb10.2019-12-16.faa.tar.gz
Placement file extraction path: galaxy_db/placement_files/supermatrix.aln.eukaryota_odb10.2019-12-16.faa
Success download from https://busco-data.ezlab.org/v5/data/placement_files/supermatrix.aln.eukaryota_odb12.2025-01-15.faa.tar.gz
Placement file extraction path: galaxy_db/placement_files/supermatrix.aln.eukaryota_odb12.2025-01-15.faa
Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree.eukaryota_odb10.2019-12-16.nwk.tar.gz
Placement file extraction path: galaxy_db/placement_files/tree.eukaryota_odb10.2019-12-16.nwk
Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree.eukaryota_odb12.2025-01-15.nwk.tar.gz
Placement file extraction path: galaxy_db/placement_files/tree.eukaryota_odb12.2025-01-15.nwk
Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree_metadata.eukaryota_odb10.2019-12-16.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/tree_metadata.eukaryota_odb10.2019-12-16.txt
Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree_metadata.eukaryota_odb12.2025-01-15.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/tree_metadata.eukaryota_odb12.2025-01-15.txt
Success download from https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb10.2024-01-08.tar.gz
Lineage file extraction path: galaxy_db/eukaryota_odb10
lineage: vertebrata_odb10
hmmsearch execute command:
 /usr/local/bin/hmmsearch

S:0.81%, 27
D:0.03%, 1
F:0.09%, 3
I:0.00%, 0
M:99.08%, 3323
N:3354

Warning: Given the potentially high diversity of the sample, compleasm results may not be reliable!We recommend reassessing the sample using BUSCO.

## Download lineage: 0.00(s)
## Run miniprot: 1196.95(s)
## Analyze miniprot: 542.87(s)
## Total runtime: 1739.82(s)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
busco_database	`"v5"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage_dataset	`"vertebrata_odb10"`
mode	`"busco"`
outputs	`["full_table_busco", "miniprot", "translated_protein", "full_table"]`
specified_contigs	`None`

Step 60: Compleasm Hap2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p 'galaxy_db/' && ln -s '/cvmfs/data.galaxyproject.org/byhand/busco/v5/lineages/vertebrata_odb10/' 'galaxy_db/vertebrata_odb10' && touch 'galaxy_db/vertebrata_odb10.done' &&  compleasm run -a '/tmp/tmp9xnm653p/files/0/a/6/dataset_0a67bfca-e372-4499-9804-d46ccefa3c62.dat' -o galaxy_output --mode busco -L 'galaxy_db' -l 'vertebrata_odb10' -t "${GALAXY_SLOTS:-1}"

Exit Code:

```
0
```

Standard Error:

[M::[email protected]*1.73] read 1473565 bases in 57 contigs
[M::[email protected]*1.69] 11572 blocks
[M::[email protected]*1.04] collected syncmers
[M::[email protected]*1.02] 677833 kmer-block pairs
[M::mp_mapopt_set_max_intron] set max intron size to 10000
[M::mp_idx_print_stat] 322886 distinct k-mers; mean occ of infrequent k-mers: 2.10; 0 frequent k-mers accounting for 0 occurrences
[M::worker_pipeline::6.588*0.83] mapped 3408 sequences
[M::worker_pipeline::12.943*0.84] mapped 3404 sequences
[M::worker_pipeline::18.902*0.85] mapped 3357 sequences
[M::worker_pipeline::25.332*0.85] mapped 3488 sequences
[M::worker_pipeline::31.598*0.85] mapped 3573 sequences
[M::worker_pipeline::37.925*0.85] mapped 3161 sequences
[M::worker_pipeline::44.459*0.84] mapped 3178 sequences
[M::worker_pipeline::50.557*0.84] mapped 3277 sequences
[M::worker_pipeline::57.200*0.84] mapped 3290 sequences
[M::worker_pipeline::63.199*0.84] mapped 3415 sequences
[M::worker_pipeline::69.068*0.84] mapped 3273 sequences
[M::worker_pipeline::75.369*0.84] mapped 3297 sequences
[M::worker_pipeline::82.374*0.84] mapped 3366 sequences
[M::worker_pipeline::88.591*0.84] mapped 3526 sequences
[M::worker_pipeline::95.286*0.84] mapped 3363 sequences
[M::worker_pipeline::101.998*0.84] mapped 3386 sequences
[M::worker_pipeline::108.236*0.84] mapped 3472 sequences
[M::worker_pipeline::114.337*0.84] mapped 3375 sequences
[M::worker_pipeline::120.805*0.84] mapped 3337 sequences
[M::worker_pipeline::126.979*0.84] mapped 3452 sequences
[M::worker_pipeline::132.609*0.84] mapped 3598 sequences
[M::worker_pipeline::138.401*0.84] mapped 3363 sequences
[M::worker_pipeline::145.068*0.84] mapped 3385 sequences
[M::worker_pipeline::151.679*0.84] mapped 3335 sequences
[M::worker_pipeline::157.727*0.83] mapped 3434 sequences
[M::worker_pipeline::164.354*0.83] mapped 3323 sequences
[M::worker_pipeline::170.475*0.83] mapped 3415 sequences
[M::worker_pipeline::177.543*0.83] mapped 3310 sequences
[M::worker_pipeline::183.688*0.83] mapped 3376 sequences
[M::worker_pipeline::189.778*0.83] mapped 3489 sequences
[M::worker_pipeline::196.869*0.83] mapped 3313 sequences
[M::worker_pipeline::202.797*0.83] mapped 3450 sequences
[M::worker_pipeline::208.835*0.83] mapped 3456 sequences
[M::worker_pipeline::215.405*0.83] mapped 3301 sequences
[M::worker_pipeline::221.929*0.83] mapped 3463 sequences
[M::worker_pipeline::227.952*0.83] mapped 3439 sequences
[M::worker_pipeline::234.012*0.83] mapped 3267 sequences
[M::worker_pipeline::240.355*0.83] mapped 3484 sequences
[M::worker_pipeline::246.864*0.83] mapped 3767 sequences
[M::worker_pipeline::253.331*0.83] mapped 3506 sequences
[M::worker_pipeline::259.617*0.83] mapped 3561 sequences
[M::worker_pipeline::266.243*0.83] mapped 3335 sequences
[M::worker_pipeline::272.411*0.83] mapped 3436 sequences
[M::worker_pipeline::278.445*0.83] mapped 3410 sequences
[M::worker_pipeline::284.914*0.83] mapped 3504 sequences
[M::worker_pipeline::290.531*0.83] mapped 3821 sequences
[M::worker_pipeline::296.977*0.83] mapped 3426 sequences
[M::worker_pipeline::303.539*0.83] mapped 3341 sequences
[M::worker_pipeline::310.626*0.83] mapped 3484 sequences
[M::worker_pipeline::317.303*0.83] mapped 3276 sequences
[M::worker_pipeline::323.597*0.84] mapped 3314 sequences
[M::worker_pipeline::330.039*0.84] mapped 3277 sequences
[M::worker_pipeline::336.431*0.84] mapped 3697 sequences
[M::worker_pipeline::343.527*0.84] mapped 3334 sequences
[M::worker_pipeline::350.010*0.84] mapped 3323 sequences
[M::worker_pipeline::356.490*0.84] mapped 3927 sequences
[M::worker_pipeline::362.998*0.84] mapped 3655 sequences
[M::worker_pipeline::369.128*0.84] mapped 3385 sequences
[M::worker_pipeline::374.971*0.84] mapped 3395 sequences
[M::worker_pipeline::380.153*0.84] mapped 3382 sequences
[M::worker_pipeline::385.502*0.84] mapped 3341 sequences
[M::worker_pipeline::390.125*0.84] mapped 3366 sequences
[M::worker_pipeline::394.606*0.84] mapped 3334 sequences
[M::worker_pipeline::399.910*0.85] mapped 3281 sequences
