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Hello!
I'm trying to use coverm v6.1 to calculate the RPKM of several MAGs with the following command:
coverm genome -m rpkm --coupled /scratch/vilardi.k/katiefiles/clean_reads2/all_fq/combined2…
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#### Proposed solution
Supporting encryption for objects upon upload will be a necessary feature for the userbase. This should probably be implemented with WASM to enable faster performance for pro…
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#### Are you using the latest version of [samtools](https://github.com/samtools/samtools/releases/latest) and [HTSlib](https://github.com/samtools/htslib/releases/latest)? If not, please specify.
```…
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Hi,
Issue:
1) I ran samtools merge -O CRAM --reference ref.fasta output.cram input1.bam input2.bam
2) Then I ran samtools sort output.cram > output.sorted.cram
3) Then I ran samtools index outpu…
gevro updated
3 years ago
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#### Are you using the latest version of [samtools](https://github.com/samtools/samtools/releases/latest) and [HTSlib]
Using both samtools 1.11-12 and 1.13
```
[diego.terrones@clip-login-1 3bec…
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I installed the repo today and get this early error during pre-run tests
`Need samtools --version >= 1.7 but you have 1.12 - please upgrade it.`
```
snippy --check
[11:51:23] This is snippy 4.…
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Hi all,
I have a pipeline to call variants using both haplotypecaller and deepvariant, and I am trying to evaluate its performance by using samples from the genome in a bottle dataset. The issue is…
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I have a version of samtools and htslib compiled with clang and using libdeflate 1.7. When I try to pipe the output of hisat2-3n directly into `samtools sort`, I'm getting this error:
```
[E::sam_…
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iRODS support in Dockerfile below works for the version 1.10.2, but not for 1.11.
```
ARG htsversion=1.10.2
ARG samversion=1.10
ARG bcfversion=1.10.2
```
Specifically, when loading an irods file…
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Hello @erinyoung
The pipeline fails at ivar trim step.
Here's the log:
WARNING: The BED file provided did not have the expected score column, but iVar will continue trimming
iVar uses the s…