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Trouble running index_pfam_domain_info.pl #14
Comments
Hi,
couple questions.
Are the 'Skipping' messages appearing because it failed earlier and you're
rerunning the original command? If so, that would make sense.
Do you find the file:
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz
?
or is PFAM.domtblout.dat.gz found in the working directory where you're
running the prep command?
best,
~b
…On Thu, Mar 2, 2023 at 11:44 AM Emily Hoskins ***@***.***> wrote:
Hello!
I'm building a ctat_genome_library in preparation to run STAR-Fusion, but
I came across an error when I ran "prep_genome_lib.pl". It ran into an
issue when trying to run "index_pfam_domain_info.pl". I'm not sure how to
resolve this issue, could you help figure out what I need to do? Here is
implementation:
/fs/project/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/
prep_genome_lib.pl --genome_fa GRCh38.d1.vd1.fa --pfam_db current --gtf
gencode.v36.annotation.gtf --fusion_annot_lib fusion_lib.Mar2021.dat.gz
--dfam_db human
And here is the output (error on the last line):
-found STAR at
/fs/project/PAS0854/Software/STAR_Latest/STAR-2.7.0f/bin/Linux_x86_64/STAR
-found makeblastdb at /usr/local/blast/2.10.0+/bin/makeblastdb
-found blastn at /usr/local/blast/2.10.0+/bin/blastn
-found dfamscan.pl at /users/PAS0854/hosk13/.conda/envs/orien/bin/
dfamscan.pl
-found nhmmscan at /usr/local/hmmer/3.3.2/bin/nhmmscan
-found hmmscan at /usr/local/hmmer/3.3.2/bin/hmmscan
-- Skipping CMD: wget
http://dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/homo_sapiens_dfam.hmm,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_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
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_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
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_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
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_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
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_dfam_db_prep_chckpts/dfam.h3p.ok]
exists.
-- Skipping CMD: wget
ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_pfam_db_prep_chckpts/pfam_wget.ok]
exists.
-- Skipping CMD: gunzip Pfam-A.hmm.gz, checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_pfam_db_prep_chckpts/pfam_gunzip.ok]
exists.
-- Skipping CMD: hmmpress Pfam-A.hmm, checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_pfam_db_prep_chckpts/pfam_hmmpress.ok]
exists.
-- Skipping CMD: cp
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/GRCh38.d1.vd1.fa
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_genome.fa,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/ref_genome.fa.ok]
exists.
-- Skipping CMD: samtools faidx
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_genome.fa,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/ref_genome_fai.ok]
exists.
-- Skipping CMD: makeblastdb -in
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_genome.fa
-dbtype nucl, checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/makeblastdb.ok]
exists.
-- Skipping CMD: cp
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/gencode.v36.annotation.gtf
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.ok]
exists.
-- Skipping CMD: bash -c " set -euxo pipefail;
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
gtf_to_exon_gene_records.pl
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf
| sort -k 1,1 -k4,4g -k5,5g | uniq >
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
" , checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.mini.sortu.ok]
exists.
-- Skipping CMD: STAR --runThreadN 4 --runMode genomeGenerate --genomeDir
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_genome.fa.star.idx
--genomeFastaFiles
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/GRCh38.d1.vd1.fa
--limitGenomeGenerateRAM 40419136213 --genomeChrBinNbits 16 --sjdbGTFfile
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/gencode.v36.annotation.gtf
--sjdbOverhang 150 , checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/build.ok]
exists.
-- Skipping CMD:
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
gtf_to_gene_spans.pl
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf
>
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.gene_spans.ok]
exists.
-- Skipping CMD:
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
gtf_file_to_feature_seqs.pl --gtf_file
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf
--genome_fa
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_genome.fa
--seqType CDSplus > ref_annot.cdsplus.fa, checkpoint
[__loc_chkpts/ref_annot.cdsplus.fa.ok] exists.
-- Skipping CMD:
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
dfam_repeat_masker.pl --dfam_hmm homo_sapiens_dfam.hmm --target_fa
ref_annot.cdsplus.fa --out_masked ref_annot.cdsplus.dfam_masked.fa --CPU 4,
checkpoint [__loc_chkpts/ref_annot.cdsplus.dfam_masked.fa.ok] exists.
-- Skipping CMD: cp ref_annot.cdsplus.dfam_masked.fa
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/ref_annot.cdsplus.dfam_masked.fa.cp.ok]
exists.