[M::worker_pipeline::405.213*0.85] mapped 3362 sequences
[M::worker_pipeline::409.603*0.85] mapped 3686 sequences
[M::worker_pipeline::414.365*0.85] mapped 3406 sequences
[M::worker_pipeline::419.232*0.85] mapped 3262 sequences
[M::worker_pipeline::424.239*0.85] mapped 3312 sequences
[M::worker_pipeline::429.283*0.86] mapped 3308 sequences
[M::worker_pipeline::434.654*0.86] mapped 3392 sequences
[M::worker_pipeline::439.875*0.86] mapped 3346 sequences
[M::worker_pipeline::445.059*0.86] mapped 3408 sequences
[M::worker_pipeline::449.849*0.86] mapped 3200 sequences
[M::worker_pipeline::455.068*0.86] mapped 3425 sequences
[M::worker_pipeline::459.425*0.86] mapped 3425 sequences
[M::worker_pipeline::464.163*0.86] mapped 3367 sequences
[M::worker_pipeline::469.001*0.87] mapped 3464 sequences
[M::worker_pipeline::473.778*0.87] mapped 3250 sequences
[M::worker_pipeline::478.476*0.87] mapped 3312 sequences
[M::worker_pipeline::483.507*0.87] mapped 3806 sequences
[M::worker_pipeline::488.564*0.87] mapped 3475 sequences
[M::worker_pipeline::493.323*0.87] mapped 3685 sequences
[M::worker_pipeline::498.599*0.87] mapped 3335 sequences
[M::worker_pipeline::504.195*0.87] mapped 3353 sequences
[M::worker_pipeline::509.525*0.87] mapped 3356 sequences
[M::worker_pipeline::514.988*0.88] mapped 3291 sequences
[M::worker_pipeline::520.490*0.88] mapped 3309 sequences
[M::worker_pipeline::527.328*0.88] mapped 3204 sequences
[M::worker_pipeline::533.408*0.88] mapped 3319 sequences
[M::worker_pipeline::539.821*0.88] mapped 3381 sequences
[M::worker_pipeline::546.751*0.87] mapped 3312 sequences
[M::worker_pipeline::553.207*0.87] mapped 3247 sequences
[M::worker_pipeline::560.143*0.87] mapped 3342 sequences
[M::worker_pipeline::566.915*0.87] mapped 3305 sequences
[M::worker_pipeline::573.603*0.87] mapped 3425 sequences
[M::worker_pipeline::579.864*0.87] mapped 3646 sequences
[M::worker_pipeline::586.332*0.87] mapped 3250 sequences
[M::worker_pipeline::592.896*0.87] mapped 3404 sequences
[M::worker_pipeline::599.502*0.87] mapped 3324 sequences
[M::worker_pipeline::605.794*0.87] mapped 3530 sequences
[M::worker_pipeline::612.186*0.87] mapped 3330 sequences
[M::worker_pipeline::619.064*0.87] mapped 3432 sequences
[M::worker_pipeline::625.066*0.87] mapped 3830 sequences
[M::worker_pipeline::631.887*0.87] mapped 3937 sequences
[M::worker_pipeline::638.644*0.87] mapped 3391 sequences
[M::worker_pipeline::645.371*0.87] mapped 3562 sequences
[M::worker_pipeline::651.786*0.87] mapped 3605 sequences
[M::worker_pipeline::658.309*0.87] mapped 3897 sequences
[M::worker_pipeline::664.195*0.87] mapped 4068 sequences
[M::worker_pipeline::670.160*0.87] mapped 3511 sequences
[M::worker_pipeline::676.715*0.87] mapped 3324 sequences
[M::worker_pipeline::682.149*0.87] mapped 3395 sequences
[M::worker_pipeline::688.507*0.87] mapped 3394 sequences
[M::worker_pipeline::694.844*0.87] mapped 3273 sequences
[M::worker_pipeline::700.998*0.87] mapped 3211 sequences
[M::worker_pipeline::706.806*0.87] mapped 3338 sequences
[M::worker_pipeline::713.154*0.87] mapped 3208 sequences
[M::worker_pipeline::719.090*0.87] mapped 3294 sequences
[M::worker_pipeline::725.460*0.87] mapped 3415 sequences
[M::worker_pipeline::732.475*0.87] mapped 3446 sequences
[M::worker_pipeline::739.035*0.87] mapped 3498 sequences
[M::worker_pipeline::744.607*0.87] mapped 3417 sequences
[M::worker_pipeline::751.033*0.87] mapped 3417 sequences
[M::worker_pipeline::757.665*0.87] mapped 3328 sequences
[M::worker_pipeline::764.669*0.87] mapped 3448 sequences
[M::worker_pipeline::771.566*0.87] mapped 3569 sequences
[M::worker_pipeline::777.418*0.87] mapped 4045 sequences
[M::worker_pipeline::784.223*0.87] mapped 3258 sequences
[M::worker_pipeline::790.899*0.87] mapped 3320 sequences
[M::worker_pipeline::797.491*0.87] mapped 3321 sequences
[M::worker_pipeline::803.846*0.87] mapped 3223 sequences
[M::worker_pipeline::810.669*0.87] mapped 3193 sequences
[M::worker_pipeline::817.004*0.87] mapped 3310 sequences
