Bug report

[zoubinok]

• mbin version: 1.1.0
• Python version: 2.7.3
• Operating System: Ubuntu 12.04 LTS

Description

Dear sir, I used the virtual environment and installed thses packages: backports.functools-lru-cache (1.5) biopython (1.70) cycler (0.10.0) Cython (0.28) h5py (2.7.1) kiwisolver (1.0.1) matplotlib (2.2.0) mbin (1.1.0) numpy (1.13.3) pbcore (1.2.10) pip (9.0.2) pyparsing (2.2.0) pysam (0.14) python-dateutil (2.7.0) pytz (2018.3) scipy (1.0.0) setuptools (38.6.0) six (1.11.0) subprocess32 (3.2.7) wheel (0.30.0)

I want to use buildcontrols. And I used data in the github. But something is wrong. Would you like to help me? Thank you.

What I Did

(venv) zoubinserver@ubuntuZ:~/mbin/mbin/data$ buildcontrols -i aligned_reads.cmp.h5 Traceback (most recent call last): File "/home/zoubinserver/venv/bin/buildcontrols", line 11, in sys.exit(launch()) File "/home/zoubinserver/venv/local/lib/python2.7/site-packages/mbin/controls.py", line 17, in launch opts,control_aln_fn = parseArgs() File "/home/zoubinserver/venv/local/lib/python2.7/site-packages/mbin/controls.py", line 206, in parseArgs opts.ref = os.path.abspath(opts.ref) File "/home/zoubinserver/venv/lib/python2.7/posixpath.py", line 343, in abspath if not isabs(path): File "/home/zoubinserver/venv/lib/python2.7/posixpath.py", line 53, in isabs return s.startswith('/') AttributeError: 'NoneType' object has no attribute 'startswith' (venv) zoubinserver@ubuntuZ:~/mbin/mbin/data$ buildcontrols m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.cmp.h5 Traceback (most recent call last): File "/home/zoubinserver/venv/bin/buildcontrols", line 11, in sys.exit(launch()) File "/home/zoubinserver/venv/local/lib/python2.7/site-packages/mbin/controls.py", line 17, in launch opts,control_aln_fn = parseArgs() File "/home/zoubinserver/venv/local/lib/python2.7/site-packages/mbin/controls.py", line 206, in parseArgs opts.ref = os.path.abspath(opts.ref) File "/home/zoubinserver/venv/lib/python2.7/posixpath.py", line 343, in abspath if not isabs(path): File "/home/zoubinserver/venv/lib/python2.7/posixpath.py", line 53, in isabs return s.startswith('/') AttributeError: 'NoneType' object has no attribute 'startswith'

[jbeaulaurier]

Hello,

Sorry about that. This should be fixed with 7263defd6c7ecc78da48d1fa6fa06ef6273c652c. Let me know if you encounter any additional problems.

Thanks, John

[zoubinok]

Hello, I tried again. New bugs appear. So I am wandering if I used the right input file. Have you offer the wga_aligned_reads.cmp.h5? The first warning is :

2018-03-25 13:44:41 [WARNING] Failed command: cut -d$'\t' -f14295-16336 control_ipds.tmp > control_ipds.tmp.sub.7

But interestingly, I can run it in the terminal directly.

(venv) zoubinserver@ubuntuZ:~/mbin/mbin/data$ buildcontrols -i --procs=4 --control_pkl_name=control_means.pkl aligned_reads.cmp.h5 2018-03-25 13:42:06 [INFO] Initiating dictionary of all possible motifs... 2018-03-25 13:42:06 [INFO] - Adding 256 4-mer motifs... 2018-03-25 13:42:06 [INFO] Done: 256 possible contiguous motifs

2018-03-25 13:42:06 [INFO] - Adding 1024 5-mer motifs... 2018-03-25 13:42:06 [INFO] Done: 1536 possible contiguous motifs

2018-03-25 13:42:06 [INFO] - Adding 4096 6-mer motifs... 2018-03-25 13:42:06 [INFO] Done: 7680 possible contiguous motifs

2018-03-25 13:42:06 [INFO] - Adding bipartite motifs to search space... 2018-03-25 13:42:07 [INFO] Done: 194560 possible bipartite motifs

