Dear Developer,
First, thank you for creating such an amazing pipeline—it has made our work significantly easier. However, I encountered an issue while using it for my data: several of my samples did not progress through the assembly steps and were subsequently removed from further analysis. I’m not certain what caused this problem and would greatly appreciate any guidance you can provide.
Thank you in advance for your help.
Regards,
Achal
Here is the **
tormes.log
** for tormes:
This is tormes version 1.3.0
Script used:
/cluster/work/users/cpaiva/tormes-env/bin/tormes --output tormes_results --threads 16 --genera Klebsiella --config /cluster/work/users/cpaiva/tormes-env/files/config_file.txt --assembler spades --min_contig_len 200 --gene_min_cov 80 --gene_min_id 80 --max_cpus_per_assembly 8 -m /cluster/work/users/cpaiva/my-metadata.txt
Parameters set:
- Metadata file: /cluster/work/users/cpaiva/my-metadata.txt
- Output directory: /cluster/work/users/cpaiva/tormes_results
- Number of threads to use: 16
- Special analysis enabled for: Klebsiella
The analysis will be performed for:
- Number of samples from raw reads: 38
- Number of samples from genomes: 0
TORMES pipeline started at: 2025-02-20 09:54
Quality filtering process started at: 2025-02-20 10:09
- Software for filtering chosen: prinseq
- Minimum quality of reads to survive: 25
- Minimum length of reads to survive: 125
- Number of reads surviving for sample 10-4B_S10_L002: 40190996
- Number of reads surviving for sample 11-4C_S11_L002: 43838682
- Number of reads surviving for sample 1-1A_S1_L002: 39361682
- Number of reads surviving for sample 12-5A_S12_L002: 43571154
- Number of reads surviving for sample 13-5B_S13_L002: 41996326
- Number of reads surviving for sample 14-5C_S14_L002: 34985302
- Number of reads surviving for sample 15-6A_S15_L002: 42856254
- Number of reads surviving for sample 16-6B_S16_L002: 41232732
- Number of reads surviving for sample 17-6C_S17_L002: 31946684
- Number of reads surviving for sample 18-7A_S18_L002: 35486012
- Number of reads surviving for sample 19-7B_S19_L002: 31174260
- Number of reads surviving for sample 20-7C_S20_L002: 42018180
- Number of reads surviving for sample 21-8A_S21_L002: 42815422
- Number of reads surviving for sample 2-1B_S2_L002: 36242638
- Number of reads surviving for sample 22-8B_S22_L002: 41133466
- Number of reads surviving for sample 23-8C_S23_L002: 42737434
- Number of reads surviving for sample 24-9A_S24_L002: 44092550
- Number of reads surviving for sample 25-9B_S25_L002: 46538466
- Number of reads surviving for sample 26-9C_S26_L002: 40167136
- Number of reads surviving for sample 27-10A_S27_L002: 44833104
- Number of reads surviving for sample 28-10B_S28_L002: 36873478
- Number of reads surviving for sample 29-10C_S29_L002: 37313030
- Number of reads surviving for sample 30-11A_S30_L002: 37973762
- Number of reads surviving for sample 31-11B_S31_L002: 41278790
- Number of reads surviving for sample 3-1C_S3_L002: 40002416
- Number of reads surviving for sample 32-11C_S32_L002: 45108118
- Number of reads surviving for sample 33-12A_S33_L002: 39894538
- Number of reads surviving for sample 34-12B_S34_L002: 40846526
- Number of reads surviving for sample 35-12C_S35_L002: 39310426
- Number of reads surviving for sample 36-13A_S36_L002: 42251808
- Number of reads surviving for sample 37-13B_S37_L002: 36852038
- Number of reads surviving for sample 38-13C_S38_L002: 45201272
- Number of reads surviving for sample 4-2A_S4_L002: 38103326
- Number of reads surviving for sample 5-2B_S5_L002: 44310708
- Number of reads surviving for sample 6-3A_S6_L002: 38992798
- Number of reads surviving for sample 7-3B_S7_L002: 35820490
- Number of reads surviving for sample 8-3C_S8_L002: 45626052
- Number of reads surviving for sample 9-4A_S9_L002: 31423044
Assembly started at: 2025-02-21 06:48
- Software for genome assembly chosen: spades
