These are chat archives for dereneaton/ipyrad

21st
Jul 2016
Deren Eaton
@dereneaton
Jul 21 2016 02:16
Hey @zacforsman, I'm looking into it. It seems a lot of clusters are aligning poorly in step3. This may have to do with the use a common cutter and so high-overlap of reads. I may have some tricks to reduce this problem. But the initial formatting could be an issue as well. We now implement pair-merging in ipyrad itself (using vsearch) in step3. And you could also use the 'reference' method in ipyrad to pull out the data that matches to the transcriptome. All of our testing has been on non-filtered input data, where we let ipyrad do the filtering, and so if the data are highly heterogeneous to begin with it may cause problems. I'll have to test.
jianlizhao
@jianlizhao
Jul 21 2016 03:40
@isaacovercast Hi, Isaac. Thanks for your response. There are three massages in ipyrad_log.txt: 2016-07-21 11:16:13,486 pid=141518 [parallel.py] INFO ['ipcluster', 'start', '--daemon', '--cluster-id=ipyrad-141518', '--engines=Local', '--n=60']
2016-07-21 11:16:30,236 pid=141518 [assembly.py] ERROR Command '/lustre/home/zhaojianli/miniconda2/lib/python2.7/site-packages/bin/smalt-linux-x86_64 index -k 8 /lustre/home/zhaojianli/jianli/RAD/chloroplast/RHcopy.fasta /lustre/home/zhaojianli/jianli/RAD/chloroplast/RHcopy.fasta' returned non-zero exit status 1
2016-07-21 11:16:30,379 pid=141518 [parallel.py] INFO Shutting down [ipyrad-141518] remote Engines
Zac Forsman
@zacforsman
Jul 21 2016 05:23
Hey @dereneaton, I also had errors with the ipyrad reference assembly approach as well, which I tried first (should I send you that as well?). I have two references: a nearly invariant mitochondrial genome, and a transcriptome (about 20K contigs concatenated together with about two hundred NNNs between contigs). Let me know however I can help with troubleshooting. -Zac
Cycadales
@Cycadales
Jul 21 2016 23:38
Hi Guys, hope you can help I have a problems with step six while trying to run a single population. This is the error: Traceback (most recent call last):
File "/data/miniconda2/bin/ipyrad", line 9, in <module>
load_entry_point('ipyrad==0.3.21', 'console_scripts', 'ipyrad')()
File "/data/miniconda2/lib/python2.7/site-packages/ipyrad/main.py", line 456, in main
data.run(steps=steps, force=args.force, preview=args.preview)
File "/data/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 1418, in run
self.step6(force=force)
File "/data/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 1372, in step6
randomseed], 45)
File "/data/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 862, in _clientwrapper
stepfunc(*args)
File "/data/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 1155, in _step6func
force, randomseed, ipyclient)
File "/data/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/cluster_across.py", line 1270, in run
build_h5_array(data, samples, ipyclient)
File "/data/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/cluster_across.py", line 465, in build_h5_array
multicat(data, samples, ipyclient)
File "/data/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/cluster_across.py", line 542, in multicat
with lbview.temp_flags(after=cleaning[last_sample]):
KeyError: 'Ccal-15-17-9_S22_001.fastq'
bash-4.2$
at happened after this step: Step6: Clustering across 10 samples at 0.8 similarity
[####################] 100% concat/shuffle input | 0:00:05
[####################] 100% clustering across | 0:10:27
[####################] 100% building clusters | 0:00:27
[####################] 100% aligning clusters | 0:01:41
[## ] 10% indexing clusters | 0:57:57
Caught unknown exception - 'Ccal-15-17-9_S22_001.fastq'