[M::worker_pipeline::823.801*0.87] mapped 3206 sequences
[M::worker_pipeline::830.204*0.87] mapped 3287 sequences
[M::worker_pipeline::836.655*0.87] mapped 3460 sequences
[M::worker_pipeline::843.599*0.87] mapped 3243 sequences
[M::worker_pipeline::850.197*0.87] mapped 3284 sequences
[M::worker_pipeline::856.535*0.87] mapped 3268 sequences
[M::worker_pipeline::863.243*0.87] mapped 3430 sequences
[M::worker_pipeline::870.084*0.87] mapped 3283 sequences
[M::worker_pipeline::877.222*0.87] mapped 3136 sequences
[M::worker_pipeline::884.103*0.87] mapped 3340 sequences
[M::worker_pipeline::889.909*0.87] mapped 4104 sequences
[M::worker_pipeline::895.922*0.87] mapped 3490 sequences
[M::worker_pipeline::902.192*0.87] mapped 3360 sequences
[M::worker_pipeline::908.733*0.86] mapped 3363 sequences
[M::worker_pipeline::915.271*0.86] mapped 3384 sequences
[M::worker_pipeline::922.060*0.86] mapped 3202 sequences
[M::worker_pipeline::928.156*0.86] mapped 3294 sequences
[M::worker_pipeline::934.256*0.86] mapped 3435 sequences
[M::worker_pipeline::940.546*0.86] mapped 3481 sequences
[M::worker_pipeline::946.398*0.86] mapped 3337 sequences
[M::worker_pipeline::952.663*0.86] mapped 3380 sequences
[M::worker_pipeline::958.765*0.86] mapped 3308 sequences
[M::worker_pipeline::964.997*0.86] mapped 3347 sequences
[M::worker_pipeline::971.055*0.86] mapped 3455 sequences
[M::worker_pipeline::977.786*0.86] mapped 3245 sequences
[M::worker_pipeline::983.833*0.86] mapped 3481 sequences
[M::worker_pipeline::990.214*0.86] mapped 3502 sequences
[M::worker_pipeline::997.071*0.86] mapped 3248 sequences
[M::worker_pipeline::1003.097*0.86] mapped 3540 sequences
[M::worker_pipeline::1009.750*0.86] mapped 3491 sequences
[M::worker_pipeline::1015.788*0.86] mapped 3322 sequences
[M::worker_pipeline::1022.092*0.86] mapped 3485 sequences
[M::worker_pipeline::1028.322*0.86] mapped 3884 sequences
[M::worker_pipeline::1035.442*0.86] mapped 3447 sequences
[M::worker_pipeline::1041.615*0.86] mapped 3294 sequences
[M::worker_pipeline::1047.434*0.86] mapped 3422 sequences
[M::worker_pipeline::1054.175*0.86] mapped 3318 sequences
[M::worker_pipeline::1060.071*0.86] mapped 3210 sequences
[M::worker_pipeline::1066.222*0.86] mapped 3264 sequences
[M::worker_pipeline::1072.121*0.86] mapped 3572 sequences
[M::worker_pipeline::1078.343*0.86] mapped 3309 sequences
[M::worker_pipeline::1084.572*0.86] mapped 3235 sequences
[M::worker_pipeline::1090.878*0.86] mapped 3246 sequences
[M::worker_pipeline::1096.978*0.86] mapped 3349 sequences
[M::worker_pipeline::1102.723*0.86] mapped 3240 sequences
[M::worker_pipeline::1108.872*0.86] mapped 3161 sequences
[M::worker_pipeline::1115.030*0.86] mapped 3259 sequences
[M::worker_pipeline::1121.536*0.86] mapped 3252 sequences
[M::worker_pipeline::1128.173*0.86] mapped 3149 sequences
[M::worker_pipeline::1134.671*0.86] mapped 3595 sequences
[M::worker_pipeline::1140.750*0.86] mapped 3485 sequences
[M::worker_pipeline::1146.350*0.86] mapped 3287 sequences
[M::worker_pipeline::1152.507*0.86] mapped 3200 sequences
[M::worker_pipeline::1159.164*0.86] mapped 3249 sequences
[M::worker_pipeline::1166.123*0.86] mapped 3273 sequences
[M::worker_pipeline::1172.361*0.86] mapped 3329 sequences
[M::worker_pipeline::1178.650*0.86] mapped 3150 sequences
[M::worker_pipeline::1185.141*0.86] mapped 3282 sequences
[M::worker_pipeline::1191.129*0.86] mapped 3128 sequences
[M::worker_pipeline::1197.152*0.86] mapped 3144 sequences
[M::worker_pipeline::1202.844*0.86] mapped 3451 sequences
[M::worker_pipeline::1208.352*0.86] mapped 3466 sequences
[M::worker_pipeline::1214.810*0.86] mapped 3277 sequences
[M::worker_pipeline::1219.288*0.86] mapped 2560 sequences
[M::main] Version: 0.13-r248
[M::main] CMD: /usr/local/bin/miniprot --trans -u -I --outs=0.95 -t 1 --gff /tmp/tmp9xnm653p/files/0/a/6/dataset_0a67bfca-e372-4499-9804-d46ccefa3c62.dat galaxy_db/vertebrata_odb10/refseq_db.faa.gz
[M::main] Real time: 1219.300 sec; CPU: 1045.924 sec; Peak RSS: 0.209 GB