- WARNING: 14-5C_S14_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 15-6A_S15_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 16-6B_S16_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 17-6C_S17_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 18-7A_S18_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 19-7B_S19_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 20-7C_S20_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 21-8A_S21_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 22-8B_S22_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 23-8C_S23_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 24-9A_S24_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 25-9B_S25_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 26-9C_S26_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 27-10A_S27_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 28-10B_S28_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 29-10C_S29_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 30-11A_S30_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 31-11B_S31_L002 did not generate an assembly file and will be excluded for further analysis
- Number of contigs in genome 10-4B_S10_L002: 260
- Number of contigs in genome 11-4C_S11_L002: 200
- Number of contigs in genome 1-1A_S1_L002: 333
- Number of contigs in genome 12-5A_S12_L002: 239
- Number of contigs in genome 13-5B_S13_L002: 296
- Number of contigs in genome 2-1B_S2_L002: 173
- Number of contigs in genome 3-1C_S3_L002: 243
- Number of contigs in genome 32-11C_S32_L002: 171
- Number of contigs in genome 33-12A_S33_L002: 151
- Number of contigs in genome 34-12B_S34_L002: 131
- Number of contigs in genome 35-12C_S35_L002: 200
- Number of contigs in genome 36-13A_S36_L002: 139
- Number of contigs in genome 37-13B_S37_L002: 140
- Number of contigs in genome 38-13C_S38_L002: 144
- Number of contigs in genome 4-2A_S4_L002: 281
- Number of contigs in genome 5-2B_S5_L002: 179
- Number of contigs in genome 6-3A_S6_L002: 120
- Number of contigs in genome 7-3B_S7_L002: 598
- Number of contigs in genome 8-3C_S8_L002: 180
- Number of contigs in genome 9-4A_S9_L002: 205
Taxonomic identification started at: 2025-02-23 01:53
MLST started at: 2025-02-23 03:02
Antimicrobial resistance and virulence genes search started at: 2025-02-23 03:02
Gene prediction and nnotation started at: 2025-02-23 03:04
Pangenome analysis started at: 2025-02-23 06:55
Surface polysaccharide locus typing started at: 2025-02-23 07:07
WARNING: K-locus typing was not performed
WARNING: O-locus typing was not performed
Plasmid search started at: 2025-02-23 07:08
Point mutation search started at: 2025-02-23 07:08
Tormes report started at: 2025-02-23 07:17
TORMES pipeline finished at: 2025-02-23 07:18
Thank you for using TORMES!
Dear Developer,
First, thank you for creating such an amazing pipeline—it has made our work significantly easier. However, I encountered an issue while using it for my data: several of my samples did not progress through the assembly steps and were subsequently removed from further analysis. I’m not certain what caused this problem and would greatly appreciate any guidance you can provide.
Thank you in advance for your help.
Regards,
Achal
Here is the **
tormes.log
** for tormes:
This is tormes version 1.3.0
Script used:
/cluster/work/users/cpaiva/tormes-env/bin/tormes --output tormes_results --threads 16 --genera Klebsiella --config /cluster/work/users/cpaiva/tormes-env/files/config_file.txt --assembler spades --min_contig_len 200 --gene_min_cov 80 --gene_min_id 80 --max_cpus_per_assembly 8 -m /cluster/work/users/cpaiva/my-metadata.txt
Parameters set:
- Metadata file: /cluster/work/users/cpaiva/my-metadata.txt
- Output directory: /cluster/work/users/cpaiva/tormes_results
- Number of threads to use: 16
- Special analysis enabled for: Klebsiella
The analysis will be performed for:
- Number of samples from raw reads: 38
- Number of samples from genomes: 0
TORMES pipeline started at: 2025-02-20 09:54
Quality filtering process started at: 2025-02-20 10:09
- Software for filtering chosen: prinseq
- Minimum quality of reads to survive: 25
- Minimum length of reads to survive: 125
- Number of reads surviving for sample 10-4B_S10_L002: 40190996
- Number of reads surviving for sample 11-4C_S11_L002: 43838682
- Number of reads surviving for sample 1-1A_S1_L002: 39361682
- Number of reads surviving for sample 12-5A_S12_L002: 43571154
- Number of reads surviving for sample 13-5B_S13_L002: 41996326
- Number of reads surviving for sample 14-5C_S14_L002: 34985302
- Number of reads surviving for sample 15-6A_S15_L002: 42856254
- Number of reads surviving for sample 16-6B_S16_L002: 41232732
- Number of reads surviving for sample 17-6C_S17_L002: 31946684
- Number of reads surviving for sample 18-7A_S18_L002: 35486012
- Number of reads surviving for sample 19-7B_S19_L002: 31174260
- Number of reads surviving for sample 20-7C_S20_L002: 42018180
- Number of reads surviving for sample 21-8A_S21_L002: 42815422
- Number of reads surviving for sample 2-1B_S2_L002: 36242638
