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Trouble running index_pfam_domain_info.pl #14

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nadia35 opened this issue Mar 2, 2023 · 7 comments
Open

Trouble running index_pfam_domain_info.pl #14

nadia35 opened this issue Mar 2, 2023 · 7 comments

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@nadia35
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nadia35 commented Mar 2, 2023

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!!
@brianjohnhaas
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brianjohnhaas commented Mar 2, 2023 via email

@nadia35
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nadia35 commented Mar 3, 2023

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

@brianjohnhaas
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brianjohnhaas commented Mar 3, 2023 via email

@nadia35
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nadia35 commented Mar 3, 2023 •
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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:
${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/ most up to date file for 'fusion_annot_lib'? I downloaded it from this site: https://github.com/FusionAnnotator/CTAT_HumanFusionLib/releases

Thank you,
Emily

@brianjohnhaas
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brianjohnhaas commented Mar 3, 2023 via email

@nadia35
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nadia35 commented Mar 6, 2023

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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brianjohnhaas commented Mar 6, 2023 via email

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