You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
A year ago I have successfully installed nextflow and used the scrnaseq pipeline. Today I have tried to run the basic test for the rnaseq pipeline, and I am getting an error (127) that says either the fastq or the trim_galore command cannot be found. Which command it is depends on the run. They switch if I retry. The error persists regardless of whether I use singularity (what I used a year ago), docker (installed today) or apptainer (also installed today). I have even tried an install of nextflow as a dedicated conda environment, and am still getting the same error. I would be very grateful if someone could help me shed some light on this, as these pipelines are a great tool. Thank you in advance!
Command used and terminal output
nextflow run nf-core/rnaseq -profile test, docker --outdir ~/Bioinformatics/BulkRnaSeqNfTest-[nf-core/rnaseq] Pipeline completed with errors-ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)'Caused by: Process `NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)` terminated with an error exit status (127)Command executed: [ ! -f RAP1_UNINDUCED_REP1.fastq.gz ] && ln -s SRR6357073_1.fastq.gz RAP1_UNINDUCED_REP1.fastq.gz trim_galore \ --fastqc_args '-t 2' \ --cores 1 \ --gzip \ RAP1_UNINDUCED_REP1.fastq.gz cat <<-END_VERSIONS > versions.yml "NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE": trimgalore: $(echo $(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*$//') cutadapt: $(cutadapt --version) END_VERSIONSCommand exit status: 127Command output: (empty)Command error: .command.sh: line 4: trim_galore: command not foundWork dir: /home/mgoiko/work/6f/9d1d0c3b77e45f3166fe47dc09ece3Tip: 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
Relevant files
System information
Ubuntu 22.04.4 LTS
The text was updated successfully, but these errors were encountered:
Hello everyone, I have finally sorted out the issue. Want to leave this up for people in case it helps someone. If you are getting the error, please make sure there is no space between the words in
Description of the bug
Hello everyone,
A year ago I have successfully installed nextflow and used the scrnaseq pipeline. Today I have tried to run the basic test for the rnaseq pipeline, and I am getting an error (127) that says either the fastq or the trim_galore command cannot be found. Which command it is depends on the run. They switch if I retry. The error persists regardless of whether I use singularity (what I used a year ago), docker (installed today) or apptainer (also installed today). I have even tried an install of nextflow as a dedicated conda environment, and am still getting the same error. I would be very grateful if someone could help me shed some light on this, as these pipelines are a great tool. Thank you in advance!
Command used and terminal output
Relevant files
System information
Ubuntu 22.04.4 LTS
The text was updated successfully, but these errors were encountered: