These are chat archives for dereneaton/ipyrad

Jul 2017
Jul 12 2017 12:02
Hi @eaton-lab sorry to hear about the libraries issues. on my side I discovered something funky... I had issues with subsampling using a text file, today even the simple command with names in the end of the line was not working! Then I thought about checking the json file of my whole dataset and realized that some names were modified... For example an individual with raw data file as bogdanii_BCC2063_859963_TACTTAG_L005_R1_001.fastq.gz appeared in the json file as bogdanii_BCC2063_859963_TACTTAG_L005001 so using the latter name worked fine when subsampling. I know the names are kind of stupid and not informative but I don't understand why the R1 is dropped
Jul 12 2017 13:58

Hi @eaton-lab, unfortunately the step 6 error keeps happening, I tried your advices:


create a new branch with a subsample of taxa for testing

ipyrad -p params-all_ind_2017.txt -b new sampleA sampleB sampleC sampleD sampleE

run test on new branch that should finish very quickly

ipyrad -p params-new.txt -s 67 -f -c 32

If all goes well, try again with the full data set requesting fewer resources this time

ipyrad -p params-all_ind_2017.txt -s 67 -c 20

Subsampling works fine through those steps but the whole dataset still fails with the same error:

-bash-4.2$ ipyrad -p params-all_ind_2017.txt -s 67 -c 2

  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
  host compute node: [2 cores] on

  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     | 0:05:06
ERROR:ipyrad.assemble.cluster_across:ValueError(need more than 2 values to unpack)
ERROR:ipyrad.core.assembly:IPyradWarningExit: ValueError(need more than 2 values to unpack)

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

I was worried about the first error so I reran step 6 with -fbut after one week computing time the output is still the same.

Any idea?

Isaac Overcast
Jul 12 2017 18:40
@joqb When reads are pre-demux'd the sample name is generated by dropping the R1/R2 from the sample raw data file names.
Isaac Overcast
Jul 12 2017 18:57
Mm, well that error indicates the all_ind_2017.utemp file doesn't exist. I would try rerunning step 6 with the -f flag to regenerate this file:
ipyrad -p params-all_ind_2017.txt -s 67 -c 2 -f
Jul 12 2017 20:17
Hi @eaton-lab I'm getting the same updating error of 0.7.2 with 0.7.1. Should I go back to a previous version?
Isaac Overcast
Jul 12 2017 20:35
@JStarrett I have a fix for the 3rad barcode problem that will go out in the next release, should be the next day or two. Assuming you don't have duplicate sample names in the pre-merged assemblies you could also just concatenate all the individual barcodes files into one big one, then edit the merged params file and set the barcodes_path param to point to this file. I haven't tested this, but it should work.