Rnaseq: -profile standard needed for base config

[tiagochst]

Running the last version crashes in the get_software_versions function. There are also a couple of warnings.

nf-core/rnaseq : RNA-Seq Best Practice v1.5dev
=======================================================
WARN: Access to undefined parameter `max_time` -- Initialise it to a default value eg. `params.max_time = some_value`
WARN: Access to undefined parameter `maxMultiqcEmailFileSize` -- Initialise it to a default value eg. `params.maxMultiqcEmailFileSize = some_value`
Run Name       : ecstatic_tuckerman
Reads          : data/*{1,2}.fastq.gz
Data Type      : Paired-End
Genome         : false
Strandedness   : None
Trim R1        : 0
Trim R2        : 0
Trim 3' R1     : 0
Trim 3' R2     : 0
Aligner        : STAR
STAR Index     : /home/houtan/genome/hg38/
GTF Annotation : /home/houtan/genome/hg38/gencode.v28.primary_assembly.annotation.gtf
Save Reference : No
Save Trimmed   : No
Save Intermeds : No
Max Memory     : 30.GB
Max CPUs       : 1
Max Time       : null
Output dir     : data_results_hg38_gencodev28/
Working dir    : /home/houtan/ESCA/RNA-seq/PPARG/work
Container      : [:]
Current home   : /home/houtan
Current user   : root
Current path   : /home/houtan/ESCA/RNA-seq/PPARG
Script dir     : /home/houtan/my-pipelines/rnaseq
Config Profile : docker
E-mail Address : [email protected]
MultiQC maxsize: null
=========================================
[warm up] executor > local
[88/047082] Submitted process > fastqc (33-siPPARG-SA09470_S74_L008_R)
[39/296ecf] Submitted process > makeBED12 (gencode.v28.primary_assembly.annotation.gtf)
[be/69df32] Submitted process > fastqc (33-Negative-SA09464_S68_L008_R)
[25/a0191b] Submitted process > trim_galore (33-Negative-SA09464_S68_L008_R)
[f7/0072a3] Submitted process > trim_galore (33-siPPARG-SA09470_S74_L008_R)
[bc/bbf9df] Submitted process > get_software_versions
[4c/82642e] Cached process > workflow_summary_mqc
ERROR ~ Error executing process > 'get_software_versions'

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

Command executed:

  echo 1.5dev &> v_ngi_rnaseq.txt
  echo 0.30.1 &> 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
  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:
  127

Command output:
  (empty)

[ewels]

Hi @tiagochst,

Is this with nextflow version 0.30.0 by any chance? If so then try updating to 0.30.1 as there was some problem with the way it handles params.

I also pushed a bunch of changes to the pipeline earlier today, so may be worth pulling those again.

Phil

[tiagochst]

The problem happend using nextflow version0.30.1.4844. Let me try to update everything. But I'm quite sure I have the last version.

[tiagochst]

Yes, both last versions.

[ewels]

Thanks for this, I'll clear up the warnings about the missing param values. What command and config profiles are you using when you launch this? I'm confused about the get_software_versions thing as it works in my tests. Are you using docker / singularity / conda etc for your software?

[tiagochst]

I'm using docker. I was able to run the docker and run all the get_software_versions code.
I'm not sure what the problem is.

nextflow run  /home/houtan/my-pipelines/rnaseq \
     -profile docker \
     --star_index "/home/houtan/genome/hg38/" \
     --fasta "/home/houtan/genome/hg38/GRCh38.primary_assembly.genome.fa" \
     --gtf "/home/houtan/genome/hg38/gencode.v28.primary_assembly.annotation.gtf" \
     --max_memory 30.GB  \
     --memory 30.GB \
     --max_cpus 1 \
     --reads 'data/*{1,2}.fastq.gz' \
     --email  '[email protected]' \
     -resume \
     --outdir 'data_results_hg38_gencodev28/'

[tiagochst]

Also, the container is in the log is shown to be: Container : [:].

[ewels]

I think you need -profile standard,docker. Currently the docker profile doesn’t have the base config and is designed to be combined with others. This is very new and not documented yet. It’s also not ideal - I think I will look into updating this so that it does work with -profile docker in the future.

[tiagochst]

Thanks! It is working!

[apeltzer]

Hm, not sure how to proceed with this:

Should we have a central profile for this now? I'd also be happy to say the default profile is using -profile standard,docker and just document it for example. Any ideas on that @ewels ?

[apeltzer]

Discussion with phil:

• get rid of standard profile
• import base in general (independent of profile)
• Just use hardware specific configs for each entity

Take care of iGenomes stuff.

[apeltzer]

This is done in the new release coming 👍

[cailiangliang765]

This is done in the new release coming 👍

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]

Hi @cailiangliang765,

I've moved your comment to a new issue (#186), we can discuss there.

Phil