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I am running NextSV2 and I get these issues in the log files:
Traceback (most recent call last):
File "/BiO/Access/home/bioapps/nextsv/nextsv2.py", line 553, in
main()
File "/BiO/Access…
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samtools version : 1.8, using htslib 1.8
Run on
- Singularity container with gcc 5.4.0-6 on ubuntu 16.04.11
- The host is Centos 7.7 with the kernel 3.10.0-957.27.2.el7.x86_64
When running…
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Related to #2273.
(using commit 19f556177d47f9c78c34b5bdc1dc49131791b181).
When using jumpToRegion() with BAI files created by Picard tools or samtools-0.1.7, __getMinFileOffset() return 0 for the f…
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The remaining dependencies let we need to patch are:
- [ ] openssl
- [ ] libdeflate
The goal is to patch older htslib and samtools releases.
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Hi,
are these errors known? First seems to be a missing include path, second is that configure likely did not record path to site-wide htslib installation? I have gcc-4.9.4.
```
>>> Configuring…
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Dear all,
First of all, thanks for this very nice development.
I just wanted to report the fact that on some quite heavy ONT runs from bovine, NGMLR followed by sort was very slow (about 4 days …
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This error is throwing when i try a .bam output file from samtools.
Any ideas??
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Hello, Teacher Guo,
I didn't find the section for submitting questions in your github, so I posted it here (https://github.com/ZhangLabSZ/RES-Scanner2/issues/). I didn't choose the original transcrip…
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We may need a new CWL hint to collect the version number
```
hints:
VersionQuery: [samtools, --version]
```
- [ ] Write SchemaSalad for this as an extension
- [ ] Implement in `cwltool`
-…
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Somehow I'm ending up with a very low number of duplex reads after using Dorado duplex basecalling with the following command (used the ligation sequencing kit V14 SQK-LSK114):
`dorado duplex dna_r…