Rnaseq: get_software_versions error in v1.3 release

[ewels]

_Originally posted by @cailiangliang765 in https://github.com/nf-core/rnaseq/issues/33#issuecomment-478321926_

---

I still met the "ERROR ~ Error executing process > 'get_software_versions'".:

cailiangliang@clldebian:~/dd22$ nextflow run nf-core/rnaseq --reads '*_R{1,2}.fq.gz' --genome GRCh37 -profile docker
N E X T F L O W  ~  version 19.01.0
Launching `nf-core/rnaseq` [sad_hoover] - revision: 37f260d360 [master]
----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq v1.3
----------------------------------------------------

Pipeline Release  : master
Run Name          : sad_hoover
Reads             : *_R{1,2}.fq.gz
Data Type         : Paired-End
Genome            : GRCh37
Strandedness      : None
Trimming          : 5'R1: 0 / 5'R2: 0 / 3'R1: 0 / 3'R2: 0
Aligner           : STAR
STAR Index        : /home/cailiangliang/demo111/references/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/
GTF Annotation    : /home/cailiangliang/demo111/references/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf
BED Annotation    : /home/cailiangliang/demo111/references/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed
Save prefs        : Ref Genome: No / Trimmed FastQ: No / Alignment intermediates: No
Max Resources     : 128 GB memory, 16 cpus, 10d time per job
Container         : docker - nfcore/rnaseq:1.3
Output dir        : ./results
Launch dir        : /home/cailiangliang/dd22
Working dir       : /home/cailiangliang/dd22/work
Script dir        : /home/cailiangliang/.nextflow/assets/nf-core/rnaseq
User              : cailiangliang
Config Profile    : docker
----------------------------------------------------
[warm up] executor > local
[a9/b83ac8] Submitted process > get_software_versions
[9e/2f401e] Submitted process > fastqc (sample1)
[ad/7036e3] Submitted process > trim_galore (sample1)
[d1/0b3e28] Submitted process > output_documentation (1)
[a9/b83ac8] NOTE: Process `get_software_versions` terminated with an error exit status (139) -- Execution is retried (1)
[49/ef121b] Re-submitted process > get_software_versions
ERROR ~ Error executing process > 'get_software_versions'

Caused by:
  Process `get_software_versions` terminated with an error exit status (139)

Command executed:

  echo 1.3 &> v_ngi_rnaseq.txt
  echo 19.01.0 &> v_nextflow.txt
  fastqc --version &> v_fastqc.txt
  cutadapt --version &> v_cutadapt.txt
  trim_galore --version &> v_trim_galore.txt
  STAR --version &> v_star.txt
  hisat2 --version &> v_hisat2.txt
  stringtie --version &> v_stringtie.txt
  preseq &> v_preseq.txt
  read_duplication.py --version &> v_rseqc.txt
  echo $(bamCoverage --version 2>&1) > v_deeptools.txt
  featureCounts -v &> v_featurecounts.txt
  picard MarkDuplicates --version &> v_markduplicates.txt  || true
  samtools --version &> v_samtools.txt
  multiqc --version &> v_multiqc.txt
  scrape_software_versions.py &> software_versions_mqc.yaml

Command exit status:
  139

Command output:
  (empty)

Command error:
  .command.sh: line 7:   202 Segmentation fault      (core dumped) STAR --version &> v_star.txt

Work dir:
  /home/cailiangliang/dd22/work/49/ef121b60936abba428e3cec8e49a92

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
[nf-core/rnaseq] Pipeline completed with errors
WARN: Killing pending tasks (2)
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
cailiangliang@clldebian:~/dd22$ 

[ewels]

This error seems to be unrelated to the previous problem we had with get_software_versions. The key line in the log is this:

202 Segmentation fault      (core dumped) STAR --version &> v_star.txt

So basically, STAR is failing for some reason (it's not a problem with the configs as discussed in #33).

[ewels]

Ok, I just tested the container and it works fine for me:

$ docker run -it nfcore/rnaseq:1.3 bash -c "STAR --version"
STAR_2.6.1d

@cailiangliang765 - could you try the same command in your terminal please? Also pasting the output from docker image ls would be helpful:

$ docker image ls
REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
nfcore/rnaseq       1.3                 e7839e32cee9        4 days ago          3.54GB

[cailiangliang765]

this is the same with you.

cailiangliang@clldebian:$ docker image ls
nfcore/rnaseq 1.3 e7839e32cee9 4 days ago 3.54GB

but i can not get the version info like you.

cailiangliang@clldebian:$ docker run -it nfcore/rnaseq:1.3 bash -c "STAR --version"
cailiangliang@clldebian:~$

then i enter the docker container, it shows,

cailiangliang@clldebian:~$ docker run -it nfcore/rnaseq:1.3 bash
(base) root@2a0cbaf0ee30:/# STAR --version
Segmentation fault (core dumped)
(base) root@2a0cbaf0ee30:/# 

[ewels]

Bah, this is very strange. I thought the whole point of docker was that stuff should work the same on every system 😞

What system are you running on @cailiangliang765? How is docker installed?

[cailiangliang765]

I am on Debian.

cailiangliang@clldebian:$ cat /etc/issue
Debian GNU/Linux buster/sid \n \l

I met this error when i remove the nfcore/rnaseq (e7839e32cee9). i do not know why this happened. this error happens to other images too. so i think i need to try reinstall docker.

cailiangliang@clldebian:$ docker rmi e7839e32cee9
Error response from daemon: conflict: unable to delete e7839e32cee9 (must be forced) - image is being used by stopped container dee8ec9a8738

[cailiangliang765]

Bah, this is very strange. I thought the whole point of docker was that stuff should work the same on every system 😞

What system are you running on @cailiangliang765? How is docker installed?

@ewels I find the reason for this issue. The docker support the kernel version 4.9.0 not 4.19.0. This issue can be closed now. Many thanks for your help.

[apeltzer]

Thanks for the info :-)