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PacificBiosciences / FALCON

FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
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tan-runs cannot find build/raw_reads.db under tan-chunks #666

Closed jasmynp closed 6 years ago

jasmynp commented 6 years ago

My latest binary runs fails in tan-runs. Looking at the stderr under tan-00* subdir, it is looking for a build/raw_reads.db under tan-chunks that does not exist:

INFO]ln -sf ../../tan-chunks/build/raw_reads.db raw_reads.db
Traceback (most recent call last):
  File "/miniconda/miniconda2/envs/qaqc2/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/miniconda/miniconda2/envs/qaqc2/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/falcon/falcon-2018.08.08-21.41/fc_env_180824/lib/python2.7/site-packages/falcon_kit/mains/dazzler.py", line 1357, 
in <module>
    main()
  File "/falcon/falcon-2018.08.08-21.41/fc_env_180824/lib/python2.7/site-packages/falcon_kit/mains/dazzler.py", line 1353, 
in main
    args.func(args)
  File "/falcon/falcon-2018.08.08-21.41/fc_env_180824/lib/python2.7/site-packages/falcon_kit/mains/dazzler.py", line 923, i
n cmd_tan_apply
    tan_apply(args.db_fn, args.script_fn, args.job_done_fn)
  File "/falcon/falcon-2018.08.08-21.41/fc_env_180824/lib/python2.7/site-packages/falcon_kit/mains/dazzler.py", line 323, in tan_apply
    db = symlink_db(db_fn)
  File "/falcon/falcon-2018.08.08-21.41/fc_env_180824/lib/python2.7/site-packages/falcon_kit/mains/dazzler.py", line 232, in symlink_db
    all_basenames = os.listdir(db_dirname)
OSError: [Errno 2] No such file or directory: '../../tan-chunks/build'
WARNING:root:Call '/bin/bash user_script.sh' returned 256.

The build/raw_reads.db is located in the top-level 0-rawreads and the rawreads.db is symlinked under tan-split subdir. I'm guessing it needs to symlink the build dir under tan-chunks or link directly from 0-rawreads?

Thanks.

pb-cdunn commented 6 years ago

What version of pypeflow/falcon_kit? (You should see falcon_kit and pypeflow version strings in stderr.)

jasmynp commented 6 years ago

I hope this is correct: falcon-kit 1.2.2+git.00e8272b663d32a0962ae92ab92324a3b3eb4b46

I couldn't find the pypeflow version string in stderr. Where is it printed in? I'm using the develop version that you requested I try out. Same issue whether I use fs_based or blocking.

jasmynp commented 6 years ago

I see someone else's stderr that reports the pypeflow version below it. But mine doesn't. Not sure why.

pb-cdunn commented 6 years ago 
commit 00e8272b663d32a0962ae92ab92324a3b3eb4b46
Merge: b72db27 6b1ac0b
Author: Christopher Dunn <cdunn@pacificbiosciences.com>
Date:   Thu Aug 2 20:59:37 2018

I'm not sure if there was a bug there, but since there is already a new tarball, you might have better luck with that.