TACC: Setting memory limits for job 987598 to unlimited KB TACC: Dumping job script: -------------------------------------------------------------------------------- #!/bin/bash #$ -N abyss_fish546_pe-2013-01-24-11-50-07639 #$ -cwd #$ -V #$ -o abyss_fish546_pe-2013-01-24-11-50-07639-6353.out #$ -e abyss_fish546_pe-2013-01-24-11-50-07639-6353.err #$ -l h_rt=08:00:00 #$ -A iPlant-Master #$ -pe 12way 48 #$ -q normal curl -k "https://foundation.iplantcollaborative.org/apps-v1/trigger/job/6353/token/71f2c9cb-0f08-48df-b59f-facf0f9b3d5e/status/RUNNING" cd /scratch/0004/iplant/sr320/job-6353-abyss_fish546_pe-2013-01-24-11-50-07639/sr320-6353-1359028226000 # Environmental settings for abyss-lonestar-1.3.3u1: module purge module load TACC module load abyss/1.3.3 module load bwa/0.5.9 module load bowtie/0.12.7 module load irods # We support presentation of multiple PE libraries, each # of which has a different insert size. However, we can't automatically # parameterize this yet using the API. The workaround is to # require the following # # 1. Lane files representing paired-end sequences must be # combined into interlaced single files # 2. If a sequence library for a given insert size is comprised # of multiple interlaced files, they must be concatenated into single # files # 3. All single-end sequences resulting from primary sequencing # or from failure in the interlacing process must be combined into a # single single-end file and presented as such lib1=/iplant/home//sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz lib2=/iplant/home//sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz lib3=${lib3} se=${se} ARGS="" # kmer if [ -n "25" ]; then ARGS="${ARGS} -k=25"; fi # minimum mean k-mer coverage of a unitig if [ -n "" ]; then ARGS="${ARGS} -c=${C}"; fi # minimum erosion k-mer coverage if [ -n "" ]; then ARGS="${ARGS} -e="; fi # minimum erosion k-mer coverage per strand if [ -n "0" ]; then ARGS="${ARGS} -E=0"; fi # allowable error of a distance estimate if [ -n "6" ]; then ARGS="${ARGS} -d=6"; fi # maximum number of branches of a bubble if [ -n "2" ]; then ARGS="${ARGS} -a=2"; fi # minimum alignment length of a read (bp) if [ -n "" ]; then ARGS="${ARGS} -l="; fi # minimum overlap of two unitigs (bp) if [ -n "30" ]; then ARGS="${ARGS} -m=30"; fi # minimum number of pairs required for building contigs if [ -n "10" ]; then ARGS="${ARGS} -n=10"; fi # minimum number of pairs required for building scaffolds if [ -n "" ]; then ARGS="${ARGS} -N="; fi # minimum sequence identity of a bubble if [ -n "0.9" ]; then ARGS="${ARGS} -p=0.9"; fi # maximum length of a bubble (bp) if [ -n "10000" ]; then ARGS="${ARGS} -b=10000"; fi # minimum base quality if [ -n "3" ]; then ARGS="${ARGS} -q=3"; fi # minimum unitig size required for building contigs (bp) if [ -n "200" ]; then ARGS="${ARGS} -s=200"; fi # minimum contig size required for building scaffolds (bp) if [ -n "" ]; then ARGS="${ARGS} -S="; fi # minimum tip size (bp) if [ -n "2000" ]; then ARGS="${ARGS} -t=2000"; fi # aligner if [ -n "bwa" ]; then ARGS="${ARGS} --aligner=bwa"; fi # name if [ -n "assembly" ]; then ARGS="${ARGS} --name=assembly"; fi # Unpack bin/ directory tar -zxf bin.tgz # Path stuff export CWD=${PWD} export PATH="${PATH}:${PWD}/bin" # Create local temp directory export TMPDIR="${CWD}/tmp" mkdir -p $TMPDIR # Create the Abyss-PE executable script perl bin/param2abyss-shell.pl --xlib1=/iplant/home//sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz --xlib2=/iplant/home//sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz --xlib3=${lib3} --xse=${se} $ARGS # iRODS fetch echo "iRODS fetch starting..." if [ -n "/iplant/home//sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz" ]; then echo "lib1" lib1_f=$(basename /iplant/home//sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz) iget -frPVT /iplant/home//sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz . fi if [ -n "/iplant/home//sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz" ]; then echo "lib2" lib2_f=$(basename /iplant/home//sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz) iget -frPVT /iplant/home//sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz . fi if [ -n "${lib3}" ]; then echo "lib3" lib1_3=$(basename ${lib3}) iget -frPVT ${lib3} . fi if [ -n "${se}" ]; then echo "se" se_f=$(basename ${se}) iget -frPVT ${se} . fi echo "iRODS fetch complete" # Fire off the Abyss-PE job. bash abyss-shell.sh # Remove bin, tmp directory, and input files # Do this first in case user has named their input files the same as # their assembly name rm -rf tmp abyss-shell.sh bin $lib1_f $lib2_f $lib3_f $se_f # Move work files into kmer directory mkdir -p "k25" mv assembly-* k25/ mv coverage.hist k25/ mv lib*-* k25/ curl -k "https://foundation.iplantcollaborative.org/apps-v1/trigger/job/6353/token/71f2c9cb-0f08-48df-b59f-facf0f9b3d5e/status/FINISHED" curl -k "https://foundation.iplantcollaborative.org/apps-v1/trigger/job/6353/token/71f2c9cb-0f08-48df-b59f-facf0f9b3d5e/status/ARCHIVING" imkdir -p /iplant/home/sr320/analyses/Abyss_fish546_PE-2013-01-24-11-50-07.639 for i in `find . -maxdepth 1`; do exists=`grep -x "$i" .iplant.archive` if [ ! -n "$exists" ]; then iput -T -v -f -r $i /iplant/home/sr320/analyses/Abyss_fish546_PE-2013-01-24-11-50-07.639 fi done curl -k "https://foundation.iplantcollaborative.org/apps-v1/trigger/job/6353/token/71f2c9cb-0f08-48df-b59f-facf0f9b3d5e/status/ARCHIVING_FINISHED" -------------------------------------------------------------------------------- TACC: Done. {"status":"success","message":"","result":{"id":6353,"name":"Abyss_fish546_PE-2013-01-24-11-50-07.639","owner":"sr320","system":"lonestar4.tacc.teragrid.org","software":"abyss-lonestar-1.3.3u1","processors":48,"requestedTime":"08:00:00","memory":2,"callbackUrl":null,"archive":true,"archivePath":"/sr320/analyses/Abyss_fish546_PE-2013-01-24-11-50-07.639","outputPath":null,"outputUrl":"https://foundation.iplantcollaborative.org/apps-v1/job/6353/output/list","status":"RUNNING","submitTime":1359028240000,"startTime":1359028272012,"endTime":null,"inputs":[{"lib2":"/sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz"},{"lib1":"/sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz"}],"parameters":[{"littleE":""},{"minOver":"30"},{"minUnitig":"200"},{"cov":""},{"maxBranch":"2"},{"scaffPairs":""},{"minAlign":""},{"maxBubble":"10000"},{"aligner":"bwa"},{"distErr":"6"},{"contigPairs":"10"},{"minContig":""},{"kmer":"25"},{"name":"assembly"},{"minTip":"2000"},{"qual":"3"},{"bigE":"0"},{"seqidBubble":"0.9"}],"permissions":[]}}iRODS fetch starting... lib1 NOTICE: irodsHost=data.iplantcollaborative.org NOTICE: irodsPort=1247 NOTICE: irodsUserName=ipcservices NOTICE: irodsZone=iplant NOTICE: irodsDefResource=homeResc NOTICE: created irodsHome=/iplant/home/ipcservices NOTICE: created irodsCwd=/iplant/home/ipcservices 0/1 - 0.00% of files done 0.000/2619.908 