segmentation fault core dumped when using bamCompare
Clarkson, Christopher T
Hi,
I tried implementing an analysis with your package deepToools- bamCompare. This was after merging a number of bam files together:
samtools merge H1.5_formatted.bam -@ H1.5/*sorted.bam
samtools sort -o H1.5_formatted_sorted.bam -@ 6 H1.5_formatted.bam
samtools index H1.5_formatted_sorted.bam
[gh@chromosome-0-8 ~]$ samtools view -h H1.5_formatted_sorted.bam |head -n30
@HD VN:1.0 SO:coordinate
@SQ SN:chrM LN:16571
@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: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:chr19 LN:59128983
@SQ SN:chr20 LN:63025520
@SQ SN:chr21 LN:48129895
@SQ SN:chr22 LN:51304566
@SQ SN:chrX LN:155270560
@SQ SN:chrY LN:59373566
@PG ID:bowtie2 PN:bowtie2 VN:2.2.6 CL:"/usr/local/bowtie2/bowtie2-align-s --wrapper basic-0 -x hg19 --very-fast -p 8 -S ChIPI_H1_dot_5_11-25-14_GCCAAT.sam -1 ChIPI_H1_dot_5_11-25-14_GCCAAT_L003_R1_complete_filtered.fastq -2 ChIPI_H1_dot_5_11-25-14_GCCAAT_L003_R2_complete_filtered.fastq"
@PG ID:bowtie2-4CA82BBB PN:bowtie2 VN:2.2.6 CL:"/usr/local/bowtie2/bowtie2-align-s --wrapper basic-0 -x hg19 --very-fast -p 8 -S ChIPII_H1_dot_5_11-25-14_CAGAT.sam -1 ChIPII_H1_dot_5_11-25-14_CAGATC_L003_R1_complete_filtered.fastq -2 ChIPII_H1_dot_5_11-25-14_CAGATC_L003_R2_complete_filtered.fastq"
HWI-ST1437:123:C69MTACXX:3:1104:7568:77851 163 chrM 1 23 4M5I92M = 123 223 CGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGAC CCCFFFFFHHHHHJIIJJJJJJJJJJJJJJJJIJJJJJIIIJJJJJIJJJHIIIJJJJJIIJJJJJHGHFFFFDDD5@>@DEDDDDDDBDDDEDDDDDDDB AS:i:-40 XN:i:0 XM:i:4 XO:i:1 XG:i:5 NM:i:9 MD:Z:0G0A0T0C92 YS:i:-11 YT:Z:CP
HWI-ST1437:123:C69MTACXX:3:1108:18364:3150 69 chrM 1 0 CTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCT CCCFFFFFHHGHHJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJIJIJHHCEHHFFF@DEDEEEEEDDDDDDDDDDDBDDDDA YT:Z:UP
I performed the same operation for the corresponding (-b2) input files as above:
bamCompare -b1 H1.5_formatted_sorted.bam -b2 input_formatted_sorted.bam -o test.bw
An error is immediately returned:
bamCompare -b1 H1.5_formatted_sorted.bam -b2 input_formatted_sorted.bam -o test.bw
Segmentation fault (core dumped)
ls -ltrh
-rw-rw-r-- 1 cc16956 r_cc16956 11G Oct 5 14:05 input_formatted_sorted.bam
-rw-rw-r-- 1 cc16956 r_cc16956 11G Oct 5 15:56 H1.5_formatted_sorted.bam
However when I try this with just a pair of the individual files that were used to make the merged bam files the process works...
Can you help me out with this?
Chris
Devon Ryan
BTW, if the input files are already sorted then you don't need to
resort after running "samtools merge".
Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany
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