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CGI-stLFR / CompleteWGS

Pipeline for combining stLFR and PCR free data
GNU General Public License v3.0
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The issues for relative and absolute path for the fast files in the sample list #2

Open wzhang42 opened 2 months ago

wzhang42 commented 2 months ago

Thanks you so much for your developing this stLFR pipelines. I just downloaded the demo fastq and use the same data to generate two types of sample list with relative file path and absolute file path respectively. The relative path can run successfully, but the version with absolute path do not work. Do not know how to solve and move forward. Thank you in advance The details:
I .) Sample list using relative path is as the following sample stlfr1 stlfr2 pcrfree1 pcrfree2 demo demo/stLFR_demo_1M_1.fq.gz demo/stLFR_demo_1M_2.fq.gz demo/PF_demo_1M_1.fq.gz demo/PF_demo_1M_2.fq.gz 2.) Sample list using the absolute path is as the following sample stlfr1 stlfr2 pcrfree1 pcrfree2 demo /research/groups/cab/projects/automapper/common/tchang1/Softwares/CompleteWGS/demo/stLFR_demo_1M_1.fq.gz /research/groups/cab/projects/automapper/common/tchang1/Softwares/CompleteWGS/demo/stLFR_demo_1M_2.fq.gz /research/groups/cab/projects/automapper/common/tchang1/Softwares/CompleteWGS/demo/PF_demo_1M_1.fq.gz /research/groups/cab/projects/automapper/common/tchang1/Softwares/CompleteWGS/demo/PF_demo_1M_2.fq.gz 3.) I used the same command to run. 4.) I found the nextflow pipeline run through step 1 parse_sample:toCsv. and generated a sample list.csv with delimiter as ','. The process > CWGS:fq (demo) for the two cases generated the same softlink for all the fast.gz (both link with the absolute file paths). with exitcode 0. 5.) But the nextflow.log indicate that the running using the absolute path is failed. the failure messages as the following :

[bc/d9cd18] NOTE: Missing output file(s) demo_stlfr_1.fq.gz expected by process CWGS:fq (demo) -- Execution is retried (1) [f7/3d66fd] Re-submitted process > CWGS:fq (demo) ERROR ~ Error executing process > 'CWGS:fq (demo)'

Caused by: Missing output file(s) demo_stlfr_1.fq.gz expected by process CWGS:fq (demo)

Command executed:

mv stLFR_demo_1M_1.fq.gz demo_stlfr_1.fq.gz mv stLFR_demo_1M_2.fq.gz demo_stlfr_2.fq.gz mv PF_demo_1M_1.fq.gz demo_pcrfree_1.fq.gz mv PF_demo_1M_2.fq.gz demo_pcrfree_2.fq.gz

Command exit status: 0

Command output: (empty)

Command error: -- env MBP_USAGE_LOGDIR|MBP_TASK_WORKSPACE='/research_jude/rgs01_jude/groups/cab/projects/automapper/common/tchang1/Softwares/CompleteWGS/CWGS_run_wz_fullpath/usage' -- writing USAGE to file: /research_jude/rgs01_jude/groups/cab/projects/automapper/common/tchang1/Softwares/CompleteWGS/CWGS_run_wz_fullpath/usage/tmpnxf.DoJ4h3xOuh..noderome157.1179913.USAGE

biancai3939 commented 1 month ago

@wzhang42 Please add -B /research/groups/cab/projects/automapper/common/tchang1/Softwares/CompleteWGS/demo in the command line. Sorry for the inconvenience, we will fix that in the next update.