error TranscriptAssembly.nf with fastp

[LucileSol]

I am running the following command : nextflow run -c params_scriptseq.config -profile nbis,singularity ~/git/NBIS/pipelines-nextflow/TranscriptAssembly/TranscriptAssembly.nf

param file : // Workflow parameters params.reads = 'Gb*_{R1,R2}.fastq.gz' params.genome = 'genome.fa' params.single_end = false params.outdir = 'results_scriptseq_Gb' params.skip_trimming = false params.trimmer = 'fastp' params.fastp_options = ' -Q -L' params.trimmomatic_adapter_path = '/projects/references/adapters/TruSeq3_all.fa' params.trimmomatic_clip_options = 'LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36' params.hisat2_options = ' --fr' params.stringtie_options = ' --fr' params.multiqc_config = "/home/lucso605/git/NBIS/pipelines-nextflow/TranscriptAssembly/config/multiqc_conf.yml"

and get the following error

Error executing process > 'transcript_assembly:fastp (Gb_ROV6_3)'

Caused by: Process transcript_assembly:fastp (Gb_ROV6_3) terminated with an error exit status (127)

Command executed:

fastp -Q -L -w 2 -i Gb_ROV6_3_R1.fastq.gz -I Gb_ROV6_3_R2.fastq.gz \ -o Gb_ROV6_3_fastp-trimmed_R1.fastq.gz \ -O Gb_ROV6_3_fastp-trimmed_R2.fastq.gz \ --json Gb_ROV6_3_fastp.json

Command exit status: 127

Command output: (empty)

Command error: WARNING: Skipping mount /sw/easybuild/software/Singularity/3.8.0/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container /bin/bash: line 0: cd: /scratch/nxf.XCNzlbfCs9: No such file or directory /bin/bash: .command.run: No such file or directory

Work dir: /projects/annotation/species/RNAseq/work/e2/abcd73a4279e144994b22926615f69

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

[mahesh-panchal]

This is confusing. Nextflow isn't able to find the scratch directory it created.

[LucileSol]

If I use conda instead of singularity

Error executing process > 'transcript_assembly:multiqc'

Caused by: Process transcript_assembly:multiqc terminated with an error exit status (1)

Command executed:

multiqc . -c multiqc_conf.yml

Command exit status: 1

Command output: (empty)

Command error: Traceback (most recent call last): File "/projects/annotation/geodia_baretti/RNAseq/work/conda/multiqc-c98eb6b85dda6e7c6d0116ad2fc6861c/bin/multiqc", line 6, in from multiqc.main import multiqc File "/projects/annotation/geodia_baretti/RNAseq/work/conda/multiqc-c98eb6b85dda6e7c6d0116ad2fc6861c/lib/python3.9/site-packages/multiqc/init.py", line 16, in from .multiqc import run File "/projects/annotation/geodia_baretti/RNAseq/work/conda/multiqc-c98eb6b85dda6e7c6d0116ad2fc6861c/lib/python3.9/site-packages/multiqc/multiqc.py", line 37, in from .plots import table File "/projects/annotation/geodia_baretti/RNAseq/work/conda/multiqc-c98eb6b85dda6e7c6d0116ad2fc6861c/lib/python3.9/site-packages/multiqc/plots/table.py", line 9, in from multiqc.utils import config, report, util_functions, mqc_colour File "/projects/annotation/geodia_baretti/RNAseq/work/conda/multiqc-c98eb6b85dda6e7c6d0116ad2fc6861c/lib/python3.9/site-packages/multiqc/utils/mqc_colour.py", line 7, in import spectra File "/projects/annotation/geodia_baretti/RNAseq/work/conda/multiqc-c98eb6b85dda6e7c6d0116ad2fc6861c/lib/python3.9/site-packages/spectra/init.py", line 1, in from .core import COLOR_SPACES, Color, Scale File "/projects/annotation/geodia_baretti/RNAseq/work/conda/multiqc-c98eb6b85dda6e7c6d0116ad2fc6861c/lib/python3.9/site-packages/spectra/core.py", line 1, in from colormath import color_objects, color_conversions File "/projects/annotation/geodia_baretti/RNAseq/work/conda/multiqc-c98eb6b85dda6e7c6d0116ad2fc6861c/lib/python3.9/site-packages/colormath/color_conversions.py", line 13, in import networkx File "/projects/annotation/geodia_baretti/RNAseq/work/conda/multiqc-c98eb6b85dda6e7c6d0116ad2fc6861c/lib/python3.9/site-packages/networkx/init.py", line 114, in import networkx.generators File "/projects/annotation/geodia_baretti/RNAseq/work/conda/multiqc-c98eb6b85dda6e7c6d0116ad2fc6861c/lib/python3.9/site-packages/networkx/generators/init.py", line 14, in from networkx.generators.intersection import File "/projects/annotation/geodia_baretti/RNAseq/work/conda/multiqc-c98eb6b85dda6e7c6d0116ad2fc6861c/lib/python3.9/site-packages/networkx/generators/intersection.py", line 13, in from networkx.algorithms import bipartite File "/projects/annotation/geodia_baretti/RNAseq/work/conda/multiqc-c98eb6b85dda6e7c6d0116ad2fc6861c/lib/python3.9/site-packages/networkx/algorithms/init.py", line 16, in from networkx.algorithms.dag import File "/projects/annotation/geodia_baretti/RNAseq/work/conda/multiqc-c98eb6b85dda6e7c6d0116ad2fc6861c/lib/python3.9/site-packages/networkx/algorithms/dag.py", line 23, in from fractions import gcd ImportError: cannot import name 'gcd' from 'fractions' (/projects/annotation/geodia_baretti/RNAseq/work/conda/multiqc-c98eb6b85dda6e7c6d0116ad2fc6861c/lib/python3.9/fractions.py)

Work dir: /projects/annotation/geodia_baretti/RNAseq/work/38/0a84313fb783662f65c4e11cdd7f64

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

[mahesh-panchal]

Is /scratch visible inside a singularity container? Could you test it please?

[LucileSol]

no it is not

[mahesh-panchal]

Check if someone updated Singularity and didn't include scratch in the automounts. I think that has happened before.

[LucileSol]

Yes it solved the singularity problem!

[mahesh-panchal]

Re: MultiQC Can you make a pull request and update it to the latest version please?

[LucileSol]

all fixed with new MultiQC version and Singularity fix