Omar Abou Saada

Have you checked line 20892 in your sam file? I think it's very likely that you'll find the mapping quality is given as a negative integer. If you do, then...

That means your problem is that newer versions of samtools do some file formats format checks that 1.09 doesn't do. So they see a negative mapQ and presume that the...

Before starting over from scratch, you should check if the long read mapping, short read mapping and variant calling steps were over. If so, then you can save a lot...

If the long reads are mapped and the short reads are mapped and variant called, then you can run `nphase partial --sampleName SAMPLE_NAME --reference REFERENCE --output OUTPUT_FOLDER --longReads LONG_READ_FILE --vcf...

Based on your output it looks like, for some reason, the GATK variant selection is happening twice simultaneously. Is there any possible way you somehow ran the same command line...

So, looking at the output log, you can see that a lot of lines are duplicated, which shouldn't happen and I also presume didn't happen with the example dataset? ```...

I usually use `screen` rather than `nohup` so I'm not familiar with how it proceeds. How do you get the STDOUT, did you just stay logged in? Do you also...

I think there's the slightest little chance that STDERR isn't redirected to nohup.out and that it's hiding an error from us that would help us understand what's going on here....

Okay, let's troubleshoot. First making sure we're on the same page. Initially, the issue was that your machine restarted by accident in the middle of a run and my advice...

Haha, I mean, from my perspective it's weird that it wasn't working before! Hopefully it all runs fine again with your other sample. Are you saying you have a total...