[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).