These are chat archives for dereneaton/ipyrad

28th
Oct 2016
James Clugston
@Cycadales_twitter
Oct 28 2016 08:40
@dereneaton @isaacovercast Hi Guys, I have got another problem with a separate analysis two (not the one mentioned yesterday!). This problem is occurring during step 2 where some samples are just not filtering when when I re-run the step it is unsuccessful. I know there is nothing wrong with the samples as they have worked before. But it is quite strange is seems to happen since the update. Basically what is happening is some samples show 0 reads filtered and the step fail completely. I am using PairGBS setting and its 150 PE samples. I think a total of 73 samples.
James Clugston
@Cycadales_twitter
Oct 28 2016 13:23
@dereneaton @isaacovercast ok kind of figured out the above problem. One sample just was not filtering and I am not sure why as it worked fine before. Also it has been quality trimmed and filter already so its a little strange.
Amely Martins
@amelymartins
Oct 28 2016 15:22
Hi @dereneaton and @isaacovercast . I'm having the same error that @Cycadales_twitter was having. I'm using ipyrad for denovo assembly of ddRAD PE 150bp reads. Any ideas?
The error messages in my ipyrad_log.txt file are:
2016-10-27 20:05:18,171 pid=38509 [cluster_across.py] ERROR error in singlecat (CAQ2_sample) MemoryError()
2016-10-28 02:58:26,714 pid=32808 [cluster_across.py] ERROR error in singlecat (CAQ2_sample) MemoryError()
So, it sounds that one sample is not indexing. But I don't know why.
Amanda Haponski
@ahaponski_twitter
Oct 28 2016 15:42
Hi @dereneaton. I am just switching over from pyrad to ipyrad and I had a couple of questions. In pyrad I was able to specify my outgroups and also a subset of my taxa. I have been looking through the readthedocs file and saw information on subsampling my dataset, but is there anyway to specify my outgroups. I know in the past specifying the outgroups for my dataset has made a big difference in the # of loci the program recovers.
Deren Eaton
@dereneaton
Oct 28 2016 16:14
@Cycadales_twitter do you mean zero reads pass the filter or zero reads are filtered from the data?
@/all pretty sure we know the source of the memoryerror in step6 and we're working on it.
James Clugston
@Cycadales_twitter
Oct 28 2016 17:16
Untitled.pdf
@dereneaton Hi Daren this is what I get (see above). Did you get the files I sent you via Wetranfer? for the other analysis I have running. Its not that reads don't pass its that it seems that nothing happens with that sample and it fails.
James Clugston
@Cycadales_twitter
Oct 28 2016 22:58
@dereneaton @isaacovercast Ok so I have done some further testing on my own system to see how it handles this data what it give me back. This is the error Encountered an error, see ./ipyrad_log.txt. IPyradError((' error in %s, %s', ['cutadapt', '--quality-cutoff', '20,20', '-u', '0', '-U', '0', '--trim-n', '--quality-base', '30', '--max-n', '15', '--minimum-length', '40', '-o', '/Volumes/LaCie/PhD/RAD_data/Ccal_test/Ccal_test/Ccal_test_edits/Ccal-15-23-7_S70_001_PairedTrim.trimmed_R1_.fastq.gz', '-p', '/Volumes/LaCie/PhD/RAD_data/Ccal_test/Ccal_test/Ccal_test_edits/Ccal-15-23-7_S70_001_PairedTrim.trimmed_R2_.fastq.gz', '/Volumes/LaCie/PhD/RAD_data/Ccal_test/Ccal_fastq/Ccal-15-23-7_S70_R1_001_PairedTrim.fastq.gz', '/Volumes/LaCie/PhD/RAD_data/Ccal_test/Ccal_fastq/Ccal-15-23-7_S70_R2_001_PairedTrim.fastq.gz'], "This is cutadapt 1.11 with Python 2.7.12\nCommand line parameters: --quality-cutoff 20,20 -u 0 -U 0 --trim-n --quality-base 30 --max-n 15 --minimum-length 40 -o /Volumes/LaCie/PhD/RAD_data/Ccal_test/Ccal_test/Ccal_test_edits/Ccal-15-23-7_S70_001_PairedTrim.trimmed_R1_.fastq.gz -p /Volumes/LaCie/PhD/RAD_data/Ccal_test/Ccal_test/Ccal_test_edits/Ccal-15-23-7_S70_001_PairedTrim.trimmed_R2_.fastq.gz /Volumes/LaCie/PhD/RAD_data/Ccal_test/Ccal_fastq/Ccal-15-23-7_S70_R1_001_PairedTrim.fastq.gz /Volumes/LaCie/PhD/RAD_data/Ccal_test/Ccal_fastq/Ccal-15-23-7_S70_R2_001_PairedTrim.fastq.gz\nTrimming 0 adapters with at most 10.0% errors in paired-end mode ...\ncutadapt: error: Reads are improperly paired. Read name 'NS500799:97:HTV37BGXX:4:11401:6904:1031 1:N:0:TAATGCGC+AGGCTATA' in file 1 does not match 'NS500799:97:HTV37BGXX:2:11101:16232:1067 1:N:0:TAATGCGC+AGGCTATA' in file 2.\ngzip: error writing to output: Broken pipe\ngzip: /Volumes/LaCie/PhD/RAD_data/Ccal_test/Ccal_fastq/Ccal-15-23-7_S70_R2_001_PairedTrim.fastq.gz: uncompress failed\ngzip: error writing to output: Broken pipe\ngzip: /Volumes/LaCie/PhD/RAD_data/Ccal_test/Ccal_fastq/Ccal-15-23-7_S70_R1_001_PairedTrim.fastq.gz: uncompress failed\n"))
@dereneaton this is unlinked to the question a posted about step six (which I did send in an email)