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canu_run.log
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canu_run.log
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KEVINs-MacBook-Pro-2:genome_assemblies ksb$ mkdir runs
KEVINs-MacBook-Pro-2:genome_assemblies ksb$ cd runs/
KEVINs-MacBook-Pro-2:runs ksb$ canu -p jb418 -d jb418-auto genomeSize=4.7m -pacbio-raw ../raw_reads/pb.fastq.gz
contigFilter 2 1000 0.75 0.75 2 num 5
-- Canu snapshot v1.5 +60 changes (r8260 4523567eb791caa2dcc781f172dae5c1c935a783)
--
-- CITATIONS
--
-- Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM.
-- Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
-- Genome Res. 2017 May;27(5):722-736.
-- http://doi.org/10.1101/gr.215087.116
--
-- Read and contig alignments during correction, consensus and GFA building use:
-- Šošic M, Šikic M.
-- Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.
-- Bioinformatics. 2017 May 1;33(9):1394-1395.
-- http://doi.org/10.1093/bioinformatics/btw753
--
-- Overlaps are generated using:
-- Berlin K, et al.
-- Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.
-- Nat Biotechnol. 2015 Jun;33(6):623-30.
-- http://doi.org/10.1038/nbt.3238
--
-- Myers EW, et al.
-- A Whole-Genome Assembly of Drosophila.
-- Science. 2000 Mar 24;287(5461):2196-204.
-- http://doi.org/10.1126/science.287.5461.2196
--
-- Li H.
-- Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.
-- Bioinformatics. 2016 Jul 15;32(14):2103-10.
-- http://doi.org/10.1093/bioinformatics/btw152
--
-- Corrected read consensus sequences are generated using an algorithm derived from FALCON-sense:
-- Chin CS, et al.
-- Phased diploid genome assembly with single-molecule real-time sequencing.
-- Nat Methods. 2016 Dec;13(12):1050-1054.
-- http://doi.org/10.1038/nmeth.4035
--
-- Contig consensus sequences are generated using an algorithm derived from pbdagcon:
-- Chin CS, et al.
-- Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
-- Nat Methods. 2013 Jun;10(6):563-9
-- http://doi.org/10.1038/nmeth.2474
--
-- CONFIGURE CANU
--
-- Detected Java(TM) Runtime Environment '1.8.0_131' (from 'java').
-- Detected gnuplot version '5.0 patchlevel 6' (from 'gnuplot') and image format 'png'.
-- Detected 8 CPUs and 16 gigabytes of memory.
-- No grid engine detected, grid disabled.
--
-- (tag)Concurrency
-- (tag)Threads |
-- (tag)Memory | |
-- (tag) | | | algorithm
-- ------- ------ -------- -------- -----------------------------
-- Local: meryl 8 GB 4 CPUs x 2 jobs (k-mer counting)
-- Local: cormhap 6 GB 8 CPUs x 1 job (overlap detection with mhap)
-- Local: obtovl 8 GB 8 CPUs x 1 job (overlap detection)
-- Local: utgovl 8 GB 8 CPUs x 1 job (overlap detection)
-- Local: cor 8 GB 2 CPUs x 4 jobs (read correction)
-- Local: ovb 2 GB 1 CPU x 8 jobs (overlap store bucketizer)
-- Local: ovs 8 GB 1 CPU x 8 jobs (overlap store sorting)
-- Local: red 2 GB 4 CPUs x 2 jobs (read error detection)
-- Local: oea 1 GB 1 CPU x 8 jobs (overlap error adjustment)
-- Local: bat 8 GB 4 CPUs x 2 jobs (contig construction)
-- Local: cns 8 GB 4 CPUs x 2 jobs (consensus)
-- Local: gfa 8 GB 4 CPUs x 2 jobs (GFA alignment and processing)
--
-- Generating assembly 'jb418' in '/Users/ksb/computation/science/genome_assemblies/runs/jb418-auto'
--
-- Parameters:
--
-- genomeSize 4700000
--
-- Overlap Generation Limits:
-- corOvlErrorRate 0.2400 ( 24.00%)
-- obtOvlErrorRate 0.0450 ( 4.50%)
-- utgOvlErrorRate 0.0450 ( 4.50%)
--
-- Overlap Processing Limits:
-- corErrorRate 0.3000 ( 30.00%)
-- obtErrorRate 0.0450 ( 4.50%)
-- utgErrorRate 0.0450 ( 4.50%)
-- cnsErrorRate 0.0750 ( 7.50%)
--
--
-- BEGIN CORRECTION
--
----------------------------------------
-- Starting command on Thu Jun 8 11:25:05 2017 with 25.91 GB free disk space
cd correction
/Users/ksb/computation/science/canu/Darwin-amd64/bin/gatekeeperCreate \
-minlength 1000 \
-o ./jb418.gkpStore.BUILDING \
./jb418.gkpStore.gkp \
> ./jb418.gkpStore.BUILDING.err 2>&1
-- Finished on Thu Jun 8 11:25:12 2017 (7 seconds) with 25.746 GB free disk space
----------------------------------------
--
-- In gatekeeper store 'correction/jb418.gkpStore':
-- Found 68971 reads.
-- Found 641540394 bases (136.49 times coverage).
