These are chat archives for dereneaton/ipyrad

29th
Jun 2017
Nora Mitchell
@noracmitchell
Jun 29 2017 16:27
Hi all, I'm running ipyrad v 0.7.1 remotely on a linux cluster on RADseq data. Everything seems to be running smoothly until I hit Step 6, indexing clusters, and get an input/output error. (always at 37% I've tried running by submitting a bash script to the cluster, and also running it semi-interactively using qlogin. alt. The log file says essentially the same thing '2017-06-29 11:57:33,485 pid=24240 [assembly.py] ERROR IPyradWarningExit: singlecat error: 679.1 RuntimeError(Can't decrement id ref count (Unable to close file, errno = 5, error message = 'input/output error'))'. Any insight? Thanks!
Deren Eaton
@dereneaton
Jun 29 2017 20:32
Hi @noracmitchell , I haven't seen this error before, but I'm guessing that it might occur if you have a sample at this step which has no consensus reads that passed filtering. If so, it's something we should catch and report better. Can you check the step 5 stats results to see if any samples have zero consensus reads? If so, you will want to create a new branch which excludes those samples before proceeding with step 6.