Hello there,
having started pick_closed_reference_otus.py on a large dataset - 14.8GB fna - the process is now sleeping after some 12h of working.
The command was:
pick_closed_reference_otus.py \
-i demulti_seqs_chimerafree.fna \
-r $reference_seqs \
-t $reference_tax \
-p $uclust_params \
-a \
-O 6 \
-o ./cr_otus
refs were according to SILVA 123,
uclust params is: pick_otus:otu_picking_method uclust_ref
Outputs so far are:
POTU_ggMo_ POTU_ggMo_.2_clusters.uc POTU_ggMo_.3_otus.log POTU_ggMo_.5_clusters.uc
POTU_ggMo_.0_clusters.uc POTU_ggMo_.2_failures.txt POTU_ggMo_.3_otus.txt POTU_ggMo_.5_failures.txt
POTU_ggMo_.0_failures.txt POTU_ggMo_.2_otus.log POTU_ggMo_.4_clusters.uc POTU_ggMo_.5_otus.log
POTU_ggMo_.0_otus.log POTU_ggMo_.2_otus.txt POTU_ggMo_.4_failures.txt POTU_ggMo_.5_otus.txt
POTU_ggMo_.0_otus.txt POTU_ggMo_.3_clusters.uc POTU_ggMo_.4_otus.log
POTU_ggMo_.1_clusters.uc POTU_ggMo_.3_failures.txt POTU_ggMo_.4_otus.txt
Right now I can see the following processes:
poller.py - Sleeping - 79.7MB RAM, 0% CPU
parallel_pick_otus_uclust_ref.py - Sleeping - 10.4MB RAM, 0% CPU
The last files were created 4h ago....
- What should I do here? Wait?
Here's my print_qiime_config -f:
print_qiime_config.py -f
System information
==================
Platform: linux2
Python version: 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC 4.8.2]
Python executable: /usr/bin/python
QIIME default reference information
===================================
For details on what files are used as QIIME's default references, see here:
https://github.com/biocore/qiime-default-reference/releases/tag/0.1.3Dependency versions
===================
QIIME library version: 1.9.1
QIIME script version: 1.9.1
qiime-default-reference version: 0.1.3
NumPy version: 1.11.0
SciPy version: 0.17.1
pandas version: 0.18.1
matplotlib version: 1.4.3
biom-format version: 2.1.5
h5py version: 2.5.0 (HDF5 version: 1.8.11)
qcli version: 0.1.1
pyqi version: 0.3.2
scikit-bio version: 0.2.3
PyNAST version: 1.2.2
Emperor version: 0.9.51
burrito version: 0.9.1
burrito-fillings version: 0.1.1
sortmerna version: SortMeRNA version 2.0, 29/11/2014
sumaclust version: SUMACLUST Version 1.0.00
swarm version: Swarm 1.2.19 [May 13 2016 21:04:23]
gdata: Installed.
RDP Classifier version (if installed): Not installed.
Java version (if installed): 1.8.0_91
QIIME config values
===================
For definitions of these settings and to learn how to configure QIIME, see here:
http://qiime.org/install/qiime_config.html http://qiime.org/tutorials/parallel_qiime.html blastmat_dir: None
pick_otus_reference_seqs_fp: /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
sc_queue: all.q
topiaryexplorer_project_dir: None
pynast_template_alignment_fp: /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta
cluster_jobs_fp: start_parallel_jobs.py
pynast_template_alignment_blastdb: None
assign_taxonomy_reference_seqs_fp: /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
torque_queue: friendlyq
jobs_to_start: 1
slurm_time: None
denoiser_min_per_core: 50
assign_taxonomy_id_to_taxonomy_fp: /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir: /tmp/
slurm_memory: None
slurm_queue: None
blastall_fp: blastall
seconds_to_sleep: 1