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Rayan CHIKHI
serratus-batch-dl
Commits
262e1ba3
Commit
262e1ba3
authored
Jun 20, 2020
by
Rayan CHIKHI
Browse files
apparently docker doesnt like my args
parent
bbd3cdb7
Changes
1
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Inline
Side-by-side
src/batch_processor.py
View file @
262e1ba3
...
...
@@ -79,12 +79,12 @@ def process_file(accession, region):
prefetch_start
=
datetime
.
now
()
# 'is larger than maximum allowed: skipped' solved by:
# https://wiki.rc.hms.harvard.edu/display/O2/Aspera+to+download+NCBI+SRA+data
os
.
system
(
'prefetch -
-max-size
35G '
+
accession
)
os
.
system
(
'prefetch -
X
35G '
+
accession
)
prefetch_time
=
datetime
.
now
()
-
prefetch_start
sdb_log
(
sdb
,
accession
,
'prefetch_time'
,
int
(
prefetch_time
.
seconds
))
os
.
system
(
'mkdir -p tmp/'
)
pfqdump_start
=
datetime
.
now
()
os
.
system
(
'/parallel-fastq-dump --skip-technical --split-
3
--outdir out/ --tmpdir tmp/ --threads 4 --sra-id '
+
accession
)
os
.
system
(
'/parallel-fastq-dump --skip-technical --split-
e
--outdir out/ --tmpdir tmp/ --threads 4 --sra-id '
+
accession
)
pfqdump_time
=
datetime
.
now
()
-
pfqdump_start
sdb_log
(
sdb
,
accession
,
'pfqdump_time'
,
int
(
pfqdump_time
.
seconds
))
...
...
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