--
-- Read length histogram (one '*' equals 73.14 reads):
-- 0 999 0
-- 1000 1999 5120 **********************************************************************
-- 2000 2999 5006 ********************************************************************
-- 3000 3999 4542 **************************************************************
-- 4000 4999 4473 *************************************************************
-- 5000 5999 4643 ***************************************************************
-- 6000 6999 4419 ************************************************************
-- 7000 7999 4351 ***********************************************************
-- 8000 8999 4136 ********************************************************
-- 9000 9999 4039 *******************************************************
-- 10000 10999 3781 ***************************************************
-- 11000 11999 3588 *************************************************
-- 12000 12999 3376 **********************************************
-- 13000 13999 3100 ******************************************
-- 14000 14999 2898 ***************************************
-- 15000 15999 2403 ********************************
-- 16000 16999 2012 ***************************
-- 17000 17999 1491 ********************
-- 18000 18999 1195 ****************
-- 19000 19999 965 *************
-- 20000 20999 789 **********
-- 21000 21999 628 ********
-- 22000 22999 501 ******
-- 23000 23999 368 *****
-- 24000 24999 301 ****
-- 25000 25999 233 ***
-- 26000 26999 164 **
-- 27000 27999 125 *
-- 28000 28999 95 *
-- 29000 29999 60
-- 30000 30999 49
-- 31000 31999 31
-- 32000 32999 24
-- 33000 33999 29
-- 34000 34999 11
-- 35000 35999 10
-- 36000 36999 4
-- 37000 37999 4
-- 38000 38999 4
-- 39000 39999 1
-- 40000 40999 0
-- 41000 41999 1
-- 42000 42999 1
-- Finished stage 'cor-gatekeeper', reset canuIteration.
-- Finished stage 'merylConfigure', reset canuIteration.
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Thu Jun 8 11:25:13 2017 with 25.744 GB free disk space (1 processes; 2 concurrently)
cd correction/0-mercounts
./meryl.sh 1 > ./meryl.000001.out 2>&1
-- Finished on Thu Jun 8 11:29:28 2017 (255 seconds) with 24.055 GB free disk space
----------------------------------------
-- Meryl finished successfully.
-- Finished stage 'merylCheck', reset canuIteration.
--
-- 16-mers Fraction
-- Occurrences NumMers Unique Total
-- 1- 1 325626582 *******************************************************************--> 0.7636 0.5084
-- 2- 2 65712451 ********************************************************************** 0.9176 0.7136
-- 3- 4 24584106 ************************** 0.9600 0.7982
-- 5- 7 5403190 ***** 0.9821 0.8614
-- 8- 11 2306304 ** 0.9897 0.8956
-- 12- 16 1643585 * 0.9943 0.9278
-- 17- 22 837495 0.9977 0.9609
-- 23- 29 246923 0.9993 0.9824
-- 30- 37 52113 0.9998 0.9904
-- 38- 46 15797 0.9999 0.9926
-- 47- 56 7636 0.9999 0.9935
-- 57- 67 4850 0.9999 0.9941
-- 68- 79 4451 0.9999 0.9946
-- 80- 92 4462 1.0000 0.9951
-- 93- 106 3225 1.0000 0.9957
-- 107- 121 1842 1.0000 0.9962
-- 122- 137 941 1.0000 0.9965
-- 138- 154 721 1.0000 0.9966
-- 155- 172 666 1.0000 0.9968
-- 173- 191 764 1.0000 0.9970
-- 192- 211 1014 1.0000 0.9972
-- 212- 232 1165 1.0000 0.9975
-- 233- 254 1027 1.0000 0.9979
-- 255- 277 791 1.0000 0.9983
-- 278- 301 535 1.0000 0.9986
-- 302- 326 320 1.0000 0.9989
-- 327- 352 166 1.0000 0.9990
-- 353- 379 73 1.0000 0.9991
-- 380- 407 63 1.0000 0.9992
-- 408- 436 39 1.0000 0.9992
-- 437- 466 13 1.0000 0.9992
-- 467- 497 13 1.0000 0.9992
-- 498- 529 15 1.0000 0.9992
-- 530- 562 11 1.0000 0.9993
-- 563- 596 16 1.0000 0.9993
-- 597- 631 5 1.0000 0.9993
-- 632- 667 12 1.0000 0.9993
-- 668- 704 17 1.0000 0.9993
-- 705- 742 9 1.0000 0.9993
-- 743- 781 7 1.0000 0.9993
-- 782- 821 5 1.0000 0.9993
--
-- 112503 (max occurrences)
-- 314879247 (total mers, non-unique)
-- 100836977 (distinct mers, non-unique)
-- 325626582 (unique mers)
-- For mhap overlapping, set repeat k-mer threshold to 6405.
--
-- Found 640505829 16-mers; 426463559 distinct and 325626582 unique. Largest count 112503.
-- Finished stage 'cor-meryl', reset canuIteration.
--
-- OVERLAPPER (mhap) (correction)
--
-- Set corMhapSensitivity=low based on read coverage of 136.
--
-- PARAMETERS: hashes=256, minMatches=3, threshold=0.8
--
-- Given 6 GB, can fit 18000 reads per block.
-- For 5 blocks, set stride to 2 blocks.
-- Logging partitioning to 'correction/1-overlapper/partitioning.log'.
-- Configured 4 mhap precompute jobs.
-- Configured 5 mhap overlap jobs.
-- Finished stage 'cor-mhapConfigure', reset canuIteration.
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Thu Jun 8 11:29:40 2017 with 25.73 GB free disk space (4 processes; 1 concurrently)
cd correction/1-overlapper
./precompute.sh 1 > ./precompute.000001.out 2>&1
./precompute.sh 2 > ./precompute.000002.out 2>&1
./precompute.sh 3 > ./precompute.000003.out 2>&1
./precompute.sh 4 > ./precompute.000004.out 2>&1
-- Finished on Thu Jun 8 11:56:05 2017 (1585 seconds) with 23.407 GB free disk space
----------------------------------------
-- All 4 mhap precompute jobs finished successfully.
-- Finished stage 'cor-mhapPrecomputeCheck', reset canuIteration.
