Colby Chiang
Colby Chiang
I think this is because you're running CNVnator on the example file, which has nonsense contigs ("20_slice"). CNVnator expects human contigs from GRCh37 (without "chr" prefixes). I think it will...
is your fasta file indexed?
To answer your question, "speedseq align" ought to work on non-human genomes. Some downstream modules (like VEP variant annotation with the -A flag or CNVnator read-depth annotation) might have problems...
do you need to change "V9\" to "V9 \" (with a space)? also, maybe try running it with "-v" for verbose output
Did the command print anything out to the screen while it was running? It might help diagnose the problem
also, it should have created a temp directory while it was working. Did it?
First, you should ensure that your BAM file is not corrupt. Also, speedseq -v will print out its internal commands while it is running. Use that information to diagnose the...
good to hear. Regarding the seg fault, I know that Ryan made a modification to LUMPY recently (https://github.com/arq5x/lumpy-sv/commit/d4e15812566b0cc0cac34f478f04a6ff54d0bfce) to address some of these issues. I incorporated it into speedseq (https://github.com/hall-lab/speedseq/commit/be664483a2533b21ffd373ffe8137c2a069b105b)...
if you have the error log (run with -v) could you also post it? can't e certain that that is the problem, but it's my best guess at the moment...
I don't have much experience with different versions of ROOT, but we're using v5.34.20 on our system so I can confirm it works with that. I don't have any ideas...