tophat 2.0.0 CIGAR and sequence length are inconsistent

[laxman]

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

[GenoMax]

You appear to be running older versions of both programs. Any possibility you can upgrade both (Tophat now in v.2.0.8 and Bowtie2 v.2.1.0) and see if the error goes away.

[laxman]

i already have upgraded version but another sample from the same batch worked fine with older versions I used. I will give it a try too
-best
-Lax

[dylkot]

I am having the exact same issue. Has anyone else seen or resolved this? In my case, the offending mapped read looks as follows:

59 69 * 0 255 * * 0 0 CGCAAGGGCATCTCTGGGAAAGGACCTGGGGCTGGTGAGGGGCCCGGAGGAGTCTTTGCCCGCGCGTGAGACTCCA @?@BD@DDB?B;CCCF3C3AAF>AEFFB?C0?D@<)99?FFFI@;;/'=B;5(6>;>B################## ZN:Z:SRR821602.59

and the output is:

and the output is:

[2013-07-18 13:34:28] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2013-07-18 13:34:28] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-07-18 13:34:28] Checking for Samtools
Samtools version: 0.1.19.0
[2013-07-18 13:34:28] Checking for Bowtie index files
[2013-07-18 13:34:28] Checking for Bowtie index files
[2013-07-18 13:34:28] Checking for reference FASTA file
[2013-07-18 13:34:28] Generating SAM header for /home/unix/dylkot/genomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome
format: fastq
quality scale: phred33 (default)
[2013-07-18 13:35:31] Reading known junctions from GTF file
[2013-07-18 13:35:37] Preparing reads
left reads: min. length=76, max. length=76, 2500 kept reads (0 discarded)
right reads: min. length=76, max. length=76, 2498 kept reads (2 discarded)
[2013-07-18 13:35:37] Using pre-built transcriptome index..
[2013-07-18 13:35:41] Mapping left_kept_reads to transcriptome genome with Bowtie2
[2013-07-18 13:35:49] Mapping right_kept_reads to transcriptome genome with Bowtie2
[2013-07-18 13:35:56] Reporting output tracks
[FAILED]
Error running /home/unix/dylkot/bin/tophat-2.0.8b.Linux_x86_64/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir /broad/hptmp/dkotliar/GTEX/mapped/debug/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 5 --read-gap-length 2 --read-edit-dist 7 --read-realign-edit-dist 8 --max-insertion-length 3 --max-deletion-length 3 -z gzip --inner-dist-mean 67 --inner-dist-std-dev 231 --gtf-annotations /home/unix/dylkot/genomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.gff --gtf-juncs /home/unix/dylkot/mapped/debug/tmp/genome.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header /home/unix/dylkot/mapped/debug/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/home/unix/dylkot/bin/samtools-0.1.19/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /home/unix/dylkot/genomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa /home/unix/dylkot/mapped/debug/junctions.bed /home/unix/dylkot/mapped/debug/insertions.bed /home/unix/dylkot/mapped/debug/deletions.bed /home/unix/dylkot/mapped/debug/fusions.out /home/unix/dylkot/mapped/debug/tmp/accepted_hits /home/unix/dylkot/mapped/debug/tmp/left_kept_reads.m2g.bam /home/unix/dylkot/mapped/debug/tmp/left_kept_reads.bam /home/unix/dylkot/mapped/debug/tmp/right_kept_reads.m2g.bam //home/unix/dylkot/mapped/debug/tmp/right_kept_reads.bam
Error: CIGAR and sequence length are inconsistent!(CGCAAGGGCATCTCTGGGAAAGGACCTGGGGCTGGTGAGGGGCCCGGAGGAGTCTTTGCCCGCGCGTGAGACTCCA)

Any idea what could be going on or how I can best get around this problem?