bcftools error

[Jay-Leung]

Hello! I was following the step by step installation from https://www.biostarhandbook.com/step-by-step.html#step-by-step.

However, when I ran ./bin/doctor.py, it gave an error for bcftools:

Doctor! Doctor! Give me the news.
Checking symptoms ...
bwa ... OK
datamash ... OK
fastqc -h ... OK
hisat2 ... OK
seqret -h ... OK
featureCounts ... OK
efetch ... OK
esearch ... OK
samtools ... OK
fastq-dump ... OK
bowtie2 ... OK
bcftools ... ERROR
seqtk ... OK
seqkit ... OK
bio ... OK
fastq-dump -X 1 -Z SRR1553591 ... OK

Your system shows 1 error!

Run the command that has failed for more details.

When I ran bcftools, it gave:
bcftools: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory

Could you advise on this? I am using a Linux Ubuntu LTS 20.04 LTS virtual machine. I have tried to install the latest gsl 2.7 but it doesn't seem to work as well.

Thanks!

[ialbert]

sounds like some sort of library version mismatch, sometimes this can be fixed by forcing either the tool or the library to the correct version:

mamba install bcftools=1.4

or , since this looks like it is looking for an older version of gsl (25 most likely means 2.5)

mamba install gsl=2.5

another possibility is to install bcftools into a separate environment and switch to that when running bcftools

[Jay-Leung]

Hi Albert!

Thanks for the prompt response! I installed gsl 25 and bcftools works, but samtools did not. I resolved it by running conda update --all, so now all is okay. Thanks!

Regards,
Jay

[ialbert]

sound good, glad it worked out