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patrickwest / EukRep_Pipeline

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'InsideOut.pm line 1953 during global destruction' error running genemark-ES #3

Closed drelo closed 2 years ago

drelo commented 4 years ago

Dear Patrick

I used CONCOT to obtain the bins during this pipeline and now I had a problem using GeneMark-ES. I reduced the '_mincontig' to try with my dataset and I edited the gmes.cfg file accordingly using min_contig: 2500 . Following the advice in another github issue I run change_path_in_perl_scripts.pl with my perl executable in my conda environment, I also installed cpanm Hash::Merge and that seemed to fix a previous error. Now I run perl ../gmes_linux_64/gmes_petap.pl --ES -min_contig 2500 --sequence 14.fa

This is the last part of the output of this stage:

Intergenic: 130 25510
SvsM  0.121518987341772 vs 0.878481012658228
genes in IvsT all and selected: 1260 330
1, -1.56498614986327
2, -1.57958494928442
3, -1.44238382777093
4, -2.11021320034659
5, -2.03789253876696
6, -3.09104245335832
7, -2.96587931040431
# estimate 1: 0.721428571428571
# estimate 2: 0.75629398124262
# value: 0.75629398124262
IvsT  0.75629398124262 vs 0.24370601875738
    (in cleanup)    (in cleanup)  at /mnt/ubi/andres/miniconda3/envs/eukarya/lib/site_perl/5.26.2/Object/InsideOut.pm line 1953 during global destruction.
(eukarya) [andrespara@nagual clusters]$ vim /mnt/ubi/andres/miniconda3/envs/eukarya/lib/site_perl/5.26.2/Object/InsideOut.pm

Please find attached a file of one of the bins. 16.fa.txt

This is the length of the sequences inside the file (I already filtered those <2500)

NODE_423_length_9247_cov_24.787859 9247 NODE_4198_length_2911_cov_22.738796 2911

Do you know how to fix this? Thanks for your help.

Jiangjiangzhang6 commented 2 years ago

Dear my friend, how did you solve this err, I met the same bug,

drelo commented 2 years ago

I couldn't fix it and the lab moved onto analyzing another dataset instead. Sorry