Conda profile FastQC crash

[jfy133]

Describe the bug
When using the following flag -profile standard,conda the pipeline crashes at FastQC with th exit status 127, and the following command error:

Command error:
  java: symbol lookup error: /projects1/users/fellows/nextflow/eager2/my_test/work/conda/nf-core-eager-2.0.0-a95ee9548e4a04d99b07955eabaa0afe/jre/lib/amd64/../../../lib/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var

Furthermore, one 'Tip' message provided is to check .command.out file in the work directory. However, this file doesn't exist. Note, the tip message seems to change when re-running so it would be good to know if this is a random 'help of the day' type message from Nextflow, and if so make that clearer.

To Reproduce
The command I used was
run nf-core/eager --reads 'EXB015.A1701/*_R{1,2}*fastq.gz' --pairedEnd --fasta '~References/hg19_MT.fasta' -profile standard,conda --max_cpus 4 --max_memory 32G

(Sending input files privately)

Expected behavior

Not to crash and possibly for the conda environment downloaded having the correct library contents

Screenshots
NA

Operating System:
Ubuntu 14.04

Additional context
Please provide me with the following files:

• .nextflow.log
• results/pipeline_info/...

eager2_error_20181018.tar.gz

[apeltzer]

Could be related to bioconda/bioconda-recipes#5026

[apeltzer]

Looks to me a bit like a bioconda issue

[apeltzer]

Apparently its an issue if you have reversed conda channels.

- defaults
- bioconda
- conda-forge

is the correct order. I had the latter two switched, thus potentially causing that issue. I'll run a local test with the updated recipe and might push a new release to resolve the problem if that helps!

[apeltzer]

Could you give it a try please @jfy133 ? Please use the switch -r dev to run the pipeline with the otherwise identical command as before. If you confirm this to work, I'll push 2.0.1 :-)

[jfy133]

Sadly same error. Also with fresh nextflow depencies and nf-core/eager2 files
nextflow.log

[yassineS]

I have a similar issue on a Slurm based cluster, and reproduced the issue using conda, and singularity with a pre-build image (singularity pull) as well as a build image on the system itself. Here's the command and the error message:

> nextflow run nf-core/eager -with-singularity /apps/containers/nf-core-eager.simg  --pairedEnd --reads "/path/sample_{1,2}.fastq.gz" --trim_bam 3 --max_time 12.h --max_cpus 4 --max_memory 32G --snpcapture false --udg true --udg_type Half --bwamem --genome ${ref} --saveReference true  -name textEager3
N E X T F L O W  ~  version 0.32.0
Launching `nf-core/eager` [textEager3] - revision: 897fca777a [master]
WARN: Access to undefined parameter `readPaths` -- Initialise it to a default value eg. `params.readPaths = some_value`
=========================================
 nf-core/eager v2.0.0dev
=========================================
Pipeline Name  : nf-core/eager
Pipeline Version: 2.0.0
Run Name       : textEager3
Reads          : /path/sample_{1,2}.fastq.gz
Fasta Ref      : false
Data Type      : Paired-End
Max Memory     : 32G
Max CPUs       : 4
Max Time       : 12.h
Output dir     : ./results
Working dir    : /fast/users/user/eager/work
Container Engine: singularity
Container      : /apps/containers/nf-core-eager.simg
Current home   : /home/user
Current user   : user
Current path   : /home/user/fastdir/eager
Script dir     : /home/user/.nextflow/assets/nf-core/eager
Config Profile : standard
=========================================
[warm up] executor > SLURM
[c5/898ed5] Submitted process > get_software_versions
[e1/cadfbc] Submitted process > fastqc (sample)
[06/d3a688] Submitted process > adapter_removal (sample)
[7f/7a6a9a] Submitted process > output_documentation
ERROR ~ Error executing process > 'get_software_versions'

Caused by:
  Process `get_software_versions` terminated with an error exit status (127)

Command executed:

  echo 2.0.0 &> v_pipeline.txt
  echo 0.32.0 &> v_nextflow.txt
  fastqc --version &> v_fastqc.txt 2>&1 || true
  multiqc --version &> v_multiqc.txt 2>&1 || true
  bwa &> v_bwa.txt 2>&1 || true
  samtools --version &> v_samtools.txt 2>&1 || true
  AdapterRemoval -version  &> v_adapterremoval.txt 2>&1 || true
  picard MarkDuplicates --version &> v_markduplicates.txt  2>&1 || true
  dedup -v &> v_dedup.txt 2>&1 || true
  preseq &> v_preseq.txt 2>&1 || true
  gatk BaseRecalibrator --version 2>&1 | grep Version: > v_gatk.txt 2>&1 || true
  vcf2genome &> v_vcf2genome.txt 2>&1 || true
  fastp --version &> v_fastp.txt 2>&1 || true
  bam --version &> v_bamutil.txt 2>&1 || true
  qualimap --version &> v_qualimap.txt 2>&1 || true

  scrape_software_versions.py &> software_versions_mqc.yaml

Command exit status:
  127

Command output:
  (empty)

Command error:
  env: singularity: No such file or directory

Work dir:
  /fast/users/user/eager/work/c5/898ed52fe4a02f48caaf2f0130963b

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
[e1/cadfbc] NOTE: Process `fastqc (sample)` terminated with an error exit status (127) -- Error is ignored
[nf-core/eager] Pipeline Complete

[apeltzer]

@yassineS thats a bit of a different issue - can you open a separate ticket for that one?

@jfy133 We found a solution for this and I'll try to push an update for that soonish to test again.

[apeltzer]

The dev branch is currently updating itself and will need a couple of minutes to run this through. Docker and Singularity images are being rebuilt, which is going to take another ~30min-1hour from now on.

@jfy133 Can you test again in ~1 hour maybe using the -r devswitch? I'll push release 2.0.1 then.

@yassineS I opened a new issue for you #68 and will continue there. Its something else than this error actually..

[apeltzer]

This is fixed in release 2.0.1 #69