brianjohnhaas
commented
2 years ago Hi,
The system was built around gencode data. You can probably get it to work with your inputs, but you might need to remove the --human_gencode_filter parameter. The --human_gencode_filter helps deal with a handful of otherwise difficult to capture fusions with human data.
On Tue, Sep 7, 2021 at 1:38 PM anoronh4 @.***> wrote:
i am seeing the error:
Error, cmd: bash -c "set -euxo pipefail; cat /refbuild/GRCh37/starfusion/../annotation/Homo_sapiens.GRCh37.75.gtf | egrep 'IG_V_gene|IG_C_gene|IG_D_gene|IG_J_gene' | awk '{ if (\$3 == \"exon\") { print } }' | egrep ^chr14 > __gencode_refinement_chkpts/IGH_locus.gtf" died with ret 256 No such file or directory at /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/util/../lib/Pipeliner.pm line 186. Pipeliner::run(Pipeliner=HASH(0x55e9885d75a8)) called at /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/util/revise_gencode_annotations.pl line 115 Error, cmd: /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/util/revise_gencode_annotations.pl --gencode_gtf /refbuild/GRCh37/starfusion/../annotation/Homo_sapiens.GRCh37.75.gtf --out_gtf /refbuild/GRCh37/starfusion/../annotation/Homo_sapiens.GRCh37.75.gtf.revised.gtf died with ret 512 No such file or directory at /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/lib/Pipeliner.pm line 186. Pipeliner::run(Pipeliner=HASH(0x560a404fd2a8)) called at /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl line 460
the singularity cmd i am running with is certainly able to access the gtf file:
singularity exec \ -B /refbuild \ /toolsdir/starfusion_1.10.1.sif \ /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl \ --genome_fa /refbuild/GRCh37/genome/Homo_sapiens.GRCh37.dna.primary_assembly.fa \ --gtf /refbuild/GRCh37/annotation/Homo_sapiens.GRCh37.75.gtf \ --pfam_db current \ --dfam_db human \ --fusion_annot_lib /refbuild/other/starfusion_resources/GRCh37_gencode_v19_CTAT_lib_Mar012021.source.tar.gz \ --human_gencode_filter \ --annot_filter_rule /refbuild/other/starfusion_resources/AnnotFilterRule.pm
The output file __gencode_refinement_chkpts/IGH_locus.gtf is created but has no content. Could the cause be that egrep ^chr14 returns no matches? The format of the chromosomes is ^14 rather than ^chr14. can that be easily fixed?
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
anoronh4
abhijitswain09
i am seeing the error:
the singularity cmd i am running with is certainly able to access the gtf file:
The output file
__gencode_refinement_chkpts/IGH_locus.gtfis created but has no content. Could the cause be thategrep ^chr14returns no matches? The format of the chromosomes is^14rather than^chr14. can that be easily fixed?