error occurred when run prep_genome_lib.pl

[HAN SAI LEE]

hi

i'm just building ctat_genome_lib 

but when i run prep_genome_lib.pl i've got error message and i can't figure it out 

please help me

my  code :

 ~/tools/STAR-Fusion-v1.9.1/ctat-genome-lib-builder/prep_genome_lib.pl --genome_fa ~/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa --gtf ~/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf --fusion_annot_lib ~/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/fusion_annot_lib.gz --annot_filter_rule ~/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/AnnotFilterRule.pm --pfam_db current --dfam_db human --human_gencode_filter

Error :

-found STAR at /users/hslee/anaconda3/bin/STAR

-found makeblastdb at /users/hslee/anaconda3/bin/makeblastdb

-found blastn at /users/hslee/anaconda3/bin/blastn

- *** ERROR, cannot locate required tool in PATH setting: dfamscan.pl ***

-found nhmmscan at /users/hslee/anaconda3/bin/nhmmscan

-found hmmscan at /users/hslee/anaconda3/bin/hmmscan

-- Skipping CMD: wget http://dfam.org/releases/Dfam_3.1/infrastructure/dfamscan/homo_sapiens_dfam.hmm, checkpoint [/users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/_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 [/users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/_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 [/users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/_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 [/users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/_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 [/users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/_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 [/users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/_pfam_db_prep_chckpts/pfam_wget.ok] exists.

-- Skipping CMD: gunzip Pfam-A.hmm.gz, checkpoint [/users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/_pfam_db_prep_chckpts/pfam_gunzip.ok] exists.

-- Skipping CMD: hmmpress Pfam-A.hmm, checkpoint [/users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/_pfam_db_prep_chckpts/pfam_hmmpress.ok] exists.

-- Skipping CMD: cp /users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa /users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ctat_genome_lib_build_dir/ref_genome.fa, checkpoint [/users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ctat_genome_lib_build_dir/__chkpts/ref_genome.fa.ok] exists.

-- Skipping CMD: samtools faidx /users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ctat_genome_lib_build_dir/ref_genome.fa, checkpoint [/users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ctat_genome_lib_build_dir/__chkpts/ref_genome_fai.ok] exists.

-- Skipping CMD: makeblastdb -in /users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ctat_genome_lib_build_dir/ref_genome.fa -dbtype nucl, checkpoint [/users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ctat_genome_lib_build_dir/__chkpts/makeblastdb.ok] exists.

* Running CMD: /users/hslee/tools/STAR-Fusion-v1.9.1/ctat-genome-lib-builder/util/revise_gencode_annotations.pl --gencode_gtf /users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf --out_gtf /users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf.revised.gtf

-revising human gencode annotations

-- Skipping CMD: bash -c "set -euxo pipefail; cat /users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf |  egrep -v 'IG_V_gene|IG_C_gene|IG_D_gene|IG_J_gene|readthrough_transcript' > __gencode_refinement_chkpts/ref_annot.gtf.feature_selected" , checkpoint [/users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/__gencode_refinement_chkpts/feature_selection.ok] exists.

-- Skipping CMD: /users/hslee/tools/STAR-Fusion-v1.9.1/ctat-genome-lib-builder/util/remove_long_intron_readthru_transcripts.pl __gencode_refinement_chkpts/ref_annot.gtf.feature_selected 100000 > __gencode_refinement_chkpts/ref_annot.gtf.feature_selected.noreadthrus, checkpoint [/users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/__gencode_refinement_chkpts/remove_readthrus.ok] exists.

* Running CMD: bash -c "set -euxo pipefail; cat /users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ref_annot.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"

+ cat /users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf

+ egrep 'IG_V_gene|IG_C_gene|IG_D_gene|IG_J_gene'

+ awk '{ if ($3 == "exon") { print } }'

+ egrep '^chr14'

Error, cmd: bash -c "set -euxo pipefail; cat /users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ref_annot.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 /users/hslee/tools/STAR-Fusion-v1.9.1/ctat-genome-lib-builder/util/../lib/Pipeliner.pm line 186.

        Pipeliner::run(Pipeliner=HASH(0x563dbd2d49f8)) called at /users/hslee/tools/STAR-Fusion-v1.9.1/ctat-genome-lib-builder/util/revise_gencode_annotations.pl line 115

Error, cmd: /users/hslee/tools/STAR-Fusion-v1.9.1/ctat-genome-lib-builder/util/revise_gencode_annotations.pl --gencode_gtf /users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf --out_gtf /users/hslee/tools/STAR-Fusion-v1.9.1/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf.revised.gtf died with ret 512 No such file or directory at /users/hslee/tools/STAR-Fusion-v1.9.1/ctat-genome-lib-builder/lib/Pipeliner.pm line 186.

        Pipeliner::run(Pipeliner=HASH(0x55869bfbc6e8)) called at /users/hslee/tools/STAR-Fusion-v1.9.1/ctat-genome-lib-builder/prep_genome_lib.pl line 460

thank you in advance 

thanks

[Brian Haas]

Hi,

If you're going to build the genome lib, you'll need to start from a source lib not the plug-n-play one.  If you have the plug-n-play library, you should be good to go w/o having to build it.

best,

~b

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--

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