2018-03-25 13:42:07 [INFO] 2018-03-25 13:42:07 [INFO] Preparing to create new control data in ctrl_tmp 2018-03-25 13:42:07 [INFO] Loading data from /home/zoubinserver/mbin/mbin/data/aligned_reads.cmp.h5... 2018-03-25 13:42:07 [INFO] Querying 246 reads using 4 chunks of size 61... 2018-03-25 13:42:07 [INFO] ...chunk 0 - mol 0/61 (0.0%) 2018-03-25 13:42:08 [INFO] ...chunk 1 - mol 0/61 (0.0%) 2018-03-25 13:42:09 [INFO] ...chunk 2 - mol 0/61 (0.0%) 2018-03-25 13:42:10 [INFO] ...chunk 3 - mol 0/61 (0.0%) 2018-03-25 13:42:17 [INFO] ...chunk 0 - mol 6/61 (9.0%) 2018-03-25 13:42:18 [INFO] ...chunk 1 - mol 6/61 (9.0%) 2018-03-25 13:42:19 [INFO] ...chunk 2 - mol 6/61 (9.0%) 2018-03-25 13:42:20 [INFO] ...chunk 3 - mol 6/61 (9.0%) 2018-03-25 13:42:38 [INFO] ...chunk 0 - mol 12/61 (19.0%) 2018-03-25 13:42:38 [INFO] ...chunk 1 - mol 12/61 (19.0%) 2018-03-25 13:42:39 [INFO] ...chunk 2 - mol 12/61 (19.0%) 2018-03-25 13:42:40 [INFO] ...chunk 3 - mol 12/61 (19.0%) 2018-03-25 13:42:47 [INFO] ...chunk 0 - mol 18/61 (29.0%) 2018-03-25 13:42:48 [INFO] ...chunk 1 - mol 18/61 (29.0%) 2018-03-25 13:42:49 [INFO] ...chunk 2 - mol 18/61 (29.0%) 2018-03-25 13:42:49 [INFO] ...chunk 3 - mol 18/61 (29.0%) 2018-03-25 13:43:06 [INFO] ...chunk 0 - mol 24/61 (39.0%) 2018-03-25 13:43:07 [INFO] ...chunk 1 - mol 24/61 (39.0%) 2018-03-25 13:43:08 [INFO] ...chunk 2 - mol 24/61 (39.0%) 2018-03-25 13:43:08 [INFO] ...chunk 3 - mol 24/61 (39.0%) 2018-03-25 13:43:25 [INFO] ...chunk 0 - mol 30/61 (49.0%) 2018-03-25 13:43:26 [INFO] ...chunk 1 - mol 30/61 (49.0%) 2018-03-25 13:43:27 [INFO] ...chunk 3 - mol 30/61 (49.0%) 2018-03-25 13:43:27 [INFO] ...chunk 2 - mol 30/61 (49.0%) 2018-03-25 13:43:35 [INFO] ...chunk 1 - mol 36/61 (59.0%) 2018-03-25 13:43:36 [INFO] ...chunk 0 - mol 36/61 (59.0%) 2018-03-25 13:43:36 [INFO] ...chunk 3 - mol 36/61 (59.0%) 2018-03-25 13:43:37 [INFO] ...chunk 2 - mol 36/61 (59.0%) 2018-03-25 13:43:55 [INFO] ...chunk 1 - mol 42/61 (68.0%) 2018-03-25 13:43:56 [INFO] ...chunk 3 - mol 42/61 (68.0%) 2018-03-25 13:43:56 [INFO] ...chunk 0 - mol 42/61 (68.0%) 2018-03-25 13:43:56 [INFO] ...chunk 2 - mol 42/61 (68.0%) 2018-03-25 13:44:05 [INFO] ...chunk 1 - mol 48/61 (78.0%) 2018-03-25 13:44:05 [INFO] ...chunk 3 - mol 48/61 (78.0%) 2018-03-25 13:44:06 [INFO] ...chunk 0 - mol 48/61 (78.0%) 2018-03-25 13:44:06 [INFO] ...chunk 2 - mol 48/61 (78.0%) 2018-03-25 13:44:24 [INFO] ...chunk 1 - mol 54/61 (88.0%) 2018-03-25 13:44:25 [INFO] ...chunk 3 - mol 54/61 (88.0%) 2018-03-25 13:44:26 [INFO] ...chunk 2 - mol 54/61 (88.0%) 2018-03-25 13:44:30 [INFO] Chunk 0: found 55 alignments (54 molecules) > 100bp in aligned_reads.cmp.h5 2018-03-25 13:44:31 [INFO] Chunk 3: found 55 alignments (55 molecules) > 100bp in aligned_reads.cmp.h5 2018-03-25 13:44:32 [INFO] Chunk 2: found 55 alignments (55 molecules) > 100bp in aligned_reads.cmp.h5 2018-03-25 13:44:33 [INFO] Chunk 1: found 58 alignments (58 molecules) > 100bp in aligned_reads.cmp.h5 2018-03-25 13:44:33 [INFO] Combining results data from all chunks... 2018-03-25 13:44:33 [INFO] ...1/4 2018-03-25 13:44:33 [INFO] ...2/4 2018-03-25 13:44:33 [INFO] ...3/4 2018-03-25 13:44:33 [INFO] ...4/4 2018-03-25 13:44:33 [INFO] Done. 2018-03-25 13:44:33 [INFO] Catting contig-specific data from parallel processes... 2018-03-25 13:44:33 [INFO] ...contig plasmid_phel3 (0/1) 2018-03-25 13:44:38 [INFO] Done. 2018-03-25 13:44:38 [INFO] 2018-03-25 13:44:38 [INFO] Building dictionary of control values for all motifs... 