bug in screen.seqs command in v. 1.22?

I am running mothur 1.22 on a 64-bit PC. I have a large dataset (>1 million seqs, 70 000 unique seqs) that refuses to complete the screen.seqs command. mothur runs it for >24 hrs, then closes without any information in the log file. However, screen.seqs will run on the same dataset in mothur v. 1.20. Any tips?

Could you send the input files and logfile to mothur.bugs@gmail.com?

This is a bug related to the Windows paralellization and will be fixed in version 1.23.0.

Is this also related? Processors has been tested for values 1, 2, 20 (22 available) and all end with the same result.
Datafile is 10G, but I was about to test with a smaller dataset.

Otherwise, is you recommendation to just use a previous mothur version for the screen.seqs command?


mothur > screen.seqs(fasta=input.clean.unique.align, name=input.clean.names, group=input.groups, start=1044, end=6421, minlength=200, maxlength=400, processors=20)

[arnist:04731] *** Process received signal ***
[arnist:04731] Signal: Segmentation fault (11)
[arnist:04731] Signal code: Address not mapped (1)
[arnist:04731] Failing at address: 0xfc8000
[arnist:04731] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10060) [0x7fe928600060]
[arnist:04731] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x138864) [0x7fe928389864]
[arnist:04731] [ 2] mothur(_ZN17ScreenSeqsCommand9driverMPIEiiRP11ompi_file_tS2_S2_RSt6vectorIySaIyEERSt3setISsSt4lessISsESaISsEE+0x497) [0xa0de37]
[arnist:04731] [ 3] mothur(_ZN17ScreenSeqsCommand7executeEv+0xbd4) [0xa1d674]
[arnist:04731] [ 4] mothur(_ZN14InteractEngine8getInputEv+0x715) [0x6c3b75]
[arnist:04731] [ 5] mothur(main+0xab9) [0x475e49]
[arnist:04731] [ 6] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fe92827230d]
[arnist:04731] [ 7] mothur() [0x478731]
[arnist:04731] *** End of error message ***
Segmentation fault

Can you try it with version 1.23.0?

Okay, 1.21 was just sitting there doing nothing.
But with 1.23.0 it works fine for me!