Genome build -

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Elad Herz

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Nov 28, 2025, 10:56:07 AM11/28/25

to Trinity_CTAT_users

Hello CTAT users and Brian,

Thanks for this tool and the support.

I'm trying to build human genome for GRCh38 - release 49 (genecode)

Since I didn't found the resources fusion_annot_lib , annot_filter_rule I have used those from previous plug and play (I'm not really sure if there are any updates)

I have ran this command:

prep_genome_lib.pl --genome_fa /home/ec2-user/work/star-fusion/Homo_sapiens_GRCh38_49_dna_primary_assembly.fa \
--gtf /home/ec2-user/work/star-fusion/Homo_sapiens_GRCh38_49.filtered.gtf \
--fusion_annot_lib /home/ec2-user/work/star-fusion/ctat_genome_lib_build_dir/GRCh38_gencode_v44_CTAT_lib_Oct292023.source/fusion_annot_lib.gz \
--annot_filter_rule /home/ec2-user/work/star-fusion/ctat_genome_lib_build_dir/GRCh38_gencode_v44_CTAT_lib_Oct292023.source/AnnotFilterRule.pm \
--pfam_db current \
--dfam_db human \
--max_readlength 150 \
--CPU 24

unfortunately the following step seems to be running forever:
* 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

Have any one saw it before?

dfamscan.pl --version
version 1.4
nhmmscan : version HMMER 3.4 (Aug 2023)

Best regards,

Elad

Brian Haas

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Nov 28, 2025, 12:16:48 PM11/28/25

to Elad Herz, Trinity_CTAT_users

Hi Elad,

The dfam step can run for a long time, but assuming it does actually finish at some point, it only needs to be run once thankfully. Try checking the __dfam_ref_annot.cdsplus.fa/dfam.out to see if it's still being written to, or if it's somehow ceased activity without crashing for some reason. If it's still going, then I'd just wait it out. If it takes longer than a couple days, I might worry.

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