-- Skipping CMD:
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
index_cdna_seqs.pl
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/ref_annot.cdsplus.dfam_masked.fa.idx.ok]
exists.
-- Skipping CMD: makeblastdb -in ref_annot.cdsplus.dfam_masked.fa -dbtype
nucl, checkpoint [__loc_chkpts/ref_annot.cdsplus.dfam_masked.fa.blidx.ok]
exists.
-- Skipping CMD: blastn -query ref_annot.cdsplus.dfam_masked.fa -db
ref_annot.cdsplus.dfam_masked.fa -max_target_seqs 10000 -outfmt 6 -evalue
1e-10 -num_threads 4 -dust no -lcase_masking >
ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6, checkpoint
[__loc_chkpts/ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.ok] exists.
-- Skipping CMD: bash -c " set -euxo pipefail;
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
blast_outfmt6_replace_trans_id_w_gene_symbol.pl
ref_annot.cdsplus.dfam_masked.fa
ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6 | gzip >
ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.gz" , checkpoint
[__loc_chkpts/ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.gz.ok]
exists.
-- Skipping CMD: bash -c " set -euxo pipefail;
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
blast_select_single_per_gene_pair.pl
ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.gz | gzip >
ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.best.gz" ,
checkpoint
[__loc_chkpts/ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.best.gz.ok]
exists.
-- Skipping CMD: bash -c " set -euxo pipefail;
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
filter_overlapping_blast_hits.pl
ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.best.gz
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans
| gzip >
ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.best.overlaps_filt.gz"
, checkpoint
[__loc_chkpts/ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.best.overlaps_filt.ok]
exists.
-- Skipping CMD: cp
ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.best.overlaps_filt.gz
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/blast_pairs.dat.gz,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/cp_gene_blast_pairs.ok]
exists.
-- Skipping CMD:
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
index_blast_pairs.pl
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/blast_pairs.idx
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/blast_pairs.dat.gz,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/blast_pairs.idx.ok]
exists.
-- Skipping CMD:
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
gtf_file_to_feature_seqs.pl --gtf_file
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/gencode.v36.annotation.gtf
--genome_fa
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/GRCh38.d1.vd1.fa
--seqType cDNA > ref_annot.cdna.fa, checkpoint
[__loc_chkpts/ref_annot.cdna.fa.ok] exists.
-- Skipping CMD: cp ref_annot.cdna.fa
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.cdna.fa,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/cp_ref_annot_cdna.ok]
exists.
-- Skipping CMD:
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
index_cdna_seqs.pl
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.cdna.fa,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/index_ref_annot_cdna.ok]
exists.
-- Skipping CMD: makeblastdb -in ref_annot.cdna.fa -dbtype nucl,
checkpoint [__loc_chkpts/ref_annot.cdna.fa.blastidx.ok] exists.
-- Skipping CMD: blastn -query ref_annot.cdna.fa -db ref_annot.cdna.fa
-max_target_seqs 10000 -outfmt 6 -evalue 1e-10 -num_threads 4 -dust no >
ref_annot.cdna.fa.allvsall.outfmt6, checkpoint
[__loc_chkpts/ref_annot.cdna.fa.blastn.allvsall.outfmt6.ok] exists.
-- Skipping CMD:
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
isoform_blast_gene_chr_conversion.pl --blast_outfmt6
ref_annot.cdna.fa.allvsall.outfmt6 --gtf
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/gencode.v36.annotation.gtf
> ref_annot.cdna.fa.allvsall.outfmt6.toGenes, checkpoint
[__loc_chkpts/ref_annot.cdna.fa.allvsall.blastn.outfmt6.toGenes.ok] exists.
-- Skipping CMD: sort -k2,2 -k7,7
ref_annot.cdna.fa.allvsall.outfmt6.toGenes >
ref_annot.cdna.fa.allvsall.outfmt6.toGenes.sorted, checkpoint
[__loc_chkpts/ref_annot.cdna.fa.allvsall.blastn.outfmt6.toGenes.sorted.ok]
exists.
-- Skipping CMD: gzip -f
ref_annot.cdna.fa.allvsall.outfmt6.toGenes.sorted, checkpoint
[__loc_chkpts/ref_annot.cdna.fa.allvsall.blastn.outfmt6.toGenes.sorted.gzip.ok]
exists.
