maker tool get stucks forever

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4.5 years ago

hafiz.talhamalik ▴ 350

I am doing denovo annotation using maker tool. It gives me the following error

****deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  trnascan.

Widget::trnascan:
/media/user/drive/Softwares/maker-softs/trnascan-se-2.0.5/tRNAscan-SE-2.0/tRNAscan-SE -b -q /tmp/maker_ZnR2uW/7.abinit_nomask.0 > /tmp/maker_ZnR2uW/7.abinit_nomask.0.eukaryotic.trnascan

WARNING: -q exists already.
 (O)verwrite file, (A)ppend to file, or (Q)uit program?****

no matter i chose an option from these it gets stuck there. I left the terminal opened for 2 days even and nothing happened. i deleted the temporary files as well from the above mentioned path but that didn't worked.

any solution ??

annotation maker • 1.1k views

ADD COMMENT • link updated 4.5 years ago by lieven.sterck 15k • written 4.5 years ago by hafiz.talhamalik ▴ 350

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Do not hesitate to stop MAKER and restart. It will continue where it stopped. Maybe it will pass over the problem this time.

ADD REPLY • link 4.5 years ago by Juke34 8.9k

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I stopped it and tried running again. It get's stuck again with same warning.

ADD REPLY • link 4.5 years ago by hafiz.talhamalik ▴ 350

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deactivate tRNAscan
trna=0 #find tRNAs with tRNAscan, 1 = yes, 0 = no

or if you really want to annotate tRNA use another version. I used tRNAscan-1.3.1 successfully.

ADD REPLY • link 4.5 years ago by Juke34 8.9k

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ok. let me try this..!

ADD REPLY • link 4.5 years ago by hafiz.talhamalik ▴ 350

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ok. let me try this..!

ADD REPLY • link 4.5 years ago by hafiz.talhamalik ▴ 350

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