Samtools Segmentation error while using samtools index

AnushaC · 06-17-2014, 03:30 PM

Hi ,
I did re header my bam file and I did sort my file and trying to index my new bam file it is giving me the segmentation error .

################
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chrX LN:155270560
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chr10 LN:135534747
@SQ SN:chr11 LN:135006516
@SQ SN:chr12 LN:133851895
@SQ SN:chr13 LN:115169878
@SQ SN:chr14 LN:107349540
@SQ SN:chr15 LN:102531392
@SQ SN:chr16 LN:90354753
@SQ SN:chr17 LN:81195210
@SQ SN:chr18 LN:78077248
@SQ SN:chr20 LN:63025520
@SQ SN:chrY LN:59373566
@SQ SN:chr19 LN:59128983
@SQ SN:chr22 LN:51304566
@SQ SN:chr21 LN:48129895
@RG ID:SRR203401 PL:ROADMAP PU

GF LB:brain.SRR203401 SM:brain.SRR203401
achimmiri@idash-cloud-707:/mnt/oncogxA/anusha/ReadGroup_Bam$
##############
this is my header , I checked with samtools flagstat my new bam file after I did reheader

15158685 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
13730482 + 0 mapped (90.58%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

I checked my bam file manually but I don't see any problem . I am not sure why I am getting segmentation error

dpryan · 06-18-2014, 01:16 AM

Please give the exact command that produced this and the version of samtools that you're using.

vishnuamaram · 06-18-2014, 02:33 AM

hey anusha,

there is no error in general while using samtools index, the command line is very simple. let us know what command r u using.

Cross verify whether ur previous steps of samtools are correct or not.

AnushaC · 06-18-2014, 08:01 AM

Hi,
Thanks it is working . Bam header is not sorted that why it give segmentation error .

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06-17-2014, 03:30 PM	#1
AnushaC Member Location: San Diego Join Date: Sep 2013 Posts: 78	Samtools Segmentation error while using samtools index Hi , I did re header my bam file and I did sort my file and trying to index my new bam file it is giving me the segmentation error . ################ @SQ SN:chr1 LN:249250621 @SQ SN:chr2 LN:243199373 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 @SQ SN:chr5 LN:180915260 @SQ SN:chr6 LN:171115067 @SQ SN:chr7 LN:159138663 @SQ SN:chrX LN:155270560 @SQ SN:chr8 LN:146364022 @SQ SN:chr9 LN:141213431 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ SN:chr12 LN:133851895 @SQ SN:chr13 LN:115169878 @SQ SN:chr14 LN:107349540 @SQ SN:chr15 LN:102531392 @SQ SN:chr16 LN:90354753 @SQ SN:chr17 LN:81195210 @SQ SN:chr18 LN:78077248 @SQ SN:chr20 LN:63025520 @SQ SN:chrY LN:59373566 @SQ SN:chr19 LN:59128983 @SQ SN:chr22 LN:51304566 @SQ SN:chr21 LN:48129895 @RG ID:SRR203401 PL:ROADMAP PUGF LB:brain.SRR203401 SM:brain.SRR203401 achimmiri@idash-cloud-707:/mnt/oncogxA/anusha/ReadGroup_Bam$ ############## this is my header , I checked with samtools flagstat my new bam file after I did reheader 15158685 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 13730482 + 0 mapped (90.58%:-nan%) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (-nan%:-nan%) 0 + 0 with itself and mate mapped 0 + 0 singletons (-nan%:-nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) I checked my bam file manually but I don't see any problem . I am not sure why I am getting segmentation error

06-18-2014, 01:16 AM	#2
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	Please give the exact command that produced this and the version of samtools that you're using.

06-18-2014, 02:33 AM	#3
vishnuamaram Member Location: india Join Date: Jun 2013 Posts: 42	hey anusha, there is no error in general while using samtools index, the command line is very simple. let us know what command r u using. Cross verify whether ur previous steps of samtools are correct or not.

06-18-2014, 08:01 AM	#4
AnushaC Member Location: San Diego Join Date: Sep 2013 Posts: 78	Hi, Thanks it is working . Bam header is not sorted that why it give segmentation error .