error loading sam header

[Marina Kasaikina]

Hi! I'm very new here and I apologize for very basic question/

 I've got a problem with loading of the custom reference file to the IGV. I indexed fasta file with and aligned the fastq files using  bowtie 2.3.0, tranformed to bam file and sorted bam file using samtools 1.3. (samtools view -ubSh $here$sam.sam > $here${sam}.bam)  When loading to the igv (2.3.97), I'm getting the repeated error: "Error loading sam file. For sequence 6 text and binary have different lenghts in file path/to sorted/bam/file."

My guess is that the problem in the different ways of indexing and sorting by IGV and samtools. When I'm loading .fasta to IGV, it generated .fai index itself. What can be done here?

Thank you so much in advance!!!

[James Robinson]

Hi,

Could you attach your igv.log file?  The error message indicates a problem with the bam file.  It has nothing to do with indexes or IGV vs samtools.   

Jim

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[Marina Kasaikina]

Hi Jim,

Please see the attached file.

Thanks!

Marina. 

On Tuesday, August 1, 2017 at 4:04:04 PM UTC-4, Jim Robinson wrote:

Hi,

Could you attach your igv.log file?  The error message indicates a problem with the bam file.  It has nothing to do with indexes or IGV vs samtools.   

Jim

On Tue, Aug 1, 2017 at 9:39 AM, Marina Kasaikina <kasa...@gmail.com> wrote:

Hi! I'm very new here and I apologize for very basic question/

 I've got a problem with loading of the custom reference file to the IGV. I indexed fasta file with and aligned the fastq files using  bowtie 2.3.0, tranformed to bam file and sorted bam file using samtools 1.3. (samtools view -ubSh $here$sam.sam > $here${sam}.bam)  When loading to the igv (2.3.97), I'm getting the repeated error: "Error loading sam file. For sequence 6 text and binary have different lenghts in file path/to sorted/bam/file."

My guess is that the problem in the different ways of indexing and sorting by IGV and samtools. When I'm loading .fasta to IGV, it generated .fai index itself. What can be done here?

Thank you so much in advance!!!

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[James Robinson]

Something has gone wrong in the creation of your bam file, but I can't tell you what.   The error indicates that the sequence length specified in the "SAM" file header differs from the sequence length specfied in the SAM text header for the 7th sequence in your file.  In other words the "LN" parameter specfied for  @SQ entry in the SAM header differs from the l_ref value for the same sequence in the BAM header.  

I don't know how this can occur.   You might try asking in the samtools or htsjdk forums.

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[Marina Kasaikina]

Jim,

Thank you. Whatever happened - this is very reproducible. I repeated the alignment and the genome indexing a couple of times with the same result.

[James Robinson]

Post your question here  https://gatkforums.broadinstitute.org/wdl/discussions/tagged/htsjdk.    I edited it slightly as you can see below.  

You might also try the samtools mailing list  https://sourceforge.net/p/samtools/mailman/samtools-help/.    It looks like the error is created by samtools,  but detected by the htsjdk,  so I don't know which is the right forum to start.

"I have a repeatable error from the htsjdk when I try to load my bam file in IGV.   I indexed fasta file with and aligned the fastq files using  bowtie 2.3.0, tranformed to bam file and sorted bam file using samtools 1.3. (samtools view -ubSh $here$sam.sam > $here${sam}.bam)  When loading to the igv (2.3.97), I'm getting the repeated error: "Error loading sam file. For sequence 6 text and binary have different lenghts in file path/to sorted/bam/file.""