{"action":"opened","issue":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON_unzip/issues/56","repository_url":"https://api.github.com/repos/PacificBiosciences/FALCON_unzip","labels_url":"https://api.github.com/repos/PacificBiosciences/FALCON_unzip/issues/56/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/FALCON_unzip/issues/56/comments","events_url":"https://api.github.com/repos/PacificBiosciences/FALCON_unzip/issues/56/events","html_url":"https://github.com/PacificBiosciences/FALCON_unzip/issues/56","id":193213869,"number":56,"title":"python -m not finding function for get_read_ctg_map","user":{"login":"YourePrettyGood","id":13870588,"avatar_url":"https://avatars.githubusercontent.com/u/13870588?v=3","gravatar_id":"","url":"https://api.github.com/users/YourePrettyGood","html_url":"https://github.com/YourePrettyGood","followers_url":"https://api.github.com/users/YourePrettyGood/followers","following_url":"https://api.github.com/users/YourePrettyGood/following{/other_user}","gists_url":"https://api.github.com/users/YourePrettyGood/gists{/gist_id}","starred_url":"https://api.github.com/users/YourePrettyGood/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/YourePrettyGood/subscriptions","organizations_url":"https://api.github.com/users/YourePrettyGood/orgs","repos_url":"https://api.github.com/users/YourePrettyGood/repos","events_url":"https://api.github.com/users/YourePrettyGood/events{/privacy}","received_events_url":"https://api.github.com/users/YourePrettyGood/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-12-02T20:46:03Z","updated_at":"2016-12-02T20:46:03Z","closed_at":null,"body":"Hi,\r\nFirst off, thanks a ton for all your work on FALCON and FALCON_unzip!  I've been using FALCON for about a year now, and the results are great!\r\n\r\n--Note--\r\nThis may be related to FALCON issue #499: https://github.com/PacificBiosciences/FALCON/issues/499\r\n\r\nI've run into a series of issues trying to run FALCON_unzip on one of my assemblies (genome size estimate of between 380 and 430 Mb, but the p_ctg.fa comes out near 580-590 Mb, so I suspect haplotigs are being kept together in p_ctg.fa).\r\n\r\nThe first error involves a Python exception being thrown (an AttributeError) that the 'module' object does not have attribute 'get_read_ctg_map'.  This seems to trace back to the `python -m get_read_ctg_map` call in track_reads.sh generated by `task_track_reads()` in unzip.py.  I've also tried manually calling `python -m get_read-ctg_map` with and without deleting mypwatcher and other relevant directories and files, basically resetting the FALCON_unzip run to 0.\r\n\r\nWhat did succeed from there was running the DBshow commands manually, and running the (slightly-modified) contents of the `generate_read_to_ctg_map()` function.\r\n\r\nAfter that, I'm able to run `python -m rr_ctg_track` and `python -m pr_ctg_track`successfully, but then hit another error running `python -m fetch_reads` complaining about input.fofn not existing as a file.  I used a non-canonical input FOFN name, and included this in my fc_unzip.cfg, but it doesn't seem to be used in `task_track_reads()` in unzip.py (should be easy to tack into the config[] dictionary in `main()` in unzip.py, assign it to a variable in `task_track_reads()`, and then throw that after a `--fofn` in the script definition for track_reads.sh).\r\n\r\nAnd a third note (not an error, but a suggestion), maybe pypeFLOW already does this, but it'd be good to avoid repeating get_read_ctg_map, rr_ctg_track, pr_ctg_track, and fetch_reads if their output files already exist.  Since I manually ran the steps, as soon as I tried to re-run fc_unzip.py to get to alignment and phasing, FALCON_unzip tried to redo all the steps I had run manually, and failed again on get_read_ctg_map.\r\n\r\nVersion info:\r\nI tried first with FALCON_unzip c936cb9 on the p_ctg.fa generated by FALCON 0.4.0 (don't remember which commit), and then installed the newest via FALCON-integrate a few days ago and re-ran to see what might be happening.  Newest versions used:\r\nFALCON-integrate: 3b36fd91d36149ec000ab35fbd1e8b7646f8e95c\r\nFALCON: 87b6262607a885979727592c5aa0dad459085f33\r\nFALCON-make: 02ed9dedb0d5bc7bec75bfad8aa0a92629ad0099\r\nFALCON_unzip: c936cb94a63cc763f9733d2f497ccc00a68ba02c\r\npypeFLOW: bdd41dbc5ac4e4cf1dec1fa57e52850b399d85aa\r\n\r\nInstall was via PYTHONUSERBASE, I'm using SLURM, and I unset PYTHONPATH and source env.sh prior to running fc_unzip.py each time.  I've tried with Python 2.7.3 and 2.7.12 to see if that makes a difference (maybe they fiddled with the handling of the -m flag?).\r\n\r\nPotential source for the first error:\r\nComparing the scripts getting called with `python -m`, it looks like get_read_ctg_map.py is the only one that uses any makePypeLocalFile() calls and runs functions via a PypeTask.  Is this even necessary?  It seems that get_read_ctg_map.py isn't terribly computationally intensive compared to the others, so adding extra Pype tasks seems an unnecessary additional complexity.  Attached is an example (and apologies, but I forgot to remove the PypeProcWatcherWorkflow part).\r\n[get_read_ctg_map.py.txt](https://github.com/PacificBiosciences/FALCON_unzip/files/628179/get_read_ctg_map.py.txt)\r\n\r\nAgain, thanks for your time and all your great work!\r\n\r\nBest regards,\r\nPatrick Reilly"}}
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