dDocent stops at creating alignment intervals

[a.w...@uni-bayreuth.de]

Dear all,

a dDocent project stops, and the last messages are:

Creating alignment intervals
mawk: cannot open "mapped.2046.bed" for output (Too many open files)
Genomic interval creation failed.  This may be related to the maximum number of open files.

See also attached log files. I am not sure whether this message is correct as the main log file states earlier that bam files failed to open. However, thy are present.

I have testet dDocent with a small dataset from earlier projects, and the entire process completed without errors.

I have also increased the ulimit by 'ulimit - n 2048', but the problem persists.

Is there any advice how to proceed?

[a.w...@uni-bayreuth.de]

Let me add a detail: The dDocent_mail.log states the following:

mawk: cannot open "mapped.1022.bed" for output (Too many open files)

Although this file is present in the log_ls-l.txt file, this might be misleading. A second dDocent run has been started in this directory and the mapped bed files were created with increasing number. I Tested dDocent on another machine with only one run, and the same error appears and the mapped bed file is indeed missing.

Best