I am getting this error message when running Cufflinks on a Tophat created BAM file. Tophat version 1.3.3 and Cufflinks version 1.1.0. Bowtie 0.12.7 and Samtools 0.1.18
Tophat command:
Cufflinks:
Tophat finishes without error, but Cufflinks does not..
You are using Cufflinks v1.1.0, which is the most recent release.
Warning: BAM header too large
File /media/hd2/tuco/tophat/406A/tophat_out/accepted_hits.bam doesn't appear to be a valid BAM file, trying SAM...
[21:18:11] Inspecting reads and determining fragment length distribution.
SAM error on line 25873: CIGAR op has zero length
SAM error on line 26633: CIGAR op has zero length
...
Tophat command:
Code:
/home/matthew/tophat-1.3.3/tophat -p 16 -r 195 -z pbzip2 --mate-std-dev 50 /media/hd2/tuco/bowtie.index/tuco7 \ /media/hd2/tuco/unshuff/sgatrim/nocontam/MDM01_index1_qualshuff.nohomo.1.fq /media/hd2/tuco/unshuff/sgatrim/nocontam/MDM01_index1_qualshuff.nohomo.2.fq
Code:
/home/matthew/cufflinks/cufflinks -p16 -u -o /media/hd2/tuco/tophat/406A/cuff \ -b /media/hd2/tuco/bowtie.index/tuco.fa --upper-quartile-norm --max-mle-iterations 20000 \ --num-importance-samples 10000 /media/hd2/tuco/tophat/406A/tophat_out/accepted_hits.bam
You are using Cufflinks v1.1.0, which is the most recent release.
Warning: BAM header too large
File /media/hd2/tuco/tophat/406A/tophat_out/accepted_hits.bam doesn't appear to be a valid BAM file, trying SAM...
[21:18:11] Inspecting reads and determining fragment length distribution.
SAM error on line 25873: CIGAR op has zero length
SAM error on line 26633: CIGAR op has zero length
...
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