These are chat archives for dereneaton/ipyrad

5th
Aug 2016
RobertaDamasceno
@RobertaDamasceno
Aug 05 2016 18:19
This message was deleted
RobertaDamasceno
@RobertaDamasceno
Aug 05 2016 18:29

Thanks tons, @isaacovercast and @dereneaton! I think I got the logic behind branching. For many reasons, I decided to start running ipyrad from step 1 with my data, but I get an error. Conda and ipyrd are updated. By using the -d flag I was able to fix some problems my params file had (pasted below), but it still doesn't work (error pasted below as well). Maybe there is stil something wrong with the params?... I'm also pasting the contents of the log file. Thanks a lot!

#

params file problems I fixed

#

yeti:ipyrad_test_3 Yeti$ ipyrad -n data3 -f

New file 'params-data3.txt' created in /Users/Yeti/Documents/damasceno/ipyrad_test_3

yeti:ipyrad_test_3 Yeti$ ipyrad -p params-data3.txt -s 1 -d

Enabling debug mode


ipyrad [v.0.3.25]

Interactive assembly and analysis of RAD-seq data

New Assembly: data3

Error setting parameter edit_cutsites: list index out of range
You entered: TGCAG

yeti:ipyrad_test_3 Yeti$ ipyrad -p params-data3.txt -s 1 -d

Enabling debug mode


ipyrad [v.0.3.25]

Interactive assembly and analysis of RAD-seq data

New Assembly: data3

Error setting parameter max_SNPs_locus: invalid literal for int() with base 10: ''
You entered: 8,
#

error in step 1

#

yeti:ipyrad_test_3 Yeti$ ipyrad -p params-data3.txt -s 1 -d

Enabling debug mode


ipyrad [v.0.3.25]

Interactive assembly and analysis of RAD-seq data

New Assembly: data3
ipyparallel setup: Local connection to 24 Engines

Step1: Demultiplexing fastq data to Samples
[####################] 100% chunking large files | 0:25:01
[ ] 0% sorting reads | 0:00:20
Caught unknown exception - IndexError(index 1000000 is out of bounds for axis 0 with size 1000000)

Traceback (most recent call last):
File "/Users/Yeti/miniconda2/bin/ipyrad", line 9, in <module>
load_entry_point('ipyrad==0.3.25', 'console_scripts', 'ipyrad')()
File "/Users/Yeti/miniconda2/lib/python2.7/site-packages/ipyrad/main.py", line 457, in main
data.run(steps=steps, force=args.force, preview=args.preview)
File "/Users/Yeti/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 1405, in run
self.step1(force=force, preview=preview)
File "/Users/Yeti/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 1223, in step1
self._clientwrapper(self._step1func, [force, preview], 45)
File "/Users/Yeti/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 859, in _clientwrapper
stepfunc(*args)
File "/Users/Yeti/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 993, in _step1func
assemble.demultiplex.run(self, preview, ipyclient, force)
File "/Users/Yeti/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/demultiplex.py", line 599, in run
wrapped_run(data, preview, ipyclient, force)
File "/Users/Yeti/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/demultiplex.py", line 755, in wrapped_run
result = async.result()
File "/Users/Yeti/miniconda2/lib/python2.7/site-packages/concurrent/futures/_base.py", line 398, in result
return self.get_result()
File "/Users/Yeti/miniconda2/lib/python2.7/site-packages/concurrent/futures/_base.py", line 357, in
get_result
raise type(self._exception), self._exception, self._traceback
ipyparallel.error.RemoteError: IndexError(index 1000000 is out of bounds for axis 0 with size 1000000)

#

log file

#

2016-08-05 13:36:29,156 pid=1048 [assembly.py] INFO Assembly.tuplecheck() failed to cast to <type 'int'> - 8,
2016-08-05 13:37:02,667 pid=1073 [parallel.py] INFO ['ipcluster', 'start', '--daemon', '--cluster-id=ipyrad-1073', '--engines=Local', '--n=24']
2016-08-05 13:37:11,754 pid=1073 [demultiplex.py] INFO ncpus 24
2016-08-05 13:37:11,755 pid=1073 [demultiplex.py] INFO optim 36675000
2016-08-05 13:37:11,757 pid=1073 [demultiplex.py] INFO chunks size = 36675000 lines, on 24 cpus
2016-08-05 14:02:13,424 pid=1073 [demultiplex.py] INFO chunkfiles {0: [('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaaa', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaab', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaac', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaad', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaae', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaaf', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaag', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaah', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaai', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaaj', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaak', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaal', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaam', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaan', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaao', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaap', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaaq', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaar', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaas', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaat', 0), ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaau', 0)]}
2016-08-05 14:02:13,424 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaaa', 0)
2016-08-05 14:02:13,427 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaab', 0)
2016-08-05 14:02:13,431 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaac', 0)
2016-08-05 14:02:13,433 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaad', 0)
2016-08-05 14:02:13,436 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaae', 0)
2016-08-05 14:02:13,439 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaaf', 0)
2016-08-05 14:02:13,442 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaag', 0)
2016-08-05 14:02:13,445 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaah', 0)
2016-08-05 14:02:13,448 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaai', 0)
2016-08-05 14:02:13,451 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaaj', 0)
2016-08-05 14:02:13,454 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaak', 0)

2016-08-05 14:02:13,458 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaal', 0)
2016-08-05 14:02:13,466 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaam', 0)
2016-08-05 14:02:13,469 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaan', 0)
2016-08-05 14:02:13,472 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaao', 0)
2016-08-05 14:02:13,475 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaap', 0)
2016-08-05 14:02:13,479 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaaq', 0)
2016-08-05 14:02:13,481 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaar', 0)
2016-08-05 14:02:13,485 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaas', 0)
2016-08-05 14:02:13,488 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaat', 0)
2016-08-05 14:02:13,491 pid=1073 [demultiplex.py] INFO tups ('/Users/Yeti/Documents/damasceno/ipyrad_test_3/tmp-chunks-data3/chunk1_0_aaau', 0)
2016-08-05 14:02:35,183 pid=1073 [assembly.py] ERROR IndexError(index 1000000 is out of bounds for axis 0 with size 1000000)
2016-08-05 14:02:35,363 pid=1073 [parallel.py] INFO Shutting down [ipyrad-1073] remote Engines