Menu
▾
▴
#5 Segmentation fault : Failed to read ebd file by varisite
Hello,
I'm getting the following error when i'm running varisite. Kindly let me know how to fix this.
[ngb@NEO mapping_bwa]$ /data1/snptools/varisite ebd.list chr hg19.fa
binding 5
groups 1
loading hg19.fa
fail to read 1.sorted.bam.ebd
fail to read 2.sorted.bam.ebd
fail to read 3.sorted.bam.ebd
fail to read 4.sorted.bam.ebd
fail to read 5.bam.ebd
Segmentation fault
[ngb@NEO mapping_bwa]$
Thanks,
Ashwani
Related
Discussion
Anonymous
Ashwani, does the ebd files have the right path?
Dear Jin, yes they are in the same folder from where they are being run later i tried putting them with complete/full path but still gave the same error. the "chr" option in the syntax does it points to any particular file (genome file or chromosome file) i dont have ant file having the name chr currently in my directory.
[ngb@NEO mapping_bwa]$ ~/Downloads/snptools/varisite ebd.list chr hg19.fa
binding 3
groups 1
loading hg19.fa
fail to read #/data3/J-Human/mapping_bwa/1_sorted.bam
fail to read fail to read #/data3/J-Human/mapping_bwa/2.sorted.bam.ebd
/data3/J-Human/mapping_bwa/3.sorted.bam.ebd
Segmentation fault
[ngb@NEO mapping_bwa]$ vi ebd.list
Ashwani, "chr" is actually "$chr", it is 19 in your case.
Hi Ashwani,
Can you check if the 3rd field in your BAM files is "19" or "chr19"? You need to use that as the 2nd argument of varisite consistently. Hope it helps.
Zhuoyi
You did not post the reads data section but only the BAM header. From this, I guess the 3rd field of reads data section should be named such that, for chromosome 19, it is "chr19" instead of "19". Therefore, you probably want to try the following commands:
$ /data1/snptools/varisite ebd.list chr19 hg19.fa
Zhuoyi
hi all:
please be careful, the following command does not works correctly, as
hg19.fa is a big fasta file containing multiple chromosomes.
$ /data1/snptools/varisite ebd.list chr19 hg19.fa
we need separated fasta file for each chromosome. please use the following
command:
$ /data1/snptools/varisite ebd.list chr19 ch19.fa
On Wed, Apr 16, 2014 at 3:58 AM, Zhuoyi Huang zyhuang@users.sf.net wrote:
Related
Tickets: #5
Hello,
I have run all the commands of SNPtools and imputation step is currently going on. I need to know one thing though. after the varisite step when we get the output of SNP files in vcf format for each chromosome. How do we know the genotype of Individual samples in this vcf file? I have 9 samples which i have processed using SNPTOOLS and after varisite step i get 24 vcf files each corresponding to one chromosome but when i open these VCF files i do see the genotype column but there is only one column for refernce genotype and there is no information related to sample and sample specific genotype. Can you let me know how to get the sample specific snp information from the vcf file. My sample output file for chr10 after varisite step is as follows:
[ngb@NEO J-Human]$ head chr10.sites.vcf
chr10 61419 . G A 4.64292 PASS SNP
chr10 62057 . G A 3.74172 PASS SNP
chr10 66183 . G A 1.92568 PASS SNP
chr10 66397 . C T 1.82326 PASS SNP
chr10 68575 . C T 4.27638 PASS SNP
chr10 69071 . G A 5.63506 PASS SNP
chr10 69083 . C T 13.5143 PASS SNP
chr10 71160 . C T 1.72429 PASS SNP
chr10 71667 . C T 3.50066 PASS SNP
chr10 71776 . T C 3.07973 PASS SNP
[ngb@NEO J-Human]$
Hi, Ashwani
The next step is GL.
Please check the wiki:
https://sourceforge.net/p/snptools/wiki/Best%20practices%20of%20integrated%20SNP%20analysis/
The workflow of SNPtools was explained there.