MB - 0.00% of file sizes done Processing filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz - 2619.908 MB From server: NumThreads=16, addr:128.196.172.157, port:20030, cookie=721723935 filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz - 639.985/2619.908 MB - 24.43% done filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz - 1279.971/2619.908 MB - 48.86% done filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz - 1879.957/2619.908 MB - 71.76% done filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz - 2519.942/2619.908 MB - 96.18% done filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz - 2616.160/2619.908 MB - 99.86% done filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz - 2619.908/2619.908 MB - 100.00% done filtered_106A_Female_Mix_ 2619.908 MB | 125.336 sec | 16 thr | 20.903 MB/s lib2 NOTICE: irodsHost=data.iplantcollaborative.org NOTICE: irodsPort=1247 NOTICE: irodsUserName=ipcservices NOTICE: irodsZone=iplant NOTICE: irodsDefResource=homeResc NOTICE: created irodsHome=/iplant/home/ipcservices NOTICE: created irodsCwd=/iplant/home/ipcservices 0/1 - 0.00% of files done 0.000/2500.568 MB - 0.00% of file sizes done Processing filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz - 2500.568 MB From server: NumThreads=16, addr:128.196.172.157, port:20037, cookie=204919485 filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz - 599.986/2500.568 MB - 23.99% done filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz - 1239.972/2500.568 MB - 49.59% done filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz - 1839.958/2500.568 MB - 73.58% done filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz - 2427.991/2500.568 MB - 97.10% done filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz - 2500.568/2500.568 MB - 100.00% done filtered_106A_Female_Mix_ 2500.568 MB | 121.316 sec | 16 thr | 20.612 MB/s iRODS fetch complete /opt/apps/intel11_1/mvapich2/1.6/bin/mpirun -np 48 ABYSS-P -k25 -q3 -E0 -t2000 -b10000 --coverage-hist=coverage.hist -s assembly-bubbles.fa -o assembly-1.fa filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz ABySS 1.3.3 ABYSS-P -k25 -q3 -E0 -t2000 -b10000 --coverage-hist=coverage.hist -s assembly-bubbles.fa -o assembly-1.fa filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz Running on 48 processors 0: Running on host c329-114.ls4.tacc.utexas.edu 1: Running on host c329-114.ls4.tacc.utexas.edu36: Running on host c338-105.ls4.tacc.utexas.edu12: Running on host c303-206.ls4.tacc.utexas.edu 24: Running on host c333-114.ls4.tacc.utexas.edu 437: Running on host c338-105.ls4.tacc.utexas.edu 13: Running on host c303-206.ls4.tacc.utexas.edu 25: Running on host c333-114.ls4.tacc.utexas.edu 5: Running on host c329-114.ls4.tacc.utexas.edu 38: Running on host c338-105.ls4.tacc.utexas.edu 14: Running on host c303-206.ls4.tacc.utexas.edu 26: Running on host c333-114.ls4.tacc.utexas.edu 6: Running on host c329-114.ls4.tacc.utexas.edu 39: Running on host c338-105.ls4.tacc.utexas.edu 15: Running on host c303-206.ls4.tacc.utexas.edu 27: Running on host c333-114.ls4.tacc.utexas.edu 7: Running on host c329-114.ls4.tacc.utexas.edu 41: Running on host c338-105.ls4.tacc.utexas.edu 17: Running on host c303-206.ls4.tacc.utexas.edu 288: Running on host c329-114.ls4.tacc.utexas.edu 42: Running on host c338-105.ls4.tacc.utexas.edu 18: Running on host c303-206.ls4.tacc.utexas.edu 29: Running on host c333-114.ls4.tacc.utexas.edu 9: Running on host c329-114.ls4.tacc.utexas.edu 43: Running on host c338-105.ls4.tacc.utexas.edu 19: Running on host c303-206.ls4.tacc.utexas.edu 30: Running on host c333-114.ls4.tacc.utexas.edu 10: Running on host c329-114.ls4.tacc.utexas.edu 44: Running on host c338-105.ls4.tacc.utexas.edu 20: Running on host c303-206.ls4.tacc.utexas.edu 31: Running on host c333-114.ls4.tacc.utexas.edu 45: Running on host c338-105.ls4.tacc.utexas.edu 21: Running on host c303-206.ls4.tacc.utexas.edu 32: Running on host c333-114.ls4.tacc.utexas.edu 2: Running on host c329-114.ls4.tacc.utexas.edu 46: Running on host c338-105.ls4.tacc.utexas.edu 22: Running on host c303-206.ls4.tacc.utexas.edu 33: Running on host c333-114.ls4.tacc.utexas.edu 3: Running on host c329-114.ls4.tacc.utexas.edu 47: Running on host c338-105.ls4.tacc.utexas.edu 23: Running on host c303-206.ls4.tacc.utexas.edu 34: Running on host c333-114.ls4.tacc.utexas.edu : 35: Running on host c333-114.ls4.tacc.utexas.edu Running on host c329-114.ls4.tacc.utexas.edu 11: Running on host c329-114.ls4.tacc.utexas.edu 16: Running on host c303-206.ls4.tacc.utexas.edu : Running on host c333-114.ls4.tacc.utexas.edu 40: Running on host c338-105.ls4.tacc.utexas.edu 0: Reading `filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz'... 1: Reading `filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz'... 0: Loaded 5790971 k-mer. 1: Loaded 5781348 k-mer. 2: Loaded 5788657 k-mer. 3: Loaded 5778652 k-mer. 412: Loaded 5784379 k-mer. 5: Loaded 5784048 k-mer. 36: Loaded 5782110 k-mer. 13: Loaded 5781830 k-mer. 24: Loaded 5790229 k-mer. 6: Loaded 5783327 k-mer. 37: Loaded 5780357 k-mer. 14: Loaded 5777641 k-mer. 25: Loaded 5780942 k-mer. 7: Loaded 5784834 k-mer. 38: Loaded 5780393 k-mer. 15: Loaded 5778182 k-mer. 26: Loaded 5791264 k-mer. 8: Loaded 5787863 k-mer. 39: Loaded 5777838 k-mer. 1627: Loaded 5773227 k-mer. 9: Loaded 5779939 k-mer. 4017: Loaded 5779465 k-mer. 2810: Loaded 5795290 k-mer. 41: Loaded 5785362 k-mer. 18: Loaded 5787073 k-mer. 29: Loaded 5780085 k-mer. 11: Loaded 42: Loaded 5792132 k-mer. 19: Loaded 5778707 k-mer. 30: Loaded 5774883 k-mer. : 43: Loaded 5779455 k-mer. 20: Loaded 5787524 k-mer. 31: Loaded 5783457 k-mer. Loaded 44: Loaded 5785456 k-mer. 21: Loaded 5779136 k-mer. 32: Loaded 5792479 k-mer. 578690145: Loaded 5784295 k-mer. 22: Loaded 5787292 k-mer. 33: Loaded 5779402 k-mer. k-mer. 46: Loaded 5779608 k-mer. 23: Loaded 5776692 k-mer. 34: Loaded 5790313 k-mer. 47: Loaded 5777467 k-mer. : 35: Loaded 5775952 k-mer. : Loaded : Loaded 5786922Loaded 5789481 k-mer. 5786581 k-mer. k-mer. 5777273 k-mer. Loaded 277596714 k-mer. At least 8.88 GB of RAM is required. Minimum k-mer coverage is 284 Using a coverage threshold of 4... The median k-mer coverage is 13 The reconstruction is 71685093 The k-mer coverage threshold is 3.60555 Setting parameter e (erode) to 4 Setting parameter c (coverage) to 3.60555 Finding adjacenct k-mer... 0: Added 11865866 edges. Added 1: Added 11842937 edges. 36: Added 11848811 edges. 12: Added 11851996 edges. 24: Added 11865487 edges. 2: Added 11860506 edges. 37: Added 11843770 edges. 13: Added 11846573 edges. 25: Added 11845182 edges. 3: Added 11836478 edges. 38: Added 11844976 edges. 14: Added 11835628 edges. 26: Added 11866833 edges. 439: Added 11837557 edges. 15: Added 11839195 edges. 27: Added 11825598 edges. 5: Added 11850099 edges. 4016286: Added 11849619 edges. 41: Added 11851272 edges. 