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hasindu2008 / f5c

Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)

Home Page:https://hasindu2008.github.io/f5c/docs/overview

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Error Running Call Methylation

katiestoker opened this issue · comments

commented

Hello,

Indexing seems to have worked well, however I receive the error "[init_core::ERROR] sam_itr_queryi failed. A problem with the BAM index?" when running f5c call-methylation.

Thanks!
Katie.

commented

How was the BAM file and the BAM index created?
Could you please try after reindexing the BAM file, samtools index file.bam?

commented

The BAM file was created using samtools sort .sam > .bam
I then indexed using samtools index .bam

I reindexed the bam file in this way and am still getting the error.

commented

Is this dataset pretty large? Wondering if you can share an example so I can reproduce the error on my side.

ALternatively, could you try executing scripts/test.sh under f5c repository directory to see if you encounter the same error for the example dataset?

commented

@katiestoker Also could you please copy-paste the exact command you executed so I can have a look?

commented

@katiestoker Any updates on this?

commented

Hello,

I was actually using test data to check everything was set up before using my own data. I started again from download and the issue seems to be resolved. Hopefully everything works ok on my own data now.

Thanks for your help!

Best,

Katie