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fc_ovlp_stats adding DB argument #614

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mictadlo opened this issue Mar 8, 2018 · 0 comments
Open

fc_ovlp_stats adding DB argument #614

mictadlo opened this issue Mar 8, 2018 · 0 comments

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@mictadlo
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mictadlo commented Mar 8, 2018

Hi,
Could you please add an argument for DB rather use a hardcoded path?

fc_ovlp_stats --stream --n_core 4 --fofn preads_lasfiles.fofn --min_len 6973 > ovlp.stats

[12684]u'LA4Falcon -mo ../1-preads_ovl/preads.db assemblyDB.129.las'
    raise value
Exception: Traceback (most recent call last):
  File "/lustre/work-lustre/waterhouse_team/apps/FALCON-integrate/FALCON/falcon_kit/util/io.py", line 60, in run_func
    ret = func(*args)
  File "/lustre/work-lustre/waterhouse_team/apps/FALCON-integrate/FALCON/falcon_kit/mains/ovlp_stats.py", line 70, in run_filter_stats
    return fn, filter_stats(reader.readlines, min_len)
  File "/lustre/work-lustre/waterhouse_team/apps/FALCON-integrate/FALCON/falcon_kit/util/io.py", line 148, in __exit__
    raise Exception(msg)
Exception: 1 <- u'LA4Falcon -mo ../1-preads_ovl/preads.db assemblyDB.6.las'

LA4Falcon: Could not open database ../1-preads_ovl/preads.db
LA4Falcon: Could not open database ../1-preads_ovl/preads.db
LA4Falcon: Could not open database ../1-preads_ovl/preads.db
LA4Falcon: Could not open database ../1-preads_ovl/preads.db

Thank you in advance.

Michal

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