These are chat archives for dereneaton/ipyrad

3rd
Sep 2016
Isaac Overcast
@isaacovercast
Sep 03 2016 00:46
@SheaML I couldn't reproduce this error, but I added some code to set the vsearch max qscore arbitrarily high. I pushed a new package to conda, so if you could dl it and try it out that would be great (0.3.39): conda install -c ipyrad ipyrad
Matt McElroy
@Mattalac_twitter
Sep 03 2016 02:04
Hi @isaacovercast and @dereneaton - quick easy one for you. I'm running ipyrad on a 32 core computer, but other analysis are using some of the cores. How can I limit ipyrad to only a subset of cores as to not crash the computer? I recall that in pyrad the params file had a line to do this... thanks!
Deren Eaton
@dereneaton
Sep 03 2016 02:06
in ipyrad you can use the -c arguments to the command line: e.g., ipyrad -p params-data.txt -s 2 -c 4
Matt McElroy
@Mattalac_twitter
Sep 03 2016 02:07
@dereneaton thanks! glitter is cool!
Deren Eaton
@dereneaton
Sep 03 2016 02:07
ha, yeah, good for quick response.
jianlizhao
@jianlizhao
Sep 03 2016 08:41
@dereneaton this is the first line in ipyrad_log.txt file: 2016-09-03 16:09:21,682 pid=38826 [load.py] WARNING skipping: no svd results present in old assembly ...........these are the last four lines:016-09-03 16:10:21,684 pid=38826 [write_outfiles.py] INFO superedge is (1094929, 5)
2016-09-03 16:10:24,965 pid=38826 [write_outfiles.py] INFO finished filtering
2016-09-03 16:10:34,210 pid=38826 [write_outfiles.py] INFO Writing .vcf file
2016-09-03 16:22:20,076 pid=38826 [parallel.py] INFO Shutting down [ipyrad-38826] remote Engines
Isaac Overcast
@isaacovercast
Sep 03 2016 17:06
@jianlizhao Can you re-run step 7 with the -d flag and email me the ipyrad_log.txt: iovercast@gc.cuny.edu
Edgardo M. Ortiz
@edgardomortiz
Sep 03 2016 17:07

I guess this is a conda issue? tetrad can't find a package, and error stays the same after reinstalling ipyrad:

Traceback (most recent call last):
  File "/home1/02728/emo347/miniconda2/bin/tetrad", line 11, in <module>
    load_entry_point('ipyrad==0.3.39', 'console_scripts', 'tetrad')()
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 542, in load_entry_point

  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2569, in load_entry_point

  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2229, in load

  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2235, in resolve

  File "/home1/02728/emo347/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/__init__.py", line 3, in <module>
    from . import tetrad
  File "/home1/02728/emo347/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/tetrad.py", line 40, in <module>
    from bitarray import bitarray
ImportError: No module named bitarray

Is there a way to force all the ipyrad associated packages to be reinstalled as well?

Isaac Overcast
@isaacovercast
Sep 03 2016 17:31

@edgardomortiz Looks like we missed a dependency. I will add this to the next package. For now you can work around it by:

conda install bitarray

You'll also need to do this:

conda install -c etetoolkit ete3
Edgardo M. Ortiz
@edgardomortiz
Sep 03 2016 17:33
Thanks, it is working now
Deren Eaton
@dereneaton
Sep 03 2016 18:52
Oh, yeah, the current package for tetrad is not ready for use.
I would consider it in development mode still.
Shea Lambert
@SheaML
Sep 03 2016 23:26
@isaacovercast Thanks - I've updated to 0.3.39, but I'm still getting the same error, and it appears the qmax is unchanged, e.g.: "Fatal error: FASTQ quality value (69) above qmax (41)."
Shea Lambert
@SheaML
Sep 03 2016 23:36

@isaacovercast Perhaps I should mention that the read merging is specifically where the error occurs - and that I don't see the fastq_qmax parameter being set for this step.

Here's an example of the command that's failing (paths modified for readability):
bin/vsearch-linux-x86_64 --fastq_mergepairs edits/XXXR1.fastq --reverse edits/XXXR2.fastq --fastqout edits/XXXmerged.fastq --fastqout_notmerged_fwd edits/tmp92S8pZ_nonmergedR1.fastq --fastqout_notmerged_rev edits/tmpOwJlYf_nonmergedR2.fastq --fasta_width 0 --fastq_allowmergestagger --fastq_minmergelen 35 --fastq_maxns 10 --fastq_minovlen 20 --fastq_maxdiffs 4 --label_suffix _m1 --threads 0