These are chat archives for dereneaton/ipyrad

16th
Nov 2016
Deren Eaton
@dereneaton
Nov 16 2016 15:06
@edgardomortiz if possible, try requesting more time for now. 600 samples is a lot! But we should be able to better parallelize the 'building database' step if we put some more time into it. So far we focused most of our effort just on making the indexing step faster. But major improvements to it might take a little while, I'll be in the field for the next week. Although we haven't built in checkpoints for the substeps within step 6 [yet], you could restart from just the 'build database' step by editing the code manually for now.
Edgardo M. Ortiz
@edgardomortiz
Nov 16 2016 16:21
Thanks @dereneaton, I will give it a try
R2C2.lab
@R2C2_Lab_twitter
Nov 16 2016 17:11
Hi I got this error in step 6

regina@ccmar-r2c2-01:~/ipyrad_individual> ipyrad -p params-individual.txt -s 6


ipyrad [v.0.4.1]

Interactive assembly and analysis of RAD-seq data

loading Assembly: individual
from saved path: ~/ipyrad_individual/individual.json
local compute node: [20 cores] on ccmar-r2c2-01

Step 6: Clustering across 5 samples at 0.85 similarity
[####################] 100% concat/shuffle input | 0:00:32
[####################] 100% clustering across | 10:26:15
[####################] 100% building clusters | 0:00:30
[####################] 100% aligning clusters | 0:11:08
[####################] 100% database indels | 0:04:12
[ ] 0% indexing clusters | 1:05:59
Encountered an unexpected error (see ./ipyrad_log.txt)
Error message is below -------------------------------
tuple index out of range

thanks for any advice; and it seems that is still running...
Edgardo M. Ortiz
@edgardomortiz
Nov 16 2016 19:16
Hi @R2C2_Lab_twitter that looks like a memory error, try reducing to 10 cores, that worked for me in the past (you need to add -c 10 to your ipyrad command). Also notice there is version 0.5.2 out now, you may want to update.
Sam Borstein
@sborstein
Nov 16 2016 20:59

Hi ipyrad community. I am currently having some issues with step three for a dataset containing 380 individuals I am analyzing on a mac with 24 cores and 64 GB memory with ipyrad 0.5.0. I am getting errors in my ipyrad log with regards to muscle_align and it seems to prevent step 3 from finishing properly. While I have clustS.gz files in the directory for most of my samples, I am missing it for a few samples and the step 3 summary stats brought up by -r state that all sample are in step 2 although some have info in the clusters and clusters_hidepth columns. The ipyrad.log has the following:

2016-11-15 18:38:49,189 pid=18915 [cluster_within.py] ERROR sample [Nruf_LLandUp160_3] failed in step [muscle_align]; error: ImpossibleDependency()
2016-11-15 18:38:49,189 pid=18915 [cluster_within.py] ERROR sample [Nruf_LLandUp160_9] failed in step [muscle_align]; error: IndexError(list index out of range)
2016-11-15 18:38:49,190 pid=18915 [cluster_within.py] ERROR sample [Nruf_LLandUp160_8] failed in step [muscle_align]; error: IndexError(list index out of range)

and continues with eleven more samples with entries of "ERROR failed in step [muscle_align]; error" IndexError(list index out range)"

If anyone has any tips on what might be causing the errors and how to proceed that would be greatly appreciated.