Closed NishatTamana51 closed 9 months ago
It appears that Braker failed to run. Could you please attach the log file here?
/home/cblast/Documents/7_f_proj/testrun_fungap_to_be_removed/fungap_out/logs/braker_SRR1198667.log
Update: The problem was with corrupted pfam database file and proteome file from sister orgs. I ran the commands several times for fetching them correctly. After that, the error vanished. Thanks for suggesting checking the braker_SRR1198667.log file.
Sure. Here is the log file:
#********* # WARNING: # The hints file(s) for GeneMark-EX contain less than 150 introns with multiplicity >= 10! (In total, 54 unique introns are contained. 19 have a multiplicity >= 10.) Possibly, you are trying to run braker.pl on data that does not provide sufficient multiplicity information. This will e.g. happen if you try to use introns generated from assembled RNA-Seq transcripts; or if you try to run braker.pl in epmode with mappings from proteins without sufficient hits per locus. Or if you use the example data set (orthodb_small.fa). # A low number of intron hints with sufficient multiplicity may result in a crash of GeneMark-EX (it should not crash with the example data set). #********* ln: failed to create symbolic link '/home/cblast/Documents/7_f_proj/testrun_fungap_to_be_removed/fungap_out/braker_out/SRR1198667/traingenes.gtf': File exists ERROR in file /home/cblast/miniconda3/envs/fungap/bin/braker.pl at line 6918 failed to execute: ln -s /home/cblast/Documents/7_f_proj/testrun_fungap_to_be_removed/fungap_out/braker_out/SRR1198667/GeneMark-ET/genemark.gtf /home/cblast/Documents/7_f_proj/testrun_fungap_to_be_removed/fungap_out/braker_out/SRR1198667/traingenes.gtf!
Is the problem related to fetching genome assembly and protein dataset files from NCBI? I faced problem while using extracting the gz contents for the protein file. But after several attempt, It worked.
Initially. I encountered the following output while trying to download protein files for test run using download_sister_orgs.py: `Validate input taxon...
Downloading protein sequence files... [Run] wget --quiet -nc ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/949/124/435/GCA_949124435.1_AIF_collapsed.nuclear_genome.ScRAP/*protein.faa.gz [Run] mv GCA_949124435.1_AIF_collapsed.nuclear_genome.ScRAP_protein.faa.gz /home/cblast/Documents/7_f_proj/testrun_fungap_to_be_removed/sister_orgs/GCA_949124435.1_protein.faa.gz
Done. Check "sister_orgs.list" for downloaded files details`
But the sister_orgs.lists file gave me no entries for the columns: `asm_id organism genbank_acc kingdom phylum subphylum class order family file_name'
Did braker fail for this?
Glad to hear that you resolved it! Let me know if you have further questions!
After configuring FunGAP, I did the test run but got the following error in BRAKER step. What could be the problem?
During handling of the above exception, another exception occurred: