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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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BRAKER error on call: parse_ET.pl #5

Closed Edison2021 closed 5 years ago

Edison2021 commented 6 years ago

I'm trying the BRAKER v2.1.0, but it stops at the GeneMark-ET step. Here's the exact error: error, file not found ~/src/gm_et_linux_64/gmes_petap/parse_ET.pl: set.out error on call: ~/src/gm_et_linux_64/gmes_petap/parse_ET.pl --section ET_A --cfg ~/src/BRAKER2/BRAKER_v2.1.0/example/run.cfg --v However, if i run ~/src/gm_et_linux_64/gmes_petap/parse_ET.pl, it will work.

Any help or suggestions would be appreciated!

PS: where can i downloade the BRAKER v1

KatharinaHoff commented 6 years ago

Please update to BRAKER 2.1.2 (https://github.com/Gaius-Augustus/BRAKER/releases/tag/v2.1.2)

The first BRAKER versions are still archieved at http://bioinf.uni-greifswald.de/augustus/binaries/old/ but I really don't recommend using old versions. The commands for calling tools from within BRAKER have changed over time. Also, the old versions contained numerous bugs that have long been fixed in the current version.

Do you observe the problem (in current version of BRAKER) when using the example data set, too?

Edison2021 commented 6 years ago

I tried the BRAKER v2.1.0 using the example data set from current version of BRAKER. I will update and let you know what will happen.

Edison2021 commented 6 years ago

I tried the latest one and the previous error disappears. Thanks!

KatharinaHoff commented 6 years ago

Excellent!

tiramisutes commented 5 years ago

Hi, I use the latest BRAKER 2.1.2 and have the same stder in gmes.log file.

/public/home/software/gm_et_linux_64/gmes_petap/gmes_petap.pl : [Mon Oct 22 10:17:59 2018] /public/home/software/gm_et_linux_64/gmes_petap/parse_ET.pl --section ET_A --cfg  /public/home/BRAKER2/GeneMark-ETP/run.cfg  --v
/public/home/software/gm_et_linux_64/gmes_petap/gmes_petap.pl : [Mon Oct 22 10:17:59 2018] error
KatharinaHoff commented 5 years ago

Can you please give some more information? Your post does not contain the actual error, it does not contain the braker call.

ersgupta commented 5 years ago

Hi Katharina,

I get the same error using v2.1.2. Any help would be great.

concatenate predictions: /<path>/gene_prediction/braker/braker/<spec>/GeneMark-ET/run/ET_A_1
training level ET_A: /<path>/gene_prediction/braker/braker/<spec>/GeneMark-ET/run/ET_A_1
error, file not found /<path>/apps/genemark/gm_et_linux_64/gmes_petap/parse_ET.pl: set.out
error on call: /<path>/apps/genemark/gm_et_linux_64/gmes_petap/parse_ET.pl --section ET_A --cfg  /<path>/gene_prediction/braker/braker/<spec>/GeneMark-ET/run.cfg  --v
ersgupta commented 5 years ago

Got it sorted. There are no files in hmmout folder and upon inspecting a bit I found out that genemark's 400-day license period had ended.

KatharinaHoff commented 5 years ago

Ok, that's good to know. I will close this issue, then.