Docker image issue

[YasirKusay]

I am running Docker to create a new CTAT resource lib. Here is my command:

docker run -v `pwd`:/data --rm trinityctat/starfusion /bin/bash -c "chmod 770 /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/lib/Pipeliner.pm; ./STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl --genome_fa /data/refs/GRCh38_masked_v2_decoy_gene.fasta --gtf /data/refs/gencode.v39.annotation.gtf --fusion_annot_lib /data/refs/fusion_lib.Mar2021.dat.gz --annot_filter_rule /data/refs/AnnotFilterRule.pm --pfam_db current --dfam_db human --human_gencode_filter --output_dir /data/custom_ctat"

I am using a custom hg38 fasta reference, the gencode v39 annotation and the fusion_lib.Mar2021.dat.gz fusion annotation lib. However, during this step:

* 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 4

It seems to hang infinitely. During another trial, it thew an error (I will try and replicate it). Could you please help me understand this issue?

[brianjohnhaas]

Hi, The dfam step can take a long while.... like possibly a day to complete. I wonder if it's really hanging, or just taking a long time. You can run 'tail -f' on the __dfam_ref_annot.cdsplus.fa/dfam.out file to see if it's continuing to be written to.

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On Tue, Aug 27, 2024 at 7:51 PM YasirKusay ***@***.***> wrote: I am running Docker to create a new CTAT resource lib. Here is my command: docker run -v `pwd`:/data --rm trinityctat/starfusion /bin/bash -c "chmod 770 /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/lib/Pipeliner.pm; ./STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl --genome_fa /data/refs/GRCh38_masked_v2_decoy_gene.fasta --gtf /data/refs/gencode.v39.annotation.gtf --fusion_annot_lib /data/refs/fusion_lib.Mar2021.dat.gz --annot_filter_rule /data/refs/AnnotFilterRule.pm --pfam_db current --dfam_db human --human_gencode_filter --output_dir /data/custom_ctat" I am using a custom hg38 fasta reference, the gencode v39 annotation and the fusion_lib.Mar2021.dat.gz fusion annotation lib. However, during this step: * 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 4 It seems to hang infinitely. During another trial, it thew an error (I will try and replicate it). Could you please help me understand this issue? — Reply to this email directly, view it on GitHub <#407>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX45CCFH2ABDFBSXIDDZTUGGRAVCNFSM6AAAAABNHEARCCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4TANJVGQZTEMY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[YasirKusay]

Strange, I dont see this in my ctat folder that is being generated

[YasirKusay]

Just an update to this, I did see some new files created after 11 hours, so it seems to be progressing.

If my build fails, is it possible to resume the process from what I have so far, every single time I retry it it starts from scratch.