Bonjour,
j'ai une erreur en écriture et je sais pas trop d'où ça vient. A priori il y a de la place dans le projet. Est-ce que ça vient de la RAM ou du fait que j'ai trop de jobs en parallèle qui écrivent au même endroit?
Je vous mets la sortie de snakemake:
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 mergeGTF
1
[Thu Jul 29 12:38:29 2021]
rule mergeGTF:
input: /shared/projects/bi4edc/mm39/gencode.vM27.annotation.gtf
output: /shared/projects/repeats/RASflow_IFB/results/Dnmt1/mapping_HISAT2/repeats_featureCounts/merge_genes_te.gtf, /shared/projects/repeats/RASflow_IFB/results/Dnmt1/mapping_HISAT2/repeats_featureCountsNgenes.txt
jobid: 0
cat: erreur d'écriture: Ne peut allouer de la mémoire
[Thu Jul 29 12:38:42 2021]
Error in rule mergeGTF:
jobid: 0
output: /shared/projects/repeats/RASflow_IFB/results/Dnmt1/mapping_HISAT2/repeats_featureCounts/merge_genes_te.gtf, /shared/projects/repeats/RASflow_IFB/results/Dnmt1/mapping_HISAT2/repeats_featureCountsNgenes.txt
shell:
mkdir -p /shared/projects/repeats/RASflow_IFB/results/Dnmt1/mapping_HISAT2/repeats_featureCounts
cat /shared/projects/bi4edc/mm39/gencode.vM27.annotation.gtf /shared/projects/bi4edc/mm39/mm39_TE_rmsk.gtf > /shared/projects/repeats/RASflow_IFB/results/Dnmt1/mapping_HISAT2/repeats_featureCounts/merge_genes_te.gtf
awk '$3=="gene"' /shared/projects/bi4edc/mm39/gencode.vM27.annotation.gtf | wc -l > /shared/projects/repeats/RASflow_IFB/results/Dnmt1/mapping_HISAT2/repeats_featureCountsNgenes.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Removing output files of failed job mergeGTF since they might be corrupted:
/shared/projects/repeats/RASflow_IFB/results/Dnmt1/mapping_HISAT2/repeats_featureCounts/merge_genes_te.gtf
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Merci de votre aide!
Magali