longtianpy / skewgd_v1 Goto Github PK

aurebg@begonia:/data/aurebg_projects/WGD$ python /data/software/SkewGD/WGD_detection.py -i Athaliana_Phytozome167_TAIR10.cds.fa -o WGD_Atha/Atha_MCL -d WGD_Atha/ -y /usr/local/bin/yn00

** (WGD_detection.py:10372): WARNING **: Couldn't connect to accessibility bus: Failed to connect to socket /tmp/dbus-Cf5K2FmXPG: Connection refused
Translating CDS to proteins...

/usr/local/lib/python2.7/dist-packages/Bio/Seq.py:2041: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.
BiopythonWarning)
Self-blasting, this may take long...

Building a new DB, current time: 05/06/2016 16:25:21
New DB name: /data/aurebg_projects/WGD/Athaliana_Phytozome167_TAIR10.cds.fa.protein
New DB title: Athaliana_Phytozome167_TAIR10.cds.fa.protein
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 27416 sequences in 1.65178 seconds.
Clustering...
..[mcl] new tab created
[mcl] pid 19353
ite ------------------- chaos time hom(avg,lo,hi) expa expb expc fmv
1 ................... 30.09 0.08 1.02/0.02/3.66 2.17 2.17 2.17 0
2 ................... 47.06 0.18 0.90/0.19/1.55 2.34 1.35 2.94 7
3 ................... 25.04 0.22 0.83/0.11/2.87 2.30 0.69 2.02 10
4 ................... 17.66 0.12 0.82/0.17/3.61 1.93 0.69 1.40 6
5 ................... 20.96 0.06 0.85/0.21/2.28 1.28 0.72 1.01 1
6 ................... 10.83 0.04 0.88/0.20/2.51 1.06 0.74 0.74 0
7 ................... 5.50 0.03 0.91/0.39/2.26 1.02 0.74 0.55 0
8 ................... 2.18 0.02 0.94/0.46/1.36 1.01 0.75 0.41 0
9 ................... 1.39 0.01 0.96/0.54/1.34 1.00 0.80 0.33 0
10 ................... 0.95 0.01 0.98/0.52/1.19 1.00 0.86 0.28 0
11 ................... 0.64 0.01 0.99/0.63/1.22 1.00 0.90 0.26 0
12 ................... 0.48 0.01 0.99/0.58/1.00 1.00 0.94 0.24 0
13 ................... 0.34 0.01 1.00/0.76/1.00 1.00 0.97 0.23 0
14 ................... 0.25 0.01 1.00/0.76/1.00 1.00 0.98 0.23 0
15 ................... 0.25 0.01 1.00/0.76/1.00 1.00 0.99 0.22 0
16 ................... 0.24 0.01 1.00/0.76/1.00 1.00 0.99 0.22 0
17 ................... 0.37 0.01 1.00/0.75/1.00 1.00 1.00 0.22 0
18 ................... 0.50 0.01 1.00/0.63/1.00 1.00 1.00 0.22 0
19 ................... 0.28 0.01 1.00/0.80/1.00 1.00 1.00 0.22 0
20 ................... 0.03 0.01 1.00/0.97/1.00 1.00 1.00 0.22 0
21 ................... 0.00 0.01 1.00/1.00/1.00 1.00 1.00 0.22 0
22 ................... 0.00 0.01 1.00/1.00/1.00 1.00 1.00 0.22 0
[mcl] jury pruning marks: <99,99,99>, out of 100
[mcl] jury pruning synopsis: <99.0 or perfect> (cf -scheme, -do log)
[mcl] output is in Athaliana_Phytozome167_TAIR10.cds.fa.protein.mcl_out
[mcl] 5055 clusters found
[mcl] output is in Athaliana_Phytozome167_TAIR10.cds.fa.protein.mcl_out

Please cite:
Stijn van Dongen, Graph Clustering by Flow Simulation. PhD thesis,
University of Utrecht, May 2000.
( http://www.library.uu.nl/digiarchief/dip/diss/1895620/full.pdf
or http://micans.org/mcl/lit/svdthesis.pdf.gz)
OR
Stijn van Dongen, A cluster algorithm for graphs. Technical
Report INS-R0010, National Research Institute for Mathematics
and Computer Science in the Netherlands, Amsterdam, May 2000.
( http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z
or http://micans.org/mcl/lit/INS-R0010.ps.Z)

Matching clusters...
5049
Traceback (most recent call last):
File "/data/software/SkewGD/WGD_detection.py", line 125, in
main()
File "/data/software/SkewGD/WGD_detection.py", line 41, in main
afa_file_list = Hong_wrapper(nucleotide_cds=nucleotide_cds, identity=identity, coverage=coverage, output_prefix=out_prefix,working_dir=working_dir)
File "/data/software/SkewGD/WGD_detection.py", line 95, in Hong_wrapper
process_cluster_all.process_cluster(mcl_out=mcl_out, protein_cds=protein_cds, output_prefix=output_prefix,working_dir=working_dir)
File "/data/software/SkewGD/process_cluster_all.py", line 41, in process_cluster
with open(output_prefix+str(i)+'.txt','w') as output:
IOError: [Errno 2] No such file or directory: 'WGD_Atha/Atha_MCL1.txt'

I have these warning messages:
1- ** (WGD_detection.py:10372): WARNING **: Couldn't connect to accessibility bus: Failed to connect to socket /tmp/dbus-Cf5K2FmXPG: Connection refused
Translating CDS to proteins...
2- usr/local/lib/python2.7/dist-packages/Bio/Seq.py:2041: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.
BiopythonWarning)

The pipeline runs over different steps. It will informative for the user if while the pipeline is running, it get messages like:

====================
SkewGB pipeline starts
Date XXXXXXXX
====================

Step 1 of Z: Translating CDS to proteins start (date)
XXXXXX CDS have been translated to proteins

Step 2 of Z: Building the selfblast database (date)

Step 3 of Z: Performing selfblast (date)
XXXXX hits were detected excluding selfhits.

....

The pipeline can be modified in the future, It should have the program version number.

The number of threads should be configurable. For example process_blast.py uses '-num_threads 8' but the program should be able to use any number specified by the user depending of the resources (for example, the Bombarely lab's server has 64 threads).