PBJelly fails: no gaps to fill
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Get the following output in PBJelly/mapping/pacbio.fasta/err:
2017-05-04 00:00:07,700 [INFO] Running /home/ubuntu/PBSuite_15.8.24/bin/m4pie.py /home/ubuntu/blasr/PBJelly/mapping/pacbio.fasta.m4 /home/ubuntu/blasr/pacbio.fasta /home/ubuntu/blasr/b1-flavo_cerulean.fasta --nproc 31 -i
2017-05-04 00:00:10,253 [INFO] Extracting tails
Traceback (most recent call last):
File "/home/ubuntu/PBSuite_15.8.24/bin/m4pie.py", line 209, in
run(sys.argv[1:])
File "/home/ubuntu/PBSuite_15.8.24/bin/m4pie.py", line 188, in run
r, t, m = extractTails(aligns, reads, outFq=tailfastq, minLength=args.minTail)
File "/home/ubuntu/PBSuite_15.8.24/bin/m4pie.py", line 53, in extractTails
seq = reads[read.qname][:pTail]
KeyError: 'm140309_015740_42141_c100633532550000001823121009121460_s1_p0/140091/0_9074/7986_8567/0_581'
PBJelly discussion pages indicate this is typically a problem with the long-read header files containing white space, but pacbio.fasta does not contain white space anywhere in the header or body of the file (checked by vim "ESC/ ").
This error is associated with PBJelly failing to enumerate gaps to fill using long reads.