--- a/test-data/out_paired.log	Thu Aug 10 06:37:09 2017 -0400
+++ b/test-data/out_paired.log	Tue Aug 29 17:37:07 2017 -0400
@@ -1,116 +1,36 @@
-# output generated by extract --bc-pattern=NNNXXX --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --log=/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_863.dat
-# job started at Tue Aug  8 15:14:12 2017 on packer-test -- cba9bf6d-f8cd-49c4-8184-3f4a090cbc3e
-# pid: 32709, system: Linux 4.4.0-83-generic #106-Ubuntu SMP Mon Jun 26 17:54:43 UTC 2017 x86_64
+# output generated by extract --bc-pattern=NNNXXX --stdin=input_read1.gz --read2-in=input_read2.gz --stdout out1.gz --read2-out=out2.gz --log=/tmp/tmpREDhtd/files/003/dataset_3773.dat
+# job started at Tue Aug 29 14:20:44 2017 on gaius -- 5913ff4c-b1d1-4f65-abec-66ca6684bdbd
+# pid: 21437, system: Linux 4.10.0-33-generic #37-Ubuntu SMP Fri Aug 11 10:55:28 UTC 2017 x86_64
+# blacklist                               : None
+# compresslevel                           : 6
+# error_correct_cell                      : False
+# extract_method                          : string
+# filter_cell_barcode                     : None
+# filter_cell_barcodes                    : False
 # log2stderr                              : False
 # loglevel                                : 1
 # pattern                                 : NNNXXX
 # pattern2                                : None
-# prime3                                  : False
+# prime3                                  : None
 # quality_encoding                        : None
+# quality_filter_mask                     : None
 # quality_filter_threshold                : None
 # random_seed                             : None
 # read2_in                                : input_read2.gz
 # read2_out                               : out2.gz
+# read2_stdout                            : False
+# reads_subset                            : None
+# reconcile                               : False
 # short_help                              : None
-# split                                   : False
-# stats                                   : True
 # stderr                                  : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'>
 # stdin                                   : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'>
-# stdlog                                  : <_io.TextIOWrapper name='/home/ubuntu/mount/git/temp/galaxy/database/files/000/dataset_863.dat' mode='a' encoding='UTF-8'>
+# stdlog                                  : <_io.TextIOWrapper name='/tmp/tmpREDhtd/files/003/dataset_3773.dat' mode='a' encoding='UTF-8'>
 # stdout                                  : <_io.TextIOWrapper name='out1.gz' encoding='ascii'>
 # timeit_file                             : None
 # timeit_header                           : None
 # timeit_name                             : all
-Barcode	UMI	Sample	Count
-AAAAGT	AAA	AGT	1
-TTTTTT	TTT	TTT	1
-TTGGTT	TTG	GTT	1
-AAGTTT	AAG	TTT	1
-ATATAA	ATA	TAA	1
-GTTTTT	GTT	TTT	4
-GTTTTA	GTT	TTA	1
-TATAGA	TAT	AGA	1
-AAGTAT	AAG	TAT	1
-TTATTT	TTA	TTT	1
-AGATGA	AGA	TGA	1
-TTTTAG	TTT	TAG	2
-GTGTTT	GTG	TTT	1
-GTATGT	GTA	TGT	1
-AGTGTT	AGT	GTT	1
-AGAAAT	AGA	AAT	1
-TATAAA	TAT	AAA	1
-TGTATC	TGT	ATC	1
-TAAAAT	TAA	AAT	1
-ATTATT	ATT	ATT	1
-ATTTAG	ATT	TAG	1
-TATATT	TAT	ATT	1
-ATTTGG	ATT	TGG	1
-AAAATA	AAA	ATA	1
-AAGTTA	AAG	TTA	1
-GTTGTA	GTT	GTA	1
-TTTGAA	TTT	GAA	1
-ATTTGA	ATT	TGA	1
-TTTATA	TTT	ATA	2
-ATACGT	ATA	CGT	1
-GGTTAG	GGT	TAG	1
-GGTGTT	GGT	GTT	1
-TGGTTG	TGG	TTG	1
-AGTTAT	AGT	TAT	1
-GAGTAG	GAG	TAG	1
-TGTGTT	TGT	GTT	1
-TGAATT	TGA	ATT	1
-TTTAGG	TTT	AGG	2
-TAGATG	TAG	ATG	1
-TTGGAT	TTG	GAT	1
-TTGGAC	TTG	GAC	1
-TGTATG	TGT	ATG	1
-AGAGTG	AGA	GTG	1
-AGAATA	AGA	ATA	1
-TTGTTT	TTG	TTT	1
-AATATA	AAT	ATA	1
-TTATTA	TTA	TTA	1
-TTAAAG	TTA	AAG	2
-AGGAGT	AGG	AGT	1
-ATAAGT	ATA	AGT	1
-TTGTGG	TTG	TGG	1
-GTATTA	GTA	TTA	1
-AGTGGA	AGT	GGA	1
-TTTGGG	TTT	GGG	1
-TAAGAG	TAA	GAG	1
-TTGGGA	TTG	GGA	1
-TATAGG	TAT	AGG	1
-TTTTTG	TTT	TTG	1
-AAGAGG	AAG	AGG	1
-GAGAGA	GAG	AGA	1
-TTGGTG	TTG	GTG	1
-TAGAGG	TAG	AGG	1
-ATTTTG	ATT	TTG	1
-TGGATG	TGG	ATG	1
-ATTTTT	ATT	TTT	1
-TTATAT	TTA	TAT	1
-TGTTTG	TGT	TTG	1
-GTTGGT	GTT	GGT	1
-TCTTTA	TCT	TTA	1
-ATTGTT	ATT	GTT	2
-ATAAGA	ATA	AGA	1
-TATCGA	TAT	CGA	1
-TTTGTT	TTT	GTT	1
-GTGTAT	GTG	TAT	1
-AGTGAA	AGT	GAA	1
-GTTGTG	GTT	GTG	1
-TAGTGA	TAG	TGA	1
-TATTGA	TAT	TGA	1
-TTAATG	TTA	ATG	1
-TTTAAA	TTT	AAA	2
-AGAAAG	AGA	AAG	1
-TTTTGT	TTT	TGT	1
-TTATAG	TTA	TAG	1
-AGGTGT	AGG	TGT	1
-TTAGTT	TTA	GTT	1
-TTTAAT	TTT	AAT	1
-AGGATG	AGG	ATG	1
-ATATAT	ATA	TAT	1
-AGAGTT	AGA	GTT	1
-GAGAAA	GAG	AAA	1
-ATATGA	ATA	TGA	1
-# job finished in 0 seconds at Tue Aug  8 15:14:12 2017 --  0.41  0.02  0.00  0.00 -- cba9bf6d-f8cd-49c4-8184-3f4a090cbc3e
+# whitelist                               : None
+2017-08-29 14:20:44,451 INFO Starting barcode extraction
+2017-08-29 14:20:44,461 INFO Input Reads: 100
+2017-08-29 14:20:44,461 INFO Reads output: 100
+# job finished in 0 seconds at Tue Aug 29 14:20:44 2017 --  0.73  0.05  0.00  0.00 -- 5913ff4c-b1d1-4f65-abec-66ca6684bdbd