Hi, I am comparing transcriptome assemblies from a few different assemblers and have been using BUSCO (http://busco.ezlab.org/) to characterize the completeness of assembly compared to a set of orthologues.
All seems to work well for some transcriptome assemblies (e.g. Trinity) but not for others (Oases) - I get this error:
*** Extracting candidate transcripts! *** Traceback (most recent call last): File "/root/Downloads/BUSCO_v1.22/BUSCO_v1.22.py", line 565, in <module> out = open('%s%s%s_.temp' % (args['tmp'],i,args['abrev']),'w') IOError: [Errno 2] No such file or directory: './Locus_1_Transcript_5/10_Confidence_0.455_Length_2461new_.temp'
after running this
root@:~ python /root/Downloads/BUSCO_v1.22/BUSCO_v1.22.py -o new -in ./transcripts-l200.fasta -l /root/Downloads/BUSCO_v1.22/metazoa/ -m trans
All dependencies installed, and I as I said, works for some fasta assemblies but not others. I thought it might be issues with the long fasta headers, but that error does not suggest such a problem. Looking at that line in the python code;
if i in scaff_list: 565 out = open('%s%s%s_.temp' % (args['tmp'],i,args['abrev']),'w') out.write('>%s\n' % (i)) check = 1
Thanks for any help.