17: Added 11842363 edges. 29: Added 11842089 edges. 7: Added 11852294 edges. 42: Added 11870185 edges. 18: Added 11856148 edges. 30: Added 11829722 edges. 8: Added 11860045 edges. 43: Added 11839621 edges. 19: Added 11834874 edges. 31: Added 11850032 edges. 9: Added 11840279 edges. 44: Added 11855181 edges. 20: Added 11864236 edges. 32: Added 11869013 edges. 10: Added 11877834 edges. 45: Added 11850539 edges. 21: Added 11840202 edges. 33: Added 11840418 edges. 11: Added 11833571 edges. 46: Added 11837409 edges. 22: Added 11859658 edges. 34: Added 11863002 edges. : 47: Added 11836867 edges. 23: Added 11835488 edges. 35: Added 11829625 edges. Added : : : 11862595Added Added Added edges. 118664481185658611858791568763498 edges. Eroding tips... edges. edges. edges. 22: Eroded 2323793 tips. 11: Eroded 2340760 tips. 35: Eroded 2343842 tips. 10: Eroded 2352924 tips. 23: Eroded 2352873 tips. 34: Eroded 2368365 tips. 47: Eroded 2369851 tips. 17: Eroded 2368174 tips. 8: Eroded 2376421 tips. 5: Eroded 2375817 tips. 28: Eroded 2387071 tips. 6: Eroded 2386645 tips. 24: Eroded 2390139 tips. 26: Eroded 2390737 tips. 40: Eroded 2393707 tips. 29: Eroded 2391282 tips. 4: Eroded 2393194 tips. 13: Eroded 2392731 tips. 33: Eroded 2392025 tips. 1: Eroded 2396859 tips. 16: Eroded 2395564 tips. 7: Eroded 2399215 tips. 38: Eroded 2395884 tips. 31: Eroded 2401961 tips. 3: Eroded 2400922 tips. 41: Eroded 2402962 tips. 30: Eroded 2400834 tips. 27: Eroded 2402003 tips. 39: Eroded 2405688 tips. 46: Eroded 2405041 tips. 36: Eroded 2405128 tips. 2: Eroded 2410955 tips. 14: Eroded 2406558 tips. 45: Eroded 2407228 tips. 21: Eroded 2407974 tips. 42: Eroded 2410467 tips. 18: Eroded 2414639 tips. 15: Eroded 2410115 tips. 37: Eroded 2413153 tips. 43: Eroded 2412960 tips. 19: Eroded 2415402 tips. 25: Eroded 2416387 tips. 9: Eroded 2418069 tips. 0: Eroded 2423080 tips. 12: Eroded 2420162 tips. 20: Eroded 2420475 tips. 32: Eroded 2426285 tips. 44: Eroded 2423649 tips. 0: Eroded 39481 tips. 1: Eroded 63764 tips. 36: Eroded 52444 tips. 12: Eroded 38671 tips. 2: Eroded 51213 tips. 37: Eroded 44249 tips. 13: Eroded 65697 tips. 3: Eroded 55896 tips. 38: Eroded 59749 tips. 14: Eroded 51207 tips. 24: Eroded 70235 tips. 439: Eroded 53497 tips. 15: Eroded 46220 tips. 25: Eroded 41543 tips. 5: Eroded 82627 tips. 401626: Eroded 70729 tips. 6: Eroded 72210 tips. 41: Eroded 55785 tips. 17: Eroded 85966 tips. 27: Eroded 54541 tips. 7: Eroded 60598 tips. 42: Eroded 49416 tips. 18: Eroded 47691 tips. 288: Eroded 83739 tips. 43: Eroded 43661 tips. 19: Eroded 41866 tips. 29: Eroded 66872 tips. 9: Eroded 39728 tips. 44: Eroded 37544 tips. 20: Eroded 39079 tips. 30: Eroded 54966 tips. 10: Eroded 109873 tips. 45: Eroded 50838 tips. 21: Eroded 49607 tips. 32: Eroded 37866 tips. 11: Eroded 116483 tips. 46: Eroded 53005 tips. 22: Eroded 136035 tips. 33: Eroded 64703 tips. : 47: Eroded 90034 tips. 23: Eroded 103645 tips. 34: Eroded 93360 tips. Eroded : : 35: Eroded 114089 tips. 66499Eroded Eroded 31: Eroded 57858 tips. tips. 6799263687: Eroded 118030563 tips. tips. tips. Eroded 74135 tips. Pruning tips shorter than 1 bp... 11: Pruned 507 tips. 23: Pruned 502 tips. 17: Pruned 505 tips. 5: Pruned 519 tips. 34: Pruned 503 tips. 46: Pruned 512 tips. 8: Pruned 504 tips. 28: 10: Pruned 484 tips. Pruned 497 tips. 35: Pruned 496 tips. 19: Pruned 494 tips. 27: Pruned 476 tips. 47: Pruned 535 tips. 30: Pruned 506 tips. 41: Pruned 565 tips. 29: Pruned 503 tips. 43: Pruned 502 tips. 1: Pruned 503 tips. 18: Pruned 508 tips. 22: Pruned 506 tips. 38: Pruned 539 tips. 33: Pruned 498 tips. 9: Pruned 559 tips. 36: Pruned 498 tips. 40: Pruned 476 tips. 7: Pruned 521 tips. 31: Pruned 538 tips. 26: Pruned 504 tips. 6: Pruned 504 tips. 2: Pruned 530 tips. 39: Pruned 505 tips. 16: Pruned 3: Pruned 537 tips. 504 tips. 25: Pruned 493 tips. 42: Pruned 535 tips. 37: Pruned 502 tips. 13: Pruned 568 tips. 15: Pruned 504 tips. 32: Pruned 530 tips. 0: Pruned 520 tips. 14: Pruned 499 tips. 45: Pruned 521 tips. 4: Pruned 548 tips. 44: Pruned 525 tips. 20: Pruned 537 tips. 12: Pruned 498 tips. 21: Pruned 509 tips. 24: Pruned 544 tips. Pruned 24673 k-mer in 24673 tips. Pruning tips shorter than 2 bp... 11: Pruned 118 tips. 23: Pruned 138 tips. 17: Pruned 128 tips. 5: Pruned 141 tips. 46: Pruned 152 tips. 19: Pruned 158 tips. 27: Pruned 137 tips. 8: Pruned 161 tips. 28: Pruned 147 tips. 35: Pruned 164 tips. 30: Pruned 133 tips. 10: Pruned 147 tips. 41: Pruned 148 tips. 47: Pruned 153 tips. 34: Pruned 135 tips. 43: Pruned 134 tips. 38: Pruned 155 tips. 18: Pruned 135 tips. 40: Pruned 29: Pruned 170 tips. 15033: Pruned 166 tips. tips. 22: Pruned 165 tips. 13: Pruned 156 tips. 26: Pruned 155 tips. 9: Pruned 154 tips. 36: Pruned 141 tips. 3: Pruned 145 tips. 2: Pruned 145 tips. 1: Pruned 168 tips. 31: Pruned 166 tips. 25: Pruned 128 tips. 7: Pruned 140 tips. 6: Pruned 171 tips. 16: 32: Pruned 125 tips. 0: Pruned 160 tips. Pruned 156 tips. 37: Pruned 157 tips. 42: Pruned 135 tips. 15: Pruned 148 tips. 39: Pruned 140 tips. 14: Pruned 142 tips. 20: Pruned 144 tips. 44: Pruned 160 tips. 4: Pruned 155 tips. 45: Pruned 161 tips. 21: Pruned 149 tips. 12: Pruned 151 tips. 24: Pruned 138 tips. Pruned 12123 k-mer in 7125 tips. Pruning tips shorter than 4 bp... 23: Pruned 207 tips. 17: Pruned 241 tips. 19: Pruned 200 tips. 13: Pruned 230 tips. 22: Pruned 223 tips. 40: Pruned 18: Pruned 227 tips. 21216 tips. : Pruned 203 tips. 15: Pruned 225 tips. 14: Pruned 262 tips. 20: Pruned 211 tips. 38: Pruned 230 tips. 47: Pruned 218 tips. 41: Pruned 215 tips. 46: Pruned 223 tips. 37: Pruned 240 tips. 12: Pruned 234 tips. 21: Pruned 243 tips. 42: Pruned 207 tips. 45: Pruned 179 tips. 36: Pruned 233 tips. 44: Pruned 201 tips. 39: Pruned 210 tips. 43: Pruned 221 tips. 28: Pruned 35: Pruned 245 tips. 207 tips. 29: Pruned 190 tips. 27: Pruned 249 tips. 31: Pruned 212 tips. 30: Pruned 204 tips. 33: Pruned 223 tips. 5: Pruned 212 tips. 25: Pruned 211 tips. 7: Pruned 239 tips. 4: Pruned 237 tips. 8: Pruned 240 tips. 24: Pruned 208 tips. 0: Pruned 223 tips. 2: Pruned 218 tips. 11: Pruned 201 tips. 6: Pruned 227 tips. 34: Pruned 220 tips. 32: Pruned 230 tips. 3: Pruned 229 tips. 26: Pruned 226 tips. 1: Pruned 233 tips. 10: Pruned 215 tips. 9: Pruned 236 tips. Pruned 30698 k-mer in 10630 tips. Pruning tips shorter than 8 bp... 17: Pruned 268 tips. 13: Pruned 249 tips. 23: Pruned 227 tips. 19: Pruned 275 tips. 20: Pruned 252 tips. 15: Pruned 268 tips. 22: Pruned 263 tips. 18: Pruned 276 tips. 14: Pruned 269 tips. 12: Pruned 249 tips. 16: Pruned 259 tips. 21: Pruned 263 tips. 4: Pruned 294 tips. 42: Pruned 269 tips. 39: Pruned 270 tips. 41: Pruned 263 tips. 38: Pruned 267 tips. 40: Pruned 236 tips. 37: Pruned 274 tips. 45: Pruned 274 tips. 36: Pruned 270 tips. 43: Pruned 252 tips. 47: Pruned 241 tips. 46: Pruned 289 tips. 11: Pruned 243 tips. 9: Pruned 264 tips. 44: Pruned 257 tips. 3: Pruned 254 tips. 