STAR index issues to the step 4
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0
Entering edit mode
5 months ago
aka ▴ 10

I am trying to index a reference genome on a pipeline with snakemake and I made this rule:

rule reference_faidx_star:
input:
"../resources/reference/Qrob_PM1N.fa"
output:
"../resources/reference/ref/"
log:
"../results/logs/star/star_index.log"
params:
gtf= "../resources/reference/gff_gtf/Qrob_PM1N_genes_20161004.gtf"
# resources:
#     mem_mb=25000
message:
"""
INDEX STAR
"""
shell:
"STAR --runMode genomeGenerate --runThreadN {threads} --genomeDir {output} --genomeFastaFiles {input} --sjdbGTFfile {params.gtf} --sjdbOverhang 149 --genomeSAindexNbases 12 " # Logging


At first everything works but there is a break at step 4. Only 4 files are created in my folder: chrLength.txt, chrNameLength.txt, chrName.txt, chrStart.txt, and the terminal displays this:

[Tue Apr 20 09:09:30 2021]
Job 4:
INDEX STAR

Apr 20 09:09:30 ..... started STAR run
Apr 20 09:09:30 ... starting to generate Genome files
Apr 20 09:09:50 ... starting to sort Suffix Array. This may take a long time...
Apr 20 09:09:55 ... sorting Suffix Array chunks and saving them to disk...
/usr/bin/bash : ligne 1 :  7343 Processus arrêté      STAR --runMode genomeGenerate --runThreadN 1 --genomeDir ../resources/reference/ref/ --genomeFastaFiles ../resources/reference/Qrob_PM1N.fa --sjdbGTFfile ../resources/reference/gff_gtf/Qrob_PM1N_genes_20161004.gtf --sjdbOverhang 149 --genomeSAindexNbases 12 -limitGenomeGenerateRAM 25000000000
[Tue Apr 20 09:10:01 2021]
Error in rule reference_faidx_star:
jobid: 4
output: ../resources/reference/ref/
log: ../results/logs/star/star_index.log (check log file(s) for error message)
shell:
STAR --runMode genomeGenerate --runThreadN 1 --genomeDir ../resources/reference/ref/ --genomeFastaFiles ../resources/reference/Qrob_PM1N.fa --sjdbGTFfile ../resources/reference/gff_gtf/Qrob_PM1N_genes_20161004.gtf --sjdbOverhang 149 --genomeSAindexNbases 12
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)


I don't understand what is wrong with this rule, where I don't write in bash?

I hope you can help me. Thank you, Have a nice day!

pipeline snakemake STAR mapping • 246 views
1
Entering edit mode

The error has nothing to do with bash. Snakmake is telling you that it runs in bash strict mode, which is information you might need for debugging,

AFAIK, to state that a directory would exist at the end of a rule, you need to specify directory("../resources/reference/ref/"), not just ../resources/reference/ref/. Check the files under the .snakemake directory to see if any of them have the exact error message.

Also, step 4 has nothing to do with your error. What is the content of ../results/logs/star/star_index.log?

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Entering edit mode

Apparently, the problem is that I was not running it with multiple threads. I need 4 threads.

For the directory it is not necessary to specify directory("../resources/reference/ref/") I can use the path directly normally.