failed executing genemark

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Ambreen
Posts: 1
Joined: Thu Oct 05, 2017 1:24 pm

failed executing genemark

Post by Ambreen »

I am trying to run braker for my mouse data. i have got my .fa file from ensemble and have bam files. when i run braker, the following error shows up:
NEXT STEP: execute GeneMark-ET
failed to execute: perl /media/ambreen/D206B4E906B4CFA9/gm_et_linux_64/gmes_petap/gmes_petap.pl --sequence=/home/ambreen/braker/newone7/genome.fa --ET=/home/ambreen/braker/newone7/hintsfile.gff --cores=4 1>/home/ambreen/braker/newone7/GeneMark-ET.stdout 2>/home/ambreen/braker/newone7/errors/GeneMark-ET.stderr

gmes.log file created shows error at the following line:
/media/ambreen/D206B4E906B4CFA9/gm_et_linux_64/gmes_petap/gmes_petap.pl : [Thu Oct 5 12:20:25 2017] /media/ambreen/D206B4E906B4CFA9/gm_et_linux_64/gmes_petap/make_nt_freq_mat.pl --cfg /home/ambreen/braker/newone6/GeneMark-ET/run.cfg --section start_ATG --format INI
/media/ambreen/D206B4E906B4CFA9/gm_et_linux_64/gmes_petap/gmes_petap.pl : [Thu Oct 5 12:20:25 2017] /media/ambreen/D206B4E906B4CFA9/gm_et_linux_64/gmes_petap/make_nt_freq_mat.pl --cfg /home/ambreen/braker/newone6/GeneMark-ET/run.cfg --section stop_TAA --format TERM_TAA
/media/ambreen/D206B4E906B4CFA9/gm_et_linux_64/gmes_petap/gmes_petap.pl : [Thu Oct 5 12:20:25 2017] error

when i tried to run genemark.pl seperately, it showed the following error:
perl gmes_petap.pl --ET /media/ambreen/D206B4E906B4CFA9/Mouse/TG_TS_RNA/ali
gnment/TS9/hints.gff --sequence /media/ambreen/D206B4E906B4CFA9/Mouse/genome/mousechr2.fa --et_score 10
error, no valid sequences were found
error on call: /media/ambreen/D206B4E906B4CFA9/gm_et_linux_64/gmes_petap/make_nt_freq_mat.pl --cfg /media/ambreen/D206B4E906B4CFA9/gm_et_linux_64/gmes_petap/run.cfg --section donor_GT --format DONOR

i am stuck here. Any help will be appreciated. T
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katharina
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Re: failed executing genemark

Post by katharina »

For issues that reproducibly exist with running GeneMark outside of BRAKER, please contact the GeneMark team (http://exon.gatech.edu/GeneMark/), directly.
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