Segmentation fault (core dumped) about bamdst

[shiquan]

hi, can you give me a demo to repeat this issue? Thx

[stroke1989]

链接：https://pan.baidu.com/s/10LO66IMXjMclHDdYpXM6pw
提取码：m2rw
--来自百度网盘超级会员V1的分享
the line include bam file and bed file. Hope your response

[shiquan]

I didn't test your data; it's huge for me to download all of it. But I found the chromosome name in the bed is inconsistent with BAM. You should check that.

[stroke1989]

yes, as you point out, I have revised chromosome name in bed file, the attachement is my bed file. However, again., error occurred:
(base) ug0416@gs72:~/software/bamdst$ /home/ug0416/software/bamdst/bamdst -p /home/ug0416/mydata/genome/hg19/hg19_bed/IDTV2.chr.bed -o /home/ug0416/software/bamdst/coverage/ /home/ug0416/mydata/05.gatk/a.BQSR/2nd_BQSR/SCA_271_N.sorted.markdup.bam
Segmentation fault (core dumped)

Hope youre reponse!Appreciate!

[nameOnStone]

Hi, I'm a newer to bamdst. This is a excellent tool. I runned the example file succefully. However, when I runned the following code: ~/software/bamdst$ /home/ug0416/software/bamdst/bamdst -p /home/ug0416/mydata/genome/hg19/hg19_bed/IDTV2.chr.bed -o /home/ug0416/software/bamdst/coverage/ /home/ug0416/mydata/04.mapping/2nd_geneseed_mapping/SCA_876_T.sorted.bam error occurred: Segmentation fault (core dumped) Hope your repose! Appreciate

same with you

[shiquan]

Fixed. Please pull the updated repo.

[stroke1989]

Fixed. Please pull the updated repo.

Great!. Now, it can run successfully

[ZhangJiePKU]

Hi, a small question:
Does Bamdst need 1-based bed file？ I wanted to calculate the depth for whole genome using 0-based bed, but I got a same error as stroke1989.
Thanks.

[shiquan]

How many base pairs in your bed file? I didn't test bamdst with a WGS bam, but I think the memory limitation may cause some issue. Maybe to shrink your bed file or split it by chromosomes can help.