samFilter Shows CoreDump

Hi, am trying to run pbalign on my data with the --ForQuiver option on. However, am encountering a problem. Everytime blasr reaches on samFilter it shows Segmentation Fault (CoreDumped)

quiver pbalign samfilter

• 1,536 views • link

written 9.7 years ago by anniiee9 •

Segmentation fault is usually because of less memory.You should provide more memory and re run.

• 0 views • link

written 9.7 years ago by Ron

0 answers

No answers yet.

More posts like this

Kaiju database download
written 2.7 years ago by 10mz1 •

Hi all, I'm trying to operationalize Kaiju on my local PC. I downloaded the non-redundant database and extracted locally. I am now trying to run …
HH-suite: Segmentation fault (core dumped)
written 7.2 years ago by max_19

Hi all, Everytime I try to run HHblits from HH-suite (https://github.com/soedinglab/hh-suite/wiki#hh-suite-databases), it runs to a certain point then fails with this message: **Segmentation fault (core …
pbalign does not produce output
written 7.5 years ago by misterie

Hi, During run pbalign, I see that pbalign does not produce output. I tried different options — print to stdout, to file, by tmp files …
FastTree on Mac - Segmentation Fault 11
written 7.5 years ago by celine.petitjean •

Hello all, I am trying to run FastTree 2.1.10 on my mac and constantly have a Segmentation Fault 11. I reinstalled it several time, including …
bedtools intersect segmentation fault
written 8.7 years ago by ambarishnag •

Hi, I am trying to run a command: bedtools intersect -wao -f 0.75 -a A.gtf -b B.gtf > output.bed and I get segmentation fault. The …
SamFilter core dump Issue
written 9.6 years ago by madhuratathode •

Hello, I am using Pbalign for aligning pacbio reads in PacBio assembly correction where Blasr and samFilter is used by pbalign in the background. Blasr …
Help Needed with Pbalign SamFIlter
written 9.7 years ago by anniiee9 •

Hi all. I have been trying to run Pbalign with bax.h5 files from my PacBio data. I am facing this problem: 2016-12-04 08:45:37,051 [INFO] FilterService: …
pbalign - SortService returned a non-zero exit status
written 9.8 years ago by mjp •

I'm following [pbalign tutorial on large datasets][1]. I split my original fofn into subsets containing only three bax.h5 files, there is 14 of them. I …
Segmentation fault error while running extractPIRs from ShapeIT
written 9.9 years ago by kirannbishwa01

I am getting 'segmentation fault error' while trying to run subcommand from ShapeIt **$extractPIRs --bam bamlist --vcf sequence.multiple.vcf.gz --out myPIRsList** Reading genotypes in [sequence.multiple.vcf.gz] in …
velveth segmentation fault
written 11.6 years ago by emma.berdan •

Hi everyone, I am trying to run velveth on some paired end data I have but as soon as I submit the command I get …