-- Skipping CMD: cp ref_annot.cdna.fa.allvsall.outfmt6.toGenes.sorted.gz
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/trans.blast.dat.gz,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/trans.blast.dat.cp.ok]
exists.
-- Skipping CMD:
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
build_chr_gene_alignment_index.pl --blast_genes
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/trans.blast.dat.gz
--out_prefix
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/trans.blast.align_coords,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/trans.blast.dat.index.ok]
exists.
-- Skipping CMD:
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
build_prot_info_db.pl --gtf
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/gencode.v36.annotation.gtf
--genome_fa
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/GRCh38.d1.vd1.fa
--out_prefix
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/_prot_info_db.ok]
exists.
-- Skipping CMD: cp
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/AnnotFilterRuleLib/AnnotFilterRule.pm
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/.,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/annotfiltrule_cp.ok]
exists.
-- Skipping CMD: cp
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/fusion_lib.Mar2021.dat.gz
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/fusion_annot_lib.gz,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/fusion_annot_lib.cp.ok]
exists.
-- Skipping CMD:
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
build_fusion_annot_db_index.pl --gene_spans
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans
--out_db_file
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/fusion_annot_lib.idx
--key_pairs
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/fusion_annot_lib.gz,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/_fusion_annot_lib.idx.ok]
exists.
-- Skipping CMD:
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
gtf_file_to_feature_seqs.pl --gtf_file
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/gencode.v36.annotation.gtf
--genome_fa
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/GRCh38.d1.vd1.fa
--seqType prot > ref_annot.pep.fa, checkpoint
[__loc_chkpts/make_pep_file.ok] exists.
-- Skipping CMD: hmmscan --cpu 4 --domtblout PFAM.domtblout.dat Pfam-A.hmm
ref_annot.pep.fa, checkpoint [__loc_chkpts/hmmscan.ok] exists.
-- Skipping CMD: gzip PFAM.domtblout.dat, checkpoint
[__loc_chkpts/gzip_pfam.ok] exists.
-- Skipping CMD: cp PFAM.domtblout.dat.gz
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz,
checkpoint
[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/cp_pfam_dat.ok]
exists.
- Running CMD:
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
index_pfam_domain_info.pl --pfam_domains
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz
--genome_lib_dir
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir
Error, cmd:
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/
index_pfam_domain_info.pl --pfam_domains
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz
--genome_lib_dir
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir
died with ret 139 No such file or directory at
/fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/lib/Pipeliner.pm
line 186.
Pipeliner::run(Pipeliner=HASH(0x5597b8206e40)) called at
/fs/project/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/
prep_genome_lib.pl line 460
Thank you in advance!!
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The Broad Institute
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|
Thank you for the quick reply! I believe that the 'Skipping' messages appear because the files/directories they generate already exist (I ran this a few times trying to download the correct dependencies for each script). Here is one example: -- Skipping CMD: wget http://dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/homo_sapiens_dfam.hmm, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_dfam_db_prep_chckpts/dfam..ok] exists. I double checked, I was able to locate /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz. I run the command (from the previous comment) from this directory: /fs/project/PAS0854/Emily/kinase_fusions/tcga/star_rerun, which does include PFAM.domtblout.dat.gz. Would it help to unzip the file? Or am I missing other dependencies? Thank you again for your help! |
Hi Emily,
Just for some more context - are you trying to build the ctat genome lib
from a 'source' lib that we provide, or are you trying to build your own
given a different set of genome resources?
best,
~b
…On Fri, Mar 3, 2023 at 11:25 AM Emily Hoskins ***@***.***> wrote:
Thank you for the quick reply!
I believe that the 'Skipping' messages appear because the
files/directories they generate already exist (I ran this a few times
trying to download the correct dependencies for each script). Here is one
example: -- Skipping CMD: wget
http://dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/homo_sapiens_dfam.hmm,
checkpoint *[/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_dfam_db_prep_chckpts/dfam..ok]
exists.*
I double checked, I was able to locate
/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz.
I run the command (from the previous comment) from this directory:
/fs/project/PAS0854/Emily/kinase_fusions/tcga/star_rerun, which does
include PFAM.domtblout.dat.gz. Would it help to unzip the file? Or am I
missing other dependencies?
Thank you again for your help!
