falcon_kit.mains.fasta_filter is crashing about pbbioconda

[gconcepcion]

Did the test case work successfully?

It's always better to test the install on the test case rather than your own dataset first

[gconcepcion]

FYI: I am able to replicate this bug - however. In your fc_run.cfg you should use
pa_fasta_filter_option=streamed-median
instead of
pa_fasta_filter_option=median

[roblehmann]

The test case works. I am trying to isolate the problem by using the same fc_run.cfg from the example for my data. However, I get the same error. Strange...
I'll try the pa_fasta_filter_option

[roblehmann]

The error does not occur when I use the greg200k-sv2 example fc_run.cfg with my data, but it does occur when I use the human genome example fc_run.cfg. I will have to go through the different options and see who the culprit is.

Thanks for the quick reply!

[gconcepcion]

It's because I have the fc_run_human.cfg w/ the bad option specified.
pa_fasta_filter_option=median
I've changed the config to:
pa_fasta_filter_option=streamed-median

The example fc_run_human.cfg has been fixed and should now work.

[roblehmann]

I can confirm, the correct pa_fasta_filter_option fixed the issue.
Thanks for the quick help Greg!

[gconcepcion]

Great! Glad it works!
Hope you assemble some great genomes :)

[roblehmann]

Thanks, in fact I did already - the Nemo genome came out quite good! I’m glad you guys are working to improve Falcon further.