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vpc-ccg / sedef

Identification of segmental duplications in the genome
MIT License
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Error with number of jobs completed (zebrafish genome) #22

Closed jmuribes closed 3 years ago

jmuribes commented 3 years ago

Hello,

I have run sedef on the zebrafish reference without issues in the past, but I tried running it using a recently published version of its chromosome 4 (reference: https://www.nature.com/articles/s41586-020-2962-9, Supplementary Dataset 1) and the job fails to complete.

First, I soft-masked the sequence of the new chromosome using RepeatMasker and then used that file for sedef. The issue seems to be with 2 align jobs that do not finish and indicate the exit non-zero status 1. The log file indicates “Error:vector:_M_default_append” (log file attached).

Any ideas or suggestions about what could be going on?

Thank you in advance for the help!

sedef_zfish_error bucket_0210.log

José

saraebell commented 2 years ago

I am having the same issue with zebrafish reference genome danRer10 and mouse reference genome mm10, both have the same 'Error: launched 1000 jobs but completed only 998 jobs; exiting...'

What would be the appropriate solution? Thank you.

Screen Shot 2022-02-22 at 11 56 36 AM

inumanag commented 2 years ago

Hi all,

can you please try BISER (https://github.com/0xTCG/biser/), which is a better version of SEDEF, and see if it works— it should be able to handle this issue? We are not maintaining SEDEF anymore.

saraebell commented 2 years ago

I am having issues installing BISER and therefore have continued to try and debug this issue with SEDEF, any possible suggestions?

Error: launched 1000 jobs but completed only 998 jobs; exiting...

inumanag commented 2 years ago

Hi @saraebell

I have just fixed the issues with BISER. Can you please give it another try?

This bug won't be fixed in SEDEF (but the fix is basically part of BISER).

saraebell commented 2 years ago

Yes, I can confirm that I successfully installed BISER.