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nf-core / rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
https://nf-co.re/rnaseq
MIT License
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All results are empty! #778

Closed Raysun61 closed 2 years ago

Raysun61 commented 2 years ago

Description of the bug

My results are empty! But I find that it's available when the process is running.

I'm trying to run nf-core/rnaseq. There is nothing about error when it's running, however, all files are blank!

Command used and terminal output

nextflow run nf-core-rnaseq-7106bd7/ -name rnaseq_test_6 -profile docker -params-file nf-params.json

Relevant files

image image

Below's what it looks like when it's running

image

System information

N E X T F L O W version 22.02.0-edge build 5682 created 25-02-2022 10:37 UTC (18:37 CDT) cite doi:10.1038/nbt.3820 http://nextflow.io

I forgot "--outdir" in rnaseq_test_6, and the PATH of input_data is wrong, so there are three runs. $ nextflow log TIMESTAMP DURATION RUN NAME STATUS REVISION ID SESSION ID COMMAND 2022-03-05 17:03:38 - rnaseq_test_6 - 6b989c60f8 21b87a94-4801-442d-a9d8-aa6480bc26eb nextflow run nf-core-rnaseq-7106bd7/ -name rnaseq_test_6 -profile docker -params-file nf-params.json 2022-03-05 17:05:58 - rnaseq_test_7 - 6b989c60f8 bf99c073-5479-4c8a-ac42-f9ad97a55888 nextflow run nf-core-rnaseq-7106bd7/ -name rnaseq_test_7 -profile docker -params-file nf-params.json --outdir /home/sunlei/tmp/nextflow_v3 2022-03-05 17:14:18 8h 39m 40s rnaseq_test_8 OK 6b989c60f8 04466156-b30d-4c85-9779-5285be85f182 nextflow run nf-core-rnaseq-7106bd7/ -name rnaseq_test_8 -profile docker -params-file nf-params.json --outdir /home/sunlei/tmp/nextflow_v3

I changed the name (such as .nextflow.log.1 to nextflow_1.log ...) nextflow.log nextflow_1.log nextflow_2.log nextflow_3.log

$ cat nf-params.json { "input": "\/home\/sunlei\/tmp\/nextflow_v3\/input.csv", "fasta": "\/home\/sunlei\/rna-seq\/PRJNA547876\/0.raw_data\/hic\/genome.fasta", "gff": "\/home\/sunlei\/rna-seq\/PRJNA547876\/0.raw_data\/New_Out.GeneModels.gff", "aligner": "hisat2", }

$ cat /etc/centos-release CentOS Linux release 7.6.1810 (Core) $ cat /proc/version Linux version 3.10.0-957.el7.x86_64 (mockbuild@kbuilder.bsys.centos.org) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-36) (GCC) ) #1 SMP Thu Nov 8 23:39:32 UTC 2018

drpatelh commented 2 years ago

Initial tests with the latest stable version of NF don't show any issues. I tested this with Gitpod using the master branch which is the same code as v3.6.

nf-core/rnaseq :v3.6 Nextflow: version 21.10.6 build 5660

$ nextflow run main.nf -profile test,docker --outdir ./results
$ ls -la results/fastqc/
total 7612
drwxr-xr-x 2 gitpod gitpod   4096 Mar  7 08:58 .
drwxr-xr-x 9 gitpod gitpod    122 Mar  7 09:16 ..
-rw-r--r-- 1 gitpod gitpod 605617 Mar  7 08:54 RAP1_IAA_30M_REP1_1_fastqc.html
-rw-r--r-- 1 gitpod gitpod 361805 Mar  7 08:54 RAP1_IAA_30M_REP1_1_fastqc.zip
-rw-r--r-- 1 gitpod gitpod 612191 Mar  7 08:54 RAP1_IAA_30M_REP1_2_fastqc.html
-rw-r--r-- 1 gitpod gitpod 354078 Mar  7 08:54 RAP1_IAA_30M_REP1_2_fastqc.zip
-rw-r--r-- 1 gitpod gitpod 607358 Mar  7 08:54 RAP1_UNINDUCED_REP1_fastqc.html
-rw-r--r-- 1 gitpod gitpod 362502 Mar  7 08:54 RAP1_UNINDUCED_REP1_fastqc.zip
-rw-r--r-- 1 gitpod gitpod 604612 Mar  7 08:58 RAP1_UNINDUCED_REP2_fastqc.html
-rw-r--r-- 1 gitpod gitpod 363643 Mar  7 08:58 RAP1_UNINDUCED_REP2_fastqc.zip
-rw-r--r-- 1 gitpod gitpod 609132 Mar  7 08:58 WT_REP1_1_fastqc.html
-rw-r--r-- 1 gitpod gitpod 366447 Mar  7 08:58 WT_REP1_1_fastqc.zip
-rw-r--r-- 1 gitpod gitpod 614432 Mar  7 08:58 WT_REP1_2_fastqc.html
-rw-r--r-- 1 gitpod gitpod 356587 Mar  7 08:58 WT_REP1_2_fastqc.zip
-rw-r--r-- 1 gitpod gitpod 607871 Mar  7 08:56 WT_REP2_1_fastqc.html
-rw-r--r-- 1 gitpod gitpod 361600 Mar  7 08:56 WT_REP2_1_fastqc.zip
-rw-r--r-- 1 gitpod gitpod 614095 Mar  7 08:56 WT_REP2_2_fastqc.html
-rw-r--r-- 1 gitpod gitpod 354509 Mar  7 08:56 WT_REP2_2_fastqc.zip

$ head results/fastqc/RAP1_IAA_30M_REP1_1_fastqc.html

<html><head><title>RAP1_IAA_30M_REP1_1.fastq.gz FastQC Report</title><style type="text/css">
 @media screen {
  div.summary {
    width: 18em;
    position:fixed;
    top: 3em;
    margin:1em 0 0 1em;
  }

  div.main {

I tried to test with version 22.02.0-edge but encountered an unrelated error as reported in https://github.com/nf-core/tools/issues/1428 with the Gitpod environment so need to find a way to test with this version.

In the meantime, it would be great to have more information please @Raysun61 including the .nextflow.log file, nf-params.json and some more information about your infrastructure. It may also be worth testing the latest stable version of NF which worked for me:

NXF_VER=21.10.6 nextflow run nf-core-rnaseq-7106bd7/ -name rnaseq_test_6 -profile docker -params-file nf-params.json
Raysun61 commented 2 years ago

Thanks, I'll try to run with version 21.10.6. And I added some information in description. @drpatelh

drpatelh commented 2 years ago

Hi @Raysun61 ! This appears to be an issue with your local set-up because the files for the full-sized tests for v3.6 are published as expected and available on the website for browsing e.g. FastQC.

Will close this for now but let me know if the problem persists.