search

RahmanTeamDevelopment / CoverView

A coverage and base/mapping quality evaluation tool for panel and whole exome next-generation sequencing
MIT License
4 stars 0 forks source link

CoverView hangs when loading reads into in-memory buffer #13

Closed andyrimmer closed 7 years ago

andyrimmer commented 7 years ago

When run with the following config

{
    "outputs": { "region": true, "profiles": true },
    "reference": "/Users/munz/root/work/data/genomes/GRCh37/human_g1k_v37.fasta",
    "pass": { "MINQCOV_MIN": 15 },
    "duplicates": false,
    "direction": true
}

CoverView hangs and is unresponsive. The output is

2017-05-19 10:19:01,195 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 292 - CoverView v1.2.0 started running 2017-05-19 10:19:01,197 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 314 - Running CoverView v1.2.0 with options 2017-05-19 10:19:01,197 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 315 - Namespace(bedfile='/Users/munz/root/work/projects/CoverView/data/GIAB/TSCP_coverviewInput.bed', config='config_error3.json', input='/Users/munz/root/work/projects/CoverView/data/GIAB/15680_sorted_picard.bam', output='giab') 2017-05-19 10:19:01,197 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 316 - {'only_fail_profiles': False, 'low_bq': 10, 'direction': True, u'reference': u'/Users/munz/root/work/data/genomes/GRCh37/human_g1k_v37.fasta', 'transcript_db': None, 'low_mq': 20, 'duplicates': False, 'outputs': {'regions': True, 'gui': False, u'region': True, 'profiles': True}, 'pass': {u'MINQCOV_MIN': 15}, 'transcript': {'regions': True, 'profiles': True}} 2017-05-19 10:19:01,224 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 342 - There are 1471 target regions 2017-05-19 10:19:01,241 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 146 - Coverage metrics will be generated in a single process 2017-05-19 10:19:01,241 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 121 - Writing output headers 2017-05-19 10:19:01,251 - INFO - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 152 - Processing cluster of regions spanning 1:17345363-17380526 2017-05-19 10:19:01,252 - DEBUG - /Users/munz/root/work/projects/CoverView/test/test_18052017/CoverView/env/bin/CoverView.py - Line 152 - Loading reads into in-memory array