samtools view error after reheader

Hkins552 · 07-11-2011, 12:08 PM

I am currently having an issue with samtools view for conversion of .sam to .bam. After replacing the header of my .sam in order to match the ref contigs I think attempted the conversion and received the following output:

$ samtools view -bS 1112-1.reheader.sam > 1112-1.reheader.bam

[sam_read1] reference 'chr1' is recognized as '*'.
[sam_read1] reference 'chr1' is recognized as '*'.
[sam_read1] reference 'chr1' is recognized as '*'.
etc.

Basically for an endless number of lines.

Has anyone seen a similar error?

pasta · 07-12-2011, 02:52 AM

Maybe this can help: http://seqanswers.com/forums/showthread.php?t=4719

jjpurwar · 07-16-2011, 08:13 PM

Hi - I received the same error. I also reheadered my sam file and then tried to convert to a bam and received the [sam_read1] reference 'chrX' is recognized as '*'.

Did you ever figure out a solution to the problem?

I noticed that samtools did write a bam file. So, I visualized it (after sorting and indexing it) and it appears that the rest of the chromosomes did convert except for the chrX. I have no reads there. Not surprising.

jjpurwar · 07-17-2011, 11:32 AM

I figured out the solution to my problem. Turns out that my sam file header had to be in the right format:

The first line needs to be header.
The second line needs to be a dummy read group line
The next lines need to contain the chromosomes and their lengths.

An example of a good header is as follows:

@HD VN:1.0 SO:unsorted
@RG ID:unknownReadGroup SM:unknownSample
@SQ SN:chrI AS:ce6_32r_index LN:15072421
@SQ SN:chrII AS:ce6_32r_index LN:15279323
@SQ SN:chrIII AS:ce6_32r_index LN:13783681
@SQ SN:chrIV AS:ce6_32r_index LN:17493785
@SQ SN:chrM AS:ce6_32r_index LN:13794
@SQ SN:chrV AS:ce6_32r_index LN:20919568
@SQ SN:chrX AS:ce6_32r_index LN:17718854

Once I deleted all the @SQ , @PG, @HD lines from my sam file and appended the above header text file to my sam file and tried to convert it to a bam - it worked beautifully.

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07-11-2011, 12:08 PM	#1
Hkins552 Member Location: Baltimore MD Join Date: Jun 2011 Posts: 18	samtools view error after reheader I am currently having an issue with samtools view for conversion of .sam to .bam. After replacing the header of my .sam in order to match the ref contigs I think attempted the conversion and received the following output: $ samtools view -bS 1112-1.reheader.sam > 1112-1.reheader.bam [sam_read1] reference 'chr1' is recognized as ''. [sam_read1] reference 'chr1' is recognized as ''. [sam_read1] reference 'chr1' is recognized as '*'. etc. Basically for an endless number of lines. Has anyone seen a similar error?

07-12-2011, 02:52 AM	#2
pasta Member Location: Alps Join Date: Jan 2011 Posts: 27	Maybe this can help: http://seqanswers.com/forums/showthread.php?t=4719

07-16-2011, 08:13 PM	#3
jjpurwar Junior Member Location: Salt Lake City Join Date: Jun 2011 Posts: 9	Hi - I received the same error. I also reheadered my sam file and then tried to convert to a bam and received the [sam_read1] reference 'chrX' is recognized as '*'. Did you ever figure out a solution to the problem? I noticed that samtools did write a bam file. So, I visualized it (after sorting and indexing it) and it appears that the rest of the chromosomes did convert except for the chrX. I have no reads there. Not surprising.

07-17-2011, 11:32 AM	#4
jjpurwar Junior Member Location: Salt Lake City Join Date: Jun 2011 Posts: 9	I figured out the solution to my problem. Turns out that my sam file header had to be in the right format: The first line needs to be header. The second line needs to be a dummy read group line The next lines need to contain the chromosomes and their lengths. An example of a good header is as follows: @HD VN:1.0 SO:unsorted @RG ID:unknownReadGroup SM:unknownSample @SQ SN:chrI AS:ce6_32r_index LN:15072421 @SQ SN:chrII AS:ce6_32r_index LN:15279323 @SQ SN:chrIII AS:ce6_32r_index LN:13783681 @SQ SN:chrIV AS:ce6_32r_index LN:17493785 @SQ SN:chrM AS:ce6_32r_index LN:13794 @SQ SN:chrV AS:ce6_32r_index LN:20919568 @SQ SN:chrX AS:ce6_32r_index LN:17718854 Once I deleted all the @SQ , @PG, @HD lines from my sam file and appended the above header text file to my sam file and tried to convert it to a bam - it worked beautifully.