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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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Orthodb11 as protein hints causes an error in GeneMark-ETP #814

Closed yifeng-evo closed 2 months ago

yifeng-evo commented 2 months ago

Hi BRAKER team,

I followed the instructions to use Vertebrata.fa from orthodb11 (https://bioinf.uni-greifswald.de/bioinf/partitioned_odb11/) as protein hints, but I have an error from GeneMark-ETP:

ERROR in file /opt/BRAKER/scripts/braker.pl at line 5575
Failed to execute: /usr/bin/perl /opt/ETP/bin/gmetp.pl --cfg /lustre/fs4/casa_lab/scratch/yfeng/braker/GeneMark-ETP/etp_config.yaml --workdir /lustre/fs4/casa_lab/scratch/yfeng/braker/GeneMark-ETP --bam /lustre/fs4/casa_lab/scratch/yfeng/braker/GeneMark-ETP/etp_data/ --cores 8 --softmask  1>/lustre/fs4/casa_lab/scratch/yfeng/braker/errors/GeneMark-ETP.stdout 2>/lustre/fs4/casa_lab/scratch/yfeng/braker/errors/GeneMark-ETP.stderr
Failed to execute: /usr/bin/perl /opt/ETP/bin/gmetp.pl --cfg /lustre/fs4/casa_lab/scratch/yfeng/braker/GeneMark-ETP/etp_config.yaml --workdir /lustre/fs4/casa_lab/scratch/yfeng/braker/GeneMark-ETP --bam /lustre/fs4/casa_lab/scratch/yfeng/braker/GeneMark-ETP/etp_data/ --cores 8 --softmask  1>/lustre/fs4/casa_lab/scratch/yfeng/braker/errors/GeneMark-ETP.stdout 2>/lustre/fs4/casa_lab/scratch/yfeng/braker/errors/GeneMark-ETP.stderr
The most common problem is that GeneMark-ETP didn't receive enough evidence from the input data, in this case, see errors/GeneMark-ETP.stderr!

When I look at GeneMark-ETP.stderr, it is like this:

error, an unexpected symbol was found in the file proteins.fa in:???EVERTEBRATA.FA??ю?:RM?ﯱ?\E?D?"("EH?S?^???????>U??ާ?ܙ+ג(FĜ???????????????ߟ_G?C?}?1???C?II??{?}??9??Z?W(??~?V?U}C?{C?K????????|????????􏿎U?}=?P?{???????|N?C?????\ﱧ~_??Y??????1?5????GO{\Ǟ;?Z?{?C??G,?Z?R?|U?Zދ????U????ϵ??}[R??]C(C?Q?>?0?^??^R??W??J??~?????Udz??`?Iܼ??}?????>?5?X???Y??????3??^[^?+?9??{???8??׏?F???VNR=G?!^W{=?7??,?U?Y]ϹQ-?V=Ó??ƜZ?װ?XǙ?,?????Q_??.????QC8?=????B>??U?Z?5?K㵥?U?+R*????-?N?}??Z???®?????3?{???????S?U?K?Ϻ?W9?Z?<˘O??V?Y?֞}???9?̚?OYKMSQ?X?#ϥ?3??}???-?U?2֫?\K?%??^I?;?G9???ZF?3?XKN?R?A)A???B????G?CO'?2S?,?~??ܭ??K??Z??????.?-;???U?<ե?????5?׌A.?7>??E?RG?Z?GNI.=??8?9X"???^?V?????????????\O??!???:_???YV>X?SUFI??I-?﫾????/NU?S??3?.ｇ?C\\?ó?G'?R??]56N??U\?(7?F??Լ7??Z??C???1]+O????Y????ЮY??/V??[?|?]?:WVU-???MO=?)/F?&?XR??X?XB??R?ZO<Q^S^???C????X?R?R?^??K#??Z?,????????{֥??Q?\?;?%????G?W???\Xݣ??NT??ˎ??'Q_1?ƽ?1?8??ـL?G?S?;عW???\O.??7??Q???؄??????*?#.'?E????????'RS??N|??E?C?C???Q̀??<?5]?F?S|P??Q?5??=?9Q
error in protein file parsing: proteins.fa

There are some messy characters so it is hard to know what the unexpected symbol is. I tried to rename protein ids in Vertebrate.fa but it also generated the same error.

I think it is an issue similar to issue765 . please let me know how I could fix it. Thank you!

KatharinaHoff commented 2 months ago

Did you uncompress the OrthoDB partition prior usage?

yifeng-evo commented 2 months ago

After uncompression it works! and it seems that I had to delete the braker folder from the previous run to successfully run it.