These are chat archives for dereneaton/ipyrad

19th
Jan 2017
Francisco Pina-Martins
@StuntsPT
Jan 19 2017 14:52
Hi everyone
quick question:
while trying ipyrad I got this error:
Step 6: Clustering at 0.85 similarity across 93 samples
  [####################] 100%  concat/shuffle input  | 0:00:15
  [####################] 100%  clustering across     | 0:05:29
  [####################] 100%  building clusters     | 0:00:21
  [####################] 100%  aligning clusters     | 0:12:07
  [####################] 100%  database indels       | 0:00:36
  [####################] 100%  indexing clusters     | 0:00:49
  [####################] 100%  building database     | 0:07:22

    Step 7: Filter and write output files for 94 Samples
      The following Samples do not appear to have been clustered in step6
      (i.e., they are not in /home/francisco/GBS/ipyrad_0.5.15/qsuber01_outfiles/qsuber01.hdf5).
      Check for typos in Sample names, or try running step6 including the
      selected samples.

      Missing: Sin17

  ERROR:ipyrad.core.assembly:'Sin17' is not in list

    Encountered an unexpected error (see ./ipyrad_log.txt)
    Error message is below -------------------------------
  'Sin17' is not in list
the sample "Sin7" is not very represented
and therefore it probably has very close to 100% missing data
notice how step 6 mentions 93 samples
whereas step 7 mentions 94
any ideas on what I can do here? (besides removing the sample from the analysis altogether?)
Deren Eaton
@dereneaton
Jan 19 2017 15:03
@StuntsPT does the sample have 0 consensus reads? I think maybe ipyrad tries to exclude the sample in step 6 but then this was not consistently detected in the next step. So it's a bug. I'll look into it. We would like it to exclude empty samples. But in the mean time, yes you can just exclude the sample yourself at step 6 by using branching.
Francisco Pina-Martins
@StuntsPT
Jan 19 2017 15:04
@dereneaton Thanks!
I just create a new branch and remove the sample from the barcodes file?
or is there some other alternative?
Deren Eaton
@dereneaton
Jan 19 2017 15:07
yes, branching is the desired way because that way you still retain an Assembly that includes all of your samples, in addition to the new subsampled one.
Francisco Pina-Martins
@StuntsPT
Jan 19 2017 15:08
ok, thanks! I'll try that just now
Deren Eaton
@dereneaton
Jan 19 2017 15:08
To drop just samples A and B do this:
ipyrad -p params.txt -b newbranch - A B
Francisco Pina-Martins
@StuntsPT
Jan 19 2017 15:09
ah, cool, was already creating a new barcode file
nice! It's working
many thanks
oh wait
Deren Eaton
@dereneaton
Jan 19 2017 15:11
you can then just run steps 6 and 7 on the new branch
Francisco Pina-Martins
@StuntsPT
Jan 19 2017 15:12
ok, 6 has to go again too
of course
ok, it's running
I should get back to you in about 20 min
Francisco Pina-Martins
@StuntsPT
Jan 19 2017 15:37
Issue submitted. dereneaton/ipyrad#218
Francisco Pina-Martins
@StuntsPT
Jan 19 2017 16:07
francisco@Odin [15:02:57] [~/GBS/ipyrad_0.5.15]
-> $ ipyrad -p params-qsuber03.txt -s 7 -c 14 -b non_represented_bug - Sin17

  loading Assembly: qsuber03
  from saved path: ~/GBS/ipyrad_0.5.15/qsuber03.json
  dropping 1 samples
  creating a new branch called 'non_represented_bug' with 93 Samples
  writing new params file to params-non_represented_bug.txt
@dereneaton - the plot thickens:
And then:
francisco@Odin [15:05:31] [~/GBS/ipyrad_0.5.15]
-> $ ipyrad -p params-non_represented_bug.txt -s 67 -c 14 -f

 -------------------------------------------------------------
  ipyrad [v.0.5.15]
  Interactive assembly and analysis of RAD-seq data
 -------------------------------------------------------------
  loading Assembly: non_represented_bug
  from saved path: ~/GBS/ipyrad_0.5.15/non_represented_bug.json
  local compute node: [14 cores] on Odin

  Step 6: Clustering at 0.85 similarity across 93 samples
  [####################] 100%  concat/shuffle input  | 0:00:16
  [####################] 100%  clustering across     | 0:07:27
  [####################] 100%  building clusters     | 0:00:23
  [####################] 100%  aligning clusters     | 0:16:21
  [####################] 100%  database indels       | 0:00:37
  [####################] 100%  indexing clusters     | 0:00:48
  [####################] 100%  building database     | 0:07:25

  Step 7: Filter and write output files for 93 Samples

  Encountered an unexpected error (see ./ipyrad_log.txt)
  Error message is below -------------------------------
'Sin17'
Francisco Pina-Martins
@StuntsPT
Jan 19 2017 16:17
The number of samples is correctly counted, though.
Deren Eaton
@dereneaton
Jan 19 2017 19:12
@StuntsPT strange! I'll look into it.