Building custom genome

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Evan Conaway

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Nov 18, 2019, 7:23:48 PM11/18/19
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I'm having trouble trouble building my own genome for dog, it seems to get stuck on 

Running CMD: dfamscan.pl -fastafile ref_annot.cdsplus.fa -hmmfile ../Dfam.hmm -dfam_outfile __dfam_ref_annot.cdsplus.fa/dfam.out --masking_thresh --cpu 4

my initial command is

STAR-Fusion-v1.8.1/ctat-genome-lib-builder/prep_genome_lib.pl --genome_fa ../Canis_familiaris.CanFam3.1.dna.toplevel.fa --gtf ../Canis_familiaris.CanFam3.1.98_FIXED.gtf --pfam_db current --dfam_db ../Dfam.hmm

Brian Haas

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Nov 22, 2019, 11:24:29 AM11/22/19
to Evan Conaway, Trinity_CTAT_users
Hi Evan - sorry about the delayed response.  This got quickly buried in my inbox.

What's the error that you're encountering?

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Evan Conaway

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Nov 22, 2019, 3:02:08 PM11/22/19
to Brian Haas, Trinity_CTAT_users
IWell that’s the weird thing no error, but it’s stuck on it for house{I let it go for up to 24 house)

 
From: Brian Haas <bh...@broadinstitute.org>
Sent: Friday, November 22, 2019 11:24 AM
To: Evan Conaway
Cc: Trinity_CTAT_users
Subject: Re: Building custom genome
 

Brian Haas

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Nov 22, 2019, 6:57:04 PM11/22/19
to Evan Conaway, Trinity_CTAT_users
I wonder where it's getting stuck.  Some of the steps do take a while... it's a slow process, involving building the genome index, all-vs-all blast searches, dfam and pfam searches.   If you're using the full Dfam.hmm, see if you can instead use a 'dog' one, and that should make it go much faster in case it's getting stuck at that point.

If you can't get it to go through, I could try to make one for you.

best,

~b

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Brian Chou

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Feb 26, 2020, 5:28:41 AM2/26/20
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Hi Brian,
I have some similar troubles in building custom genome resource library for the dog, the ERROR messages are,

Error: Failed to open binary auxfiles for /PATH/Dfam.hmm: use hmmpress first

Error running command:
nhmmscan --noali --cut_ga --dfamtblout /tmp/ENboRmqVjc --cpu=4 /PATH/Dfam.hmm ref_annot.cdsplus.fa
Error, cmd: dfamscan.pl -fastafile ref_annot.cdsplus.fa -hmmfile /PATH/Dfam.hmm -dfam_outfile __dfam_ref_annot.cdsplus.fa/dfam.out --masking_thresh --cpu 4 died with ret 6400 No such file or directory at /PATH/software/STAR-Fusion-v1.8.1/ctat-genome-lib-builder/util/../lib/Pipeliner.pm line 186.
        Pipeliner::run('Pipeliner=HASH(0xa08d58)') called at /PATH/software/STAR-Fusion-v1.8.1/ctat-genome-lib-builder/util/dfam_repeat_masker.pl line 84
Error, cmd: /PATH/software/STAR-Fusion-v1.8.1/ctat-genome-lib-builder/util/dfam_repeat_masker.pl --dfam_hmm /PATH/Dfam.hmm --target_fa ref_annot.cdsplus.fa --out_masked ref_annot.cdsplus.dfam_masked.fa --CPU 4 died with ret 512 No such file or directory at /PATH/software/STAR-Fusion-v1.8.1/ctat-genome-lib-builder/lib/Pipeliner.pm line 186.
        Pipeliner::run('Pipeliner=HASH(0xdd3e38)') called at /PATH/software/STAR-Fusion-v1.8.1/ctat-genome-lib-builder/prep_genome_lib.pl line 451

I have downloaded Dfam.hmm and dfamscan.pl from https://www.dfam.org/help/tools, and Pfam file from ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz, and my command is ./prep_genome_lib.pl --genome_fa Canis_familiaris.CanFam3.1.dna.toplevel.fa --gtf Canis_familiaris.CanFam3.1.97.gtf --pfam_db /PATH/Pfam-A.hmm --dfam_db /PATH/Dfam.hmm

I would appreciate it if you could give me some help!

Best!


On Saturday, November 23, 2019 at 7:57:04 AM UTC+8, Brian Haas wrote:
I wonder where it's getting stuck.  Some of the steps do take a while... it's a slow process, involving building the genome index, all-vs-all blast searches, dfam and pfam searches.   If you're using the full Dfam.hmm, see if you can instead use a 'dog' one, and that should make it go much faster in case it's getting stuck at that point.

If you can't get it to go through, I could try to make one for you.

best,

~b

On Fri, Nov 22, 2019 at 3:02 PM Evan Conaway <evan....@gmail.com> wrote:
IWell that’s the weird thing no error, but it’s stuck on it for house{I let it go for up to 24 house)

 
From: Brian Haas <bh...@broadinstitute.org>
Sent: Friday, November 22, 2019 11:24 AM
To: Evan Conaway
Cc: Trinity_CTAT_users
Subject: Re: Building custom genome
 
Hi Evan - sorry about the delayed response.  This got quickly buried in my inbox.

What's the error that you're encountering?