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'cormhap' concurrent execution on Thu Jun 8 11:56:05 2017 with 23.407 GB free disk space (5 processes; 1 concurrently)
cd correction/1-overlapper
./mhap.sh 1 > ./mhap.000001.out 2>&1
./mhap.sh 2 > ./mhap.000002.out 2>&1
./mhap.sh 3 > ./mhap.000003.out 2>&1
./mhap.sh 4 > ./mhap.000004.out 2>&1
./mhap.sh 5 > ./mhap.000005.out 2>&1
-- Finished on Thu Jun 8 11:57:55 2017 (110 seconds) with 23.522 GB free disk space
----------------------------------------
-- Found 5 mhap overlap output files.
-- Finished stage 'cor-mhapCheck', reset canuIteration.
----------------------------------------
-- Starting command on Thu Jun 8 11:57:55 2017 with 23.522 GB free disk space
cd correction
/Users/ksb/computation/science/canu/Darwin-amd64/bin/ovStoreBuild \
-O ./jb418.ovlStore.BUILDING \
-G ./jb418.gkpStore \
-M 2-8 \
-L ./1-overlapper/ovljob.files \
> ./jb418.ovlStore.err 2>&1
-- Finished on Thu Jun 8 11:57:56 2017 (1 second) with 23.489 GB free disk space
----------------------------------------
--
-- Overlap store 'correction/jb418.ovlStore' successfully constructed.
--
-- Purged 1.179 GB in 14 overlap output files and 2 directories.
-- Overlap store 'correction/jb418.ovlStore' statistics not available (skipped in correction and trimming stages).
-- Finished stage 'cor-createOverlapStore', reset canuIteration.
-- Set corMinCoverage=4 based on read coverage of 136.
-- Computing global filter scores 'correction/2-correction/jb418.globalScores'.
----------------------------------------
-- Starting command on Thu Jun 8 11:57:57 2017 with 24.668 GB free disk space
cd correction/2-correction
/Users/ksb/computation/science/canu/Darwin-amd64/bin/filterCorrectionOverlaps \
-G ../jb418.gkpStore \
-O ../jb418.ovlStore \
-S ./jb418.globalScores.WORKING \
-c 40 \
-l 0 \
> ./jb418.globalScores.err 2>&1
-- Finished on Thu Jun 8 11:57:57 2017 (lickety-split) with 24.663 GB free disk space
----------------------------------------
-- PARAMETERS:
-- ----------
--
-- 40 (expected coverage)
-- 0 (don't use overlaps shorter than this)
-- 0.000 (don't use overlaps with erate less than this)
-- 1.000 (don't use overlaps with erate more than this)
--
-- OVERLAPS:
-- --------
--
-- IGNORED:
--
-- 0 (< 0.0000 fraction error)
-- 0 (> 0.4095 fraction error)
-- 0 (< 0 bases long)
-- 0 (> 2097151 bases long)
--
-- FILTERED:
--
-- 762145 (too many overlaps, discard these shortest ones)
--
-- EVIDENCE:
--
-- 848011 (longest overlaps)
--
-- TOTAL:
--
-- 1610156 (all overlaps)
--
-- READS:
-- -----
--
-- 18926 (no overlaps)
-- 41191 (no overlaps filtered)
-- 6125 (< 50% overlaps filtered)
-- 7785 (< 80% overlaps filtered)
-- 8664 (< 95% overlaps filtered)
-- 8854 (< 100% overlaps filtered)
--
-- Computing expected corrected read lengths 'correction/2-correction/jb418.estimate.log'.
----------------------------------------
-- Starting command on Thu Jun 8 11:57:57 2017 with 24.663 GB free disk space
cd correction/2-correction
/Users/ksb/computation/science/canu/Darwin-amd64/bin/generateCorrectionLayouts \
-G ../jb418.gkpStore \
-O ../jb418.ovlStore \
-S ./jb418.globalScores \
-c 4 \
-C 80 \
-p ./jb418.estimate.WORKING
-- Finished on Thu Jun 8 11:57:57 2017 (lickety-split) with 24.662 GB free disk space
----------------------------------------
-- Sorting reads by expected corrected length.
-- Sorting reads by uncorrected length.
-- Loading expected corrected read lengths.
-- Picking longest corrected reads.
-- Writing longest corrected reads to 'correction/2-correction/jb418.readsToCorrect'.
-- Summarizing filter.
--
-- Reads to be corrected:
-- 14075 reads longer than 14164 bp
-- 204059668 bp
-- Expected corrected reads:
-- 14075 reads
-- 188008818 bp
-- 8835 bp minimum length
-- 13358 bp mean length
-- 26590 bp n50 length
-- Using overlaps no worse than 0.3 fraction error for correcting reads (from corErrorRate parameter).
-- Finished stage 'cor-buildCorrectionLayouts', reset canuIteration.
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'cor' concurrent execution on Thu Jun 8 11:57:59 2017 with 24.659 GB free disk space (14 processes; 4 concurrently)
cd correction/2-correction
./correctReads.sh 1 > ./correctReads.000001.out 2>&1
./correctReads.sh 2 > ./correctReads.000002.out 2>&1
./correctReads.sh 3 > ./correctReads.000003.out 2>&1
./correctReads.sh 4 > ./correctReads.000004.out 2>&1
./correctReads.sh 5 > ./correctReads.000005.out 2>&1
./correctReads.sh 6 > ./correctReads.000006.out 2>&1
./correctReads.sh 7 > ./correctReads.000007.out 2>&1
./correctReads.sh 8 > ./correctReads.000008.out 2>&1
./correctReads.sh 9 > ./correctReads.000009.out 2>&1
./correctReads.sh 10 > ./correctReads.000010.out 2>&1
./correctReads.sh 11 > ./correctReads.000011.out 2>&1
./correctReads.sh 12 > ./correctReads.000012.out 2>&1
./correctReads.sh 13 > ./correctReads.000013.out 2>&1
./correctReads.sh 14 > ./correctReads.000014.out 2>&1
-- Finished on Thu Jun 8 12:38:18 2017 (2419 seconds) with 23.908 GB free disk space
----------------------------------------
-- Found 14 read correction output files.
