[maker-devel] Maker 3 stuck at "processing chunk output"

[Luca Peruzza]

Dear Maker developers,
I am posting here because we have a curious situation happening while using
maker 3.01.03 to annotate a fish genome and we have one scaffold, which is
~30.4 M bases that is problematic.

We perform 3 rounds of annotation (as suggested by the maker wikis
available). The first round uses EST and protein evidence to generate gene
models (--> we set est2genome=1 and protein2genome=1) and we do not use
gene predictors. This round always complete successfully.

In the second and third round we use the results from the previous run to
train SNAP and Augustus, plus we use gmhmm and we set runEVM=1 (and of
course we set est2genome=0 and protein2genome=0). These rounds never
finish. Maker is stuck forever as shown in Screen1.png and keeps using a
substantial amount of CPUs (as seen in Screen2.png), which I honestly do
not think is normal at that final stage of the program run (?!?).

We have noticed that if we enter the "theVOid" folder, the log file of the
contig has this error (Screen3.png).

The "curious" thing is that we have 18 other scaffolds that are between 10
and 27.6 M bases in length and maker is always able to correctly annotate
them.

Could you help us solving this issue? I could send you the fasta file and
the est and protein gff with the evidences and the gene predictor input
files if need be so you could try to replicate the error yourself (just let
me know where I can upload the relevant files).
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