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mdozmorov / genome_runner

Academic Free License v3.0
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dbcreator_encode: output url of the downloaded files #86

Closed mdozmorov closed 9 years ago

mdozmorov commented 9 years ago

When download error occur, output the URL of the file, into the genomerunner_dbcreator.log. It may be as simple as instead of INFO Downloading wgEncodeAwgSegmentationSegwayGm12878.bed.gz from UCSC output INFO Downloading wgEncodeAwgSegmentationSegwayGm12878.bed.gz from http://.....bed.gz

The error now looks like:

2015-07-22 12:57:45,442 INFO Downloading wgEncodeAwgSegmentationSegwayGm12878.bed.gz from UCSC

2015-07-22 14:18:11,994 INFO Converting into proper bed format: wgEncodeAwgSegmentationSegwayGm12878.bed.gz

2015-07-22 14:18:12,211 WARNING Unable to convert wgEncodeAwgSegmentationSegwayGm12878.bed.gz into bed

2015-07-22 14:18:12,212 WARNING Traceback (most recent call last):

File "/home/mdozmorov/genome_runner/grsnp/dbcreator_encode.py", line 601, in create_feature_set

gf_paths = gf_grp_sett[gf_group]["prep_method"](gf_outputdir,organism,gf_group,gf_file)

File "/home/mdozmorov/genome_runner/grsnp/dbcreator_encode.py", line 277, in preparebed_splitby

infile = gzip.open(dwnl_file)

File "/usr/lib/python2.7/gzip.py", line 34, in open

return GzipFile(filename, mode, compresslevel)

File "/usr/lib/python2.7/gzip.py", line 94, in init

fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')

IOError: [Errno 2] No such file or directory: '/home/mdozmorov/db_5.00_07-22-2015/downloads/hg19/wgEncodeAwgSegmentationSegwayGm12878.bed.gz'