-- Finished stage 'cor-generateCorrectedReads', reset canuIteration.
-- Found 14 read correction output files.
-- Finished stage 'cor-generateCorrectedReads', reset canuIteration.
-- Concatenating correctReads output.
-- Analyzing correctReads output.
--
-- Reads to be corrected:
-- 14075 reads longer than 14164 bp
-- 204059668 bp
-- Expected corrected reads:
-- 14075 reads
-- 188008818 bp
-- 8835 bp minimum length
-- 13358 bp mean length
-- 26590 bp n50 length
-- Actual corrected reads:
-- 14278 reads
-- 181065313 bp
-- 21 reads with 0 corrected blocks
-- 13840 reads with 1 corrected block
-- 204 reads with 2 corrected blocks
-- 10 reads with 3 corrected blocks
--
-- Purging correctReads output after merging to final output file.
-- Purged 14 .dump.success sentinels.
-- Purged 14 .fasta outputs.
-- Purged 14 .err outputs.
-- Purged 14 .out job log outputs.
-- Finished stage 'cor-dumpCorrectedReads', reset canuIteration.
--
-- Corrected reads saved in 'jb418.correctedReads.fasta.gz'.
--
--
-- BEGIN TRIMMING
--
----------------------------------------
-- Starting command on Thu Jun 8 12:38:23 2017 with 24.023 GB free disk space
cd trimming
/Users/ksb/computation/science/canu/Darwin-amd64/bin/gatekeeperCreate \
-minlength 1000 \
-o ./jb418.gkpStore.BUILDING \
./jb418.gkpStore.gkp \
> ./jb418.gkpStore.BUILDING.err 2>&1
-- Finished on Thu Jun 8 12:38:25 2017 (2 seconds) with 23.977 GB free disk space
----------------------------------------
--
-- In gatekeeper store 'trimming/jb418.gkpStore':
-- Found 14278 reads.
-- Found 181065313 bases (38.52 times coverage).
--
-- Read length histogram (one '*' equals 28.45 reads):
-- 0 999 0
-- 1000 1999 74 **
-- 2000 2999 43 *
-- 3000 3999 52 *
-- 4000 4999 49 *
-- 5000 5999 40 *
-- 6000 6999 59 **
-- 7000 7999 109 ***
-- 8000 8999 1046 ************************************
-- 9000 9999 1992 **********************************************************************
-- 10000 10999 1915 *******************************************************************
-- 11000 11999 1704 ***********************************************************
-- 12000 12999 1513 *****************************************************
-- 13000 13999 1333 **********************************************
-- 14000 14999 1140 ****************************************
-- 15000 15999 860 ******************************
-- 16000 16999 643 **********************
-- 17000 17999 472 ****************
-- 18000 18999 348 ************
-- 19000 19999 246 ********
-- 20000 20999 171 ******
-- 21000 21999 142 ****
-- 22000 22999 104 ***
-- 23000 23999 74 **
-- 24000 24999 45 *
-- 25000 25999 32 *
-- 26000 26999 26
-- 27000 27999 20
-- 28000 28999 9
-- 29000 29999 4
-- 30000 30999 4
-- 31000 31999 3
-- 32000 32999 4
-- 33000 33999 2
-- Finished stage 'obt-gatekeeper', reset canuIteration.
-- Finished stage 'merylConfigure', reset canuIteration.
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Thu Jun 8 12:38:25 2017 with 23.977 GB free disk space (1 processes; 2 concurrently)
cd trimming/0-mercounts
./meryl.sh 1 > ./meryl.000001.out 2>&1
-- Finished on Thu Jun 8 12:39:17 2017 (52 seconds) with 23.856 GB free disk space
----------------------------------------
-- Meryl finished successfully.
-- Finished stage 'merylCheck', reset canuIteration.
--
-- 22-mers Fraction
-- Occurrences NumMers Unique Total
-- 1- 1 12942715 *******************************************************************--> 0.6143 0.0716
-- 2- 2 1419870 ********************************************************************** 0.6816 0.0873
-- 3- 4 781939 ************************************** 0.7058 0.0958
-- 5- 7 497085 ************************ 0.7278 0.1071
-- 8- 11 577420 **************************** 0.7492 0.1244
-- 12- 16 732015 ************************************ 0.7767 0.1582
-- 17- 22 932531 ********************************************* 0.8119 0.2199
-- 23- 29 958268 *********************************************** 0.8559 0.3250
-- 30- 37 862263 ****************************************** 0.9001 0.4633
-- 38- 46 664995 ******************************** 0.9391 0.6190
-- 47- 56 430803 ********************* 0.9696 0.7712
-- 57- 67 187682 ********* 0.9884 0.8844
-- 68- 79 40007 * 0.9964 0.9421
-- 80- 92 15283 0.9981 0.9563
-- 93- 106 5096 0.9987 0.9630
-- 107- 121 1564 0.9989 0.9654
-- 122- 137 2490 0.9990 0.9665
-- 138- 154 2345 0.9991 0.9682
-- 155- 172 973 0.9992 0.9701
-- 173- 191 461 0.9993 0.9709
-- 192- 211 1659 0.9993 0.9714
-- 212- 232 3064 0.9994 0.9733
-- 233- 254 852 0.9995 0.9770
-- 255- 277 2835 0.9996 0.9782
-- 278- 301 1600 0.9997 0.9825
-- 302- 326 173 0.9998 0.9848
-- 327- 352 249 0.9998 0.9851
-- 353- 379 517 0.9998 0.9856
-- 380- 407 95 0.9998 0.9867
-- 408- 436 78 0.9998 0.9868
-- 437- 466 22 0.9998 0.9870
-- 467- 497 29 0.9998 0.9871
-- 498- 529 67 0.9998 0.9871
-- 530- 562 125 0.9998 0.9873
-- 563- 596 233 0.9998 0.9877
-- 597- 631 813 0.9999 0.9885
-- 632- 667 1190 0.9999 0.9914
-- 668- 704 919 1.0000 0.9956
-- 705- 742 74 1.0000 0.9990
-- 743- 781 7 1.0000 0.9993
-- 782- 821 14 1.0000 0.9993
--
-- 9052 (max occurrences)
-- 167822760 (total mers, non-unique)
-- 8127761 (distinct mers, non-unique)
-- 12942715 (unique mers)
----------------------------------------
-- Starting command on Thu Jun 8 12:39:17 2017 with 23.856 GB free disk space
cd trimming/0-mercounts
/Users/ksb/computation/science/canu/Darwin-amd64/bin/meryl \
-Dt \
-n 997 \
-s ./jb418.ms22 \
> ./jb418.ms22.frequentMers.fasta \
2> ./jb418.ms22.frequentMers.fasta.err
-- Finished on Thu Jun 8 12:39:18 2017 (1 second) with 23.856 GB free disk space
----------------------------------------
-- Reset obtOvlMerThreshold from auto to 997.
