[maker-devel] Some errors reported by Maker2

[Quanwei Zhang]

Dear Carson:

Thanks. I wonder whether smaller "max_dna_len" will split longer scaffolds.
I set max_dna_len as 1Mb, because there are quite many long scaffolds
(e.g., the longest one is about 100Mb). Would you explain whether smaller
"max_dna_len" will decrease the quality of annotation (e.g., split some
genes in the same scaffold)?


Best
Quanwei

2017-09-05 17:48 GMT-04:00 Carson Holt <carsonhh at gmail.com>:

> You ran out of memory. You probably set max_dna_len too high for the
> machines you are using. There is a note in the maker_opts.ctl file that
> tells you that this value affects memory usage.
>
> So you can either set it lower, or if running under MPI, use fewer CPUs
> per node (how you do this is MPI flavor dependent, but some flavors let you
> do this by setting process count lower combined with the round robin
> option).
>
> —Carson
>
>
>
> On Sep 5, 2017, at 2:24 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>
> 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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