Comments (3)
@bmvdgeijn
Dear owner,
I implemented WASP im my computer various time, and it performs very well, good algorithm.
However, when I run find_intersecting_snps.py (In WASP mappability filter) my account in a server
a get this error:
Traceback (most recent call last):
File "find_intersecting_snps.py", line 6, in
import pysam
File "/gpfs/home/zitoa/ChrX/apps/WASP/pysam/init.py", line 1, in
from pysam.libchtslib import *
Why ?? I did not find this module in the pysam folder.
Best,
anto
from wasp.
Hi Anto,
The error is coming from pysam, which is a wrapper around the htslib C library. The error message indicates that it is unable to import the module that wraps the C library. I suspect that the error indicates that pysam was either not compiled or installed correctly. Please try to re-build and/or re-install pysam.
Graham
from wasp.
many thanks,
best
anto
from wasp.
Related Issues (20)
- Missing step in CHT readme?
- Many reads discarded due to remapping with different CIGAR HOT 6
- CHT Snakemake workflow getting stuck at adjust_read_counts
- VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated
- find_intersecting_snps.py outputting sam files rather than bam files HOT 2
- Small sample size HOT 3
- filter_remapped_reads.py HOT 2
- find_intersecting_snps.py HOT 3
- Minor typo in Snakefile
- Represent phased blocks in VCF file HOT 1
- find_intersecting_snps.py: for pair in product(new_reads[0][group], new_reads[1][group]): IndexError: list index out of range HOT 1
- Whole genome sequencing data HOT 1
- running filter_remapped_reads.py on multiple samples all get empty bam files
- Incomplete h5 files with snp2h5
- filter_remapped_reads.py with bams created by HISAT2/ other mappers than Bowtie2 HOT 2
- running snp2h5 in the mapping snakemake HOT 1
- error in rule "get_as_counts" / bam2h5.py
- VCF to HDF5 Error
- Will rmdup_pe.py behave normally if one mate from a read pair is removed? HOT 1
- about NAs and 0s in CHT step 6 "extract_haplotype_read_counts"
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from wasp.