Command in stage minimap2_transcriptome failed with exit status = 127

[rajithadp]

Description of the bug

I tried to run the NanoSeq pipeline on a fastq.gz file using the following commands. Several steps were completed, but the minimap2 step failed.

Command used and terminal output

The commands I used:

nextflow run nf-core/nanoseq -r 3.1.0 \
    --input /samplesheet.csv \
    --outdir nanoseq \
    --protocol cDNA \
    --skip_demultiplexing \
    -profile singularity \
    --jaffal_ref_dir /for_jaffal \
    -c hpc_min2.config

The error message:

  =================================== Stage get_fasta (DRR095878) ====================================
  java -ea -Xms300m -cp /usr/local/opt/bbmap-38.96-1/current/ jgi.ReformatReads threads=16 ignorebadquality=t in=DRR095878.fastq.gz out=DRR095878.fastq/DRR095878.fastq.fasta
  Executing jgi.ReformatReads [threads=16, ignorebadquality=t, in=DRR095878.fastq.gz, out=DRR095878.fastq/DRR095878.fastq.fasta]
  
  Set threads to 16
  Input is being processed as unpaired
  Changed from ASCII-33 to ASCII-64 on input <: 60 -> 29
  Input:                        640277 reads            3101342227 bases
  Output:                       640277 reads (100.00%)  3101342227 bases (100.00%)
  
  Time:                                 459.405 seconds.
  Reads Processed:        640k  1.39k reads/sec
  Bases Processed:       3101m  6.75m bases/sec
  
  ============================= Stage minimap2_transcriptome (DRR095878) =============================
  bash: line 1: minimap2: command not found
  Cleaned up file DRR095878.fastq/DRR095878.fastq.paf to .bpipe/trash/DRR095878.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 DRR095878.fastq/DRR095878.fastq.fasta > DRR095878.fastq/DRR095878.fastq.paf ; 
  
  
  ========================================= Pipeline Failed ==========================================
  
  In stage Unknown: One or more parallel stages aborted. The following messages were reported:
  
  --------------------------- minimap2_transcriptome  ( DRR095878.fastq )  ---------------------------
  
  Command in stage minimap2_transcriptome failed with exit status = 127 : 
  
  minimap2 -t 16 -x map-ont -c for_jaffal/hg38_genCode22.fa DRR095878.fastq/DRR095878.fastq.fasta > DRR095878.fastq/DRR095878.fastq.paf ;
  
  ----------------------------------------------------------------------------------------------------
  
  Use 'bpipe errors' to see output from failed commands.

Relevant files

No response

System information

No response