--
-- Found 180765475 22-mers; 21070476 distinct and 12942715 unique. Largest count 9052.
-- Finished stage 'obt-meryl', reset canuIteration.
--
-- OVERLAPPER (normal) (trimming) erate=0.045
--
----------------------------------------
-- Starting command on Thu Jun 8 12:39:18 2017 with 23.975 GB free disk space
cd trimming/1-overlapper
/Users/ksb/computation/science/canu/Darwin-amd64/bin/overlapInCorePartition \
-g ../jb418.gkpStore \
-bl 100000000 \
-bs 0 \
-rs 2000000 \
-rl 0 \
-ol 500 \
-o ./jb418.partition \
> ./jb418.partition.err 2>&1
-- Finished on Thu Jun 8 12:39:18 2017 (lickety-split) with 23.975 GB free disk space
----------------------------------------
--
-- Configured 2 overlapInCore jobs.
-- Finished stage 'obt-overlapConfigure', reset canuIteration.
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'obtovl' concurrent execution on Thu Jun 8 12:39:18 2017 with 23.975 GB free disk space (2 processes; 1 concurrently)
cd trimming/1-overlapper
./overlap.sh 1 > ./overlap.000001.out 2>&1
./overlap.sh 2 > ./overlap.000002.out 2>&1
-- Finished on Thu Jun 8 13:10:36 2017 (1878 seconds) with 25.296 GB free disk space
----------------------------------------
-- Found 2 overlapInCore output files.
--
-- overlapInCore compute 'trimming/1-overlapper':
-- kmer hits
-- with no overlap 10217440 5108720 +- 2740846.293
-- with an overlap 1381377 690688.5 +- 387281.676
--
-- overlaps 1381377 690688.5 +- 387281.676
-- contained 0 0 +- 0
-- dovetail 0 0 +- 0
--
-- overlaps rejected
-- multiple per pair 0 0 +- 0
-- bad short window 0 0 +- 0
-- bad long window 0 0 +- 0
-- Finished stage 'obt-overlapCheck', reset canuIteration.
----------------------------------------
-- Starting command on Thu Jun 8 13:10:36 2017 with 25.296 GB free disk space
cd trimming
/Users/ksb/computation/science/canu/Darwin-amd64/bin/ovStoreBuild \
-O ./jb418.ovlStore.BUILDING \
-G ./jb418.gkpStore \
-M 2-8 \
-L ./1-overlapper/ovljob.files \
> ./jb418.ovlStore.err 2>&1
-- Finished on Thu Jun 8 13:10:37 2017 (1 second) with 25.244 GB free disk space
----------------------------------------
--
-- Overlap store 'trimming/jb418.ovlStore' successfully constructed.
--
-- Purged 0.025 GB in 6 overlap output files and 1 directories.
-- Overlap store 'trimming/jb418.ovlStore' statistics not available (skipped in correction and trimming stages).
-- Finished stage 'obt-createOverlapStore', reset canuIteration.
----------------------------------------
-- Starting command on Thu Jun 8 13:10:37 2017 with 25.262 GB free disk space
cd trimming/3-overlapbasedtrimming
/Users/ksb/computation/science/canu/Darwin-amd64/bin/trimReads \
-G ../jb418.gkpStore \
-O ../jb418.ovlStore \
-Co ./jb418.1.trimReads.clear \
-e 0.045 \
-minlength 1000 \
-ol 1 \
-oc 1 \
-o ./jb418.1.trimReads \
> ./jb418.1.trimReads.err 2>&1
-- Finished on Thu Jun 8 13:10:38 2017 (1 second) with 25.26 GB free disk space
----------------------------------------
-- PARAMETERS:
-- ----------
-- 1000 (reads trimmed below this many bases are deleted)
-- 0.0450 (use overlaps at or below this fraction error)
-- 1 (break region if overlap is less than this long, for 'largest covered' algorithm)
-- 1 (break region if overlap coverage is less than this many read, for 'largest covered' algorithm)
--
-- INPUT READS:
-- -----------
-- 14278 reads 181065313 bases (reads processed)
-- 0 reads 0 bases (reads not processed, previously deleted)
-- 0 reads 0 bases (reads not processed, in a library where trimming isn't allowed)
--
-- OUTPUT READS:
-- ------------
-- 13279 reads 166707245 bases (trimmed reads output)
-- 990 reads 12089569 bases (reads with no change, kept as is)
-- 4 reads 6410 bases (reads with no overlaps, deleted)
-- 5 reads 6115 bases (reads with short trimmed length, deleted)
--
-- TRIMMING DETAILS:
-- ----------------
-- 9434 reads 1341145 bases (bases trimmed from the 5' end of a read)
-- 11352 reads 914829 bases (bases trimmed from the 3' end of a read)
-- Finished stage 'obt-trimReads', reset canuIteration.
