Realign process running at very low CPU Usage about circle-map

[iprada]

Dear Yizhou,

Thanks a lot for reporting the issue. Which version of Circle-Map are you using?

This used to be a problem on versions before the last version (v1.1.3). However, that problem was solved on the last release. If you are not using version v1.1.3, updating to the last version should solve your problem.

Best,

Inigo

[huangyizR]

Hi Inigo,
Thanks for your quick response! I did realize that there is a closed issue with a similar problem. I do use the version 1.1.3.
I attach my code and output error of the process. This file pbs.circle_map.4.e662010.TXT, came from a finished Circle_Map realign process. There is some error:

"RuntimeWarning: invalid value encountered in XXX "

This file :pbs.circle_map.6.e662009.TXT came from an unfinished and killed job. I saw some "[E::hts_open_format] Failed to open file sorted.bam" error that may be related to samtools. However, when I check those sorted.bam, it looks fine.

I am trying to separate samtools and realign process now. In meaning time, It would be great if you can provide some advice about my problems. Thanks for your time!

pbs.circle_map.2.TXT
pbs.circle_map.4.e662010.TXT
pbs.circle_map.6.e662009.TXT

[iprada]

Dear Yizhou,

Great to hear that v 1.1.3 is working for you.

Regarding pbs.circle_map.4.e662010.TXT:

The output messages looks fine. Those are not errors, they are some warnings raised by the software during coverage calculations on the circular DNA coordinates. In some cases you will get division by zero errors, and the software will raise a warning message. But the output of that job should be fine. I assume that you have some circular DNA calls, right?

Regarding the job pbs.circle_map.6.e662009.TXT:

I have sometimes observed this error due to the node getting out of temporary disk space. I suggest you to decrease the number of threads to 16 in order to reduce the temp disk usage and see what happens. At this moment this is a limitation on Circle-Map side and on the the long run I plan to solve and handle this probem. However this will require a lot of time to be production ready.

If reducing the number of cores does not work, write me an email on this thread so that we can figure out a solution.

Best wishes,

Inigo

[huangyizR]

Dear Inigo,
Thanks for your detailed explanation. I am running on 16 thread now to see if I have any luck. I will let you know how things going.

Thanks!

Best,
Peter

[iprada]

I am closing the issue by now. Feel free to reopen if it did not work