These are chat archives for dereneaton/ipyrad

30th
May 2018
Felipe Zapata
@zapataf
May 30 2018 00:00

@isaacovercast here are the relevant lines of the log file

2018-05-24 22:40:23,136     pid=10612     [cluster_within.py]    WARNING     Bad derephandle - ~/default_params_edits/FZ116_derep.fastq
2018-05-24 22:40:23,181     pid=10610     [cluster_within.py]    WARNING     Bad derephandle - ~/default_params_edits/FZ422_derep.fastq
2018-05-24 22:40:23,219     pid=10587     [assembly.py]    ERROR     IPyradError(    Caught error while decloning 3rad data - list index out of range)

As for the files in the *_clust directory dir the .gz files are weird:

gunzip FZ116.clust.gz 
gunzip: FZ116.clust.gz: unexpected end of file
gunzip: FZ116.clust.gz: uncompress failed
Isaac Overcast
@isaacovercast
May 30 2018 17:29
The gzip files are corrupted. This would be a very expected outcome if the disk was full. This happens both on a cluster and on your local machine?
can I see an ls -ltr in the *_clust directory?
Isaac Overcast
@isaacovercast
May 30 2018 17:39
Can you send me the full log file as well? These errors could be downstream of the real problem.