[maker-devel] Output question

[Muriel Gros-Balthazard]

Hello !

After running a genome containing 7,752 scaffolds, I have some differences in outputs.
For some I have less files in the datastore.
For instance, for one, I have only :
KE337098%2E1.gff
KE337098%2E1.maker.augustus.proteins.fasta
KE337098%2E1.maker.augustus.transcripts.fasta
run.log
theVoid.KE337098.1

And others have more:
KE332545%2E1.gff
KE332545%2E1.maker.augustus_masked.proteins.fasta
KE332545%2E1.maker.augustus_masked.transcripts.fasta
KE332545%2E1.maker.augustus.proteins.fasta
KE332545%2E1.maker.augustus.transcripts.fasta
KE332545%2E1.maker.non_overlapping_ab_initio.proteins.fasta
KE332545%2E1.maker.non_overlapping_ab_initio.transcripts.fasta
KE332545%2E1.maker.proteins.fasta
KE332545%2E1.maker.transcripts.fasta
KE332545%2E1.maker.trnascan.transcripts.fasta
run.log
theVoid.KE332545.1

I checked that for these two scaffolds, it is written FINISHED in the output.
Do we agree that as long as a scaffold is written FINISHED it is OK ?
And that the process won’t start again if I relaunch Maker in the same directory ?
I am asking this second question as I had to relaunch several times…

Also, I have something weird for some scaffolds. It has failed but the FAILED is written in column 2 of the output.
For instance if I grep a single scaffold:
KE337098.1		FAILED
KE337098.1		FAILED
KE337098.1		FAILED
KE337098.1		FAILED
KE337098.1		FAILED
KE337098.1	Pdac_ref2013s_datastore/23/51/KE337098.1/	STARTED
KE337098.1	Pdac_ref2013s_datastore/23/51/KE337098.1/	FAILED
KE337098.1		FAILED
KE337098.1		FAILED
KE337098.1		FAILED
KE337098.1		FAILED
KE337098.1		FAILED
KE337098.1		FAILED
KE337098.1		FAILED
KE337098.1		FAILED
KE337098.1		FAILED
KE337098.1		FAILED
KE337098.1	Pdac_ref2013s_datastore/23/51/KE337098.1/	RETRY
KE337098.1	Pdac_ref2013s_datastore/23/51/KE337098.1/	FINISHED


Is this problematic at some point or since it’s also written FINISHED, I should not worry ?

Thanks a lot,

Muriel

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