6: Pruned 281 tips. 8: Pruned 264 tips. 0: Pruned 264 tips. 10: Pruned 277 tips. 5: Pruned 272 tips. 2: Pruned 242 tips. 7: Pruned 251 tips. 1: Pruned 240 tips. 35: Pruned 263 tips. 33: Pruned 267 tips. 32: Pruned 258 tips. 28: Pruned 275 tips. 31: Pruned 253 tips. 30: Pruned 244 tips. 34: Pruned 269 tips. 26: Pruned 234 tips. 27: Pruned 244 tips. 24: Pruned 274 tips. 29: Pruned 249 tips. 25: Pruned 265 tips. Pruned 61147 k-mer in 12521 tips. Pruning tips shorter than 16 bp... 35: Pruned 336 tips. 28: Pruned 295 tips. 27: Pruned 326 tips. 33: Pruned 345 tips. 38: Pruned 339 tips. 41: Pruned 339 tips. 42: Pruned 332 tips. 32: Pruned 349 tips. 13: Pruned 324 tips. 37: Pruned 326 tips. 17: Pruned 296 tips. 39: Pruned 310 tips. 30: Pruned 334 tips. 45: Pruned 330 tips. 43: Pruned 353 tips. 26: Pruned 338 tips. 40: Pruned 324 tips. 29: Pruned 357 tips. 31: Pruned 362 tips. 24: Pruned 315 tips. 46: Pruned 361 tips. 36: Pruned 312 tips. 25: Pruned 343 tips. 47: Pruned 299 tips. 34: Pruned 313 tips. 19: Pruned 337 tips. 44: Pruned 345 tips. 18: Pruned 373 tips. 20: Pruned 314 tips. 22: Pruned 366 tips. 23: Pruned 344 tips. 15: Pruned 306 tips. 14: Pruned 333 tips. 16: Pruned 358 tips. 21: Pruned 316 tips. 12: Pruned 338 tips. 4: Pruned 336 tips. 11: Pruned 306 tips. 8: Pruned 359 tips. 6: Pruned 381 tips. 2: Pruned 343 tips. 5: Pruned 295 tips. 0: Pruned 322 tips. 3: Pruned 320 tips. 10: Pruned 352 tips. 7: Pruned 332 tips. 1: Pruned 348 tips. 9: Pruned 322 tips. Pruned 143960 k-mer in 16004 tips. Pruning tips shorter than 32 bp... 4: Pruned 349 tips. 6: Pruned 343 tips. 13: Pruned 369 tips. 17: Pruned 382 tips. 11: Pruned 363 tips. 8: Pruned 361 tips. 18: Pruned 374 tips. 19: Pruned 372 tips. 35: Pruned 333 tips. 2: Pruned 367 tips. 7: Pruned 368 tips. 27: Pruned 355 tips. 33: Pruned 368 tips. 3: Pruned 370 tips. 10: Pruned 395 tips. 22: Pruned 379 tips. 5: Pruned 386 tips. 0: Pruned 340 tips. 16: Pruned 389 tips. 14: Pruned 374 tips. 1: Pruned 354 tips. 20: Pruned 402 tips. 28: Pruned 378 tips. 32: Pruned 372 tips. 21: Pruned 393 tips. 9: Pruned 380 tips. 15: Pruned 412 tips. 23: Pruned 414 tips. 12: Pruned 392 tips. 29: Pruned 367 tips. 30: Pruned 356 tips. 31: Pruned 394 tips. 26: Pruned 379 tips. 25: Pruned 362 tips. 24: Pruned 366 tips. 34: Pruned 405 tips. 41: Pruned 358 tips. 37: Pruned 370 tips. 42: Pruned 388 tips. 43: Pruned 354 tips. 45: Pruned 393 tips. 38: Pruned 381 tips. 39: Pruned 383 tips. 40: Pruned 370 tips. 36: Pruned 381 tips. 46: Pruned 377 tips. 44: Pruned 374 tips. 47: Pruned 410 tips. Pruned 297404 k-mer in 18002 tips. Pruning tips shorter than 64 bp... 35: Pruned 404 tips. 27: Pruned 394 tips. 32: Pruned 375 tips. 28: Pruned 384 tips. 33: Pruned 383 tips. 41: Pruned 406 tips. 31: Pruned 396 tips. 4: Pruned 376 tips. 13: Pruned 386 tips. 30: Pruned 405 tips. 6: Pruned 388 tips. 11: Pruned 384 tips. 25: Pruned 402 tips. 34: Pruned 398 tips. 29: Pruned 471 tips. 7: Pruned 407 tips. 17: Pruned 371 tips. 42: Pruned 378 tips. 19: Pruned 384 tips. 26: Pruned 413 tips. 1: Pruned 400 tips. 24: Pruned 438 tips. 2: Pruned 385 tips. 3: Pruned 412 tips. 5: Pruned 421 tips. 8: Pruned 408 tips. 10: Pruned 406 tips. 43: Pruned 411 tips. 45: Pruned 377 tips. 37: Pruned 394 tips. 38: Pruned 378 tips. 0: Pruned 394 tips. 40: Pruned 413 tips. 46: Pruned 431 tips. 39: Pruned 382 tips. 9: Pruned 395 tips. 44: Pruned 409 tips. 16: Pruned 412 tips. 22: Pruned 415 tips. 18: Pruned 414 tips. 23: Pruned 397 tips. 20: Pruned 374 tips. 36: Pruned 377 tips. 47: Pruned 407 tips. 14: Pruned 416 tips. 15: Pruned 412 tips. 21: Pruned 439 tips. 12: Pruned 432 tips. Pruned 589696 k-mer in 19254 tips. Pruning tips shorter than 128 bp... 13: Pruned 181 tips. 17: Pruned 218 tips. 27: Pruned 211 tips. 18: Pruned 216 tips. 33: Pruned 196 tips. 35: Pruned 194 tips. 21: Pruned 219 tips. 32: Pruned 197 tips. 23: Pruned 230 tips. 20: Pruned 213 tips. 16: Pruned 231 tips. 28: Pruned 210 tips. 12: Pruned 195 tips. 42: Pruned 216 tips. 19: Pruned 207 tips. 29: Pruned 220 tips. 14: Pruned 230 tips. 25: Pruned 208 tips. 26: Pruned 236 tips. 30: Pruned 223 tips. 41: Pruned 199 tips. 22: Pruned 179 tips. 15: Pruned 235 tips. 31: Pruned 213 tips. 43: Pruned 193 tips. 37: Pruned 233 tips. 46: Pruned 223 tips. 24: Pruned 213 tips. 38: Pruned 213 tips. 40: Pruned 196 tips. 39: Pruned 242 tips. 7: Pruned 204 tips. 34: Pruned 230 tips. 6: Pruned 202 tips. 8: Pruned 200 tips. 11: Pruned 220 tips. 4: Pruned 173 tips. 45: Pruned 214 tips. 2: Pruned 207 tips. 1: Pruned 244 tips. 36: Pruned 234 tips. 3: Pruned 200 tips. 44: Pruned 216 tips. 47: Pruned 212 tips. 5: Pruned 178 tips. 0: Pruned 239 tips. 10: Pruned 222 tips. 9: Pruned 216 tips. Pruned 674544 k-mer in 10201 tips. Pruning tips shorter than 256 bp... 27: Pruned 118 tips. 29: Pruned 130 tips. 31: Pruned 118 tips. 35: Pruned 129 tips. 32: Pruned 125 tips. 33: Pruned 103 tips. 30: Pruned 122 tips. 26: Pruned 120 tips. 25: Pruned 114 tips. 39: Pruned 137 tips. 28: Pruned 107 tips. 42: Pruned 101 tips. 34: Pruned 127 tips. 24: Pruned 150 tips. 13: Pruned 107 tips. 7: Pruned 110 tips. 41: Pruned 124 tips. 43: Pruned 119 tips. 45: Pruned 117 tips. 46: Pruned 115 tips. 1: Pruned 120 tips. 37: Pruned 122 tips. 38: Pruned 129 tips. 36: Pruned 123 tips. 47: Pruned 114 tips. 44: Pruned 127 tips. 6: Pruned 114 tips. 21: Pruned 108 tips. 2: Pruned 98 tips. 23: Pruned 107 tips. 40: Pruned 133 tips. 8: Pruned 120 tips. 18: Pruned 138 tips. 4: Pruned 144 tips. 11: Pruned 105 tips. 17: Pruned 118 tips. 19: Pruned 119 tips. 12: Pruned 123 tips. 16: Pruned 12510: Pruned 143 tips. tips. 14: Pruned 113 tips. 0: Pruned 134 tips. 3: Pruned 147 tips. 15: Pruned 141 tips. 5: Pruned 143 tips. 20: Pruned 132 tips. 9: Pruned 128 tips. 22: Pruned 143 tips. Pruned 687249 k-mer in 5904 tips. Pruning tips shorter than 512 bp... 18: Pruned 33 tips. 39: Pruned 27 tips. 23: Pruned 18 tips. 13: Pruned 20 tips. 32: Pruned 25 tips. 35: Pruned 30 tips. 21: Pruned 33 tips. 15: Pruned 29 tips. 31: Pruned 27 tips. 29: Pruned 32 tips. 43: Pruned 31 tips. 27: Pruned 29 tips. 17: Pruned 38 tips. 26: Pruned 29 tips. 30: Pruned 23 tips. 14: Pruned 29 tips. 16: 41: Pruned 30 tips. Pruned 31 tips. 45: Pruned 29 tips. 19: Pruned 33 tips. 42: Pruned 28 tips. 24: Pruned 27 tips. 25: Pruned 28 tips. 40: Pruned 31 tips. 33: Pruned 29 tips. 12: Pruned 28 tips. 28: Pruned 36 tips. 20: Pruned 33 tips. 22: Pruned 31 tips. 36: Pruned 26 tips. 37: Pruned 34 tips. 7: Pruned 24 tips. 44: Pruned 33 tips. 46: Pruned 28 tips. 38: Pruned 25 tips. 1: Pruned 29 tips. 8: Pruned 19 tips. 34: Pruned 30 tips. 2: Pruned 28 tips. 6: Pruned 36 tips. 10: Pruned 24 tips. 3: Pruned 28 tips. 4: Pruned 31 tips. 0: Pruned 34 tips. 47: Pruned 41 tips. 11: Pruned 33 tips. 5: Pruned 27 tips. 9: Pruned 29 tips. Pruned 289946 k-mer in 1406 tips. Pruning tips shorter than 1024 bp... 39: Pruned 0 tips. 29: Pruned 1 tips. 45: