STAR-Fusion error in tutorial

[Tadashi Kondo]

Hello !

I'm getting an error message in tutorial on STAR-FUSION.

I installed STAR-FUSION 1.6.1 via bioconda on supercomputer two weeks ago.

./prep_genome_lib.pl --genome_fa ../STAR-Fusion-Tutorial-0.0.1/minigenome.fa --gtf ../STAR-Fusion-Tutorial-0.0.1/minigenome.gtf --fusion_annot_lib ../STAR-Fusion-Tutorial-0.0.1/CTAT_HumanFusionLib.mini.dat.gz --dfam_db human

The error message is below:

-found STAR at /home/renoguch/miniconda3/envs/star-fusion/bin/STAR

-found makeblastdb at /home/renoguch/miniconda3/envs/star-fusion/bin/makeblastdb

-found blastn at /home/renoguch/miniconda3/envs/star-fusion/bin/blastn

-found dfamscan.pl at /home/renoguch/miniconda3/envs/star-fusion/bin/dfamscan.pl

-found nhmmscan at /home/renoguch/miniconda3/envs/hmmer/bin/nhmmscan

-- Skipping CMD: wget http://dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/homo_sapiens_dfam.hmm, checkpoint [/rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/_dfam_db_prep_chckpts/dfam..ok] exists.
-- Skipping CMD: wget http://dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3f, checkpoint [/rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/_dfam_db_prep_chckpts/dfam.h3f.ok] exists.
-- Skipping CMD: wget http://dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3i, checkpoint [/rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/_dfam_db_prep_chckpts/dfam.h3i.ok] exists.
-- Skipping CMD: wget http://dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3m, checkpoint [/rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/_dfam_db_prep_chckpts/dfam.h3m.ok] exists.
-- Skipping CMD: wget http://dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3p, checkpoint [/rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/_dfam_db_prep_chckpts/dfam.h3p.ok] exists.
-- Skipping CMD: cp /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/../STAR-Fusion-Tutorial-0.0.1/minigenome.fa /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/ctat_genome_lib_build_dir/ref_genome.fa, checkpoint [/rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/ctat_genome_lib_build_dir/__chkpts/ref_genome.fa.ok] exists.
-- Skipping CMD: samtools faidx /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/ctat_genome_lib_build_dir/ref_genome.fa, checkpoint [/rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/ctat_genome_lib_build_dir/__chkpts/ref_genome_fai.ok] exists.
-- Skipping CMD: makeblastdb -in /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/ctat_genome_lib_build_dir/ref_genome.fa -dbtype nucl, checkpoint [/rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/ctat_genome_lib_build_dir/__chkpts/makeblastdb.ok] exists.
-- Skipping CMD: cp /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/../STAR-Fusion-Tutorial-0.0.1/minigenome.gtf /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/ctat_genome_lib_build_dir/ref_annot.gtf, checkpoint [/rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.ok] exists.
-- Skipping CMD: bash -c " set -euxo pipefail; /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/util/gtf_to_exon_gene_records.pl /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/ctat_genome_lib_build_dir/ref_annot.gtf  | sort -k 1,1 -k4,4g -k5,5g | uniq  > /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu " , checkpoint [/rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.mini.sortu.ok] exists.
* Running CMD: STAR --runThreadN 4 --runMode genomeGenerate --genomeDir /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/ctat_genome_lib_build_dir/ref_genome.fa.star.idx   --genomeFastaFiles /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/../STAR-Fusion-Tutorial-0.0.1/minigenome.fa  --limitGenomeGenerateRAM 40419136213  --genomeChrBinNbits 16  --sjdbGTFfile /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/../STAR-Fusion-Tutorial-0.0.1/minigenome.gtf  --sjdbOverhang 150
        /home/renoguch/miniconda3/envs/star-fusion/bin/STAR-avx2 --runThreadN 4 --runMode genomeGenerate --genomeDir /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --genomeFastaFiles /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/../STAR-Fusion-Tutorial-0.0.1/minigenome.fa --limitGenomeGenerateRAM 40419136213 --genomeChrBinNbits 16 --sjdbGTFfile /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/../STAR-Fusion-Tutorial-0.0.1/minigenome.gtf --sjdbOverhang 150
        STAR version: 2.7.10b   compiled: 2023-05-25T06:56:23+0000 :/opt/conda/conda-bld/star_1684997536154/work/source
Jun 21 16:39:21 ..... started STAR run
Jun 21 16:39:21 ... starting to generate Genome files
Jun 21 16:39:22 ..... processing annotations GTF
!!!!! WARNING: --genomeSAindexNbases 14 is too large for the genome size=11114668, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 10
Jun 21 16:39:23 ... starting to sort Suffix Array. This may take a long time...
Jun 21 16:39:23 ... sorting Suffix Array chunks and saving them to disk...
Jun 21 16:39:26 ... loading chunks from disk, packing SA...
Jun 21 16:39:26 ... finished generating suffix array
Jun 21 16:39:26 ... generating Suffix Array index
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
/home/renoguch/miniconda3/envs/star-fusion/bin/STAR: 8 行: 50743 中止                  (コアダンプ) "${cmd}" "$@"
Error, cmd: STAR --runThreadN 4 --runMode genomeGenerate --genomeDir /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/ctat_genome_lib_build_dir/ref_genome.fa.star.idx   --genomeFastaFiles /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/../STAR-Fusion-Tutorial-0.0.1/minigenome.fa  --limitGenomeGenerateRAM 40419136213  --genomeChrBinNbits 16  --sjdbGTFfile /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/../STAR-Fusion-Tutorial-0.0.1/minigenome.gtf  --sjdbOverhang 150  died with ret 34304 No such file or directory at /rshare1/ZETTAI_path_WA_slash_home_KARA/home/renoguch/miniconda3/envs/star-fusion/lib/STAR-Fusion/ctat-genome-lib-builder/lib/Pipeliner.pm line 186.
        Pipeliner::run(Pipeliner=HASH(0x5610a6789400)) called at ./prep_genome_lib.pl line 460

What should I do for solution of the error message ?

Ray

 

[Brian Haas]

Looks like an out of memory error. It needs 40 to 50 G of Ram 

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Tadashi Kondo]

Thanks for your quick reply.

Your advice made my run successful.

Sincerely yours,

Ray

2023年6月21日水曜日 21:56:39 UTC+9 bh...@broadinstitute.org: