ERROR: stage minimap2_transcriptome failed: Command in stage minimap2_transcriptome failed with exit status = 127

[KRothamel]

Description of the bug

ERROR ~ Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:RNA_FUSIONS_JAFFAL:JAFFAL (1)'

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

Command executed:

bpipe run -p refBase=for_jaffal for_jaffal/JAFFAL.groovy BC01.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 2024-11-13 18:58 |
╘══════════════════════════════════════════════════════════════════════════════════════════════════╛

========================================= 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 (BC01) ======================================
java -ea -Xms300m -cp /usr/local/opt/bbmap-38.96-1/current/ jgi.ReformatReads threads=16 ignorebadquality=t in=BC01.fastq.gz out=BC01.fastq/BC01.fastq.fasta
Executing jgi.ReformatReads [threads=16, ignorebadquality=t, in=BC01.fastq.gz, out=BC01.fastq/BC01.fastq.fasta]

Set threads to 16
Input is being processed as unpaired
Input: 33 reads 3450 bases
Output: 33 reads (100.00%) 3450 bases (100.00%)

Time: 0.229 seconds.
Reads Processed: 33 0.14k reads/sec
Bases Processed: 3450 0.02m bases/sec

=============================== Stage minimap2_transcriptome (BC01) ================================
bash: line 1: minimap2: command not found
Cleaned up file BC01.fastq/BC01.fastq.paf to .bpipe/trash/BC01.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 BC01.fastq/BC01.fastq.fasta > BC01.fastq/BC01.fastq.paf ;

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

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

----------------------------- minimap2_transcriptome ( BC01.fastq ) ------------------------------

Command in stage minimap2_transcriptome failed with exit status = 127 :

minimap2 -t 16 -x map-ont -c for_jaffal/hg38_genCode22.fa BC01.fastq/BC01.fastq.fasta > BC01.fastq/BC01.fastq.paf ;

Command used and terminal output

nextflow run nf-core/nanoseq \--input /tscc/lustre/ddn/scratch/krothamel/ASO_testrun_November2024/ASOtestrun_111224.csv \--protocol cDNA \--skip_demultiplexing \-profile singularity \-resume \--jaffal_ref_dir /tscc/lustre/ddn/scratch/krothamel/ASO_testrun_November2024/nanoseq/for_jaffal

Relevant files

No response

System information

No response