On Mon, Nov 18, 2019 at 7:23 PM Evan Conaway <evan....@gmail.com> wrote:
I'm having trouble trouble building my own genome for dog, it seems to get stuck on 

Running CMD: dfamscan.pl -fastafile ref_annot.cdsplus.fa -hmmfile ../Dfam.hmm -dfam_outfile __dfam_ref_annot.cdsplus.fa/dfam.out --masking_thresh --cpu 4

my initial command is

STAR-Fusion-v1.8.1/ctat-genome-lib-builder/prep_genome_lib.pl --genome_fa ../Canis_familiaris.CanFam3.1.dna.toplevel.fa --gtf ../Canis_familiaris.CanFam3.1.98_FIXED.gtf --pfam_db current --dfam_db ../Dfam.hmm

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Brian Haas

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Feb 26, 2020, 7:33:04 AM2/26/20
to Brian Chou, Trinity_CTAT_users
Hi,

You might just need to run
   hmmpress Dfam.hmm

and then give it another try

best,

~b
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Bio info

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Jul 28, 2020, 1:10:18 PM7/28/20
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Hi Brian,

I am having similar issue. Unfortunately I could not find Dfam database for dog so I am using Dfam.hmm instead. I was wondering if you were able to generate a canine library for STAR fusion?

Here is my detailed issue:
I am running:
~/STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl \
    --genome_fa ~/dPHAM/Canis_familiaris.CanFam3.1.dna.fa \
    --gtf ~/dPHAM/Canis_familiaris.CanFam3.1.99.chr.gtf \
    --pfam_db current \
    --dfam_db ../dPHAM/Dfam.hmm \
    --output_dir CanineStarFusionDB


But I keep getting this error:

* Running CMD: dfamscan.pl -fastafile ref_annot.cdsplus.fa -hmmfile ../dPHAM/Dfam.hmm -dfam_outfile __dfam_ref_annot.cdsplus.fa/dfam.out --masking_thresh --cpu 4

Error: GA bit thresholds unavailable on model DR0006969

Error I get from running this command:

nhmmscan --noali --cut_ga --dfamtblout /tmp/Vz2MEp3HJU --cpu=4 ../dPHAM/Dfam.hmm ref_annot.cdsplus.fa
Error, cmd: dfamscan.pl -fastafile ref_annot.cdsplus.fa -hmmfile ../dPHAM/Dfam.hmm -dfam_outfile __dfam_ref_annot.cdsplus.fa/dfam.out --masking_thresh --cpu 4 died with ret 6400 No such file or directory at /home/sdas/STAR-Fusion/ctat-genome-lib-builder/util/../lib/Pipeliner.pm line 186.
Pipeliner::run(Pipeliner=HASH(0x55ed8280ddd8)) called at /home/sdas/STAR-Fusion/ctat-genome-lib-builder/util/dfam_repeat_masker.pl line 84
Error, cmd: /home/sdas/STAR-Fusion/ctat-genome-lib-builder/util/dfam_repeat_masker.pl --dfam_hmm ../dPHAM/Dfam.hmm --target_fa ref_annot.cdsplus.fa --out_masked ref_annot.cdsplus.dfam_masked.fa --CPU 4 died with ret 512 No such file or directory at /home/sdas/STAR-Fusion/ctat-genome-lib-builder/lib/Pipeliner.pm line 186.
Pipeliner::run(Pipeliner=HASH(0x555b2034fe18)) called at /home/sdas/STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl line 460

So I tired running  nhmmscan --noali  --dfamtblout /tmp/Vz2MEp3HJU --cpu=4 ../dPHAM/Dfam.hmm ref_annot.cdsplus.fa (wothout the --cut_ga option) and it works. But I am not sure if that is the solution and how do I incorporate into the pipeline.

If you have already been successful in generating the Canine library, please let me know. It will be great if you can share that with me.

Thank you for your help,
SD


On Friday, November 22, 2019 at 4:57:04 PM UTC-7, Brian Haas wrote:
I wonder where it's getting stuck.  Some of the steps do take a while... it's a slow process, involving building the genome index, all-vs-all blast searches, dfam and pfam searches.   If you're using the full Dfam.hmm, see if you can instead use a 'dog' one, and that should make it go much faster in case it's getting stuck at that point.

If you can't get it to go through, I could try to make one for you.

best,

~b

On Fri, Nov 22, 2019 at 3:02 PM Evan Conaway <evan....@gmail.com> wrote:
IWell that’s the weird thing no error, but it’s stuck on it for house{I let it go for up to 24 house)

 
From: Brian Haas <bh...@broadinstitute.org>
Sent: Friday, November 22, 2019 11:24 AM
To: Evan Conaway
Cc: Trinity_CTAT_users
Subject: Re: Building custom genome
 
Hi Evan - sorry about the delayed response.  This got quickly buried in my inbox.

What's the error that you're encountering?

On Mon, Nov 18, 2019 at 7:23 PM Evan Conaway <evan....@gmail.com> wrote:
I'm having trouble trouble building my own genome for dog, it seems to get stuck on 

Running CMD: dfamscan.pl -fastafile ref_annot.cdsplus.fa -hmmfile ../Dfam.hmm -dfam_outfile __dfam_ref_annot.cdsplus.fa/dfam.out --masking_thresh --cpu 4

my initial command is

STAR-Fusion-v1.8.1/ctat-genome-lib-builder/prep_genome_lib.pl --genome_fa ../Canis_familiaris.CanFam3.1.dna.toplevel.fa --gtf ../Canis_familiaris.CanFam3.1.98_FIXED.gtf --pfam_db current --dfam_db ../Dfam.hmm

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The Broad Institute
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Brian Haas

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Jul 28, 2020, 2:04:54 PM7/28/20
to Bio info, Trinity_CTAT_users
I'm wondering if you give the full path to the dfam hmm file, will it work ok then?    It might be that the relative path is throwing it off.

Does it crash right away, or does it run for hours and then crash?



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