[maker-devel] Some errors reported by Maker2

[Quanwei Zhang]

Hello:

We are doing genome annotation for a new rodent species. We have finished
the training of the ab initio gene predictors successful by setting the
following parameters (split_hit=40000, max_dna_len=1000000, and 99k
mammalian Swiss protein sequences as evidences.

But when I used the trained model to do the genome annotation, I got the
following kinds of errors (shown in red). I used the same parameters as
those for training, except for addition of 340k rodent TrEMBL protein
sequences for protein evidences (i.e., I use both 99k mammalian Swiss
protein sequences and 340k rodent TrEMBL protein sequences).

I am doing the annotation on a cluster and started multiple Maker in the
same directory (I had tried to use MPI but met some problems).

Do you have any suggestions? Many thanks
#some kinds of errors
open3: fork failed: Cannot allocate memory at
/gs/gsfs0/hpc01/apps/MAKER/2.31.9/bin/../lib/Widget/blastx.pm line 40.
--> rank=NA, hostname=n520
ERROR: Failed while doing blastx of proteins
ERROR: Chunk failed at level:8, tier_type:3
FAILED CONTIG:Contig2


setting up GFF3 output and fasta chunks
doing repeat masking
Can't kill a non-numeric process ID at
/gs/gsfs0/hpc01/apps/MAKER/2.31.9/bin/../lib/File/NFSLock.pm line 1050.
--> rank=NA, hostname=n513
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:Contig12378


Best
Quanwei
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