Hi,
I'm using bowtie 0.12.7 to align 100bp PE reads. I'm crashing with the error:
Too few quality values for read: -
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'
Aside from finding out why this happened, I'd be particularly happy for bowtie to report this error as a warning and then continue with the run.
Is it possible to set a flag to get bowtie to throw the read instead of crashing?
Here's my call with arguments:
bowtie -X 20000 -q -p 12 -k 2 -m 2 --un no_align.fq --max mult_align.fq hg18.index -1 fastq_1 -2 fastq_2 align.aln
The last reported read before terminate is called can be found in no_align.fq (bowtie reports 2 files - 1 for each mate) :
tail -4 no_align_1.fq
@HWI-ST1096:2181WHPACXX:5:2316:16714:101026 1:N:0:TAAGGCG
NGATGAGATGATCGACGTCATCGGGGTGACCAAGGGCAAAGGCTACAAAGGGGTCACCAGTCGTTGGCACACCAAGAAGCTGCCCCGCAAGACCCACCGA
+
#1=?DDDDFFFFFDFII@@GFBCFEE@FDFFFEFFEFFFIIIIIIIIIEFFFDBDCCCCCBBB?BBBBBBBBBBBBBBBBABBBBBBBBBBBBBBBBB@9
&
tail -4 no_align_2.fq
@HWI-ST1096:2181WHPACXX:5:2316:16714:101026 2:N:0:TAAGGCG
CCAGAGCCCGCCGCTTCGTCTGCACCAGCAAGGACTTGCGGAGGGTGAGCGCCCGCTTCTTGGTTCCCACCGCACAGCCTTTCGGCATGACGGAGTCATT
+
1:?A1ADDF1@D1<CG<EHHEGHGJ@GD?)?DD2DG>=CHIIHFD;?=@@',33;@BBBA>>:@+>A@:A9&)09<(28CCDD(&&)08>A(&)0<9CCC
I've noticed other threads mentioning stretches of multiple B's at the end of sequences being a trigger for low quality reads. Not sure if this is the case here. Either way, can I force bowtie to not terminate on this instance if indeed this is the case.
One other thing, I have checked all reported align files (max-align, un-align & align) to see whether the next read in the original fastq file (i.e. after the one above) is actually reported just to make sure termination is in fact called & it is not there in any file. Therefore my run is incomplete.
Any ideas or fixes would be greatfully appreciated.
Thanks,
Sean.
I'm using bowtie 0.12.7 to align 100bp PE reads. I'm crashing with the error:
Too few quality values for read: -
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'
Aside from finding out why this happened, I'd be particularly happy for bowtie to report this error as a warning and then continue with the run.
Is it possible to set a flag to get bowtie to throw the read instead of crashing?
Here's my call with arguments:
bowtie -X 20000 -q -p 12 -k 2 -m 2 --un no_align.fq --max mult_align.fq hg18.index -1 fastq_1 -2 fastq_2 align.aln
The last reported read before terminate is called can be found in no_align.fq (bowtie reports 2 files - 1 for each mate) :
tail -4 no_align_1.fq
@HWI-ST1096:2181WHPACXX:5:2316:16714:101026 1:N:0:TAAGGCG
NGATGAGATGATCGACGTCATCGGGGTGACCAAGGGCAAAGGCTACAAAGGGGTCACCAGTCGTTGGCACACCAAGAAGCTGCCCCGCAAGACCCACCGA
+
#1=?DDDDFFFFFDFII@@GFBCFEE@FDFFFEFFEFFFIIIIIIIIIEFFFDBDCCCCCBBB?BBBBBBBBBBBBBBBBABBBBBBBBBBBBBBBBB@9
&
tail -4 no_align_2.fq
@HWI-ST1096:2181WHPACXX:5:2316:16714:101026 2:N:0:TAAGGCG
CCAGAGCCCGCCGCTTCGTCTGCACCAGCAAGGACTTGCGGAGGGTGAGCGCCCGCTTCTTGGTTCCCACCGCACAGCCTTTCGGCATGACGGAGTCATT
+
1:?A1ADDF1@D1<CG<EHHEGHGJ@GD?)?DD2DG>=CHIIHFD;?=@@',33;@BBBA>>:@+>A@:A9&)09<(28CCDD(&&)08>A(&)0<9CCC
I've noticed other threads mentioning stretches of multiple B's at the end of sequences being a trigger for low quality reads. Not sure if this is the case here. Either way, can I force bowtie to not terminate on this instance if indeed this is the case.
One other thing, I have checked all reported align files (max-align, un-align & align) to see whether the next read in the original fastq file (i.e. after the one above) is actually reported just to make sure termination is in fact called & it is not there in any file. Therefore my run is incomplete.
Any ideas or fixes would be greatfully appreciated.
Thanks,
Sean.
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