Open Enorya opened 1 month ago
Dear Enora,
Thank you for using OMArk and reporting this issue.
From a cursory look at this issue, it seems like this may be due to the protein identifiers in the FASTA file provided through the '-of' option (GCF_001465895.1_Nfu_20140520_genomic.fna) and the one in the OMAmer output being different. Is this FASTA file the original proteome FASTA file that was first provided to OMAmer? From the file name, it looks like it may be instead a FASTA file of the genomic sequence. If it is the case, please try changing this file to the proteome FASTA file that was used as input to OMAmer.
Let me know if I am mistaken or if changing this file do not solve the issue. If it does not, could you write down a few examples of the headers from this file?
If it does, I'll keep this issue open as an incentive to work on better parameter checking.
Best wishes, Yannis
Dear Yannis,
Thank you for your quick reply. I indeed used the FASTA file of the genomic sequence and when I changed this file to the proteome FASTA file the OMArK tool worked.
Best regards, Enora
Dear,
I'm trying to use OMArK to assess the quality of a genome annotation and to be able to compare multiple ones later. However, whenever I try to run OMArK with the command
omark -f killi_lifton_annot_correct3.omamer -d LUCA.h5 -o killi_lifton -t 105023 -of ../GCF_001465895.1_Nfu_20140520_genomic.fna -v
on my dataset I get the following error:I tried to change the headers of my protein sequences in the omamer file by removing special characters or removing parts of the headers multiple times but I always get the same issue. However, when I remove the specific sequence mentioned in the error the writing continue a little bit and then stop to other sequences. The only link I found between these problematic sequences is the hoglevel (Nothobranchius furzeri in this case) but I don't understand why it's causing an issue. Here is a little part of my omamer file in which sequences XM_054735811 and XM_054735812 are problematic:
Do you have any idea why I'm experiencing this issue?
Thank you in advance for your help, Enora