These are chat archives for dereneaton/ipyrad

16th
Dec 2018
tle003
@tle003
Dec 16 2018 02:11
conda install ipyrad -c ipyrad ipyrad=0.7.28
conda install toytree toytree=0.1.16 -c eaton-lab
conda install sra-tools -c bioconda
conda install entrez-direct -c bioconda
import pkg_resources
pkg_resources.require("Toytree==0.1.16")
import toytree
tle003
@tle003
Dec 16 2018 02:17

imports

import ipyrad as ip
import ipyrad.analysis as ipa
import ipyparallel as ipp
ipcluster start --n=20 - ran in terminal; all 20 cores seem to start up with no errors
ipyclient = ipp.Client()
ipyclient.ids
sra = ipa.sratools(accession="SRP021469", workdir="fastqs-Ped")
  • runs fine, no errors, makes fastqs-Ped dir
sra.run(force=True, ipyclient=ipyclient)
tle003
@tle003
Dec 16 2018 02:23

Exception in run() - index 29 is out of bounds for axis 0 with size 1

IPyradError Traceback (most recent call last)

<ipython-input-10-1e4130d69284> in <module>()
----> 1 sra.run(force=True, ipyclient=ipyclient)

/mnt/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/sratools.pyc in run(self, force, ipyclient, name_fields, name_separator, dry_run)
170 except OSError as inst:
171 ## If sra dir doesn't even exist something very bad is broken.
--> 172 raise IPyradWarningExit("Download failed. Exiting.")
173 ## remove fastq file matching to cached sra file
174 for srr in os.listdir(sradir):

/mnt/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/util.pyc in init(self, args, **kwargs)
50 def init(self,
args, kwargs):
51 if ipyrad.interactive:
---> 52 raise IPyradError(*args,
kwargs)
53 else:
54 SystemExit.init(self, args, *kwargs)

IPyradError: Download failed. Exiting.

I am running all of my applications out of the /mnt directory as advised, as well as saving all of my files there. I had no problem running the advanced cli tutorial out of that directory yesterday.