Emily
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Brian J. Haas
The Broad Institute
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Hi! I'm trying to build the ctat genome lib from the source that you provide. I followed this template to build the library: Is "fusion_lib.Mar2021.dat.gz" the correct/ most up to date file for 'fusion_annot_lib'? I downloaded it from this site: https://github.com/FusionAnnotator/CTAT_HumanFusionLib/releases Thank you, |
Hi Emily,
I think you might be working from an old tutorial containing the 'mini'
that doesn't work with the latest software.
Are you trying to run a small tutorial, or are you looking to set up a
genome lib for routine use? Based on your response, I'll be able to point
you in the right direction.
best,
~b
…On Fri, Mar 3, 2023 at 12:59 PM Emily Hoskins ***@***.***> wrote:
Hi!
I'm trying to build the ctat genome lib from the source that you provide.
I followed this template to build the library:
${STAR_FUSION_HOME}/ctat-genome-lib-builder/prep_genome_lib.pl
--genome_fa minigenome.fa
--gtf minigenome.gtf
--fusion_annot_lib CTAT_HumanFusionLib.mini.dat.gz
--dfam_db human
--pfam_db current
Is "fusion_lib.Mar2021.dat.gz" the correct file for 'fusion_annot_lib'? I
downloaded it from this site:
https://github.com/FusionAnnotator/CTAT_HumanFusionLib/releases
Thank you,
Emily
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Hi, Brian! Oh that would make sense! I'm looking to set up a genome lib for routine use. Thank you in advance! |
Gotcha. OK, in that case you can just download the plug-n-play version if
that's available:
https://github.com/STAR-Fusion/STAR-Fusion/wiki/STAR-Fusion-release-and-CTAT-Genome-Lib-Compatibility-Matrix
If you need to build your own based on some specific version of the gencode
annotation and we don't already have it set up, then you would run the
build process from scratch, starting with just the genome and the gtf file:
https://github.com/NCIP/ctat-genome-lib-builder/wiki#building-a-custom-genome-resource-library-for-fusion-detection
hope this helps,
~b
…On Mon, Mar 6, 2023 at 2:00 PM Emily Hoskins ***@***.***> wrote:
Hi, Brian!
Oh that would make sense! I'm looking to set up a genome lib for routine
use.
Thank you in advance!
Emily
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Hello!
I'm building a ctat_genome_library in preparation to run STAR-Fusion, but I came across an error when I ran "prep_genome_lib.pl". It ran into an issue when trying to run "index_pfam_domain_info.pl". I'm not sure how to resolve this issue, could you help figure out what I need to do? Here is implementation:
/fs/project/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/prep_genome_lib.pl --genome_fa GRCh38.d1.vd1.fa --pfam_db current --gtf gencode.v36.annotation.gtf --fusion_annot_lib fusion_lib.Mar2021.dat.gz --dfam_db human
And here is the output (error on the last line):
-found STAR at /fs/project/PAS0854/Software/STAR_Latest/STAR-2.7.0f/bin/Linux_x86_64/STAR
-found makeblastdb at /usr/local/blast/2.10.0+/bin/makeblastdb
-found blastn at /usr/local/blast/2.10.0+/bin/blastn
-found dfamscan.pl at /users/PAS0854/hosk13/.conda/envs/orien/bin/dfamscan.pl
-found nhmmscan at /usr/local/hmmer/3.3.2/bin/nhmmscan
-found hmmscan at /usr/local/hmmer/3.3.2/bin/hmmscan
-- Skipping CMD: wget http://dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/homo_sapiens_dfam.hmm, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_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 [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_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 [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_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 [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_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 [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_dfam_db_prep_chckpts/dfam.h3p.ok] exists.
-- Skipping CMD: wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_pfam_db_prep_chckpts/pfam_wget.ok] exists.
-- Skipping CMD: gunzip Pfam-A.hmm.gz, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_pfam_db_prep_chckpts/pfam_gunzip.ok] exists.
-- Skipping CMD: hmmpress Pfam-A.hmm, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/_pfam_db_prep_chckpts/pfam_hmmpress.ok] exists.
-- Skipping CMD: cp /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/GRCh38.d1.vd1.fa /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_genome.fa, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/ref_genome.fa.ok] exists.
-- Skipping CMD: samtools faidx /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_genome.fa, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/ref_genome_fai.ok] exists.
-- Skipping CMD: makeblastdb -in /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_genome.fa -dbtype nucl, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/makeblastdb.ok] exists.
