These are chat archives for dereneaton/ipyrad

Jul 2016
Jul 19 2016 01:18
Hi Deren/Isaac,
Hi Deren/Isaac, when I used a reference, an error occurred: "ERROR Command '/home/data/miniconda2/lib/python2.7/site-packages/bin/smalt-linux-x86_64 index -k 8 /home/data/RAD/copy.fasta /home/data/RAD/copy.fasta' returned non-zero exit status 1" . Do you have any suggestion? Thank you.
Zac Forsman
Jul 19 2016 17:47

Hi folks, amazing work with ipyrad... I have been testing it out and it is a fantastic program. I managed to get one dataset finished with some interesting results but I'm running into some errors for reference and denovo assemblies. I just updated to 3.22... any idea what this error might be about: Mean error [0.01420 sd=0.00353]
Mean hetero [0.02251 sd=0.00411]
[####################] 100% consensus calling | 0:03:11

Caught unknown exception - IndexError(index 0 is out of bounds for axis 1 with size 0)

Traceback (most recent call last):
File "/home/z/anaconda/bin/ipyrad", line 9, in <module>
load_entry_point('ipyrad==0.3.22', 'console_scripts', 'ipyrad')()
File "/home/z/anaconda/lib/python2.7/site-packages/ipyrad/", line 456, in main, force=args.force, preview=args.preview)
File "/home/z/anaconda/lib/python2.7/site-packages/ipyrad/core/", line 1416, in run
File "/home/z/anaconda/lib/python2.7/site-packages/ipyrad/core/", line 1339, in step5
self._clientwrapper(self._step5func, [samples, force], 45)
File "/home/z/anaconda/lib/python2.7/site-packages/ipyrad/core/", line 862, in _clientwrapper
File "/home/z/anaconda/lib/python2.7/site-packages/ipyrad/core/", line 1120, in _step5func, samples, force, ipyclient)
File "/home/z/anaconda/lib/python2.7/site-packages/ipyrad/assemble/", line 757, in run
statsdicts = [i.get() for i in lasyncs[]]
File "/home/z/anaconda/lib/python2.7/site-packages/ipyparallel/client/", line 166, in get
raise self.exception()
ipyparallel.error.RemoteError: IndexError(index 0 is out of bounds for axis 1 with size 0)

Deren Eaton
Jul 19 2016 17:56
Hey @zacforsman! Glad to see you're giving ipyrad a try. I'm not sure what this error is yet, but I'll look into it. Can you run ipyrad with the debugging flag turned on (-d) and send me the output that is written to 'ipyrad_log.txt' in your working directory.