bowtie2 stops during alignment

[moritzhess]

Hi everybody,

I am aligning Illumina 100bp reads to a reference transcriptome using bowtie2. When aligning certain fastq files, bowtie stops aligning always at the same position. The first read, below is the last that bowtie aligns. Afterwards bowtie stops. I ran fastqc on the files anyway and it reported no errors. Bases and Quality strings seem to have the same length so I cannot find a reason for the alignment stop. Does anybody had the same sort of errors when using bowtie2 ?

Thanks in advance,

Moritz

@HWI-ST748:1811K3YACXX:6:1101:20680:72912 1:N:0:ACTTGA
GTGCAACAGTACCAGCAACAAATGAAGGTAAAACACCTCGATTTCTGTGCATTCAATGTTCCTCGACTTCTGTGCAGCAATCTCTCTTCTGGAAAATCGT
+
@@CFDFFFHFFDDFFEBFDH?ECHGIIJAEDHICGG1?FHBGIIDHIGEEAFIGH>BBBDGEGIJJ/@EDEHHHHHEC?@C:6@C;6;>@CCCD@C>:7?
@HWI-ST748:1811K3YACXX:6:1101:20630:72949 1:N:0:ACTTGA
GTTGTAACTGACCGGATCGCAGGCAGATTGCCCCAGCTTTAAATTAGTCATTGTTGGCGATGGAGGCACTGGGAAGACGACTTTTGTCAAACGCCATCTT
+
CCCFFFFFHHHHHJJJJIJJJJJJJJIJFJEHJJJJJJJJIIIGHHIGGIJJJJJIJIHHFFFEEDBBDDCDD?C?BDDDDDDDDDDDEEDDDDDDDDCC
@HWI-ST748:1811K3YACXX:6:1101:20750:72956 1:N:0:ACTTGA
ATGAACTTCAAGCTCTGACTGAGAAAGCCGTTATTCACGATTGGAAGGAGACCGAGTCTTGGAGGCTGTTGAAGCAGCTCACTAAATCAGTTCAACATCG

[Luyi Tian]

Does the program print any error message? or it just stoped.

[moritzhess]

Hi Luyi Tian,
thanks for your fast response!
The program itself is quiet but I piped the bowtie output to samtools view to generate bam files and samtools reports: "Parse error at line 1299638: sequence and quality are inconsistent."

Moritz

[moritzhess]

Problem solved by upgrading to Version 2.0.5.