GeneMark-ES error: parse_ET.pl line 213 Invalid regression data

[elximo]

I am trying to run GeneMark-ES on a fungal genome. I get this error only when I include the intron coordinates option --ET.

When the program starts section ET_B training step, and while creating the symbolic link in the ET_C_1 to ET_B, it crashes in the parsing script with the following error:

Must input more than one data point! at /home/myname/Applications/GeneMarkES/parse_ET.pl line 213.
Invalid regression data
error on call: /home/myname/Applications/GeneMarkES/parse_ET.pl --section ET_C --cfg /home/myname/projectX/Maker/GeneMark/run.cfg --v

I am using GeneMark-ES Suite version 4.21
I used tophat2 2.0.13 to perform my alignment


As recommended, I created the introns file for GeneMark from the tophat alignment using the script /home/myname/Applications/GeneMarkES/bet_to_gff.pl --bet junctions.bed --gff tophat_introns.gff --label Tophat2

I am running GeneMark using the command

gmes_petap.pl --ES --fungus --ET tophat_introns.gff --et_score 10 --min_contig 150000 --cores 12 --sequence mydraftgenome.fasta


Has anyone came across something similar? Meanwhile I am repeating the tophat alignment and will try again.

[elximo]

I traced a little into the failing script and apparently the hash with introns gets reduced to just one entry in a noise reduction step, after which the script fails. I am not sure in this case if it is a problem with the tophat output though.

[johnng wang]

same problem

hello sir
when i trying to run GeneMark-ES on a fungal genome, i got a same problem with yours, so i wonder if you get the solution for this? and if you could give me some advises here, thank u for your time !