-- Skipping CMD: cp /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/gencode.v36.annotation.gtf /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.ok] exists.
-- Skipping CMD: bash -c " set -euxo pipefail; /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/gtf_to_exon_gene_records.pl /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf | sort -k 1,1 -k4,4g -k5,5g | uniq > /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu " , checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.mini.sortu.ok] exists.
-- Skipping CMD: STAR --runThreadN 4 --runMode genomeGenerate --genomeDir /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --genomeFastaFiles /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/GRCh38.d1.vd1.fa --limitGenomeGenerateRAM 40419136213 --genomeChrBinNbits 16 --sjdbGTFfile /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/gencode.v36.annotation.gtf --sjdbOverhang 150 , checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/build.ok] exists.
-- Skipping CMD: /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/gtf_to_gene_spans.pl /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf > /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/ref_annot.gtf.gene_spans.ok] exists.
-- Skipping CMD: /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/gtf_file_to_feature_seqs.pl --gtf_file /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_genome.fa --seqType CDSplus > ref_annot.cdsplus.fa, checkpoint [__loc_chkpts/ref_annot.cdsplus.fa.ok] exists.
-- Skipping CMD: /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/dfam_repeat_masker.pl --dfam_hmm homo_sapiens_dfam.hmm --target_fa ref_annot.cdsplus.fa --out_masked ref_annot.cdsplus.dfam_masked.fa --CPU 4, checkpoint [__loc_chkpts/ref_annot.cdsplus.dfam_masked.fa.ok] exists.
-- Skipping CMD: cp ref_annot.cdsplus.dfam_masked.fa /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/ref_annot.cdsplus.dfam_masked.fa.cp.ok] exists.
-- Skipping CMD: /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/index_cdna_seqs.pl /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.cdsplus.fa, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/ref_annot.cdsplus.dfam_masked.fa.idx.ok] exists.
-- Skipping CMD: makeblastdb -in ref_annot.cdsplus.dfam_masked.fa -dbtype nucl, checkpoint [__loc_chkpts/ref_annot.cdsplus.dfam_masked.fa.blidx.ok] exists.
-- Skipping CMD: blastn -query ref_annot.cdsplus.dfam_masked.fa -db ref_annot.cdsplus.dfam_masked.fa -max_target_seqs 10000 -outfmt 6 -evalue 1e-10 -num_threads 4 -dust no -lcase_masking > ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6, checkpoint [__loc_chkpts/ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.ok] exists.
-- Skipping CMD: bash -c " set -euxo pipefail; /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/blast_outfmt6_replace_trans_id_w_gene_symbol.pl ref_annot.cdsplus.dfam_masked.fa ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6 | gzip > ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.gz" , checkpoint [__loc_chkpts/ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.gz.ok] exists.
-- Skipping CMD: bash -c " set -euxo pipefail; /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/blast_select_single_per_gene_pair.pl ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.gz | gzip > ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.best.gz" , checkpoint [__loc_chkpts/ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.best.gz.ok] exists.
-- Skipping CMD: bash -c " set -euxo pipefail; /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/filter_overlapping_blast_hits.pl ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.best.gz /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans | gzip > ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.best.overlaps_filt.gz" , checkpoint [__loc_chkpts/ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.best.overlaps_filt.ok] exists.
-- Skipping CMD: cp ref_annot.cdsplus.dfam_masked.fa.allvsall.outfmt6.genesym.best.overlaps_filt.gz /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/blast_pairs.dat.gz, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/cp_gene_blast_pairs.ok] exists.
-- Skipping CMD: /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/index_blast_pairs.pl /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/blast_pairs.idx /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/blast_pairs.dat.gz, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/blast_pairs.idx.ok] exists.
-- Skipping CMD: /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/gtf_file_to_feature_seqs.pl --gtf_file /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/gencode.v36.annotation.gtf --genome_fa /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/GRCh38.d1.vd1.fa --seqType cDNA > ref_annot.cdna.fa, checkpoint [__loc_chkpts/ref_annot.cdna.fa.ok] exists.
-- Skipping CMD: cp ref_annot.cdna.fa /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.cdna.fa, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/cp_ref_annot_cdna.ok] exists.
-- Skipping CMD: /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/index_cdna_seqs.pl /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.cdna.fa, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/index_ref_annot_cdna.ok] exists.