Standard Output:

Searching for miniprot in the path where compleasm.py is located
Searching for miniprot in the current execution path
Searching for miniprot in $PATH
Searching for hmmsearch in the path where compleasm.py is located
Searching for hmmsearch in the current execution path
Searching for hmmsearch in $PATH
miniprot execute command:
 /usr/local/bin/miniprot
Success download from https://busco-data.ezlab.org/v5/data/file_versions.tsv
Success download from https://busco-data.ezlab.org/v5/data/placement_files/list_of_reference_markers.eukaryota_odb10.2019-12-16.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/list_of_reference_markers.eukaryota_odb10.2019-12-16.txt
Success download from https://busco-data.ezlab.org/v5/data/placement_files/list_of_reference_markers.eukaryota_odb12.2025-01-15.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/list_of_reference_markers.eukaryota_odb12.2025-01-15.txt
Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt
Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxid-lineage.eukaryota_odb12.2025-01-15.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/mapping_taxid-lineage.eukaryota_odb12.2025-01-15.txt
Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt
Success download from https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb12.2025-01-15.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb12.2025-01-15.txt
Success download from https://busco-data.ezlab.org/v5/data/placement_files/supermatrix.aln.eukaryota_odb10.2019-12-16.faa.tar.gz
Placement file extraction path: galaxy_db/placement_files/supermatrix.aln.eukaryota_odb10.2019-12-16.faa
Success download from https://busco-data.ezlab.org/v5/data/placement_files/supermatrix.aln.eukaryota_odb12.2025-01-15.faa.tar.gz
Placement file extraction path: galaxy_db/placement_files/supermatrix.aln.eukaryota_odb12.2025-01-15.faa
Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree.eukaryota_odb10.2019-12-16.nwk.tar.gz
Placement file extraction path: galaxy_db/placement_files/tree.eukaryota_odb10.2019-12-16.nwk
Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree.eukaryota_odb12.2025-01-15.nwk.tar.gz
Placement file extraction path: galaxy_db/placement_files/tree.eukaryota_odb12.2025-01-15.nwk
Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree_metadata.eukaryota_odb10.2019-12-16.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/tree_metadata.eukaryota_odb10.2019-12-16.txt
Success download from https://busco-data.ezlab.org/v5/data/placement_files/tree_metadata.eukaryota_odb12.2025-01-15.txt.tar.gz
Placement file extraction path: galaxy_db/placement_files/tree_metadata.eukaryota_odb12.2025-01-15.txt
Success download from https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb10.2024-01-08.tar.gz
Lineage file extraction path: galaxy_db/eukaryota_odb10
lineage: vertebrata_odb10
hmmsearch execute command:
 /usr/local/bin/hmmsearch