Pruned 2 tips. 41: Pruned 2 tips. 32: Pruned 1 tips. 42: Pruned 1 tips. 43: Pruned 3 tips. 35: Pruned 1 tips. 44: Pruned 5 tips. 27: Pruned 0 tips. 40: Pruned 3 tips. 31: Pruned 2 tips. 18: Pruned 3 tips. 46: Pruned 5 tips. 47: Pruned 3 tips. 26: Pruned 4 tips. 28: Pruned 4 tips. 30: Pruned 1 tips. 25: Pruned 3 tips. 13: Pruned 1 tips. 37: Pruned 6 tips. 21: Pruned 1 tips. 24: Pruned 2 tips. 34: Pruned 4 tips. 38: Pruned 7 tips. 17: Pruned 1 tips. 33: Pruned 2 tips. 23: Pruned 2 tips. 15: Pruned 3 tips. 7: Pruned 7 tips. 19: Pruned 4 tips. 16: Pruned 2 tips. 14: Pruned 0 tips. 1: Pruned 3 tips. 2: Pruned 1 tips. 36: Pruned 3 tips. 6: Pruned 2 tips. 22: Pruned 3 tips. 20: Pruned 4 tips. 3: Pruned 3 tips. 11: Pruned 1 tips. 12: Pruned 1 tips. 10: Pruned 4 tips. 4: Pruned 3 tips. 8: Pruned 4 tips. 0: Pruned 2 tips. 5: Pruned 6 tips. 9: Pruned 4 tips. Pruned 47184 k-mer in 130 tips. Pruning tips shorter than 2000 bp... 39: Pruned 0 tips. 45: Pruned 0 tips. 43: Pruned 0 tips. 7: Pruned 0 tips. 29: Pruned 0 tips. 41: Pruned 0 tips. 44: Pruned 0 tips. 40: Pruned 0 tips. 42: Pruned 0 tips. 46: Pruned 0 tips. 37: Pruned 0 tips. 31: Pruned 0 tips. 38: Pruned 0 tips. 35: Pruned 0 tips. 18: Pruned 0 tips. 26: Pruned 0 tips. 32: Pruned 0 tips. 28: Pruned 1 tips. 25: Pruned 0 tips. 27: Pruned 0 tips. 21: Pruned 0 tips. 47: Pruned 0 tips. 30: Pruned 0 tips. 19: Pruned 0 tips. 15: Pruned 0 tips. 17: Pruned 0 tips. 23: Pruned 0 tips. 33: Pruned 0 tips. 13: Pruned 0 tips. 24: Pruned 0 tips. 34: Pruned 0 tips. 16: Pruned 0 tips. 4: Pruned 0 tips. 1: Pruned 0 tips. 20: Pruned 0 tips. 2: Pruned 0 tips. 10: Pruned 1 tips. 6: Pruned 0 tips. 14: Pruned 0 tips. 11: Pruned 0 tips. 22: Pruned 0 tips. 3: Pruned 0 tips. 8: Pruned 0 tips. 36: Pruned 1 tips. 12: Pruned 0 tips. 0: Pruned 0 tips. 5: Pruned 0 tips. 9: Pruned 0 tips. Pruned 1278 k-mer in 3 tips. Pruning tips shorter than 2000 bp... 18: Pruned 0 tips. 39: Pruned 0 tips. 17: Pruned 0 tips. 21: Pruned 0 tips. 45: Pruned 0 tips. 23: Pruned 0 tips. 41: Pruned 0 tips. 43: Pruned 0 tips. 7: Pruned 0 tips. 15: Pruned 0 tips. 19: Pruned 0 tips. 16: Pruned 0 tips. 13: Pruned 0 tips. 20: Pruned 0 tips. 29: Pruned 0 tips. 44: Pruned 0 tips. 36: Pruned 0 tips. 32: Pruned 0 tips. 38: Pruned 0 tips. 42: Pruned 0 tips. 37: Pruned 0 tips. 40: Pruned 0 tips. 46: Pruned 0 tips. 26: Pruned 0 tips. 31: Pruned 0 tips. 35: Pruned 0 tips. 14: Pruned 0 tips. 28: Pruned 0 tips. 25: Pruned 0 tips. 22: Pruned 0 tips. 27: Pruned 0 tips. 47: Pruned 0 tips. 30: Pruned 0 tips. 4: Pruned 0 tips. 1: Pruned 1 tips. 24: Pruned 0 tips. 10: Pruned 0 tips. 33: Pruned 0 tips. 8: Pruned 0 tips. 6: Pruned 0 tips. 34: Pruned 0 tips. 2: Pruned 0 tips. 12: Pruned 0 tips. 3: Pruned 0 tips. 11: Pruned 0 tips. 5: Pruned 0 tips. 0: Pruned 0 tips. 9: Pruned 0 tips. Pruned 64 k-mer in 1 tips. Pruning tips shorter than 2000 bp... 7: Pruned 0 tips. 18: Pruned 0 tips. 39: Pruned 0 tips. 17: Pruned 0 tips. 45: Pruned 0 tips. 1: Pruned 0 tips. 21: Pruned 0 tips. 15: Pruned 0 tips. 23: Pruned 0 tips. 6: Pruned 0 tips. 2: Pruned 0 tips. 4: Pruned 0 tips. 8: Pruned 0 tips. 43: Pruned 0 tips. 19: Pruned 0 tips. 5: Pruned 0 tips. 10: Pruned 0 tips. 29: Pruned 0 tips. 20: Pruned 0 tips. 41: Pruned 0 tips. 13: Pruned 0 tips. 11: Pruned 0 tips. 16: Pruned 0 tips. 42: Pruned 0 tips. 46: Pruned 0 tips. 37: Pruned 0 tips. 14: Pruned 0 tips. 38: Pruned 0 tips. 22: Pruned 0 tips. 3: Pruned 0 tips. 44: Pruned 0 tips. 31: Pruned 0 tips. 32: Pruned 0 tips. 36: Pruned 0 tips. 0: Pruned 0 tips. 35: Pruned 0 tips. 28: Pruned 0 tips. 9: Pruned 0 tips. 27: Pruned 0 tips. 40: Pruned 0 tips. 25: Pruned 0 tips. 30: Pruned 0 tips. 33: Pruned 0 tips. 24: Pruned 0 tips. 47: Pruned 0 tips. 12: Pruned 0 tips. 26: Pruned 0 tips. 34: Pruned 0 tips. Pruned 125854 tips in 13 rounds. Marking ambiguous branches... 1: Marked 457849 edges of 205630 ambiguous vertices. 10: Marked 463393 edges of 207873 ambiguous vertices. 22: Marked 461424 edges of 207224 ambiguous vertices. 35: Marked 452377 edges of 203611 ambiguous vertices. 13: Marked 459447 edges of 206443 ambiguous vertices. 23: Marked 458123 edges of 205530 ambiguous vertices. 24: Marked 463402 edges of 207739 ambiguous vertices. 21: Marked 456412 edges of 204918 ambiguous vertices. 11: Marked 454101 edges of 204318 ambiguous vertices. 0: Marked 461199 edges of 207091 ambiguous vertices. 34: Marked 458434 edges of 205875 ambiguous vertices. 25: Marked 460817 edges of 206967 ambiguous vertices. 30: Marked 455529 edges of 204788 ambiguous vertices. 47: Marked 458235 edges of 205755 ambiguous vertices. 16: Marked 459909 edges of 206545 ambiguous vertices. 3: Marked 454949 edges of 204531 ambiguous vertices. 2: Marked 460527 edges of 206966 ambiguous vertices. 26: Marked 460245 edges of 206412 ambiguous vertices. 5: Marked 459026 edges of 206165 ambiguous vertices. 27: Marked 454241 edges of 204138 ambiguous vertices. 14: Marked 456024 edges of 205068 ambiguous vertices. 6: Marked 459280 edges of 206469 ambiguous vertices. 33: Marked 457267 edges of 205093 ambiguous vertices. 37: Marked 460519 edges of 206867 ambiguous vertices. 8: Marked 463113 edges of 207650 ambiguous vertices. 39: Marked 459137 edges of 205820 ambiguous vertices. 28: Marked 461883 edges of 207339 ambiguous vertices. 38: Marked 460156 edges of 206633 ambiguous vertices. 36: Marked 462226 edges of 207132 ambiguous vertices. 15: Marked 458047 edges of 205764 ambiguous vertices. 4: Marked 468394 edges of 209676 ambiguous vertices. 18: Marked 458554 edges of 206043 ambiguous vertices. 29: Marked 459450 edges of 206376 ambiguous vertices. 17: Marked 460926 edges of 206599 ambiguous vertices. 9: Marked 455038 edges of 204222 ambiguous vertices. 42: Marked 463653 edges of 208057 ambiguous vertices. 41: Marked 458035 edges of 205876 ambiguous vertices. 40: Marked 465618 edges of 208279 ambiguous vertices. 19: Marked 454261 edges of 204569 ambiguous vertices. 43: Marked 455169 edges of 204791 ambiguous vertices. 45: Marked 457534 edges of 205644 ambiguous vertices. 31: Marked 459658 edges of 206483 ambiguous vertices. 20: Marked 468730 edges of 209591 ambiguous vertices. 12: Marked 460141 edges of 206500 ambiguous vertices. 7: Marked 459119 edges of 206149 ambiguous vertices. 44: Marked 460826 edges of 206985 ambiguous vertices. 32: Marked 462064 edges of 207553 ambiguous vertices. 46: Marked 453553 edges of 204048 ambiguous vertices. Marked 9899795 ambiguous branches. Removing low-coverage contigs (mean k-mer coverage < 3.60555)... 35: Found 3252496 k-mer in 239638 contigs before removing low-coverage contigs. Removed 1801846 k-mer in 92990 low-coverage contigs. 27: Found 3240109 k-mer in 239044 contigs before removing low-coverage contigs. Removed 1788870 k-mer in 92182 low-coverage contigs. 29: Found 3248197 k-mer in 240567 contigs before removing low-coverage contigs. Removed 1801997 k-mer in 93328 low-coverage contigs. 