These are chat archives for dereneaton/ipyrad

4th
Jul 2017
joqb
@joqb
Jul 04 2017 08:45

Hi @dereneaton,

I was running version 0.6.27, any idea what the error below is about? I updated to the latest version but the error came up again

bash-4.2$ nice ipyrad -p params-all_ind_2017.txt -s 67 -c 32 --MPI -t=4
 -------------------------------------------------------------
  ipyrad [v.0.7.1]
  Interactive assembly and analysis of RAD-seq data
 -------------------------------------------------------------
  loading Assembly: all_ind_2017
  from saved path: /data/filer-5-2/brassac/Secalinum_NGS/GBS_2/raw_reads/new/all_ind_2017.json
  establishing parallel connection with hosts...
  host compute node: [32 cores] on bit-10.ipk-gatersleben.de

  Step 6: Clustering at 0.85 similarity across 99 samples
  [                    ]   0%  building clusters     | 0:00:00  sort: cannot read: /data/filer-5-2/brassac/Secalinum_NGS/GBS_2/raw_reads/new/all_ind_2017_consens/all_ind_2017.utemp: No such file or directory
  [####################] 100%  building clusters     | 0:02:55

  Encountered an error (see details in ./ipyrad_log.txt)
  Error summary is below -------------------------------
ValueError(need more than 2 values to unpack)

I don't exactly remember how fast was pyrad on basically the same dataset (only a few individual less), but I found ipyrad quite slow especially clustering during step 3 took 19 days using the command above. Am I doing something wrong (I used nice to be able to run full power without blocking completely the server for other users but it seemed that it was anyway not much used by anybody else, only a few analyses)?

Thanks