get_software_versions error in v1.3 release

[ewels]

Originally posted by @cailiangliang765 in #33 (comment)

---

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 :-)

[laureheurtevin]

Hi,
I still met the "NOTE: Process STARindex (build_star_index) failed -- Execution is retried (1)"N E X T F L O W ~ version 22.10.0
Launching https://github.com/nf-core/dualrnaseq [festering_mandelbrot] DSL1 - revision: 3e35f4722e [master]

                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | |__ __ / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,'
nf-core/dualrnaseq v1.0.0

Pipeline Release : master
Run Name : festering_mandelbrot
Input : data/*{1,2}.fastq.gz
Host Fasta Ref : /work2/project/gafl/Data/Rosaceae/Prunus_persica/DNA/Ref_Genome/Prunus_persica-genome.v2.0.a1/Prunus_persica_NCBIv2/Prunus_persica_NCBIv2_genomic.fasta
Pathogen Fasta Ref: /work2/project/gafl/DADI/Peachrnaseq/DualRNAseq/test/refgenomes/prunus_monilinia.fasta
Host tRNA gff Ref : false
Host genome gff Ref: /work2/project/gafl/Data/Rosaceae/Prunus_persica/DNA/Ref_Genome/Prunus_persica-genome.v2.0.a1/Prunus_persica_NCBIv2/Prunus_persica_NCBIv2_genomic.gff3
Pathogen genome gff Ref: /work2/project/gafl/DADI/Peachrnaseq/DualRNAseq/test/refgenomes/prunus_monilinia.gff
Data Type : Paired-End
Max Resources : 256 GB memory, 60 cpus, 5d 8h time per job
Container : singularity - nfcore/dualrnaseq:1.0.0
Output dir : ./results
Launch dir : /work2/project/gafl/DADI/Peachrnaseq/DualRNAseq/jacques/dualrnaseq
Working dir : /work2/project/gafl/DADI/Peachrnaseq/DualRNAseq/jacques/dualrnaseq/work_test
Script dir : /work2/project/gafl/DADI/Peachrnaseq/DualRNAseq/.nextflow/assets/nf-core/dualrnaseq
User : lheurtevin
Config Profile : laure
Config Profile Description: prunus vs monilia pipeline function
Config Files : /work2/project/gafl/DADI/Peachrnaseq/DualRNAseq/.nextflow/assets/nf-core/dualrnaseq/nextflow.config, /work2/project/gafl/DADI/Peachrnaseq/DualRNAseq/jacques/dualrnaseq/nextflow.config

[- ] process > get_software_versions -
[- ] process > check_replicates -
[- ] process > uncompress_pathogen_fasta_g... -
[- ] process > uncompress_host_fasta_genome -
[- ] process > uncompress_pathogen_gff -
Pulling Singularity image docker://nfcore/dualrnaseq:1.0.0 [cache /work2/project/gafl/DADI/Peachrnaseq/DualRNAseq/jacques/dualrnaseq/work_test/singularity/nfcore-dualrnaseq-1.0.0.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /work2/project/gafl/DADI/Peachrnaseq/DualRNAseq/jacques/dualrnaseq/work_test/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location
executor > local (50)
[ee/36330f] process > get_software_versions [100%] 1 of 1 ✔
[5e/7a8f66] process > check_replicates (check_rep... [100%] 1 of 1 ✔
[4d/41624b] process > uncompress_pathogen_fasta_g... [100%] 1 of 1 ✔
[3f/fb7cfc] process > uncompress_host_fasta_genom... [100%] 1 of 1 ✔
[22/e10439] process > uncompress_pathogen_gff (un... [100%] 1 of 1 ✔
[d9/6cc8d1] process > uncompress_host_gff (uncomp... [100%] 1 of 1 ✔
[67/1c9a5b] process > combine_pathogen_host_fasta... [100%] 1 of 1 ✔
[db/00db48] process > extract_reference_names_hos... [100%] 1 of 1 ✔
[2d/aa53b4] process > extract_reference_names_pat... [100%] 1 of 1 ✔
[ec/a5b1eb] process > fastqc (Bolinha_J15_R1) [100%] 12 of 12 ✔
[54/a657c3] process > bbduk (Bolinha_J15_R1) [100%] 12 of 12 ✔
[82/13b093] process > fastqc_after_trimming (Boli... [100%] 12 of 12 ✔
[e8/a4784b] process > count_total_reads (count_to... [100%] 1 of 1 ✔
[b5/ea9b42] process > count_total_read_pairs (cou... [100%] 1 of 1 ✔
[65/ae84a0] process > STARindex (build_star_index) [ 50%] 1 of 2, failed: 1...
[- ] process > ALIGNMENTstar -
[- ] process > remove_crossmapped_reads -
[- ] process > extract_processed_reads_STAR -
[- ] process > collect_processed_reads_STAR -
[- ] process > unique_mapping_stats_STAR -
[- ] process > collect_stats_STAR_uniquely... -
[- ] process > count_crossmapped_reads -
[- ] process > multi_mapping_stats -
[- ] process > collect_stats_STAR_multi_ma... -
[- ] process > star_mapping_stats -
[- ] process > plot_star_mapping_stats -
[- ] process > multiqc -
[18/5c77fd] process > output_documentation [100%] 1 of 1 ✔
[54/10f034] NOTE: Process STARindex (build_star_index) failed -- Execution is retried (1)
Many thanks for your help.