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fanglab / SMALR

SMALR: a framework for single-molecule level interrogation of the methylation status of SMRT reads.
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sort command failing in run_test_SMp.sh #6

Closed biominer closed 6 years ago

biominer commented 7 years ago

Hi John,

Great package and well-written paper, I'm looking forward to getting this working.

Installation and setting up the virtual environment went fine, but upon running the test scripts, I'm receiving an error for the sort command failing for some reason. Please see below to see if anything jumps out as the possible source of the error.

Many thanks, ---Sam 

- ref000002 (scf7180000000009|quiver)
- ref000001 (scf7180000000008|quiver)
- ref000003 (scf7180000000010|quiver)
- ref000004 (scf7180000000011|quiver)

21:29:35 [INFO] 21:29:35 [INFO] ==================================== 21:29:35 [INFO] Analyzing contig ref000002 (scf7180000000009|quiver) 21:29:35 [INFO] ==================================== 21:29:35 [INFO] ref000002 - contig_id: ref000002 21:29:35 [INFO] ref000002 - contig_name: scf7180000000009|quiver 21:29:36 [INFO] Partitioning /home/smodlin/projects/SMALR/SMALR/test/wga_longlib.cmp.h5 into 4 chunks for analysis... 21:29:36 [INFO] ...chunk 2 - 0/2 (0.0%) alignments processed... 21:29:36 [INFO] ...chunk 1 - 0/1 (0.0%) alignments processed... 21:29:36 [INFO] ...chunk 0 - 0/8 (0.0%) alignments processed... 21:29:36 [INFO] ...chunk 3 - 0/4 (0.0%) alignments processed... 21:29:36 [INFO] ...chunk 0 - 4/8 (50.0%) alignments processed... 21:29:36 [INFO] ref000002 - Combining the 4 separate ipdArray dictionaries... 21:29:36 [INFO] Partitioning /home/smodlin/projects/SMALR/SMALR/test/nat_longlib.cmp.h5 into 4 chunks for analysis... 21:29:36 [INFO] ref000002 - Separating out file-matched regions of the control IPD values dict... 21:29:36 [INFO] ...chunk 0 - processing molecules: 0/1 (0.0%) 21:29:36 [INFO] ...chunk 1 - processing molecules: 0/4 (0.0%) 21:29:36 [INFO] ...chunk 2 - processing molecules: 0/1 (0.0%) 21:29:36 [INFO] ...chunk 3 - processing molecules: 0/1 (0.0%) 21:29:36 [INFO] ref000002 - Combining chunked test output files... 21:29:36 [INFO] ref000002 - Finalizing cleanup... 21:29:36 [INFO] Sorting output by strand/position... Traceback (most recent call last): File "/home/smodlin/projects/SMALR/smalr_venv/bin/call_smalr.py", line 4, in import('pkg_resources').run_script('smalr==1.0.0', 'call_smalr.py') File "/home/smodlin/projects/SMALR/smalr_venv/local/lib/python2.7/site-packages/pkg_resources.py", line 534, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/smodlin/projects/SMALR/smalr_venv/local/lib/python2.7/site-packages/pkg_resources.py", line 1438, in run_script execfile(script_filename, namespace, namespace) File "/home/smodlin/projects/SMALR/smalr_venv/lib/python2.7/site-packages/smalr-1.0.0-py2.7.egg/EGG-INFO/scripts/call_smalr.py", line 5, in sys.exit(main()) File "/home/smodlin/projects/SMALR/smalr_venv/local/lib/python2.7/site-packages/smalr-1.0.0-py2.7.egg/smalr/smalr_multicontig.py", line 86, in main sys.exit( app.run() ) File "/home/smodlin/projects/SMALR/smalr_venv/local/lib/python2.7/site-packages/smalr-1.0.0-py2.7.egg/smalr/smalr_multicontig.py", line 81, in run runner.run() File "/home/smodlin/projects/SMALR/smalr_venv/local/lib/python2.7/site-packages/smalr-1.0.0-py2.7.egg/smalr/smalr.py", line 392, in run raise Exception("Failed sort command: %s" % sort_CMD) Exception: Failed sort command: sort -t$'\t' -nk2 SMp.out > sorting.tmp

jbeaulaurier commented 7 years ago

Hello Sam,

Sorry for the delay getting back to you. Can you tell me: is the SMp.out file being created? I'm guessing not, and this is breaking the sort command. Could you try running that same command in SMp test debug mode? You can do this by just replacing "-i" in the run_test_SMp.sh file with "-d". Please copy/paste the output from that command and I'll see if that exposes the root cause of the problem.

Thanks for using SMALR! -John

jbeaulaurier commented 6 years ago

Should be fixed by commit 34cce4b.