----------------------------------------
-- Starting command on Thu Jun 8 13:10:38 2017 with 25.26 GB free disk space
cd trimming/3-overlapbasedtrimming
/Users/ksb/computation/science/canu/Darwin-amd64/bin/splitReads \
-G ../jb418.gkpStore \
-O ../jb418.ovlStore \
-Ci ./jb418.1.trimReads.clear \
-Co ./jb418.2.splitReads.clear \
-e 0.045 \
-minlength 1000 \
-o ./jb418.2.splitReads \
> ./jb418.2.splitReads.err 2>&1
-- Finished on Thu Jun 8 13:10:40 2017 (2 seconds) with 25.258 GB free disk space
----------------------------------------
-- PARAMETERS:
-- ----------
-- 1000 (reads trimmed below this many bases are deleted)
-- 0.0450 (use overlaps at or below this fraction error)
-- INPUT READS:
-- -----------
-- 14269 reads 181052788 bases (reads processed)
-- 9 reads 12525 bases (reads not processed, previously deleted)
-- 0 reads 0 bases (reads not processed, in a library where trimming isn't allowed)
--
-- PROCESSED:
-- --------
-- 0 reads 0 bases (no overlaps)
-- 1 reads 4027 bases (no coverage after adjusting for trimming done already)
-- 0 reads 0 bases (processed for chimera)
-- 0 reads 0 bases (processed for spur)
-- 14268 reads 181048761 bases (processed for subreads)
--
-- READS WITH SIGNALS:
-- ------------------
-- 0 reads 0 signals (number of 5' spur signal)
-- 0 reads 0 signals (number of 3' spur signal)
-- 0 reads 0 signals (number of chimera signal)
-- 8 reads 9 signals (number of subread signal)
--
-- SIGNALS:
-- -------
-- 0 reads 0 bases (size of 5' spur signal)
-- 0 reads 0 bases (size of 3' spur signal)
-- 0 reads 0 bases (size of chimera signal)
-- 9 reads 1489 bases (size of subread signal)
--
-- TRIMMING:
-- --------
-- 2 reads 9727 bases (trimmed from the 5' end of the read)
-- 6 reads 16116 bases (trimmed from the 3' end of the read)
-- Finished stage 'obt-splitReads', reset canuIteration.
----------------------------------------
-- Starting command on Thu Jun 8 13:10:40 2017 with 25.258 GB free disk space
cd trimming
/Users/ksb/computation/science/canu/Darwin-amd64/bin/gatekeeperDumpFASTQ -fasta -nolibname \
-G ./jb418.gkpStore \
-c ./3-overlapbasedtrimming/jb418.2.splitReads.clear \
-o ../jb418.trimmedReads.gz \
> ../jb418.trimmedReads.err 2>&1
-- Finished on Thu Jun 8 13:10:43 2017 (3 seconds) with 25.2 GB free disk space
----------------------------------------
-- Finished stage 'obt-dumpReads', reset canuIteration.
--
-- Trimmed reads saved in 'trimming/jb418.trimmedReads.fasta.gz'
--
--
-- BEGIN ASSEMBLY
--
----------------------------------------
-- Starting command on Thu Jun 8 13:10:43 2017 with 25.2 GB free disk space
cd unitigging
/Users/ksb/computation/science/canu/Darwin-amd64/bin/gatekeeperCreate \
-minlength 1000 \
-o ./jb418.gkpStore.BUILDING \
./jb418.gkpStore.gkp \
> ./jb418.gkpStore.BUILDING.err 2>&1
-- Finished on Thu Jun 8 13:10:45 2017 (2 seconds) with 25.154 GB free disk space
----------------------------------------
--
-- In gatekeeper store 'unitigging/jb418.gkpStore':
-- Found 14269 reads.
-- Found 178770971 bases (38.03 times coverage).
--
-- Read length histogram (one '*' equals 28.31 reads):
-- 0 999 0
-- 1000 1999 69 **
-- 2000 2999 46 *
-- 3000 3999 60 **
-- 4000 4999 62 **
-- 5000 5999 60 **
-- 6000 6999 97 ***
-- 7000 7999 188 ******
-- 8000 8999 1190 ******************************************
-- 9000 9999 1982 **********************************************************************
-- 10000 10999 1878 ******************************************************************
-- 11000 11999 1647 **********************************************************
-- 12000 12999 1509 *****************************************************
-- 13000 13999 1311 **********************************************
-- 14000 14999 1085 **************************************
-- 15000 15999 815 ****************************
-- 16000 16999 640 **********************
-- 17000 17999 455 ****************
-- 18000 18999 326 ***********
-- 19000 19999 236 ********
-- 20000 20999 166 *****
-- 21000 21999 141 ****
-- 22000 22999 99 ***
-- 23000 23999 64 **
-- 24000 24999 45 *
-- 25000 25999 30 *
-- 26000 26999 26
-- 27000 27999 18
-- 28000 28999 9
-- 29000 29999 4
-- 30000 30999 4
-- 31000 31999 3
-- 32000 32999 4
-- Finished stage 'utg-gatekeeper', reset canuIteration.
-- Finished stage 'merylConfigure', reset canuIteration.
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'meryl' concurrent execution on Thu Jun 8 13:10:46 2017 with 25.154 GB free disk space (1 processes; 2 concurrently)
cd unitigging/0-mercounts
./meryl.sh 1 > ./meryl.000001.out 2>&1
-- Finished on Thu Jun 8 13:11:35 2017 (49 seconds) with 25.046 GB free disk space
----------------------------------------
-- Meryl finished successfully.
-- Finished stage 'merylCheck', reset canuIteration.
--
-- 22-mers Fraction
-- Occurrences NumMers Unique Total
-- 1- 1 11600692 *******************************************************************--> 0.5899 0.0650
-- 2- 2 1381187 ********************************************************************** 0.6601 0.0805
-- 3- 4 769511 ************************************** 0.6856 0.0889
-- 5- 7 494404 ************************* 0.7089 0.1002
-- 8- 11 581373 ***************************** 0.7317 0.1178
-- 12- 16 731109 ************************************* 0.7615 0.1522
-- 17- 22 939818 *********************************************** 0.7992 0.2147
-- 23- 29 954511 ************************************************ 0.8466 0.3218
-- 30- 37 858784 ******************************************* 0.8937 0.4614
-- 38- 46 666508 ********************************* 0.9354 0.6186
-- 47- 56 423083 ********************* 0.9681 0.7729
-- 57- 67 182695 ********* 0.9879 0.8854
-- 68- 79 39076 * 0.9962 0.9420
-- 80- 92 15170 0.9979 0.9561
-- 93- 106 5002 0.9986 0.9629
-- 107- 121 1613 0.9989 0.9652
-- 122- 137 2426 0.9990 0.9663
-- 138- 154 2417 0.9991 0.9680
-- 155- 172 850 0.9992 0.9701
-- 173- 191 480 0.9992 0.9707
-- 192- 211 1690 0.9993 0.9712
-- 212- 232 3021 0.9993 0.9733
-- 233- 254 909 0.9995 0.9769
-- 255- 277 3002 0.9995 0.9782
-- 278- 301 1373 0.9997 0.9828
-- 302- 326 184 0.9998 0.9848
-- 327- 352 300 0.9998 0.9851
-- 353- 379 484 0.9998 0.9857
-- 380- 407 59 0.9998 0.9867
-- 408- 436 74 0.9998 0.9868
-- 437- 466 24 0.9998 0.9870
-- 467- 497 28 0.9998 0.9870
-- 498- 529 66 0.9998 0.9871
-- 530- 562 136 0.9998 0.9873
-- 563- 596 259 0.9998 0.9877
-- 597- 631 923 0.9998 0.9886
-- 632- 667 1257 0.9999 0.9918
-- 668- 704 718 1.0000 0.9965
-- 705- 742 60 1.0000 0.9990
-- 743- 781 10 1.0000 0.9993
-- 782- 821 11 1.0000 0.9993
--
-- 9016 (max occurrences)
-- 166870630 (total mers, non-unique)
-- 8064659 (distinct mers, non-unique)
-- 11600692 (unique mers)
----------------------------------------
-- Starting command on Thu Jun 8 13:11:36 2017 with 25.046 GB free disk space
cd unitigging/0-mercounts
/Users/ksb/computation/science/canu/Darwin-amd64/bin/meryl \
-Dt \
-n 991 \
-s ./jb418.ms22 \
> ./jb418.ms22.frequentMers.fasta \
2> ./jb418.ms22.frequentMers.fasta.err
-- Finished on Thu Jun 8 13:11:36 2017 (lickety-split) with 25.046 GB free disk space
----------------------------------------
-- Reset utgOvlMerThreshold from auto to 991.
--
-- Found 178471322 22-mers; 19665351 distinct and 11600692 unique. Largest count 9016.
-- Finished stage 'utg-meryl', reset canuIteration.
--
-- OVERLAPPER (normal) (assembly) erate=0.045
--
----------------------------------------
-- Starting command on Thu Jun 8 13:11:36 2017 with 25.156 GB free disk space
cd unitigging/1-overlapper
/Users/ksb/computation/science/canu/Darwin-amd64/bin/overlapInCorePartition \
-g ../jb418.gkpStore \
-bl 100000000 \
-bs 0 \
-rs 2000000 \
-rl 0 \
-ol 500 \
-o ./jb418.partition \
> ./jb418.partition.err 2>&1
-- Finished on Thu Jun 8 13:11:36 2017 (lickety-split) with 25.156 GB free disk space
----------------------------------------
--
-- Configured 2 overlapInCore jobs.
-- Finished stage 'utg-overlapConfigure', reset canuIteration.
--
-- Running jobs. First attempt out of 2.
----------------------------------------
-- Starting 'utgovl' concurrent execution on Thu Jun 8 13:11:36 2017 with 25.156 GB free disk space (2 processes; 1 concurrently)
cd unitigging/1-overlapper
./overlap.sh 1 > ./overlap.000001.out 2>&1
./overlap.sh 2 > ./overlap.000002.out 2>&1
-- Finished on Thu Jun 8 13:53:21 2017 (2505 seconds) with 24.49 GB free disk space
----------------------------------------
-- Found 2 overlapInCore output files.
--
-- overlapInCore compute 'unitigging/1-overlapper':
-- kmer hits
-- with no overlap 10946958 5473479 +- 2818062.353
-- with an overlap 506843 253421.5 +- 136957.391
--
-- overlaps 506843 253421.5 +- 136957.391
-- contained 87959 43979.5 +- 23369.172
-- dovetail 418884 209442 +- 113588.219
--
-- overlaps rejected
-- multiple per pair 0 0 +- 0
-- bad short window 0 0 +- 0
-- bad long window 0 0 +- 0
-- Finished stage 'utg-overlapCheck', reset canuIteration.
