Cufflinks bam header size too large

[ramma]

When running cufflinks on my accepted_hits.bam files from tophat, I get this output, truncated as there are many CIGAR errors.

You are using Cufflinks v2.0.2, which is the most recent release.
Warning: BAM header too large
File accepted_hits.bam doesn't appear to be a valid BAM file, trying SAM...
[12:02:25] Inspecting reads and determining fragment length distribution.
SAM error on line 806: CIGAR op has zero length
SAM error on line 823: invalid CIGAR operation
SAM error on line 831: CIGAR op has zero length
SAM error on line 847: CIGAR op has zero length
SAM error on line 874: CIGAR op has zero length
SAM error on line 879: CIGAR op has zero length

It looks like I'm having the same error as this thread was.

http://seqanswers.com/forums/showthread.php?t=15676

However, I can't get cufflinks to compile with the source changes. The dependencies fail to be noticed. I'm following the guide here http://cufflinks.cbcb.umd.edu/tutorial.html and have tried on two computers now with no luck. Is there by chance a pre-compiled version with the fix, or some other way around this issue?

Thanks for any help.

[ramma]

I made it past the previous error with some help compiling cufflinks with the source change to handle headers larger than 4MB. Now another error appears when trying to run cufflinks.

You are using Cufflinks v2.0.2, which is the most recent release.
Error: sort order of reads in BAMs must be the same

I've tried sorting the accepted_hits.bam file with samtools as many threads seem to suggest, and error persists.

[JueFish]

ramma, having similar issue using cufflinks on large transcriptome sequence with lots of predicted transcripts. How did you get the program to compile? When I change the hits.cpp file, it won't compile, but if I leave it at 4 MB it still works. Any ideas on how to make this work?

Thanks.

[ramma]

ramma, having similar issue using cufflinks on large transcriptome sequence with lots of predicted transcripts. How did you get the program to compile? When I change the hits.cpp file, it won't compile, but if I leave it at 4 MB it still works. Any ideas on how to make this work?

Thanks.

Hi JueFish, I have a standalone version of cufflinks which I believe accepts up to 8 MB header size. I had help compiling it, so it's not my expertise and every time I tried compiling it myself with the header size change I had issues as well. If 8 MB is enough for your needs I'd be happy to send the stand alone version to you.

[JueFish]

ramma, 8MB is actually still smaller than what I need, but it's better than what I got. I can probably drop my reference down to get in that range. I'll send you a private message on Seqanswers and we can figure out how I might be able to get a copy of the binary from you. Thanks.

[ataraxia]

Dear ramma,
I am having a similar problem to Juefish when trying to run Cufflinks on my TopHat accepted_hits.bams output, as I am using a very fragmented genome (my bam header size is around 5.5 MB). I have tried to compile the source code changing the parameter for header size without any success. Would it be possible for you to send me your stand alone version? Which system are you using (Mac, PC, Linux)?

[ramma]

Sure ataraxia, I'll PM you a link to the download. It's compiled for a linux system.

[RNAddict]

Ramma could you supply me with your 8MB compilation?

[RNAddict]

I made it past the previous error with some help compiling cufflinks with the source change to handle headers larger than 4MB. Now another error appears when trying to run cufflinks.

You are using Cufflinks v2.0.2, which is the most recent release.
Error: sort order of reads in BAMs must be the same

I've tried sorting the accepted_hits.bam file with samtools as many threads seem to suggest, and error persists.

Did you ever find a way to fix this second error? I am experiencing it as well.

[pengchy]

Did you ever find a way to fix this second error? I am experiencing it as well.

Hi RNAddict,

here is the solution

http://seqanswers.com/forums/showthread.php?t=4058