These are chat archives for dereneaton/ipyrad

21st
Mar 2018
Ollie White
@Ollie_W_White_twitter
Mar 21 2018 15:01

Thanks for the reply @isaacovercast. I don't have a tmp file in my directory

 ls -l
total 4822816
-rw-r--r-- 1 oww1v14 bj 2418642962 Feb 16 17:05 MAC_RAW_GBS00289_L7_R1_data.fq.gz
-rw-r--r-- 1 oww1v14 bj 2518933734 Feb 16 17:08 MAC_RAW_GBS00289_L7_R2_data.fg.gz
-rw-r--r-- 1 oww1v14 bj        108 Feb 21 09:25 MD5.txt
-rw------- 1 oww1v14 bj        468 Feb 21 09:47 barcodes.txt
-rw------- 1 oww1v14 bj       4411 Mar 21 14:48 des.json
drwx------ 2 oww1v14 bj        512 Mar 21 14:47 des_fastqs
-rw------- 1 oww1v14 bj       4910 Mar 21 14:48 ipyrad_log.txt
-rw------- 1 oww1v14 bj          0 Mar 21 14:44 job-ipyrad-12.e5137251
-rw------- 1 oww1v14 bj      49791 Mar 21 14:48 job-ipyrad-12.o5137251
-rw------- 1 oww1v14 bj       3035 Feb 22 11:49 params-des.txt
drwx------ 3 oww1v14 bj      32768 Feb 22 11:52 reference-plastid-genomes
-rw------- 1 oww1v14 bj        430 Mar 21 12:59 script-ipyrad.pbs
-rw-r--r-- 1 oww1v14 bj       1050 Feb 21 09:25 seq-info.txt

I checked my system space this morning and it looked okay

mmlsquota scratch
                         Block Limits                                    |     File Limits
Filesystem type             KB      quota      limit   in_doubt    grace |    files   quota    limit in_doubt    grace  Remarks
scratch    USR       812296576  943718400 1073741824   15803264     none |    97910  360000   400000     2270     none gss1.violet12

I re ran steps one and two this morning after checking my disk space and below is the ipyrad_log.txt from the debug run

-------------------------------------------------------------
  ipyrad [v.0.7.21]
  Interactive assembly and analysis of RAD-seq data
 -------------------------------------------------------------
  Begin run: 2018-03-21 14:47
  Using args {'preview': False, 'force': True, 'threads': 16, 'results': False, 'quiet': False, 'merge': None, 'ipcluster': None, 'cores': 0, 'params': 'params-des.txt', 'branch': None, 'steps': '12', 'debug': True, 'new': None, 'download': None, 'MPI': False}
  Platform info: ('Linux', 'green0096', '2.6.32-696.10.3.el6.x86_64', '#1 SMP Thu Sep 21 12:12:50 EDT 2017', 'x86_64')2018-03-21 14:47:11,096   pid=12063       [parallel.py]   INFO    ['ipcluster', 'start', '--daemonize', '--cluster-id=ipyrad-cli-12063', '--engines=Local', '--profile=default', '--n=16']
2018-03-21 14:47:19,769         pid=12063       [demultiplex.py]        INFO    zcat is using optim = 8000000
2018-03-21 14:48:34,427         pid=12063       [assembly.py]   ERROR   R1 and R2 files are not the same length.
2018-03-21 14:48:36,498         pid=12063       [assembly.py]   INFO      shutting down engines
2018-03-21 14:48:36,537         pid=12063       [assembly.py]   INFO      finished shutdown
2018-03-21 14:48:36,538         pid=12063       [__init__.py]   INFO    debugging turned off

If you have any suggestions please do let me know, cheers Ollie

emhudson
@emhudson
Mar 21 2018 21:28
Hi Deren and Isaac, I am able to run my gbs data all the way through to step 7, but I get an "empty varcounts array" error on the last step. This happens even though the "trim_loci" values are all zero. From looking at the step 7 stats, it seems that all reads are filtered out at the "filtered_by_min_sample " step, so I changed the min_samples_locus parameter from the default down to two. I still had the exact same result, however. Any suggestions?