We get the following error while running Tophat 2.0.0 on a sequence. STAR aligner works fine on this sequence file. Here is the part of the log:
[2013-04-12 10:40:14] Preparing reads
left reads: min. length=101, max. length=101, 183210621 kept reads (230841 discarded)
....
Line 171124311, sequence length 74 vs 101 from CIGAR
Parse error at line 171124311: CIGAR and sequence length are inconsistent
[FAILED]
Error running bowtie:
The offending reads looks fine to me!
@D8CXHXP1:240:C0DBWACXX:5:1208:19908:68173 1:N:0:
CGAGGCTGGCATTTGTGTTCTCTTAGGGTCTGCATAACATCTGTCCAGGATCTTCTGGCTTTCATATTCTCTGGTGAGAAGTCTGGTGTAATTCTAATAGG
+
CCCFFFFFHGHHHJJGIIGIJJJJJJIJFGGIIJJJJIJJJJJEHJJJJEIIJJJJJJJIJJJJJJJJJJJJHHH?EEFFFFFFEECECDEEFEEEEEDDD
Any idea why this might be happening?
we are running:
TopHat v2.0.0
Bowtie2 version 2.0.0-beta5
[2013-04-12 10:40:14] Preparing reads
left reads: min. length=101, max. length=101, 183210621 kept reads (230841 discarded)
....
Line 171124311, sequence length 74 vs 101 from CIGAR
Parse error at line 171124311: CIGAR and sequence length are inconsistent
[FAILED]
Error running bowtie:
The offending reads looks fine to me!
@D8CXHXP1:240:C0DBWACXX:5:1208:19908:68173 1:N:0:
CGAGGCTGGCATTTGTGTTCTCTTAGGGTCTGCATAACATCTGTCCAGGATCTTCTGGCTTTCATATTCTCTGGTGAGAAGTCTGGTGTAATTCTAATAGG
+
CCCFFFFFHGHHHJJGIIGIJJJJJJIJFGGIIJJJJIJJJJJEHJJJJEIIJJJJJJJIJJJJJJJJJJJJHHH?EEFFFFFFEECECDEEFEEEEEDDD
Any idea why this might be happening?
we are running:
TopHat v2.0.0
Bowtie2 version 2.0.0-beta5
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