- Number of reads surviving for sample 22-8B_S22_L002: 41133466
- Number of reads surviving for sample 23-8C_S23_L002: 42737434
- Number of reads surviving for sample 24-9A_S24_L002: 44092550
- Number of reads surviving for sample 25-9B_S25_L002: 46538466
- Number of reads surviving for sample 26-9C_S26_L002: 40167136
- Number of reads surviving for sample 27-10A_S27_L002: 44833104
- Number of reads surviving for sample 28-10B_S28_L002: 36873478
- Number of reads surviving for sample 29-10C_S29_L002: 37313030
- Number of reads surviving for sample 30-11A_S30_L002: 37973762
- Number of reads surviving for sample 31-11B_S31_L002: 41278790
- Number of reads surviving for sample 3-1C_S3_L002: 40002416
- Number of reads surviving for sample 32-11C_S32_L002: 45108118
- Number of reads surviving for sample 33-12A_S33_L002: 39894538
- Number of reads surviving for sample 34-12B_S34_L002: 40846526
- Number of reads surviving for sample 35-12C_S35_L002: 39310426
- Number of reads surviving for sample 36-13A_S36_L002: 42251808
- Number of reads surviving for sample 37-13B_S37_L002: 36852038
- Number of reads surviving for sample 38-13C_S38_L002: 45201272
- Number of reads surviving for sample 4-2A_S4_L002: 38103326
- Number of reads surviving for sample 5-2B_S5_L002: 44310708
- Number of reads surviving for sample 6-3A_S6_L002: 38992798
- Number of reads surviving for sample 7-3B_S7_L002: 35820490
- Number of reads surviving for sample 8-3C_S8_L002: 45626052
- Number of reads surviving for sample 9-4A_S9_L002: 31423044
Assembly started at: 2025-02-21 06:48
- Software for genome assembly chosen: spades
- WARNING: 14-5C_S14_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 15-6A_S15_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 16-6B_S16_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 17-6C_S17_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 18-7A_S18_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 19-7B_S19_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 20-7C_S20_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 21-8A_S21_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 22-8B_S22_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 23-8C_S23_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 24-9A_S24_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 25-9B_S25_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 26-9C_S26_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 27-10A_S27_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 28-10B_S28_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 29-10C_S29_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 30-11A_S30_L002 did not generate an assembly file and will be excluded for further analysis
- WARNING: 31-11B_S31_L002 did not generate an assembly file and will be excluded for further analysis
- Number of contigs in genome 10-4B_S10_L002: 260
- Number of contigs in genome 11-4C_S11_L002: 200
- Number of contigs in genome 1-1A_S1_L002: 333
- Number of contigs in genome 12-5A_S12_L002: 239
- Number of contigs in genome 13-5B_S13_L002: 296
- Number of contigs in genome 2-1B_S2_L002: 173
- Number of contigs in genome 3-1C_S3_L002: 243
- Number of contigs in genome 32-11C_S32_L002: 171
- Number of contigs in genome 33-12A_S33_L002: 151
- Number of contigs in genome 34-12B_S34_L002: 131
- Number of contigs in genome 35-12C_S35_L002: 200
- Number of contigs in genome 36-13A_S36_L002: 139
- Number of contigs in genome 37-13B_S37_L002: 140
- Number of contigs in genome 38-13C_S38_L002: 144
- Number of contigs in genome 4-2A_S4_L002: 281
- Number of contigs in genome 5-2B_S5_L002: 179
- Number of contigs in genome 6-3A_S6_L002: 120
- Number of contigs in genome 7-3B_S7_L002: 598
- Number of contigs in genome 8-3C_S8_L002: 180
- Number of contigs in genome 9-4A_S9_L002: 205
Taxonomic identification started at: 2025-02-23 01:53
MLST started at: 2025-02-23 03:02
Antimicrobial resistance and virulence genes search started at: 2025-02-23 03:02
Gene prediction and nnotation started at: 2025-02-23 03:04
Pangenome analysis started at: 2025-02-23 06:55
Surface polysaccharide locus typing started at: 2025-02-23 07:07
WARNING: K-locus typing was not performed
WARNING: O-locus typing was not performed
Plasmid search started at: 2025-02-23 07:08
Point mutation search started at: 2025-02-23 07:08
Tormes report started at: 2025-02-23 07:17
TORMES pipeline finished at: 2025-02-23 07:18
Thank you for using TORMES!