Stopping in STEP18 -> 17.checkM_batch.pl

[sean-workman]

Hey there,

I'm trying to run the sequential method on a set of reads and the run has failed after Step 17. I am seeing the message:

Storing results for DAS in /scratch/sdwork/daniel/sequential/HB_102/intermediate/17.HB_102.checkM
Can't find /scratch/sdwork/daniel/sequential/HB_102/intermediate/17.HB_102.checkM

I am running version 1.6.5 rather than the post1 version.

HB102_syslog.gz

[fpusan]

Will look into It.
Can I assume that 1.6.5 fixed your issue at step 10 and close #927?

[sean-workman]

It would appear so! This is a different data set but it made it past step 10 so it would appear that we are all good on that front! :)

[jtamames]

Is this an eukaryotic dataset, right? Then checkM tries to evaluate the bins, and cannot because all are eukaryotic. And dies. This should not be the case, my bad, sorry about that. I will fix that for the next release.
You can restart in step 18 (--restart -step 18) to finish the analysis.
Best,
J

[sean-workman]

Ahh gotcha. There will definitely be lots of host reads (predominantly host even), but there should be at least some bacterial stuff. Is there a good way to restart the analysis if it's been submitted as a sequential job so that it continues on to the next one? I'm also taking a shot with co-assembly, which I think will work better.