JAFFAL pipeline crashes when singularity is used

[marcDabad]

Description of the bug

JAFFAL pipeline crashes when singularity is used because singularity container has not minimap2 (at least)

Command used and terminal output

nextflow run nf-core/nanoseq--input samplesheet.csv --outdir first --protocol cDNA --skip_demultiplexing --skip_vc --skip_sv -profile slurm,singularity --jaffal_ref_dir ${PWD}/for_jaffal

Relevant files

No response

System information

• Nextflow 22.10.1
• HPC
• slurm
• Singularity
• Centos
• nanoseq 3.1.0

[zya067025]

Hi, I have the same issue when I am running nanoseq 3.1.0

[Xiao-Zhong]

encountered the issue as well. "bash: line 1: minimap2: command not found"

ERROR ~ Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:RNA_FUSIONS_JAFFAL:JAFFAL (6)'

Caused by:
Process NFCORE_NANOSEQ:NANOSEQ:RNA_FUSIONS_JAFFAL:JAFFAL (6) terminated with an error exit status (1)

Command executed:

bpipe run -p refBase=for_jaffal for_jaffal/JAFFAL.groovy PVYP334523_pass_barcode03.fastq.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_NANOSEQ:NANOSEQ:RNA_FUSIONS_JAFFAL:JAFFAL":
jaffa: $( echo 'jaffa 2.0' )
END_VERSIONS

Command exit status:
1

Command output:
| Starting Pipeline at 2024-07-09 02:23 |
╘══════════════════════════════════════════════════════════════════════════════════════════════════╛

========================================= Stage run_check ==========================================
Running JAFFA version 2.1
Checking for required data files...
for_jaffal/hg38_genCode22.fa
for_jaffal/hg38_genCode22.tab
for_jaffal/known_fusions.txt
for_jaffal/hg38.fa
for_jaffal/Masked_hg38.1.bt2
for_jaffal/hg38_genCode22.1.bt2
All looking good

=========================== Stage get_fasta (PVYP334523_pass_barcode03) ============================
java -ea -Xms300m -cp /usr/local/opt/bbmap-38.96-1/current/ jgi.ReformatReads threads=16 ignorebadquality=t in=PVYP334523_pass_barcode03.fastq.gz out=PVYP334523_pass_barcode03.fastq/PVYP334523_pass_barcode03.fastq.fasta
Executing jgi.ReformatReads [threads=16, ignorebadquality=t, in=PVYP334523_pass_barcode03.fastq.gz, out=PVYP334523_pass_barcode03.fastq/PVYP334523_pass_barcode03.fastq.fasta]

Set threads to 16
Input is being processed as unpaired
Changed from ASCII-33 to ASCII-64 on input Z: 90 -> 59
Input: 5132931 reads 7327093108 bases
Output: 5132931 reads (100.00%) 7327093108 bases (100.00%)

Time: 234.195 seconds.
Reads Processed: 5132k 21.92k reads/sec
Bases Processed: 7327m 31.29m bases/sec

===================== Stage minimap2_transcriptome (PVYP334523_pass_barcode03) =====================
bash: line 1: minimap2: command not found
Cleaned up file PVYP334523_pass_barcode03.fastq/PVYP334523_pass_barcode03.fastq.paf to .bpipe/trash/PVYP334523_pass_barcode03.fastq.paf
ERROR: stage minimap2_transcriptome failed: Command in stage minimap2_transcriptome failed with exit status = 127 :

minimap2 -t 16 -x map-ont -c for_jaffal/hg38_genCode22.fa PVYP334523_pass_barcode03.fastq/PVYP334523_pass_barcode03.fastq.fasta > PVYP334523_pass_barcode03.fastq/PVYP334523_pass_barcode03.fastq.paf ;

========================================= Pipeline Failed ==========================================

In stage Unknown: One or more parallel stages aborted. The following messages were reported:

------------------- minimap2_transcriptome ( PVYP334523_pass_barcode03.fastq ) -------------------

Command in stage minimap2_transcriptome failed with exit status = 127 :

minimap2 -t 16 -x map-ont -c for_jaffal/hg38_genCode22.fa PVYP334523_pass_barcode03.fastq/PVYP334523_pass_barcode03.fastq.fasta > PVYP334523_pass_barcode03.fastq/PVYP334523_pass_barcode03.fastq.paf ;

---

Use 'bpipe errors' to see output from failed commands.

Command error:
INFO: Converting SIF file to temporary sandbox...
mkdir: cannot create directory ‘/home/xzhong/.bpipedb’: Read-only file system
ln: failed to create symbolic link '/home/xzhong/.bpipedb/jobs/91': No such file or directory
INFO: Cleaning up image...

Work dir:
/scratch/ms002/xzhong/06_nanopore/work/6b/e74e2b04ed202b4efc4dc195abe96d

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

-- Check '.nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit

[YinYangKarly]

@Xiao-Zhong, maybe you post this in a new post/issue. I am encountered the same issue as you at this moment

[Xiao-Zhong]

@Xiao-Zhong, maybe you post this in a new post/issue. I am encountered the same issue as you at this moment

I don't think the tool is being under active development or well-maintained. We have to skip the problematic step(s) at the moment, otherwise will waste too much time.

For JAFFAL, install and run it directly following the homepage: https://github.com/Oshlack/JAFFA

The NF pipeline might have a nice final report including JAFFAL output, but I don't know and gave up after the bambu step.

[YinYangKarly]

I am expanding a nextflow pipeline for my internship. I tried to implement JAFFA from the modules they used for nanoseq. I alreaday tested JAFFA separately via command line )JAFFA direct), that worked fine. My question at this moment: how to implement JAFFA in a nextflow pipeline without having these errors?