30: Found 3241802 k-mer in 239772 contigs before removing low-coverage contigs. Removed 1794991 k-mer in 93035 low-coverage contigs. 33: Found 3238109 k-mer in 240229 contigs before removing low-coverage contigs. Removed 1801728 k-mer in 93339 low-coverage contigs. 34: Found 3255108 k-mer in 241382 contigs before removing low-coverage contigs. Removed 1807722 k-mer in 93695 low-coverage contigs. 26: Found 3240525 k-mer in 240835 contigs before removing low-coverage contigs. Removed 1797550 k-mer in 93686 low-coverage contigs. 25: Found 3256655 k-mer in 240893 contigs before removing low-coverage contigs. Removed 1795552 k-mer in 93275 low-coverage contigs. 28: Found 3259711 k-mer in 241788 contigs before removing low-coverage contigs. Removed 1802816 k-mer in 93625 low-coverage contigs. 32: Found 3272605 k-mer in 242678 contigs before removing low-coverage contigs. Removed 1815999 k-mer in 93997 low-coverage contigs. 31: Found 3269255 k-mer in 241035 contigs before removing low-coverage contigs. Removed 1798733 k-mer in 93296 low-coverage contigs. 24: Found 3291470 k-mer in 242852 contigs before removing low-coverage contigs. Removed 1824697 k-mer in 94622 low-coverage contigs. 14: Found 3247171 k-mer in 239574 contigs before removing low-coverage contigs. Removed 1795006 k-mer in 92546 low-coverage contigs. 21: Found 3246248 k-mer in 239370 contigs before removing low-coverage contigs. Removed 1798475 k-mer in 92828 low-coverage contigs. 17: Found 3250913 k-mer in 241548 contigs before removing low-coverage contigs. Removed 1810363 k-mer in 93927 low-coverage contigs. 15: Found 3246006 k-mer in 240318 contigs before removing low-coverage contigs. Removed 1802151 k-mer in 93145 low-coverage contigs. 23: Found 3253103 k-mer in 240589 contigs before removing low-coverage contigs. Removed 1797912 k-mer in 93194 low-coverage contigs. 12: Found 3257857 k-mer in 240793 contigs before removing low-coverage contigs. Removed 1814012 k-mer in 93951 low-coverage contigs. 16: Found 3251044 k-mer in 241002 contigs before removing low-coverage contigs. Removed 1807228 k-mer in 93636 low-coverage contigs. 19: Found 3241603 k-mer in 239425 contigs before removing low-coverage contigs. Removed 1798523 k-mer in 92806 low-coverage contigs. 13: Found 3274370 k-mer in 241223 contigs before removing low-coverage contigs. Removed 1808248 k-mer in 93637 low-coverage contigs. 20: Found 3287672 k-mer in 243866 contigs before removing low-coverage contigs. Removed 1814103 k-mer in 94606 low-coverage contigs. 18: Found 3276728 k-mer in 241186 contigs before removing low-coverage contigs. Removed 1808046 k-mer in 93415 low-coverage contigs. 22: Found 3268395 k-mer in 241572 contigs before removing low-coverage contigs. Removed 1809922 k-mer in 93584 low-coverage contigs. 1: Found 3242663 k-mer in 240447 contigs before removing low-coverage contigs. Removed 1792515 k-mer in 93051 low-coverage contigs. 9: Found 3255863 k-mer in 240362 contigs before removing low-coverage contigs. Removed 1795773 k-mer in 93029 low-coverage contigs. 6: Found 3245147 k-mer in 241386 contigs before removing low-coverage contigs. Removed 1798320 k-mer in 93123 low-coverage contigs. 3: Found 3258907 k-mer in 240487 contigs before removing low-coverage contigs. Removed 1806435 k-mer in 92963 low-coverage contigs. 11: Found 3251548 k-mer in 239897 contigs before removing low-coverage contigs. Removed 1807144 k-mer in 93210 low-coverage contigs. 2: Found 3256327 k-mer in 241288 contigs before removing low-coverage contigs. Removed 1804507 k-mer in 93573 low-coverage contigs. 4: Found 3257091 k-mer in 242490 contigs before removing low-coverage contigs. Removed 1807944 k-mer in 94285 low-coverage contigs. 5: Found 3260666 k-mer in 240136 contigs before removing low-coverage contigs. Removed 1809840 k-mer in 93435 low-coverage contigs. 0: Found 3270063 k-mer in 241258 contigs before removing low-coverage contigs. Removed 1811480 k-mer in 93893 low-coverage contigs. 8: Found 3265174 k-mer in 241300 contigs before removing low-coverage contigs. Removed 1802956 k-mer in 93493 low-coverage contigs. 7: Found 3278134 k-mer in 241716 contigs before removing low-coverage contigs. Removed 1816365 k-mer in 93614 low-coverage contigs. 10: Found 3286476 k-mer in 243287 contigs before removing low-coverage contigs. Removed 1819936 k-mer in 94494 low-coverage contigs. 39: Found 3237712 k-mer in 240065 contigs before removing low-coverage contigs. Removed 1798794 k-mer in 92999 low-coverage contigs. 46: Found 3252954 k-mer in 239057 contigs before removing low-coverage contigs. Removed 1801747 k-mer in 92622 low-coverage contigs. 43: Found 3262535 k-mer in 240134 contigs before removing low-coverage contigs. Removed 1802226 k-mer in 93219 low-coverage contigs. 40: Found 3266229 k-mer in 241420 contigs before removing low-coverage contigs. Removed 1811177 k-mer in 93915 low-coverage contigs. 37: Found 3269767 k-mer in 241045 contigs before removing low-coverage contigs. Removed 1806034 k-mer in 93586 low-coverage contigs. 38: Found 3271575 k-mer in 241240 contigs before removing low-coverage contigs. Removed 1817747 k-mer in 93786 low-coverage contigs. 45: Found 3257082 k-mer in 240737 contigs before removing low-coverage contigs. Removed 1798335 k-mer in 93225 low-coverage contigs. 47: Found 3253832 k-mer in 239883 contigs before removing low-coverage contigs. Removed 1798853 k-mer in 92937 low-coverage contigs. 41: Found 3261530 k-mer in 241056 contigs before removing low-coverage contigs. Removed 1812752 k-mer in 93763 low-coverage contigs. 44: Found 3261273 k-mer in 241578 contigs before removing low-coverage contigs. Removed 1812785 k-mer in 94060 low-coverage contigs. 42: Found 3269054 k-mer in 242464 contigs before removing low-coverage contigs. Removed 1814463 k-mer in 94317 low-coverage contigs. 36: Found 3283817 k-mer in 242261 contigs before removing low-coverage contigs. Removed 1814785 k-mer in 94306 low-coverage contigs. Found 156442571 k-mer in 11566173 contigs before removing low-coverage contigs. Removed 86659403 k-mer in 4487243 low-coverage contigs. Splitting ambiguous branches... 1: Split 185709 ambigiuous branches. 10: Split 188485 ambigiuous branches. 35: Split 185463 ambigiuous branches. 22: Split 186971 ambigiuous branches. 24: Split 188427 ambigiuous branches. 34: Split 186689 ambigiuous branches. 47: Split 185650 ambigiuous branches. 14: Split 185273 ambigiuous branches. 2: Split 187532 ambigiuous branches. 13: Split 186808 ambigiuous branches. 11: Split 186065 ambigiuous branches. 23: Split 186068 ambigiuous branches. 25: Split 186693 ambigiuous branches. 28: Split 187153 ambigiuous branches. 26: Split 187264 ambigiuous branches. 0: Split 187507 ambigiuous branches. 31: Split 186526 ambigiuous branches. 3: Split 185126 ambigiuous branches. 36: Split 188347 ambigiuous branches. 