[maker-devel] failed contigs in master_datastore_index.log but no errors in screen output

[Valerie Soza]

Hi all

I ran 3 instances of Maker 2.31.9 on a genome assembly using a SNAP training parameters file and my training parameters from running BUSCO on our genome. The job completed on our departmental computing cluster but when I looked at the master_datastore_index.log, 4 scaffolds had FAILED and 2 were indicated as RETRY.

I previously ran Maker on this same genome just using the SNAP training parameters file and it worked fine so I am perplexed.

$ grep FAILED Rwill4_master_datastore_index.log 
LG12_ordered_scaffold_101	Rwill4_datastore/B7/F2/LG12_ordered_scaffold_101/	FAILED 
unclustered_scaffold_3148	Rwill4_datastore/62/82/unclustered_scaffold_3148/	FAILED 
unclustered_scaffold_3490	Rwill4_datastore/1D/F9/unclustered_scaffold_3490/	FAILED 
unclustered_scaffold_7506	Rwill4_datastore/69/B8/unclustered_scaffold_7506/	FAILED

$ grep RETRY Rwill4_master_datastore_index.log 
LG12_ordered_scaffold_101	Rwill4_datastore/B7/F2/LG12_ordered_scaffold_101/	RETRY 
unclustered_scaffold_7506	Rwill4_datastore/69/B8/unclustered_scaffold_7506/	RETRY

When I looked at the screen output from all 3 instances, there are no errors when I grep for Error, error, or ERROR.
None of the 3 screen outputs indicated that Maker had finished, so I restarted the job and then immediately got that "Maker is now finished!!!” 
However when I grep for the 4 failed scaffolds above in the 3 screen outputs, I only get something for 1 of the scaffolds, which also happens to be the last lines in one of the screens' output's:

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: LG12_ordered_scaffold_101
Length: 89169
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/935482.1.ravana.q/maker_ul9sWE; /net/gs/vol3/software/modules-sw/RepeatMasker/4.0.7/Linux/RHEL6/x86_64/RepeatMasker /net/shendure/vol8/projects/R.williamsianum.annotation/Maker_analyses/SNAP_training/Rwill4.maker.output/Rwill4_datastore/B7/F2/LG12_ordered_scaffold_101//theVoid.LG12_ordered_scaffold_101/0/LG12_ordered_scaffold_101.0.all.rb -species all -dir /net/shendure/vol8/projects/R.williamsianum.annotation/Maker_analyses/SNAP_training/Rwill4.maker.output/Rwill4_datastore/B7/F2/LG12_ordered_scaffold_101//theVoid.LG12_ordered_scaffold_101/0 -pa 10
#———————————————#

It seems like the run did not finish properly. Am I interpreting this correctly? Does anyone have suggestions on what I should do or how to troubleshoot? 

Thanks.

-Valerie
	
Valerie Soza, Ph.D.
c/o Hall Lab
Department of Biology
University of Washington
Johnson Hall 202A
Box 351800
Seattle, WA 98195-1800
206-543-6740
http://staff.washington.edu/vsoza/