Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

library error in smoove #237

Open
poddarharsh15 opened this issue Jan 17, 2024 · 4 comments
Open

library error in smoove #237

poddarharsh15 opened this issue Jan 17, 2024 · 4 comments

Comments

@poddarharsh15
Copy link

Screenshot from 2024-01-15 14-53-37
Hello, I am facing this error while running smoove on conda environment could you please add some suggestions to solve this issue.
Thanks in advance.

@brentp
Copy link
Owner

brentp commented Jan 17, 2024

Hi, I'm not sure how to help with this exact issue, but there's a problem with your pysam install, you might try re-installing pysam in that environment.

@poddarharsh15
Copy link
Author

I tried installing pysam several times and also created a separate environment for pysam but still it gives me the same error.

@brentp
Copy link
Owner

brentp commented Jan 18, 2024

I would check the pysam issues and/or ask there.

@poddarharsh15
Copy link
Author

poddarharsh15 commented Jan 18, 2024

I am waiting for their answer I did ask there, but at the same time I am trying to find solutions by running on different environment using this command line on terminal.
smoove call --outdir ~/HG002_bams/results_smoove/ --exclude ceph18.b37.lumpy.exclude.2014-01-15.bed --name HG002 --fasta home/tigem/h.poddar/short_reads_pipeline/reference_genome/GRCh37/GRCh37.p13.genome.fa -p 1 --genotype /home/tigem/h.poddar/HG002_bams/HG002_dragen.bam
Please let me know if I am making some error with the smoove call command.(running on just one sample obtained from HG002 golden standard data) Thanks in advance.
After running above command I am getting another panic error could please suggest me some ideas.
Screenshot from 2024-01-18 10-25-33

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants