[maker-devel] Problems with failed contigs

[p sz]

Hi
I have tried to split the fasta file in small chunks and perform a execution for each chunk. Most of executions fail as I have described previously. I have inspect the results of a random chunk with 287 contigs and there are these error lines repeated 47 times:

substr outside of string at /mnt/home/users/pab_001_uma/pedro/software/maker/bin/../lib/PhatHit_utils.pm line 850.
--> rank=15, hostname=dx095
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:Sosen1_s1284
ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:Sosen1_s1284

Can you help me to fix this problem?
Thank you in advance
Pedro Seoane

________________________________
De: p sz <seoanezonjic at hotmail.com>
Enviado: martes, 6 de marzo de 2018 9:30
Para: maker-devel at yandell-lab.org
Asunto: Problems with failed contigs

Hi
Currently i'm annotating a fish genome using the Maker 3 version and the execution don't finish properly. I execute Maker in a shared cluster trough MPI, asking for 96 cores (in order to not block the maker manager nor the file system) in 6 nodes of 16 cores each one. The work run 3 or 4 days and the output suddenly stops. The work remains 3 days more, but the index datastore is not modified and the only files that their attributes change are the lock files. When the job exceed the working time (7 days) it is cancelled. Then, I inspect the datastore index and count the uniq started and finished tags for each scaffold. The results are:
STARTED:3890
FINISHED:3378
So, there are about 500 scaffolds in which the analysis fails. When I inspect the STDERR maker output I see this error line repeated ~2000 times, at differents sites:
substr outside of string at /mnt/home/users/pab_001_uma/pedro/software/maker/bin/../lib/PhatHit_utils.pm line 850
and near this line, the following:
ERROR: Failed while annotating transcripts
My questions are, what can I do to annotate the failed scaffolds? and in addition, is the great amount of failed analysis the reason of the job freeze?
Thanks in advance




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