S:0.81%, 27
D:0.03%, 1
F:0.09%, 3
I:0.00%, 0
M:99.08%, 3323
N:3354

Warning: Given the potentially high diversity of the sample, compleasm results may not be reliable!We recommend reassessing the sample using BUSCO.

## Download lineage: 0.00(s)
## Run miniprot: 1219.31(s)
## Analyze miniprot: 505.32(s)
## Total runtime: 1724.63(s)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
busco_database	`"v5"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage_dataset	`"vertebrata_odb10"`
mode	`"busco"`
outputs	`["full_table_busco", "miniprot", "translated_protein", "full_table"]`
specified_contigs	`None`

Step 7: Meryl Database:
- step_state: scheduled

Step 61: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cut --complement -f '3' '/tmp/tmp9xnm653p/files/e/0/3/dataset_e0301968-367d-40c7-853e-d96fdd1e6a1b.dat' > '/tmp/tmp9xnm653p/job_working_directory/000/61/outputs/dataset_92abd116-9491-44dd-b089-bd0da95ba7f5.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
complement	`"--complement"`
cut_type_options	`{"__current_case__": 0, "colnames_option": {"__current_case__": 1, "header": "N", "list": ["3"]}, "cut_element": "-f", "delimiter": ""}`
dbkey	`"?"`

Step 62: output_merqury.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
input	`{"values": [{"id": 14, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 63: output_merqury.spectra-asm.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
input	`{"values": [{"id": 14, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.spectra-asm.fl", "which_dataset": "by_identifier"}`

Step 64: merqury_qv:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
input	`{"values": [{"id": 13, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury", "which_dataset": "by_identifier"}`

Step 65: output_merqury.assembly_01.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
input	`{"values": [{"id": 14, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.assembly_01.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 66: merqury_stats:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
input	`{"values": [{"id": 15, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.completeness", "which_dataset": "by_identifier"}`

Step 67: output_merqury.assembly_02.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
input	`{"values": [{"id": 14, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.assembly_02.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 68: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/6073bb457ec0/text_processing/find_and_replace' -o '/tmp/tmp9xnm653p/job_working_directory/000/62/outputs/dataset_f1df8a69-5509-495c-8bed-1eb684a34c4d.dat' -g     '#' 'Number of' '/tmp/tmp9xnm653p/files/9/2/a/dataset_92abd116-9491-44dd-b089-bd0da95ba7f5.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6e3f44083b2e11f096ae7c1e52ec831e"`
chromInfo	`"/tmp/tmp9xnm653p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 8: Database for Busco Lineage:
- step_state: scheduled
Step 9: Lineage:
- step_state: scheduled
Step 10: Name for Haplotype 1:
- step_state: scheduled

Other invocation details
- history_id
  - aedf7f6f6750dbdf
- history_state
  - ok
- invocation_id
  - aedf7f6f6750dbdf
- invocation_state
  - scheduled
- workflow_id
  - 2dc7b877046663aa

Updating workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4 fro…

6f881fb

…m 0.3.5 to 0.3.6

Delphine-L added 2 commits May 27, 2025 14:57

Correct missing parameters in ggplot

bfacefa

fix column numbers for plotting

91a267d

Delphine-L approved these changes May 27, 2025

View reviewed changes

Delphine-L merged commit 2d42cd5 into galaxyproject:main May 27, 2025
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Updating workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4 from 0.3.5 to 0.3.6 #855

Updating workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4 from 0.3.5 to 0.3.6 #855

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Updating workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4 from 0.3.5 to 0.3.6 #855

Updating workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4 from 0.3.5 to 0.3.6 #855

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