37: Split 186580 ambigiuous branches. 38: Split 187284 ambigiuous branches. 16: Split 186999 ambigiuous branches. 6: Split 186248 ambigiuous branches. 46: Split 185615 ambigiuous branches. 29: Split 186564 ambigiuous branches. 8: Split 187446 ambigiuous branches. 7: Split 186824 ambigiuous branches. 12: Split 187404 ambigiuous branches. 5: Split 186206 ambigiuous branches. 4: Split 188730 ambigiuous branches. 21: Split 185955 ambigiuous branches. 30: Split 185753 ambigiuous branches. 40: Split 187604 ambigiuous branches. 41: Split 187156 ambigiuous branches. 15: Split 186309 ambigiuous branches. 27: Split 184677 ambigiuous branches. 39: Split 185992 ambigiuous branches. 42: Split 187580 ambigiuous branches. 33: Split 186218 ambigiuous branches. 18: Split 186667 ambigiuous branches. 45: Split 185837 ambigiuous branches. 17: Split 187036 ambigiuous branches. 43: Split 185948 ambigiuous branches. 19: Split 185432 ambigiuous branches. 9: Split 185869 ambigiuous branches. 20: Split 188860 ambigiuous branches. 32: Split 187263 ambigiuous branches. 44: Split 188036 ambigiuous branches. Split 8961848 ambiguous branches. Removed 86659403 marked k-mer. Eroding tips... 24: Eroded 1248 tips. 10: Eroded 1199 tips. 2: Eroded 1167 tips. 23: Eroded 1224 tips. 1: Eroded 1242 tips. 35: Eroded 1316 tips. 36: Eroded 1268 tips. 3: Eroded 1268 tips. 13: Eroded 1335 tips. 8: Eroded 1342 tips. 14: Eroded 1436 tips. 7: Eroded 1345 tips. 31: Eroded 1354 tips. 34: Eroded 1435 tips. 38: Eroded 1494 tips. 22: Eroded 1530 tips. 18: Eroded 1565 tips. 11: Eroded 1483 tips. 33: Eroded 1640 tips. 47: Eroded 1681 tips. 25: Eroded 1570 tips. 29: Eroded 1621 tips. 21: Eroded 1645 tips. 28: Eroded 1672 tips. 27: Eroded 1807 tips. 0: Eroded 1762 tips. 5: Eroded 1775 tips. 16: Eroded 1818 tips. 39: Eroded 1795 tips. 26: Eroded 1830 tips. 40: Eroded 1825 tips. 42: Eroded 2023 tips. 17: Eroded 1935 tips. 9: Eroded 2035 tips. 6: Eroded 1955 tips. 41: Eroded 2026 tips. 46: Eroded 2040 tips. 20: Eroded 2180 tips. 4: Eroded 2144 tips. 45: Eroded 2094 tips. 19: Eroded 2235 tips. 15: Eroded 2317 tips. 12: Eroded 2249 tips. 30: Eroded 2257 tips. 37: Eroded 2413 tips. 32: Eroded 2406 tips. 43: Eroded 2447 tips. 44: Eroded 2498 tips. 0: Eroded 5545 tips. 1: Eroded 6178 tips. 36: Eroded 6073 tips. 12: Eroded 4973 tips. 24: Eroded 6182 tips. 2: Eroded 6253 tips. 37: Eroded 4948 tips. 13: Eroded 6102 tips. 25: Eroded 5653 tips. 3: Eroded 6064 tips. 38: Eroded 5813 tips. 14: Eroded 6022 tips. 26: Eroded 5544 tips. 439: Eroded 5647 tips. 15: Eroded 5079 tips. 27: Eroded 5697 tips. 5: Eroded 5632 tips. 4016286: Eroded 5348 tips. 41: Eroded 5373 tips. 17: Eroded 5323 tips. 29: Eroded 5560 tips. 7: Eroded 5943 tips. 42: Eroded 5585 tips. 18: Eroded 5777 tips. 30: Eroded 5074 tips. 8: Eroded 6101 tips. 43: Eroded 4886 tips. 19: Eroded 5083 tips. 31: Eroded 5908 tips. 9: Eroded 5309 tips. 44: Eroded 4919 tips. 20: Eroded 5243 tips. 32: Eroded 4932 tips. 10: Eroded 6172 tips. 45: Eroded 5126 tips. 21: Eroded 5585 tips. 33: Eroded 5913 tips. 11: Eroded 5933 tips. 46: Eroded 5344 tips. 22: Eroded 5972 tips. 34: Eroded 5868 tips. : 47: Eroded 5704 tips. 23: Eroded 6204 tips. 35: Eroded 6070 tips. Eroded : : : 5245Eroded Eroded Eroded tips. 548457715660Eroded 353766 tips. tips. tips. tips. Pruning tips shorter than 1 bp... 17: Pruned 1376 tips. 19: Pruned 1262 tips. 15: Pruned 1327 tips. 23: Pruned 1333 tips. 18: Pruned 1370 tips. 16: Pruned 1296 tips. 22: Pruned 1383 tips. 14: Pruned 1315 tips. 13: Pruned 1404 tips. 27: Pruned 1341 tips. 12: Pruned 1284 tips. 34: Pruned 1340 tips. 21: Pruned 1363 tips. 20: Pruned 1372 tips. 29: Pruned 1319 tips. 26: Pruned 1308 tips. 28: Pruned 1357 tips. 33: Pruned 1347 tips. 35: Pruned 1367 tips. 31: Pruned 1404 tips. 32: Pruned 1333 tips. 30: Pruned 1302 tips. 25: Pruned 1401 tips. 24: Pruned 1369 tips. 37: Pruned 1327 tips. 43: Pruned 1341 tips. 45: Pruned 1271 tips. 42: Pruned 1304 tips. 36: Pruned 1342 tips. 9: Pruned 1332 tips. 46: Pruned 1324 tips. 41: Pruned 1320 tips. 3: Pruned 1305 tips. 39: Pruned 1312 tips. 47: Pruned 1332 tips. 7: Pruned 1431 tips. 40: Pruned 1433 tips. 38: Pruned 1354 tips. 44: Pruned 1379 tips. 10: Pruned 1401 tips. 2: Pruned 1242 tips. 5: Pruned 1345 tips. 4: Pruned 6: Pruned 1339 tips. 1361 tips. 1: Pruned 1356 tips. 0: Pruned 1281 tips. 11: Pruned 1360 tips. 8: Pruned 1345 tips. Pruned 64410 k-mer in 64410 tips. Pruning tips shorter than 2 bp... 33: Pruned 671 tips. 34: Pruned 741 tips. 27: Pruned 718 tips. 26: Pruned 703 tips. 31: Pruned 744 tips. 35: Pruned 724 tips. 28: Pruned 739 tips. 30: Pruned 683 tips. 29: Pruned 752 tips. 37: Pruned 683 tips. 24: Pruned 757 tips. 9: Pruned 686 tips. 42: Pruned 693 tips. 45: Pruned 671 tips. 25: Pruned 741 tips. 32: Pruned 754 tips. 39: Pruned 723 tips. 40: Pruned 733 tips. 43: Pruned 703 tips. 36: Pruned 750 tips. 38: Pruned 752 tips. 46: Pruned 752 tips. 41: Pruned 720 tips. 47: Pruned 747 tips. 3: Pruned 723 tips. 10: Pruned 747 tips. 44: Pruned 773 tips. 5: Pruned 721 tips. 17: Pruned 721 tips. 6: Pruned 745 tips. 11: Pruned 720 tips. 1: Pruned 721 tips. 7: Pruned 718 tips. 14: Pruned 713 tips. 2: Pruned 720 tips. 19: Pruned 660 tips. 21: Pruned 702 tips. 23: Pruned 758 tips. 13: Pruned 727 tips. 18: Pruned 760 tips. 22: Pruned 730 tips. 15: Pruned 748 tips. 16: Pruned 7584 tips. : Pruned 738 tips. 8: Pruned 726 tips. 0: Pruned 784 tips. 20: Pruned 725 tips. 12: Pruned 716 tips. Pruned 54216 k-mer in 34894 tips. Pruning tips shorter than 4 bp... 27: Pruned 898 tips. 31: Pruned 930 tips. 33: Pruned 938 tips. 26: Pruned 965 tips. 28: Pruned 968 tips. 29: Pruned 958 tips. 35: Pruned 945 tips. 34: Pruned 906 tips. 30: Pruned 963 tips. 32: Pruned 1013 tips. 25: Pruned 961 tips. 24: Pruned 968 tips. 9: Pruned 923 tips. 5: Pruned 939 tips. 3: Pruned 957 tips. 14: Pruned 983 tips. 17: Pruned 924 tips. 20: Pruned 934 tips. 11: Pruned 984 tips. 18: Pruned 977 tips. 13: Pruned 940 tips. 22: Pruned 996 tips. 19: Pruned 914 tips. 1: Pruned 1003 tips. 16: 4Pruned : 958Pruned tips. 967 tips. 15: Pruned 910 tips. 6: Pruned 996 tips. 7: Pruned 984 tips. 21: Pruned 937 tips. 23: Pruned 928 tips. 2: Pruned 925 tips. 12: Pruned 1026 tips. 10: Pruned 881 tips. 0: Pruned 913 tips. 8: Pruned 944 tips. 40: Pruned 941 tips. 46: Pruned 956 tips. 42: Pruned 980 tips. 39: Pruned 968 tips. 45: Pruned 948 tips. 36: Pruned 904 tips. 41: Pruned 941 tips. 44: Pruned 1013 tips. 38: Pruned 978 tips. 37: Pruned 921 tips. 43: Pruned 975 tips. 47: Pruned 947 tips. Pruned 122243 k-mer in 45728 tips. Pruning tips shorter than 8 bp... 9: Pruned 1085 tips. 5: Pruned 1090 tips. 3: Pruned 1094 tips. 11: Pruned 1141 tips. 1: Pruned 1147 tips. 6: Pruned 1146 tips. 7: Pruned 1118 tips. 4: Pruned 1189 tips. 10: Pruned 1142 tips. 2: Pruned 1148 tips. 0: Pruned 1206 tips. 8: Pruned 1202 tips. 33: Pruned 1057 tips. 27: Pruned 1094 tips. 31: Pruned 1084 tips. 29: Pruned 