-- Skipping CMD: makeblastdb -in ref_annot.cdna.fa -dbtype nucl, checkpoint [__loc_chkpts/ref_annot.cdna.fa.blastidx.ok] exists.
-- Skipping CMD: blastn -query ref_annot.cdna.fa -db ref_annot.cdna.fa -max_target_seqs 10000 -outfmt 6 -evalue 1e-10 -num_threads 4 -dust no > ref_annot.cdna.fa.allvsall.outfmt6, checkpoint [__loc_chkpts/ref_annot.cdna.fa.blastn.allvsall.outfmt6.ok] exists.
-- Skipping CMD: /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/isoform_blast_gene_chr_conversion.pl --blast_outfmt6 ref_annot.cdna.fa.allvsall.outfmt6 --gtf /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/gencode.v36.annotation.gtf > ref_annot.cdna.fa.allvsall.outfmt6.toGenes, checkpoint [__loc_chkpts/ref_annot.cdna.fa.allvsall.blastn.outfmt6.toGenes.ok] exists.
-- Skipping CMD: sort -k2,2 -k7,7 ref_annot.cdna.fa.allvsall.outfmt6.toGenes > ref_annot.cdna.fa.allvsall.outfmt6.toGenes.sorted, checkpoint [__loc_chkpts/ref_annot.cdna.fa.allvsall.blastn.outfmt6.toGenes.sorted.ok] exists.
-- Skipping CMD: gzip -f ref_annot.cdna.fa.allvsall.outfmt6.toGenes.sorted, checkpoint [__loc_chkpts/ref_annot.cdna.fa.allvsall.blastn.outfmt6.toGenes.sorted.gzip.ok] exists.
-- Skipping CMD: cp ref_annot.cdna.fa.allvsall.outfmt6.toGenes.sorted.gz /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/trans.blast.dat.gz, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/trans.blast.dat.cp.ok] exists.
-- Skipping CMD: /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/build_chr_gene_alignment_index.pl --blast_genes /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/trans.blast.dat.gz --out_prefix /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/trans.blast.align_coords, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/trans.blast.dat.index.ok] exists.
-- Skipping CMD: /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/build_prot_info_db.pl --gtf /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/gencode.v36.annotation.gtf --genome_fa /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/GRCh38.d1.vd1.fa --out_prefix /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/_prot_info_db.ok] exists.
-- Skipping CMD: cp /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/AnnotFilterRuleLib/AnnotFilterRule.pm /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/., checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/annotfiltrule_cp.ok] exists.
-- Skipping CMD: cp /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/fusion_lib.Mar2021.dat.gz /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/fusion_annot_lib.gz, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/fusion_annot_lib.cp.ok] exists.
-- Skipping CMD: /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/build_fusion_annot_db_index.pl --gene_spans /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans --out_db_file /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/fusion_annot_lib.idx --key_pairs /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/fusion_annot_lib.gz, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/_fusion_annot_lib.idx.ok] exists.
-- Skipping CMD: /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/gtf_file_to_feature_seqs.pl --gtf_file /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/gencode.v36.annotation.gtf --genome_fa /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/GRCh38.d1.vd1.fa --seqType prot > ref_annot.pep.fa, checkpoint [__loc_chkpts/make_pep_file.ok] exists.
-- Skipping CMD: hmmscan --cpu 4 --domtblout PFAM.domtblout.dat Pfam-A.hmm ref_annot.pep.fa, checkpoint [__loc_chkpts/hmmscan.ok] exists.
-- Skipping CMD: gzip PFAM.domtblout.dat, checkpoint [__loc_chkpts/gzip_pfam.ok] exists.
-- Skipping CMD: cp PFAM.domtblout.dat.gz /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz, checkpoint [/fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/__chkpts/cp_pfam_dat.ok] exists.
Error, cmd: /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/util/index_pfam_domain_info.pl --pfam_domains /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir/PFAM.domtblout.dat.gz --genome_lib_dir /fs/ess/PAS0854/Emily/kinase_fusions/tcga/star_rerun/ctat_genome_lib_build_dir died with ret 139 No such file or directory at /fs/ess/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/lib/Pipeliner.pm line 186.
Pipeliner::run(Pipeliner=HASH(0x5597b8206e40)) called at /fs/project/PAS0854/Software/star_fusion_v1.12.0/ctat-genome-lib-builder/prep_genome_lib.pl line 460
Thank you in advance!!
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