error 6 in opening hmm file

[schmittel]

Hi,

I'm running ctat-genome-lib-builder with a specific Gencode release using the following paremeters:

/software/ctat-genome-lib-builder/prep_genome_lib.pl \
    --genome_fa /star_fusion/ctat_genome_library/GRCh38_gencode_v37_CTAT_lib_Mar012021.source/GRCh38.primary_assembly.genome.fa \
    --gtf /input_files/gencode.v33.annotation.gtf \
    --fusion_annot_lib /star_fusion/ctat_genome_library/GRCh38_gencode_v37_CTAT_lib_Mar012021.source/fusion_lib.Mar2021.dat.gz \
    --pfam_db current \
    --CPU 24 \
    --dfam_db human \
    --human_gencode_filter \
    --output_dir /star_fusion/ctat_genome_library/ctat_genome_lib_build_dir;

However, it keeps failing with the following error:

    * Running CMD: /star_fusion/ctat_genome_library/ctat-genome-lib-builder/util/gtf_to_gene_spans.pl /star_fusion/ctat_genome_library/ctat_genome_lib_build_dir/ref_annot.gtf > /star_fusion/ctat_genome_library/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans
    * Running CMD: /star_fusion/ctat_genome_library/ctat-genome-lib-builder/util/gtf_file_to_feature_seqs.pl --gtf_file /star_fusion/ctat_genome_library/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /star_fusion/ctat_genome_library/ctat_genome_lib_build_dir/ref_genome.fa --seqType CDSplus > ref_annot.cdsplus.fa
    * Running CMD: /star_fusion/ctat_genome_library/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 24
    * Running CMD: dfamscan.pl -fastafile ref_annot.cdsplus.fa -hmmfile homo_sapiens_dfam.hmm -dfam_outfile __dfam_ref_annot.cdsplus.fa/dfam.out --masking_thresh --cpu 24

    Error: Unexpected error 6 in opening hmm file homo_sapiens_dfam.hmm.

    Error running command:
    nhmmscan --noali --cut_ga --dfamtblout /tmp/i2lYFsyF9p --cpu=24 homo_sapiens_dfam.hmm ref_annot.cdsplus.fa
    Error, cmd: dfamscan.pl -fastafile ref_annot.cdsplus.fa -hmmfile homo_sapiens_dfam.hmm -dfam_outfile __dfam_ref_annot.cdsplus.fa/dfam.out --masking_thresh --cpu 24 died with ret 6400 No such file or directory at /star_fusion/ctat_genome_library/ctat-genome-lib-builder/util/../lib/Pipeliner.pm line 186.
            Pipeliner::run(Pipeliner=HASH(0x55e6f67dd2a0)) called at /star_fusion/ctat_genome_library/ctat-genome-lib-builder/util/dfam_repeat_masker.pl line 84
    Error, cmd: /star_fusion/ctat_genome_library/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 24 died with ret 512 No such file or directory at /star_fusion/ctat_genome_library/ctat-genome-lib-builder/lib/Pipeliner.pm line 186.
            Pipeliner::run(Pipeliner=HASH(0x55a7650dd140)) called at /star_fusion/ctat_genome_library/ctat-genome-lib-builder/prep_genome_lib.pl line 460

I see it is having difficulty generating the homo_sapiens_dfam.hmm file - do you think this is a memory issue or due to another reason?

Many thanks for your help.

[brianjohnhaas]

Hi,

Is the file homo_sapiens_dfam.hmm downloaded into the working directory? The builder script should be retrieving it for you given the human setting. It should be finding it here: http://dfam.org/releases/Dfam_3.1/infrastructure/dfamscan and pulling it down automatically.

On Thu, Mar 31, 2022 at 7:34 AM schmittel @.***> wrote:

Hi,

I'm running ctat-genome-lib-builder with a specific Gencode release using the following paremeters:

/software/ctat-genome-lib-builder/prep_genome_lib.pl \ --genome_fa /star_fusion/ctat_genome_library/GRCh38_gencode_v37_CTAT_lib_Mar012021.source/GRCh38.primary_assembly.genome.fa \ --gtf /input_files/gencode.v33.annotation.gtf \ --fusion_annot_lib /star_fusion/ctat_genome_library/GRCh38_gencode_v37_CTAT_lib_Mar012021.source/fusion_lib.Mar2021.dat.gz \ --pfam_db current \ --CPU 24 \ --dfam_db human \ --human_gencode_filter \ --output_dir /star_fusion/ctat_genome_library/ctat_genome_lib_build_dir;

However, it keeps failing with the following error:

• Running CMD: /star_fusion/ctat_genome_library/ctat-genome-lib-builder/util/ gtf_to_gene_spans.pl /star_fusion/ctat_genome_library/ctat_genome_lib_build_dir/ref_annot.gtf > /star_fusion/ctat_genome_library/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans
• Running CMD: /star_fusion/ctat_genome_library/ctat-genome-lib-builder/util/ gtf_file_to_feature_seqs.pl --gtf_file /star_fusion/ctat_genome_library/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /star_fusion/ctat_genome_library/ctat_genome_lib_build_dir/ref_genome.fa --seqType CDSplus > ref_annot.cdsplus.fa
• Running CMD: /star_fusion/ctat_genome_library/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 24
• Running CMD: dfamscan.pl -fastafile ref_annot.cdsplus.fa -hmmfile homo_sapiens_dfam.hmm -dfam_outfile __dfam_ref_annot.cdsplus.fa/dfam.out --masking_thresh --cpu 24

Error: Unexpected error 6 in opening hmm file homo_sapiens_dfam.hmm.

Error running command: nhmmscan --noali --cut_ga --dfamtblout /tmp/i2lYFsyF9p --cpu=24 homo_sapiens_dfam.hmm ref_annot.cdsplus.fa Error, cmd: dfamscan.pl -fastafile ref_annot.cdsplus.fa -hmmfile homo_sapiens_dfam.hmm -dfam_outfile __dfam_ref_annot.cdsplus.fa/dfam.out --masking_thresh --cpu 24 died with ret 6400 No such file or directory at /star_fusion/ctat_genome_library/ctat-genome-lib-builder/util/../lib/Pipeliner.pm line 186. Pipeliner::run(Pipeliner=HASH(0x55e6f67dd2a0)) called at /star_fusion/ctat_genome_library/ctat-genome-lib-builder/util/ dfam_repeat_masker.pl line 84 Error, cmd: /star_fusion/ctat_genome_library/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 24 died with ret 512 No such file or directory at /star_fusion/ctat_genome_library/ctat-genome-lib-builder/lib/Pipeliner.pm line 186. Pipeliner::run(Pipeliner=HASH(0x55a7650dd140)) called at /star_fusion/ctat_genome_library/ctat-genome-lib-builder/prep_genome_lib.pl line 460

I see it is having difficulty generating the homo_sapiens_dfam.hmm file - do you think this is a memory issue or due to another reason?

Many thanks for your help.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>

--

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

[schmittel]

Thanks @brianjohnhaas. I downloaded the dfam.hmm file manually and everything worked as expected. For some reason the automatically downloaded files were getting deleted, causing the error. Downloading them manually resolved it.

Thanks again.