These are chat archives for dereneaton/ipyrad

23rd
Aug 2018
danielyao12
@danielyao12
Aug 23 2018 07:34
Hi Isaac and Deren, I got an error message when I run the Step 3. It was:

Assembly: ilex56sp
[####################] 100% dereplicating | 1:13:36 | s3 |

Encountered an unexpected error (see ./ipyrad_log.txt)
Error message is below -------------------------------
IPyradError(vsearch v2.0.3_linux_x86_64, 63.0GB RAM, 20 cores
https://github.com/torognes/vsearch

Reading file /dev/stdin 100%
15273287074 nt in 51245987 seqs, min 35, max 300, avg 298
Dereplicating 100%
Sorting)

And the text storing in the ipyrad_log.txt was:

Reading file /dev/stdin 100%
15273287074 nt in 51245987 seqs, min 35, max 300, avg 298
Dereplicating 100%
Sorting 100%
30089880 unique sequences, avg cluster 1.7, median 1, max 2120
Writing output file)
2018-08-23 15:19:32,565 pid=23886 [assembly.py] ERROR IPyradError(vsearch v2.0.3_linux_x86_64, 63.0GB RAM, 20 cores
https://github.com/torognes/vsearch

Reading file /dev/stdin 100%
15273287074 nt in 51245987 seqs, min 35, max 300, avg 298
Dereplicating 100%
Sorting)


Was this because of the HPC or the dataset? I find that my dataset size of each individual differed a lot. And I just update the ipyrad version. So, this should be not about the ipyrad software. As your opinion, how should I solve this problem? Thanks.