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TrinityCTAT / ctat-mutations

Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
https://github.com/TrinityCTAT/ctat-mutations
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changing tmp directory of singularity image #93

Open ConcettaDe4 opened 3 years ago

ConcettaDe4 commented 3 years ago

Hi! I am executing the the mutation lib integration utility using the singularity image ctat_mutations.v3.0.1.simg. I used the command:

singularity exec -e -B /home/RNAseq_project/trinity_cancer_transcriptome_toolkit/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir /home/RNAseq_project/trinity_cancer_transcriptome_toolkit/ctat_mutations.v3.0.1.simg /usr/local/src/ctat-mutations/mutation_lib_prep/ctat-mutation-lib-integration.py --genome_lib_dir /home/RNAseq_project/trinity_cancer_transcriptome_toolkit/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir

After I got the following error message:

INFO:    Converting SIF file to temporary sandbox...
FATAL:   while extracting /home/RNAseq_project/trinity_cancer_transcriptome_toolkit/ctat_mutations.v3.0.1.simg: root filesystem extraction failed: failed to copy content in staging file: write /tmp/rootfs-392536996/archive-411898547: no space left on device

I was wondering how I can change the tmp directory with singularity.

Thank you!

Concetta

joshua-gould commented 3 years ago

Please see https://sylabs.io/guides/3.7/user-guide/build_env.html#temporary-folders

On Tue, May 25, 2021 at 9:42 AM ConcettaDe4 @.***> wrote:

Hi! I am executing the the mutation lib integration utility using the singularity image ctat_mutations.v3.0.1.simg. I used the command:

singularity exec -e -B /home/RNAseq_project/trinity_cancer_transcriptome_toolkit/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir /home/RNAseq_project/trinity_cancer_transcriptome_toolkit/ctat_mutations.v3.0.1.simg /usr/local/src/ctat-mutations/mutation_lib_prep/ctat-mutation-lib-integration.py --genome_lib_dir /home/RNAseq_project/trinity_cancer_transcriptome_toolkit/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir

After I got the following error message:

INFO: Converting SIF file to temporary sandbox... FATAL: while extracting /home/RNAseq_project/trinity_cancer_transcriptome_toolkit/ctat_mutations.v3.0.1.simg: root filesystem extraction failed: failed to copy content in staging file: write /tmp/rootfs-392536996/archive-411898547: no space left on device

I was wondering how I can change the tmp directory with singularity.

Thank you!

Concetta

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ConcettaDe4 commented 3 years ago

Thank you. Now it works!