From 1df08f0e33c2e7a0f59748ca8906cca699c848a7 Mon Sep 17 00:00:00 2001
From: "julie.orjuela" <julie.orjuela@ird.fr>
Date: Wed, 17 Jul 2024 15:41:02 +0200
Subject: [PATCH] adding more logs error in slurm itrop cluster test
---
RNAja/snakefiles/Snakefile | 20 +++++++++++++++-----
1 file changed, 15 insertions(+), 5 deletions(-)
diff --git a/RNAja/snakefiles/Snakefile b/RNAja/snakefiles/Snakefile
index a3e416d..d82b467 100644
--- a/RNAja/snakefiles/Snakefile
+++ b/RNAja/snakefiles/Snakefile
@@ -473,7 +473,7 @@ rule stringtie :
tools_config["SINGULARITY"]["TOOLS"]
shell:
"""
- stringtie -p 8 -e -B -G {input.gtf} -o {output.gtf} -A {output.tsv} {input.bam} > 1>{log.output} 2>{log.error}
+ stringtie -p 8 -e -B -G {input.gtf} -o {output.gtf} -A {output.tsv} {input.bam} 1>{log.output} 2>{log.error}
"""
@@ -484,9 +484,12 @@ rule stringtie_gtf_list:
list_gtf = expand(f"{output_dir}"+"/COUNT/STRINGTIE/"+"{{mappers}}"+"/"+"{{mappers}}"+"_"+"{fastq}"+".gtf", fastq = SAMPLE_NAME),
output :
gtf_out = f'{output_dir}/COUNT/STRINGTIE/{{mappers}}/{{mappers}}_gtf_list.txt',
+ log:
+ output = f'{log_dir}/COUNT/STRINGTIE/{{mappers}}/{{mappers}}_gtf_list.o',
+ error = f'{log_dir}/COUNT/STRINGTIE/{{mappers}}/{{mappers}}_gtf_list.e'
shell:
"""
- find {input.list_gtf} >> {output.gtf_out}
+ find {input.list_gtf} 1>>{output.gtf_out} 2>{log.error}
"""
# Merge stringtie GTF
@@ -517,15 +520,19 @@ rule list_for_prepDE:
gtf = rules.stringtie_gtf_list.output.gtf_out
output:
list= f'{output_dir}/COUNT/STRINGTIE/{{mappers}}/{{mappers}}_Stringtie_list.txt'
+ log:
+ output = f'{log_dir}/COUNT/STRINGTIE/{{mappers}}/{{mappers}}_Stringtie_list.o',
+ error = f'{log_dir}/COUNT/STRINGTIE/{{mappers}}/{{mappers}}_Stringtie_list.e'
params:
dir = f"{output_dir}/COUNT/STRINGTIE/{{mappers}}"
shell:
"""
- cd {params.dir}
+ (cd {params.dir}
ls *.gtf | sed 's/.gtf//' - > names.txt
realpath *gtf > paths.txt
paste names.txt paths.txt > {output.list}
- rm names.txt paths.txt
+ rm names.txt paths.txt
+ ) 2>{log.error}
"""
@@ -537,11 +544,14 @@ rule prepDE_stringtie_table:
output :
gcsv = f'{output_dir}/COUNT/STRINGTIE/{{mappers}}/{{mappers}}_STRINGTIE_gene_count_matrix.csv',
tcsv = f'{output_dir}/COUNT/STRINGTIE/{{mappers}}/{{mappers}}_STRINGTIE_transcript_count_matrix.csv',
+ log:
+ output = f'{output_dir}/COUNT/STRINGTIE/{{mappers}}/{{mappers}}_STRINGTIE_gene_count_matrix.o',
+ error = f'{output_dir}/COUNT/STRINGTIE/{{mappers}}/{{mappers}}_STRINGTIE_gene_count_matrix.e',
singularity:
tools_config["SINGULARITY"]["TOOLS"]
shell:
"""
- prepDE.py -i {input.mergelist} -t {output.tcsv} -g {output.gcsv}
+ (prepDE.py -i {input.mergelist} -t {output.tcsv} -g {output.gcsv} ) 1>{log.output} 2>{log.error}
"""
rule htseq_count:
--
GitLab