Oct 6 17:29:44 Will run velvet optimiser with the following paramters: Velveth parameter string: -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth start hash values: 19 Velveth end hash value: 31 Velveth hash step value: 2 Velvetg minimum coverage cutoff to use: 0 Read tracking for final assembly off. Oct 6 17:29:44 Beginning velveth runs. ******************************************************** Assembly id: 6 Velveth timestamp: Oct 6 2015 17:37:21 Velveth version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_29 29 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_29 Velvet hash value: 29 Roadmap file size: 556690619 ********************************************************** ******************************************************** Assembly id: 2 Velveth timestamp: Oct 6 2015 17:37:35 Velveth version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_21 21 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_21 Velvet hash value: 21 Roadmap file size: 581877722 ********************************************************** ******************************************************** Assembly id: 7 Velveth timestamp: Oct 6 2015 17:37:36 Velveth version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 ********************************************************** ******************************************************** Assembly id: 5 Velveth timestamp: Oct 6 2015 17:37:40 Velveth version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_27 27 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_27 Velvet hash value: 27 Roadmap file size: 561604992 ********************************************************** ******************************************************** Assembly id: 3 Velveth timestamp: Oct 6 2015 17:38:27 Velveth version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_23 23 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_23 Velvet hash value: 23 Roadmap file size: 573193117 ********************************************************** ******************************************************** Assembly id: 1 Velveth timestamp: Oct 6 2015 17:38:38 Velveth version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_19 19 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_19 Velvet hash value: 19 Roadmap file size: 590370224 ********************************************************** ******************************************************** Assembly id: 4 Velveth timestamp: Oct 6 2015 17:38:53 Velveth version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_25 25 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_25 Velvet hash value: 25 Roadmap file size: 566673453 ********************************************************** Oct 6 17:38:53 Beginning vanilla velvetg runs. ******************************************************** Assembly id: 7 Assembly score: 95 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:04:49 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 45877 n50: 95 length of longest contig: 950 Total bases in contigs: 4528235 Number of contigs > 1k: 0 Total bases in contigs > 1k: 0 ********************************************************** ******************************************************** Assembly id: 4 Assembly score: 79 Velveth timestamp: Oct 6 2015 17:38:53 Velvetg timestamp: Oct 6 2015 18:05:47 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_25 25 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_25 -clean yes Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_25 Velvet hash value: 25 Roadmap file size: 566673453 Total number of contigs: 77125 n50: 79 length of longest contig: 926 Total bases in contigs: 5801295 Number of contigs > 1k: 0 Total bases in contigs > 1k: 0 ********************************************************** ******************************************************** Assembly id: 5 Assembly score: 83 Velveth timestamp: Oct 6 2015 17:37:40 Velvetg timestamp: Oct 6 2015 18:06:35 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_27 27 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_27 -clean yes Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_27 Velvet hash value: 27 Roadmap file size: 561604992 Total number of contigs: 70662 n50: 83 length of longest contig: 799 Total bases in contigs: 5703655 Number of contigs > 1k: 0 Total bases in contigs > 1k: 0 ********************************************************** ******************************************************** Assembly id: 1 Assembly score: 57 Velveth timestamp: Oct 6 2015 17:38:38 Velvetg timestamp: Oct 6 2015 18:07:52 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_19 19 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_19 -clean yes Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_19 Velvet hash value: 19 Roadmap file size: 590370224 Total number of contigs: 99414 n50: 57 length of longest contig: 620 Total bases in contigs: 5594700 Number of contigs > 1k: 0 Total bases in contigs > 1k: 0 ********************************************************** ******************************************************** Assembly id: 2 Assembly score: 66 Velveth timestamp: Oct 6 2015 17:37:35 Velvetg timestamp: Oct 6 2015 18:08:36 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_21 21 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_21 -clean yes Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_21 Velvet hash value: 21 Roadmap file size: 581877722 Total number of contigs: 81536 n50: 66 length of longest contig: 846 Total bases in contigs: 5287564 Number of contigs > 1k: 0 Total bases in contigs > 1k: 0 ********************************************************** ******************************************************** Assembly id: 3 Assembly score: 72 Velveth timestamp: Oct 6 2015 17:38:27 Velvetg timestamp: Oct 6 2015 18:08:54 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_23 23 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_23 -clean yes Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_23 Velvet hash value: 23 Roadmap file size: 573193117 Total number of contigs: 82817 n50: 72 length of longest contig: 742 Total bases in contigs: 5741621 Number of contigs > 1k: 0 Total bases in contigs > 1k: 0 ********************************************************** ******************************************************** Assembly id: 6 Assembly score: 87 Velveth timestamp: Oct 6 2015 17:37:21 Velvetg timestamp: Oct 6 2015 18:10:06 