[WARNING] Couldn't find /home/sam/data/oly_BGI_scaffolds.qual... assuming there isn't a quality file for the reference
2017-11-14 09:35:54,253 [INFO] Running /home/shared/PBSuite_15.8.24//bin//Extraction.py /home/sam/analyses/20171114_oly_pbjelly/Protocol.xml
[WARNING] Couldn't find /home/sam/data/oly_BGI_scaffolds.qual... assuming there isn't a quality file for the reference
2017-11-14 09:36:34,326 [INFO] Opening GML Files
2017-11-14 09:36:34,326 [INFO] Loading Reference Sequence
2017-11-14 09:37:09,153 [INFO] Extracting Reads
2017-11-14 09:37:09,154 [INFO] Parsing /home/sam/data/m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq
2017-11-14 09:37:11,852 [INFO] Loaded 65873 Reads
2017-11-14 09:37:11,925 [INFO] Parsed 0 Reads
2017-11-14 09:37:11,925 [INFO] Parsing /home/sam/data/m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq
2017-11-14 09:37:27,888 [INFO] Loaded 220331 Reads
2017-11-14 09:37:28,139 [INFO] Parsed 0 Reads
2017-11-14 09:37:28,139 [INFO] Parsing /home/sam/data/m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq
2017-11-14 09:37:45,251 [INFO] Loaded 191252 Reads
2017-11-14 09:37:45,477 [INFO] Parsed 0 Reads
2017-11-14 09:37:45,477 [INFO] Parsing /home/sam/data/m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq
2017-11-14 09:38:01,498 [INFO] Loaded 173062 Reads
2017-11-14 09:38:01,693 [INFO] Parsed 0 Reads
2017-11-14 09:38:01,694 [INFO] Parsing /home/sam/data/m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq
2017-11-14 09:38:18,911 [INFO] Loaded 188238 Reads
2017-11-14 09:38:19,124 [INFO] Parsed 0 Reads
2017-11-14 09:38:19,124 [INFO] Parsing /home/sam/data/m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq
2017-11-14 09:38:35,460 [INFO] Loaded 215943 Reads
2017-11-14 09:38:35,707 [INFO] Parsed 0 Reads
2017-11-14 09:38:35,707 [INFO] Parsing /home/sam/data/m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq
2017-11-14 09:38:52,276 [INFO] Loaded 217233 Reads
2017-11-14 09:38:52,522 [INFO] Parsed 0 Reads
2017-11-14 09:38:52,523 [INFO] Parsing /home/sam/data/m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq
2017-11-14 09:39:09,972 [INFO] Loaded 159264 Reads
2017-11-14 09:39:10,152 [INFO] Parsed 0 Reads
2017-11-14 09:39:10,152 [INFO] Parsing /home/sam/data/m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq
2017-11-14 09:39:20,886 [INFO] Loaded 142522 Reads
2017-11-14 09:39:21,043 [INFO] Parsed 0 Reads
2017-11-14 09:39:21,043 [INFO] Parsing /home/sam/data/m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq
2017-11-14 09:39:31,108 [INFO] Loaded 130009 Reads
2017-11-14 09:39:31,253 [INFO] Parsed 0 Reads
2017-11-14 09:39:31,254 [INFO] Parsing /home/sam/data/m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq
2017-11-14 09:39:42,207 [INFO] Loaded 142063 Reads
2017-11-14 09:39:42,369 [INFO] Parsed 0 Reads
2017-11-14 09:41:06,605 [INFO] Finished