These are chat archives for dereneaton/ipyrad

20th
Jan 2019
jhoepke
@jhoepke
Jan 20 12:10
@isaacovercast @sandrahoffberg @caesantibanez @tim-oconnor I think I found a workaround for the error "ERROR IPyradWarningExit: error in filter_stacks on chunk 0: ValueError(zero-size array to reduction operation minimum which has no identity)": Then installing Miniconda in version 4.0.5, updating to version 4.3.30, cloning the root environment and installing ipyrad version 0.7.1 then step 7 worked fine for a minimum example BUT then I get the following error in step 3 (taken from ipyrad_log.txt) then I try to run my big paired gbs data set I am currently working with:

ipyrad [v.0.7.1]

Interactive assembly and analysis of RAD-seq data

Begin run: 2019-01-18 15:02
Using args {'preview': False, 'force': True, 'threads': 2, 'results': False, 'quiet': False, 'merge': None, 'ipcluster': False, 'cores': 0, 'params': 'params-all_reference_mc2.txt
', 'branch': None, 'steps': '1234567', 'debug': False, 'new': None, 'MPI': False}
Platform info: ('Linux', 'mpcb024', '3.10.0-514.el7.x86_64', '#1 SMP Wed Oct 19 11:24:13 EDT 2016', 'x86_64')2019-01-18 18:45:00,381 pid=16663 [cluster_within.py] ERROR
sample [DCA1837] failed in step [ref_build_and_muscle_chunk]; error: AttributeError('module' object has no attribute 'AlignmentFile')
2019-01-18 18:45:00,391 pid=16663 [cluster_within.py] ERROR sample [DCA0137P2] failed in step [ref_build_and_muscle_chunk]; error: AttributeError
('module' object has no attribute 'AlignmentFile')
2019-01-18 18:45:00,391 pid=16663 [cluster_within.py] ERROR sample [DCA1807] failed in step [ref_build_and_muscle_chunk]; error: Attribu
teError('module' object has no attribute 'AlignmentFile')
2019-01-18 18:45:00,391 pid=16663 [cluster_within.py] ERROR sample [DCA1510] failed in step [ref_build_and_muscle_chunk]; error: Attrib
uteError('module' object has no attribute 'AlignmentFile')
... [MUCH MORE SAMPLES WITH THE SAME ERROR] ...
2019-01-18 18:45:22,917 pid=16663 [assembly.py] ERROR No Samples ready for estimation. First run step 3.