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_29 29 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_29 -clean yes Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_29 Velvet hash value: 29 Roadmap file size: 556690619 Total number of contigs: 62179 n50: 87 length of longest contig: 920 Total bases in contigs: 5351300 Number of contigs > 1k: 0 Total bases in contigs > 1k: 0 ********************************************************** Oct 6 18:10:14 Best assembly by assembly score - assembly id: 7 Oct 6 18:10:14 Optimisation routine chosen for best assembly: shortPaired Oct 6 18:10:14 Looking for the expected coverage Oct 6 18:10:16 Expected coverage set to 252 ******************************************************** Assembly id: 7 Assembly score: 95 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:04:49 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 45877 n50: 95 length of longest contig: 950 Total bases in contigs: 4528235 Number of contigs > 1k: 0 Total bases in contigs > 1k: 0 Paired Library insert stats: ********************************************************** Oct 6 18:10:16 Setting the short insert length Oct 6 18:10:16 Setting assembly short insert length(s) to auto Oct 6 18:10:16 Beginning coverage cutoff optimisation Oct 6 18:10:18 Setting cov_cutoff to 124.589. ******************************************************** Assembly id: 7 Assembly score: 2193963 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:29:35 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 -cov_cutoff 124.5888 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 365 n50: 35560 length of longest contig: 142007 Total bases in contigs: 2227830 Number of contigs > 1k: 106 Total bases in contigs > 1k: 2193963 Paired Library insert stats: Paired-end library 1 has length: 254, sample standard deviation: 76 Paired-end library 1 has length: 254, sample standard deviation: 76 ********************************************************** Oct 6 18:29:35 Setting cov_cutoff to 77.011. ******************************************************** Assembly id: 7 Assembly score: 2193223 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:30:55 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 -cov_cutoff 77.0112 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 371 n50: 35560 length of longest contig: 141995 Total bases in contigs: 2228227 Number of contigs > 1k: 106 Total bases in contigs > 1k: 2193223 Paired Library insert stats: Paired-end library 1 has length: 254, sample standard deviation: 76 Paired-end library 1 has length: 254, sample standard deviation: 76 ********************************************************** Looking for best cutoff score between 0.000 and 201.600 Max cutoff lies between 77.011 & 201.600 Oct 6 18:30:55 Setting cov_cutoff to 154.007. ******************************************************** Assembly id: 7 Assembly score: 2193021 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:32:14 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 -cov_cutoff 154.0070784 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 369 n50: 35560 length of longest contig: 141997 Total bases in contigs: 2227267 Number of contigs > 1k: 107 Total bases in contigs > 1k: 2193021 Paired Library insert stats: Paired-end library 1 has length: 253, sample standard deviation: 76 Paired-end library 1 has length: 254, sample standard deviation: 76 ********************************************************** Max cutoff lies between 77.011 & 154.007 Oct 6 18:32:14 Setting cov_cutoff to 106.424. ******************************************************** Assembly id: 7 Assembly score: 2193828 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:33:34 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 -cov_cutoff 106.4236255488 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 366 n50: 35560 length of longest contig: 141995 Total bases in contigs: 2227757 Number of contigs > 1k: 106 Total bases in contigs > 1k: 2193828 Paired Library insert stats: Paired-end library 1 has length: 254, sample standard deviation: 76 Paired-end library 1 has length: 254, sample standard deviation: 76 ********************************************************** Max cutoff lies between 106.424 & 154.007 Oct 6 18:33:34 Setting cov_cutoff to 135.830. ******************************************************** Assembly id: 7 Assembly score: 2193642 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:34:54 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 -cov_cutoff 135.830199410842 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 370 n50: 35560 length of longest contig: 142008 Total bases in contigs: 2228170 Number of contigs > 1k: 106 Total bases in contigs > 1k: 2193642 Paired Library insert stats: Paired-end library 1 has length: 254, sample standard deviation: 76 Paired-end library 1 has length: 254, sample standard deviation: 76 ********************************************************** Max cutoff lies between 106.424 & 135.830 Oct 6 18:34:54 Setting cov_cutoff to 117.657. ******************************************************** Assembly id: 7 Assembly score: 2194014 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:36:15 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 -cov_cutoff 117.6569367641 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 365 n50: 35560 length of longest contig: 141995 Total bases in contigs: 2227881 Number of contigs > 1k: 106 Total bases in contigs > 1k: 2194014 Paired Library insert stats: Paired-end library 1 has length: 254, sample standard deviation: 76 Paired-end library 1 has length: 254, sample standard deviation: 76 ********************************************************** Max cutoff lies between 106.424 & 124.589 Oct 6 18:36:15 Setting cov_cutoff to 113.363. ******************************************************** Assembly id: 7 Assembly score: 2194044 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:37:35 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 -cov_cutoff 113.362722189158 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 365 n50: 35560 length of longest contig: 141995 Total bases in contigs: 2227911 Number of contigs > 1k: 106 Total bases in contigs > 1k: 2194044 Paired Library insert stats: Paired-end library 1 has length: 254, sample standard deviation: 76 Paired-end library 1 has length: 254, sample standard deviation: 76 ********************************************************** Max cutoff lies between 106.424 & 117.657 Oct 6 18:37:35 Setting cov_cutoff to 110.715. ******************************************************** Assembly id: 7 Assembly score: 2194046 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:38:56 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 -cov_cutoff 110.714750433045 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 365 n50: 35560 length of longest contig: 141995 Total bases in contigs: 2227913 Number of contigs > 1k: 106 Total bases in contigs > 1k: 2194046 Paired Library insert stats: Paired-end library 1 has length: 254, sample standard deviation: 76 Paired-end library 1 has length: 254, sample standard deviation: 76 ********************************************************** Max cutoff lies between 106.424 & 113.363 Oct 6 18:38:56 Setting cov_cutoff to 109.074. ******************************************************** Assembly id: 7 Assembly score: 2194046 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:40:15 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 -cov_cutoff 109.074360465417 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 365 n50: 35560 length of longest contig: 141995 Total bases in contigs: 2227913 Number of contigs > 1k: 106 Total bases in contigs > 1k: 2194046 Paired Library insert stats: Paired-end library 1 has length: 254, sample standard deviation: 76 Paired-end library 1 has length: 254, sample standard deviation: 76 ********************************************************** Max cutoff lies between 106.424 & 110.715 Oct 6 18:40:15 Setting cov_cutoff to 108.063. ******************************************************** Assembly id: 7 Assembly score: 2194048 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:41:34 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 -cov_cutoff 108.062835254581 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 365 n50: 35560 length of longest contig: 141995 Total bases in contigs: 2227915 Number of contigs > 1k: 106 Total bases in contigs > 1k: 2194048 Paired Library insert stats: Paired-end library 1 has length: 254, sample standard deviation: 76 Paired-end library 1 has length: 254, sample standard deviation: 76 ********************************************************** Max cutoff lies between 106.424 & 109.074 Oct 6 18:41:34 Setting cov_cutoff to 107.436. ******************************************************** Assembly id: 7 Assembly score: 2194048 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:42:53 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 -cov_cutoff 107.436206286948 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 365 n50: 35560 length of longest contig: 141995 Total bases in contigs: 2227915 Number of contigs > 1k: 106 Total bases in contigs > 1k: 2194048 Paired Library insert stats: Paired-end library 1 has length: 254, sample standard deviation: 76 Paired-end library 1 has length: 254, sample standard deviation: 76 ********************************************************** Max cutoff lies between 106.424 & 108.063 Oct 6 18:42:54 Setting cov_cutoff to 107.050. ******************************************************** Assembly id: 7 Assembly score: 2194048 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:44:13 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 -cov_cutoff 107.049803656409 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 365 n50: 35560 length of longest contig: 141995 Total bases in contigs: 2227915 Number of contigs > 1k: 106 Total bases in contigs > 1k: 2194048 Paired Library insert stats: Paired-end library 1 has length: 254, sample standard deviation: 76 Paired-end library 1 has length: 254, sample standard deviation: 76 ********************************************************** Max cutoff lies between 106.424 & 107.436 Oct 6 18:44:13 Setting cov_cutoff to 106.810. ******************************************************** Assembly id: 7 Assembly score: 2193828 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:45:32 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 -cov_cutoff 106.810431390772 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 366 n50: 35560 length of longest contig: 141995 Total bases in contigs: 2227757 Number of contigs > 1k: 106 Total bases in contigs > 1k: 2193828 Paired Library insert stats: Paired-end library 1 has length: 254, sample standard deviation: 76 Paired-end library 1 has length: 254, sample standard deviation: 76 ********************************************************** Max cutoff lies between 106.810 & 107.436 Oct 6 18:45:32 Setting cov_cutoff to 107.197. ******************************************************** Assembly id: 7 Assembly score: 2194048 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:46:51 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 -cov_cutoff 107.197160276609 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 365 n50: 35560 length of longest contig: 141995 Total bases in contigs: 2227915 Number of contigs > 1k: 106 Total bases in contigs > 1k: 2194048 Paired Library insert stats: Paired-end library 1 has length: 254, sample standard deviation: 76 Paired-end library 1 has length: 254, sample standard deviation: 76 ********************************************************** Optimum value of cutoff is 107.44 Took 13 iterations Oct 6 18:46:51 Final optimised assembly details: ******************************************************** Assembly id: 7 Assembly score: 2194048 Velveth timestamp: Oct 6 2015 17:37:36 Velvetg timestamp: Oct 6 2015 18:46:51 Velveth version: 1.2.09 Velvetg version: 1.2.09 Readfile(s): -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velveth parameter string: auto_data_31 31 -shortPaired -fastq -separate SRR413299_1.fastq SRR413299_2.fastq Velvetg parameter string: auto_data_31 -clean yes -exp_cov 252 -cov_cutoff 107.197160276609 Assembly directory: /mnt/bioinfohd1/tsute/collaboration/Margaret_Duncan/2013_W50_Seq/velvetoptimizer/auto_data_31 Velvet hash value: 31 Roadmap file size: 551169575 Total number of contigs: 365 n50: 35560 length of longest contig: 141995 Total bases in contigs: 2227915 Number of contigs > 1k: 106 Total bases in contigs > 1k: 2194048 Paired Library insert stats: Paired-end library 1 has length: 254, sample standard deviation: 76 Paired-end library 1 has length: 254, sample standard deviation: 76 **********************************************************