2018-03-25 13:44:38 [INFO] * Initial build requires significant time and memory. 2018-03-25 13:44:41 [INFO] - Control data: chunk 1/100 2018-03-25 13:44:41 [INFO] - Control data: chunk 8/100 2018-03-25 13:44:41 [INFO] - Control data: chunk 15/100 2018-03-25 13:44:41 [INFO] - Control data: chunk 22/100 2018-03-25 13:44:41 [WARNING] Failed command: cut -d$'\t' -f14295-16336 control_ipds.tmp > control_ipds.tmp.sub.7 2018-03-25 13:44:41 [WARNING] Failed command: cut -d$'\t' -f1-2042 control_ipds.tmp > control_ipds.tmp.sub.0 2018-03-25 13:44:41 [WARNING] Failed command: cut -d$'\t' -f42883-44924 control_ipds.tmp > control_ipds.tmp.sub.21 2018-03-25 13:44:41 [WARNING] Failed command: cut -d$'\t' -f28589-30630 control_ipds.tmp > control_ipds.tmp.sub.14 2018-03-25 13:44:41 [WARNING] Failed command: cut -d$'\t' -f1-2042 control_ipdsN.tmp > control_ipdsN.tmp.sub.0 Traceback (most recent call last): File "/home/zoubinserver/mbin2/venv/bin/buildcontrols", line 11, in load_entry_point('mbin==1.1.1', 'console_scripts', 'buildcontrols')() File "/home/zoubinserver/mbin2/venv/local/lib/python2.7/site-packages/mbin-1.1.1-py2.7.egg/mbin/controls.py", line 20, in launch 2018-03-25 13:44:41 [WARNING] Failed command: cut -d$'\t' -f42883-44924 control_ipdsN.tmp > control_ipdsN.tmp.sub.21 2018-03-25 13:44:41 [WARNING] Failed command: cut -d$'\t' -f14295-16336 control_ipdsN.tmp > control_ipdsN.tmp.sub.7 2018-03-25 13:44:41 [WARNING] Failed command: cut -d$'\t' -f28589-30630 control_ipdsN.tmp > control_ipdsN.tmp.sub.14 2018-03-25 13:44:41 [INFO] - Control data: chunk 29/100 2018-03-25 13:44:41 [WARNING] Failed command: cut -d$'\t' -f57177-59218 control_ipds.tmp > control_ipds.tmp.sub.28 2018-03-25 13:44:41 [WARNING] Failed command: cut -d$'\t' -f57177-59218 control_ipdsN.tmp > control_ipdsN.tmp.sub.28 extract_controls(opts, control_aln_fn) File "/home/zoubinserver/mbin2/venv/local/lib/python2.7/site-packages/mbin-1.1.1-py2.7.egg/mbin/controls.py", line 55, in extract_controls control_means = controls.build_control_IPD_dict(motifs, bi_motifs) File "/home/zoubinserver/mbin2/venv/local/lib/python2.7/site-packages/mbin-1.1.1-py2.7.egg/mbin/controls.py", line 488, in build_control_IPD_dict control_means,not_found = self.chunk_control_matrices(control_ipds_fn[0], control_ipds_N_fn[0], control_kmers_fn[0]) File "/home/zoubinserver/mbin2/venv/local/lib/python2.7/site-packages/mbin-1.1.1-py2.7.egg/mbin/controls.py", line 406, in chunk_control_matrices results = mbin.launch_pool(self.opts.procs, process_contig_chunk, args) File "/home/zoubinserver/mbin2/venv/local/lib/python2.7/site-packages/mbin-1.1.1-py2.7.egg/mbin/mbin.py", line 40, in launch_pool results = p.map(funct, args) File "/usr/lib/python2.7/multiprocessing/pool.py", line 227, in map return self.map_async(func, iterable, chunksize).get() File "/usr/lib/python2.7/multiprocessing/pool.py", line 528, in get raise self._value UserWarning: loadtxt: Empty input file: "control_ipds.tmp.sub.0" (venv) zoubinserver@ubuntuZ:~/mbin/mbin/data$ cd ctrl_tmp/ (venv) zoubinserver@ubuntuZ:~/mbin/mbin/data/ctrl_tmp$ cut -d$'\t' -f14295-16336 control_ipds.tmp > control_ipds.tmp.sub.7

[zoubinok]

Hello, I used CentOS to run it today. And I find that everything is OK. So I think it do not support Ubuntu well.