"Couldn't make ofstream for marker @" error

[SIJAE-WOO]

Hi, I want to use popSTR. But I got the below error.

Couldn't make ofstream for marker @ ./attributes/chr11/130017329_CACAGT
ERROR: Could not read index file for test.bam

I checked and installed dependencies. If you know how to fix it, please let me know.
Thank you very much,
Sijae

[snaedis88]

Hello Sijae and thank you for getting in touch.

This error is most likely occurring because popSTR is opening a number of files which exceeds your system's limit for open files.
Could you please tell me how many markers you are trying to run and what the limit for number of open files is on the machine you are running popSTR on?

Kind regards,
Snædís

[SIJAE-WOO]

Thank you Snædís,
I set markersPerJob lower than 10000 and it works.
But, I met additional hurdle. I ran the popSTR in CPU cluster, not local computer. PopSTR use all threads in server.
Could I set limit of threads for running popSTR?

Regards,
Sijae

[snaedis88]

Hello again,

I just pushed a new version of the runPerChrom.sh script with a new parameter which specifies the number of threads the process should run on.
I hope this helps and let me know if any further issues come up.

Kind regards,
Snædís