FastQC crash, error 127

[KochTobi]

Pipeline crashes with conda environment

Bug description

When substituting containerization by the provided conda environment the pipeline crashes at the FastQC step. The following error gets thrown:

[Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'fa
stqc (<myactualsampleid>)'

Caused by:
  Process `fastqc (<myactualsampleid>)` terminated with an error exit status (127)

Command executed:

  fastqc -q <myactualsampleid>.fastq

Command exit status:
  127

Command output:
  (empty)

Command error:
  java: symbol lookup error:/<installation directory>/miniconda/envs/nf-core-rnaseq-1.1/jre/lib/amd64/../../../lib/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var

I looked into the directory and found the following libraries:

• libfontconfig.so -> libfontconfig.so.1.12.0*
• libfontconfig.so.1 -> libfontconfig.so.1.12.0*
• libfontconfig.so.1.12.0*

Reproduce

1. Disable containers by commenting out the container specification in nextflow.config, conf/base.config as well as other profiles you use if specified there. (release 1.1)
2. install conda 4.5.11
3. create environment using the provided environment.yml file conda env create -f environment.yml
4. run the pipeline

nextflow run main.nf --aligner hisat2 -profile cfc --saveReference --singleEnd --reads <data>/*.fastq --outdir results --skip-dupradar --skip_genebody_coverage --gtf <data>/Homo_sapiens.GRCh38.92.gtf --fasta <data>/GRCh38_r92.all.fasta

Expected behaviour

The pipeline runs through with no crash similar to execution in container.

Operation System

The pipeline was executed on the cfc cluster in Tübingen Germany

Additional notes

Same error as in nf-core/eager#67

[KochTobi]

Possible fix:

I got it working by editing the environment.yml

dependencies:
  - conda-forge::openjdk=8.0.144

was replaced by

dependencies:
  - defaults::openjdk=8.0.152

[apeltzer]

I can confirm that this indeed fixed nf-core/eager#67 properly!

[apeltzer]

Reproducing the error works unfortunately for me:
I'll open a PR to fix this ...

alex@aragorn ~/I/n/r/RNAseq> nextflow run . -profile test,conda 
N E X T F L O W  ~  version 18.10.1
Launching `./main.nf` [maniac_hodgkin] - revision: 7c9a828c2b
=======================================================
                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~'
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

 nf-core/rnaseq : RNA-Seq Best Practice v1.1
=======================================================
Run Name       : maniac_hodgkin
Reads          : data/*{1,2}.fastq.gz
Data Type      : Single-End
Genome         : false
Strandedness   : None
Trim R1        : 0
Trim R2        : 0
Trim 3' R1     : 0
Trim 3' R2     : 0
Aligner        : STAR
Fasta Ref      : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa
GTF Annotation : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf
Save Reference : No
Save Trimmed   : No
Save Intermeds : No
Max Memory     : 6 GB
Max CPUs       : 2
Max Time       : 2d
Output dir     : ./results
Working dir    : /home/alex/IDEA/nf-core/rnaseq_test/RNAseq/work
Container      : nfcore/rnaseq:1.1
Current home   : /home/alex
Current user   : alex
Current path   : /home/alex/IDEA/nf-core/rnaseq_test/RNAseq
Script dir     : /home/alex/IDEA/nf-core/rnaseq_test/RNAseq
Config Profile : test,conda
=========================================
[warm up] executor > local
Creating Conda env: /home/alex/IDEA/nf-core/rnaseq_test/RNAseq/environment.yml [cache /home/alex/IDEA/nf-core/rnaseq_test/RNAseq/work/conda/nf-core-rnaseq-1.1-31cb0d16eab401414840cd3ced2c4f17]
[ec/bc9d73] Submitted process > output_documentation
[a2/e151b3] Submitted process > get_software_versions
[0e/cf4c11] Submitted process > workflow_summary_mqc
[f9/dc25b7] Submitted process > makeBED12 (genes.gtf)
[d3/8023cf] Submitted process > trim_galore (SRR4238351)
[bc/5b86c8] Submitted process > fastqc (SRR4238351)
[76/b8ed50] Submitted process > fastqc (SRR4238379)
ERROR ~ Error executing process > 'fastqc (SRR4238351)'

Caused by:
  Process `fastqc (SRR4238351)` terminated with an error exit status (127)

Command executed:

  fastqc -q SRR4238351_subsamp.fastq.gz

Command exit status:
  127

Command output:
  (empty)

Command error:
  java: symbol lookup error: /home/alex/IDEA/nf-core/rnaseq_test/RNAseq/work/conda/nf-core-rnaseq-1.1-31cb0d16eab401414840cd3ced2c4f17/jre/lib/amd64/../../../lib/libfontconfig.so.1: undefined symbol: FT_Done_MM_Var

Work dir:
  /home/alex/IDEA/nf-core/rnaseq_test/RNAseq/work/bc/5b86c8e184cceae6c80ca3ce4e0b60

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
[nfcore/rnaseq] Pipeline Complete
WARN: Killing pending tasks (1)
[bc/9df234] Submitted process > trim_galore (SRR4238379) 

[ewels]

Just merged the PR, should fix the issue. Would be great if you could confirm by trying out the dev code and image @KochTobi

[apeltzer]

All fixed :-)