Closed nservant closed 5 months ago
Hello! Is the error consistent, i.e. occurs several time at the same place?
Yes. I also try to run it manually
singularity exec --no-home --pid -B OUTDIR/nf-core OUTDIR/nf-core/work/singularity/docker.io-trinityctat-starfusion-1.12.0.img /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl --genome_fa Homo_sapiens.GRCh38.102.all.fa --gtf Homo_sapiens.GRCh38.102.chr.gtf --annot_filter_rule AnnotFilterRule.pm --fusion_annot_lib CTAT_HumanFusionLib_Mar2021.dat.gz --pfam_db Pfam-A.hmm --dfam_db homo_sapiens_dfam.hmm --max_readlength 100 --CPU 2
same error
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "fr_FR.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
-found STAR at /usr/local/bin/STAR
-found makeblastdb at /usr/local/bin/makeblastdb
-found blastn at /usr/local/bin/blastn
-found dfamscan.pl at /usr/local/bin/dfamscan.pl
-found nhmmscan at /usr/local/bin/nhmmscan
-found hmmscan at /usr/local/bin/hmmscan
-- Skipping CMD: cp /data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/Homo_sapiens.GRCh38.102.all.fa /data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/ctat_genome_lib_build_dir/ref_genome.fa, checkpoint [/data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/ctat_genome_lib_build_dir/__chkpts/ref_genome.fa.ok] exists.
-- Skipping CMD: samtools faidx /data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/ctat_genome_lib_build_dir/ref_genome.fa, checkpoint [/data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/ctat_genome_lib_build_dir/__chkpts/ref_genome_fai.ok] exists.
-- Skipping CMD: makeblastdb -in /data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/ctat_genome_lib_build_dir/ref_genome.fa -dbtype nucl, checkpoint [/data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/ctat_genome_lib_build_dir/__chkpts/makeblastdb.ok] exists.
-- Skipping CMD: cp /data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/Homo_sapiens.GRCh38.102.chr.gtf /data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/ctat_genome_lib_build_dir/ref_annot.gtf, checkpoint [/data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.ok] exists.
-- Skipping CMD: bash -c " set -euxo pipefail; /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/util/gtf_to_exon_gene_records.pl /data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/ctat_genome_lib_build_dir/ref_annot.gtf | sort -k 1,1 -k4,4g -k5,5g | uniq > /data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu " , checkpoint [/data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.mini.sortu.ok] exists.
* Running CMD: STAR --runThreadN 2 --runMode genomeGenerate --genomeDir /data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --genomeFastaFiles /data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/Homo_sapiens.GRCh38.102.all.fa --limitGenomeGenerateRAM 40419136213 --genomeChrBinNbits 16 --sjdbGTFfile /data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/Homo_sapiens.GRCh38.102.chr.gtf --sjdbOverhang 100
Dec 19 15:54:05 ..... started STAR run
Dec 19 15:54:05 ... starting to generate Genome files
Dec 19 15:54:57 ..... processing annotations GTF
Dec 19 15:55:34 ... starting to sort Suffix Array. This may take a long time...
Dec 19 15:55:49 ... sorting Suffix Array chunks and saving them to disk...
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called recursively
Error, cmd: STAR --runThreadN 2 --runMode genomeGenerate --genomeDir /data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --genomeFastaFiles /data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/Homo_sapiens.GRCh38.102.all.fa --limitGenomeGenerateRAM 40419136213 --genomeChrBinNbits 16 --sjdbGTFfile /data/kdi_prod/.kdi/project_workspace_0/1983/acl/01.00/nf-core/work/aa/10e3b22515fa47363273ec82028fe0/Homo_sapiens.GRCh38.102.chr.gtf --sjdbOverhang 100 died with ret 134 No such file or directory at /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/lib/Pipeliner.pm line 186.
Pipeliner::run(Pipeliner=HASH(0x55dae81c0b88)) called at /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl line 460
Ok, here is a first possibility: https://github.com/alexdobin/STAR/issues/1620 not enough RAM
Thanks, I'll try !
there is no CUP requirement in the STARFUSION_BUILD
module. Does it mean that it is using the default in base.config
? ie. 6 Gb ?
process STARFUSION_BUILD {
tag 'star-fusion'
conda "bioconda::dfam=3.3 bioconda::hmmer=3.3.2 bioconda::star-fusion=1.12.0 bioconda::trinity=2.13.2 bioconda::samtools=1.9 bioconda::star=2.7.8a"
container "docker.io/trinityctat/starfusion:1.12.0"
You might have found it in the meantime but the requirements are specified in conf/modules.config: https://github.com/nf-core/rnafusion/blob/ffe9c09fb070e5675361e06543ca53fa3d29c470/conf/modules.config#L322-L325
It would be great to hear if you have solved the issue and how
I will assume this was a cluster dependent error that is now closed
Description of the bug
Hi, I try to build the references as follow ;
But the pipeline crashed when trying to build the STARfusion references ...
It seems that it crashes when building the STAR index with
died with ret 9 No such file or directory at /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/lib/Pipeliner.pm line 186
. But I checked and all required input files are in the work folder ... and singularity should be able to access them as it binds the current folder ...Any idea is welcome :) Thanks
Command used and terminal output
No response
Relevant files
No response
System information
No response