Nitin123-4
Nitin123-4
You can open funannotate/predict.py script and can see the FILTERGENE condition: if lib.which("filterGenemark.pl"): FILTERGENE = "filterGenemark.pl" else: FILTERGENE = os.path.join(parentdir, "aux_scripts", "filterGenemark.pl") Just replace this code with: if lib.which("filterGenemark.pl"): FILTERGENE...
Thanks for your response. I can see in annotate step phobius uses all the available cpus and I am giving 150GB RAM still it is breaking with memory error. It's...
Hi Team, Any idea about this ?
Hi Thanks for your reply. I ran funannotate train with sqlite. I am running update with mysql.
Oh Okay. So funannotate train should also be with mysql and update also then it should be faster?
funannotate check shows ERROR: signalp not installed. Not sure how it is still taking signalp. is there any way to avoid running signalp?
I am also facing the same issue even with bed file. Both bam and bed gives the same issue.
Same issue I am also facing.
bam file has chr and it is looking for (6:29941260-29945884) so open /home/polysolver/scripts/shell_call_hla_type file and add chr (chr6:29941260-29945884) and then run it. Do the same thing for 6:31353872-31357187 and 6:31268749-31272105...
Make sure you are using /home/polysolver/scripts/shell_call_hla_type not /home/polysolver/scripts/shell_call_hla_type_test. Also, check there should not be any error after the run is over.