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Published 20 hours ago • verified publisher icon aidenlab

Java error in run-asm-pipeline.sh

Open Sparkle-27 opened this issue 5 years ago • 5 comments

Hi there I have trouble in running 3d-dna

  • bash run-asm-pipeline.sh file.fasta mnd.txt Here is the error info, do you have any suggestions, thanks a lot. QQ截图20190711084614

Sparkle-27 avatar Jul 11 '19 00:07 Sparkle-27

Hi huanfa,

This is not an error but a warning, should not cause you issues. Usually this might happen if you are running several jobs to build Hi-C maps on the same machine, at the same time.

Best, Olga

dudcha avatar Jul 12 '19 00:07 dudcha

@dudcha Thanks for your reply. I have solved the problem which caused by the lustre, and I have changed a computer that run successfully. But a new problem appears that *.FINAL.fasta file contains all N. .rawchrom.fasta file was empty, but no error in running log file. Do you have any suggestions? Thx. QQ截图20190715225229 huanfa

Sparkle-27 avatar Jul 15 '19 14:07 Sparkle-27

Can you share the .out and .err?

On Jul 15, 2019, at 9:54 AM, huanfa [email protected] wrote:

@dudcha https://github.com/dudcha Thanks for your reply. I have solved the problem which caused by the lustre, and I have changed a computer that run successfully. But a new problem appears that *.FINAL.fasta file contains all N. .rawchrom.fasta file was empty, but no error in running log file. Do you have any suggestions? Thx. https://user-images.githubusercontent.com/21327136/61225561-67604f80-a753-11e9-836f-93cb1d603b15.png huanfa

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dudcha avatar Jul 15 '19 14:07 dudcha

@dudcha Here is the run.log file run (2).log

Sparkle-27 avatar Jul 15 '19 15:07 Sparkle-27

Hi huanfa,

This does not seem to contain the error stream, so can't use this to diagnose. One thing that may cause problems on this stage is bash version: note that it needs to be >4.2 or something to be able to handle associative arrays (recently I've changed this since rather many people kept complaining but it is not yet out).

Thanks, Olga

dudcha avatar Jul 31 '19 18:07 dudcha