bug in screen.seqs command in v. 1.22?

mothur bugs
1

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?
Thanks!
Heather

2

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

3

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

4

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?

Thanks

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
5

Can you try it with version 1.23.0?

6

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

Thanks