These are chat archives for dereneaton/ipyrad

13th
Aug 2016
Zac Forsman
@zacforsman
Aug 13 2016 09:29

I've been having some success with some libraries... amazingly fast, huge speed improvements.... Seems to be a problem with libraries not finishing,: [ ] 0% inferring [H, E] | 0:00:01 ERROR:ipyrad.assemble.util: sample PHE1 did not fin
ish
ERROR:ipyrad.assemble.util: stdout:
stderr:
error: ValueError(could not broadcast input array from shape (836,4) into shape (796,4))
[####################] 100% inferring [H, E] | 0:00:01

Step5: Consensus base calling
Skipping Sample ASO4_MP11; Already has consens reads. Use force arg to overwrite.
Skipping Sample AFUS3; Already has consens reads. Use force arg to overwrite.
Skipping Sample PPR1; Already has consens reads. Use force arg to overwrite.
Skipping Sample PHE2; Already has consens reads. Use force arg to overwrite.
Skipping Sample ASO1; Already has consens reads. Use force arg to overwrite.
Skipping Sample PVA1; Already has consens reads. Use force arg to overwrite.
Skipping Sample MP12; Already has consens reads. Use force arg to overwrite.
Skipping Sample ASO2; Already has consens reads. Use force arg to overwrite.
Skipping Sample MP14; Already has consens reads. Use force arg to overwrite.
Skipping Sample {}; not yet finished step4
Skipping Sample MP16; Already has consens reads. Use force arg to overwrite.
Skipping Sample ASO6_MP13; Already has consens reads. Use force arg to overwrite.
Skipping Sample AFUL2; Already has consens reads. Use force arg to overwrite.
Skipping Sample AFUL1; Already has consens reads. Use force arg to overwrite.
Skipping Sample PSE1; Already has consens reads. Use force arg to overwrite.
Skipping Sample PTE1; Already has consens reads. Use force arg to overwrite.
Skipping Sample PRE4; Already has consens reads. Use force arg to overwrite.
Skipping Sample ASO3_MP10; Already has consens reads. Use force arg to overwrite.
Skipping Sample PRE3; Already has consens reads. Use force arg to overwrite.
Skipping Sample PRE2; Already has consens reads. Use force arg to overwrite.
Mean error [0.00929 sd=0.00469]
Mean hetero [0.04357 sd=0.00730]
[####################] 100% consensus calling | 0:00:01
ERROR:ipyrad.core.assembly:float division by zero

Caught unknown exception - float division by zero

Traceback (most recent call last):
File "/home/zac/miniconda2/bin/ipyrad", line 9, in <module>
load_entry_point('ipyrad==0.3.26', 'console_scripts', 'ipyrad')()
File "/home/zac/miniconda2/lib/python2.7/site-packages/ipyrad/main.py", line 457, in main
data.run(steps=steps, force=args.force, preview=args.preview)
File "/home/zac/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 1413, in run
self.step5(force=force)
File "/home/zac/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 1336, in step5
self._clientwrapper(self._step5func, [samples, force], 45)
File "/home/zac/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 859, in _clientwrapper
stepfunc(args)
File "/home/zac/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 1117, in _step5func
assemble.consens_se.run(self, samples, force, ipyclient)
File "/home/zac/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/consens_se.py", line 750, in run
" consensus calling | {}".format(elapsed))
File "/home/zac/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/util.py", line 538, in progressbar
progress = 100
(finished / float(njobs))
ZeroDivisionError: float division by zero

Cycadales
@Cycadales
Aug 13 2016 10:16

HI guys, I keep getting an error during step six any ideas? Step6: Clustering across 5 samples at 0.8 similarity
[####################] 100% concat/shuffle input | 0:00:01
[####################] 100% clustering across | 0:00:33
[####################] 100% building clusters | 0:00:08
[####################] 100% aligning clusters | 0:00:33
[#### ] 20% indexing clusters | 0:01:04
Caught unknown exception - 'Carm-15-1-10-z_S41_001_PairedTrim'

Traceback (most recent call last):
File "/home/jclugston/miniconda2/bin/ipyrad", line 9, in <module>
load_entry_point('ipyrad==0.3.26', 'console_scripts', 'ipyrad')()
File "/home/jclugston/miniconda2/lib/python2.7/site-packages/ipyrad/main.py", line 457, in main
data.run(steps=steps, force=args.force, preview=args.preview)
File "/home/jclugston/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 1415, in run
self.step6(force=force)
File "/home/jclugston/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 1369, in step6
randomseed], 45)
File "/home/jclugston/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 859, in _clientwrapper
stepfunc(*args)
File "/home/jclugston/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 1152, in _step6func
force, randomseed, ipyclient)
File "/home/jclugston/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/cluster_across.py", line 1274, in run
build_h5_array(data, samples, ipyclient)
File "/home/jclugston/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/cluster_across.py", line 465, in build_h5_array
multicat(data, samples, ipyclient)
File "/home/jclugston/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/cluster_across.py", line 542, in multicat
with lbview.temp_flags(after=cleaning[last_sample]):
KeyError: 'Carm-15-1-10-z_S41_001_PairedTrim'

Cycadales
@Cycadales
Aug 13 2016 10:24
Looks like there as a problem during step three where no clusters were found in some samples.... will run it agian
Isaac Overcast
@isaacovercast
Aug 13 2016 18:05
@zacforsman It looks like most of your samples finished step 4, but PHE1 failed. Looks like this error is cascading forward to step 5. This line in your output is the offender:
Skipping Sample {}; not yet finished step4
Can you re-run step 4 and include the -d flag? This will generate a file called ipyrad_log.txt, if you can do this and email me the file it'll help in troubleshooting. iovercast@gc.cuny.edu
Isaac Overcast
@isaacovercast
Aug 13 2016 18:34
@Cycadales Hi James, This is actually a bug in step 6 that I've seen before and have been meaning to fix. Working on it now.
Isaac Overcast
@isaacovercast
Aug 13 2016 18:51
v.0.3.27 now available for linux/mac: Bug fix for a race condition in step 6. @Cycadales This should fix your problem.
Cycadales
@Cycadales
Aug 13 2016 19:11
excellent thanks @isaacovercast
Isaac Overcast
@isaacovercast
Aug 13 2016 19:26
@zacforsman Also, there is a file with extension .json in your working directory, if you could email me that as well that'd be helpful.
Isaac Overcast
@isaacovercast
Aug 13 2016 23:59
v0.3.28 up for linux/max: Improved support for running on older hpc systems.