These are chat archives for dereneaton/ipyrad

20th
Oct 2016
Deren Eaton
@dereneaton
Oct 20 2016 02:59
@jldimond will look into it out for next update.
Cycadales
@Cycadales
Oct 20 2016 07:25
@isaacovercast ahh excellent that is very helpful thanks Isaac!
mtcthome
@mtcthome
Oct 20 2016 13:39

Hi @dereneaton , I'm running ipyrad on three datasets of 192 samples each. I'm using an imac and a macbook pro, but for some reason, only the macbook seems to finish step 3 (as long as I don't use gunzip for other stuff while running ipyrad). In the imac, ipyrad is having trouble finding the .clustS.gz files for some samples, but when i repeat the analysis the error occurs with other samples. Any hints on why this is happening?

Step 3: Clustering/Mapping reads
[####################] 100% dereplicating | 0:13:06
[####################] 100% clustering | 6:03:09
[####################] 100% building clusters | 0:00:14
[####################] 100% chunking | 0:00:01
[####################] 100% aligning | 6:52:13
sample [MTCT1620] failed. See error in ./ipyrad_log.txt
sample [CFBHT13461] failed. See error in ./ipyrad_log.txt
sample [MRT4852] failed. See error in ./ipyrad_log.txt
sample [MTCT1622] failed. See error in ./ipyrad_log.txt
sample [MTR14828] failed. See error in ./ipyrad_log.txt
sample [MTCT1761] failed. See error in ./ipyrad_log.txt
sample [MTR14829] failed. See error in ./ipyrad_log.txt
sample [MTCT798] failed. See error in ./ipyrad_log.txt
sample [MTCT1218] failed. See error in ./ipyrad_log.txt
sample [CFBHT15872] failed. See error in ./ipyrad_log.txt
sample [MTCT1049] failed. See error in ./ipyrad_log.txt
sample [MTR15365] failed. See error in ./ipyrad_log.txt
sample [MTCT1090] failed. See error in ./ipyrad_log.txt
sample [MTCT1488] failed. See error in ./ipyrad_log.txt
[####################] 100% concatenating | 0:00:18

Encountered an unexpected error (see ./ipyrad_log.txt)
Error message is below -------------------------------
[Errno 2] No such file or directory: '/Users/celiohaddad/Desktop/tereza/tro/c90d8m192_clust_0.9/CFBHT15872.clustS.gz'

James McDaniel
@jlmcdaniel
Oct 20 2016 19:58
Hi @isaacovercast and @dereneaton , I have a quick (and hopefully very simple) question. I was re-reading the manual and saw that for GBS datasets you recommend to set filter_adaptersto a stringent parameter. Would you recommend setting it to 1 or 2?
Also, this is for single-end reads.
vieves
@vieves
Oct 20 2016 21:46
Hi @dereneaton and @isaacovercast I have samples that were split between two different lanes, and thus have different fastq file names (when demultiplexed). If I combine each pair of files before using ipyrad (with demultiplexed fastq files), will there be any problems downstream since the read id's within each file won't always match?