----------------------------------------
-- Starting command on Thu Jun 8 13:53:21 2017 with 24.49 GB free disk space
cd unitigging
/Users/ksb/computation/science/canu/Darwin-amd64/bin/ovStoreBuild \
-O ./jb418.ovlStore.BUILDING \
-G ./jb418.gkpStore \
-M 2-8 \
-L ./1-overlapper/ovljob.files \
> ./jb418.ovlStore.err 2>&1
-- Finished on Thu Jun 8 13:53:21 2017 (lickety-split) with 24.469 GB free disk space
----------------------------------------
--
-- Overlap store 'unitigging/jb418.ovlStore' successfully constructed.
--
-- Purged 0.009 GB in 6 overlap output files and 1 directories.
----------------------------------------
-- Starting command on Thu Jun 8 13:53:21 2017 with 24.478 GB free disk space
cd unitigging
/Users/ksb/computation/science/canu/Darwin-amd64/bin/ovStoreStats \
-G ./jb418.gkpStore \
-O ./jb418.ovlStore \
-o ./jb418.ovlStore \
> ./jb418.ovlStore.summary.err 2>&1
-- Finished on Thu Jun 8 13:53:22 2017 (1 second) with 24.477 GB free disk space
----------------------------------------
-- category reads % read length feature size or coverage analysis
-- ---------------- ------- ------- ---------------------- ------------------------ --------------------
-- middle-missing 0 0.00 0.00 +- 0.00 0.00 +- 0.00 (bad trimming)
-- middle-hump 0 0.00 0.00 +- 0.00 0.00 +- 0.00 (bad trimming)
-- no-5-prime 4 0.03 11399.75 +- 2572.60 148.75 +- 297.50 (bad trimming)
-- no-3-prime 5 0.04 11466.40 +- 1739.55 44.80 +- 68.16 (bad trimming)
--
-- low-coverage 27 0.19 8673.85 +- 4067.39 5.14 +- 1.52 (easy to assemble, potential for lower quality consensus)
-- unique 7975 55.89 12245.37 +- 3717.73 28.90 +- 8.80 (easy to assemble, perfect, yay)
-- repeat-cont 1047 7.34 11666.62 +- 3055.58 67.43 +- 11.45 (potential for consensus errors, no impact on assembly)
-- repeat-dove 49 0.34 20168.82 +- 2995.48 69.57 +- 10.74 (hard to assemble, likely won't assemble correctly or even at all)
--
-- span-repeat 2041 14.30 13354.95 +- 4013.14 4599.84 +- 4266.85 (read spans a large repeat, usually easy to assemble)
-- uniq-repeat-cont 2420 16.96 12127.19 +- 2950.24 (should be uniquely placed, low potential for consensus errors, no impact on assembly)
-- uniq-repeat-dove 389 2.73 17433.67 +- 4528.65 (will end contigs, potential to misassemble)
-- uniq-anchor 311 2.18 13452.37 +- 3811.15 4456.61 +- 3737.36 (repeat read, with unique section, probable bad read)
--
-- Overlap store 'unitigging/jb418.ovlStore' contains:
--
-- category reads % read length feature size or coverage analysis
-- ---------------- ------- ------- ---------------------- ------------------------ --------------------
-- middle-missing 0 0.00 0.00 +- 0.00 0.00 +- 0.00 (bad trimming)
-- middle-hump 0 0.00 0.00 +- 0.00 0.00 +- 0.00 (bad trimming)
-- no-5-prime 4 0.03 11399.75 +- 2572.60 148.75 +- 297.50 (bad trimming)
-- no-3-prime 5 0.04 11466.40 +- 1739.55 44.80 +- 68.16 (bad trimming)
--
-- low-coverage 27 0.19 8673.85 +- 4067.39 5.14 +- 1.52 (easy to assemble, potential for lower quality consensus)
-- unique 7975 55.89 12245.37 +- 3717.73 28.90 +- 8.80 (easy to assemble, perfect, yay)
-- repeat-cont 1047 7.34 11666.62 +- 3055.58 67.43 +- 11.45 (potential for consensus errors, no impact on assembly)
-- repeat-dove 49 0.34 20168.82 +- 2995.48 69.57 +- 10.74 (hard to assemble, likely won't assemble correctly or even at all)
--
-- span-repeat 2041 14.30 13354.95 +- 4013.14 4599.84 +- 4266.85 (read spans a large repeat, usually easy to assemble)
-- uniq-repeat-cont 2420 16.96 12127.19 +- 2950.24 (should be uniquely placed, low potential for consensus errors, no impact on assembly)
-- uniq-repeat-dove 389 2.73 17433.67 +- 4528.65 (will end contigs, potential to misassemble)
-- uniq-anchor 311 2.18 13452.37 +- 3811.15 4456.61 +- 3737.36 (repeat read, with unique section, probable bad read)
-- Finished stage 'utg-createOverlapStore', reset canuIteration.
Configure RED for 2gb memory with batches of at most 5000 reads and (unlimited) bases.
RED job 1 from read 1 to read 1434 - 1.500 GB for 1434 reads - 0.219 GB for 18084506 olaps - 0.001 GB for evidence
RED job 2 from read 1435 to read 2881 - 1.500 GB for 1447 reads - 0.219 GB for 18088043 olaps - 0.001 GB for evidence
RED job 3 from read 2882 to read 4339 - 1.501 GB for 1458 reads - 0.219 GB for 18091688 olaps - 0.001 GB for evidence
RED job 4 from read 4340 to read 5789 - 1.501 GB for 1450 reads - 0.219 GB for 18094539 olaps - 0.001 GB for evidence
RED job 5 from read 5790 to read 7212 - 1.500 GB for 1423 reads - 0.219 GB for 18085417 olaps - 0.001 GB for evidence
RED job 6 from read 7213 to read 8638 - 1.501 GB for 1426 reads - 0.219 GB for 18092586 olaps - 0.001 GB for evidence
RED job 7 from read 8639 to read 10089 - 1.501 GB for 1451 reads - 0.219 GB for 18094991 olaps - 0.001 GB for evidence