1131 tips. 26: Pruned 1168 tips. 35: Pruned 1068 tips. 34: Pruned 1136 tips. 28: Pruned 1136 tips. 30: Pruned 1152 tips. 32: Pruned 1176 tips. 24: Pruned 1144 tips. 25: Pruned 1123 tips. 22: Pruned 1142 tips. 14: Pruned 1127 tips. 17: Pruned 1080 tips. 18: Pruned 1093 tips. 20: Pruned 1099 tips. 15: Pruned 1180 tips. 16: Pruned 1131 tips. 23: Pruned 1165 tips. 13: Pruned 1095 tips. 19: Pruned 1127 tips. 21: Pruned 1147 tips. 12: Pruned 1079 tips. 42: Pruned 1129 tips. 39: Pruned 1149 tips. 38: Pruned 1130 tips. 41: Pruned 1141 tips. 46: Pruned 1052 tips. 40: Pruned 1072 tips. 44: Pruned 1092 tips. 45: Pruned 1141 tips. 43: Pruned 1095 tips. 36: Pruned 1097 tips. 37: Pruned 1119 tips. 47: Pruned 1147 tips. Pruned 258119 k-mer in 54006 tips. Pruning tips shorter than 16 bp... 27: Pruned 1273 tips. 26: Pruned 1230 tips. 33: Pruned 1258 tips. 31: Pruned 1208 tips. 35: Pruned 1320 tips. 29: Pruned 1249 tips. 28: Pruned 1255 tips. 34: Pruned 1289 tips. 30: Pruned 1285 tips. 32: Pruned 1306 tips. 24: Pruned 1300 tips. 25: Pruned 1299 tips. 42: Pruned 1223 tips. 41: Pruned 1275 tips. 39: Pruned 1249 tips. 43: Pruned 1246 tips. 9: Pruned 1246 tips. 46: Pruned 1310 tips. 45: Pruned 1202 tips. 38: Pruned 1238 tips. 40: Pruned 1280 tips. 36: Pruned 1265 tips. 44: Pruned 1284 tips. 47: Pruned 1218 tips. 37: Pruned 1278 tips. 11: Pruned 1291 tips. 6: Pruned 1306 tips. 1: Pruned 1258 tips. 3: Pruned 1299 tips. 5: Pruned 1292 tips. 4: Pruned 1256 tips. 7: Pruned 1321 tips. 10: Pruned 1310 tips. 0: Pruned 1319 tips. 2: Pruned 1332 tips. 8: Pruned 1342 tips. 22: Pruned 1279 tips. 14: Pruned 1272 tips. 20: Pruned 1264 tips. 15: Pruned 1276 tips. 19: Pruned 1302 tips. 17: Pruned 1307 tips. 18: Pruned 1317 tips. 16: Pruned 1233 tips. 21: Pruned 1226 tips. 13: Pruned 1351 tips. 23: Pruned 1292 tips. 12: Pruned 1268 tips. Pruned 580341 k-mer in 61299 tips. Pruning tips shorter than 32 bp... 22: Pruned 983 tips. 17: Pruned 993 tips. 14: Pruned 1026 tips. 18: Pruned 991 tips. 13: Pruned 1022 tips. 20: Pruned 994 tips. 19: Pruned 1008 tips. 15: Pruned 1000 tips. 23: Pruned 974 tips. 12: Pruned 993 tips. 16: Pruned 992 tips. 21: Pruned 1023 tips. 27: Pruned 990 tips. 42: Pruned 965 tips. 41: Pruned 951 tips. 39: Pruned 1027 tips. 35: Pruned 965 tips. 46: Pruned 1024 tips. 38: Pruned 958 tips. 43: Pruned 1017 tips. 40: Pruned 996 tips. 44: Pruned 990 tips. 33: Pruned 993 tips. 29: Pruned 1038 tips. 36: Pruned 937 tips. 31: Pruned 1003 tips. 37: Pruned 1020 tips. 34: Pruned 1016 tips. 26: Pruned 1004 tips. 47: Pruned 990 tips. 45: Pruned 988 tips. 28: Pruned 1012 tips. 30: Pruned 1021 tips. 25: Pruned 1002 tips. 32: Pruned 1010 tips. 24: Pruned 1053 tips. 9: Pruned 971 tips. 11: Pruned 965 tips. 3: Pruned 987 tips. 5: Pruned 1031 tips. 6: Pruned 996 tips. 7: Pruned 1015 tips. 4: Pruned 1030 tips. 8: Pruned 1046 tips. 0: Pruned 1010 tips. 1: Pruned 1042 tips. 10: Pruned 1025 tips. 2: Pruned 1007 tips. Pruned 830376 k-mer in 48094 tips. Pruning tips shorter than 64 bp... 27: Pruned 744 tips. 29: Pruned 718 tips. 34: Pruned 731 tips. 26: Pruned 729 tips. 35: Pruned 695 tips. 33: Pruned 688 tips. 30: Pruned 755 tips. 31: Pruned 783 tips. 28: Pruned 712 tips. 32: Pruned 753 tips. 24: Pruned 737 tips. 25: Pruned 765 tips. 22: Pruned 691 tips. 9: Pruned 700 tips. 4: Pruned 710 tips. 11: Pruned 725 tips. 18: Pruned 729 tips. 14: Pruned 712 tips. 17: Pruned 708 tips. 42: Pruned 731 tips. 5: Pruned 699 tips. 1: Pruned 805 tips. 6: Pruned 736 tips. 46: Pruned 689 tips. 15: Pruned 761 tips. 7: Pruned 754 tips. 20: Pruned 749 tips. 16: Pruned 726 tips. 19: Pruned 686 tips. 13: Pruned 662 tips. 3: Pruned 712 tips. 8: Pruned 767 tips. 21: Pruned 740 tips. 10: Pruned 676 tips. 23: Pruned 697 tips. 0: Pruned 749 tips. 43: Pruned 758 tips. 39: Pruned 703 tips. 38: Pruned 749 tips. 12: Pruned 735 tips. 2: Pruned 718 tips. 4037: Pruned 736 tips. : Pruned 727 tips. 41: Pruned 699 tips. 44: Pruned 742 tips. 36: Pruned 688 tips. 45: Pruned 755 tips. 47: Pruned 724 tips. Pruned 1031937 k-mer in 34858 tips. Pruning tips shorter than 128 bp... 27: Pruned 480 tips. 29: Pruned 540 tips. 35: Pruned 550 tips. 34: Pruned 557 tips. 31: Pruned 514 tips. 14: Pruned 491 tips. 17: Pruned 520 tips. 26: Pruned 557 tips. 28: Pruned 545 tips. 32: Pruned 551 tips. 3: Pruned 558 tips. 6: Pruned 511 tips. 4: Pruned 530 tips. 19: Pruned 549 tips. 22: Pruned 531 tips. 33: Pruned 488 tips. 30: Pruned 497 tips. 18: Pruned 515 tips. 15: Pruned 529 tips. 24: Pruned 540 tips. 20: Pruned 512 tips. 39: Pruned 540 tips. 46: Pruned 545 tips. 11: Pruned 521 tips. 21: Pruned 545 tips. 7: Pruned 514 tips. 23: Pruned 560 tips. 16: Pruned 493 tips. 13: Pruned 506 tips. 9: Pruned 528 tips. 1: Pruned 504 tips. 5: Pruned 535 tips. 8: Pruned 502 tips. 12: Pruned 513 tips. 10: Pruned 565 tips. 42: Pruned 495 tips. 40: Pruned 559 tips. 25: Pruned 541 tips. 2: Pruned 525 tips. 43: Pruned 541 tips. 44: Pruned 537 tips. 37: Pruned 502 tips. 45: Pruned 494 tips. 0: Pruned 524 tips. 41: Pruned 512 tips. 38: Pruned 562 tips. 47: Pruned 604 tips. 36: Pruned 511 tips. Pruned 1404972 k-mer in 25343 tips. Pruning tips shorter than 256 bp... 4: Pruned 377 tips. 7: Pruned 376 tips. 3: Pruned 369 tips. 9: Pruned 360 tips. 6: Pruned 366 tips. 27: Pruned 399 tips. 11: Pruned 378 tips. 10: Pruned 400 tips. 1: Pruned 376 tips. 35: Pruned 370 tips. 29: Pruned 414 tips. 34: Pruned 372 tips. 31: Pruned 406 tips. 26: Pruned 365 tips. 33: Pruned 398 tips. 8: Pruned 385 tips. 0: Pruned 431 tips. 2: Pruned 400 tips. 5: Pruned 386 tips. 28: Pruned 390 tips. 24: Pruned 397 tips. 30: Pruned 382 tips. 32: Pruned 372 tips. 46: Pruned 376 tips. 42: Pruned 377 tips. 37: Pruned 405 tips. 39: Pruned 374 tips. 22: Pruned 404 tips. 43: Pruned 373 tips. 18: Pruned 385 tips. 40: Pruned 372 tips. 38: Pruned 407 tips. 45: Pruned 406 tips. 47: Pruned 366 tips. 25: Pruned 385 tips. 41: Pruned 431 tips. 17: Pruned 378 tips. 15: Pruned 408 tips. 19: Pruned 394 tips. 44: Pruned 375 tips. 21: Pruned 386 tips. 23: Pruned 379 tips. 36: Pruned 417 tips. 14: Pruned 359 tips. 20: Pruned 344 tips. 16: Pruned 391 tips. 13: Pruned 408 tips. 12: Pruned 403 tips. Pruned 1967620 k-mer in 18572 tips. Pruning tips shorter than 512 bp... 31: Pruned 188 tips. 29: Pruned 203 tips. 27: Pruned 219 tips. 35: Pruned 196 tips. 26: Pruned 247 tips. 18: Pruned 202 tips. 34: Pruned 211 tips. 43: Pruned 206 tips. 38: Pruned 216 tips. 33: Pruned 224 tips. 24: Pruned 214 tips. 32: Pruned 228 tips. 45: Pruned 210 tips. 22: Pruned 206 tips. 37: Pruned 229 tips. 17: Pruned 180 tips. 42: Pruned 233 tips. 15: Pruned 213 tips. 28: Pruned 203 tips. 46: Pruned 220 tips. 21: Pruned 199 tips. 30: Pruned 247 tips. 41: Pruned 212 tips. 44: Pruned 216 tips. 39: Pruned 197 tips. 40: Pruned 222 tips. 19: Pruned 226 tips. 4: Pruned 206 tips. 25: Pruned 243 tips. 14: Pruned 244 tips. 47: Pruned 224 tips. 16: Pruned 231 tips. 36: Pruned 246 tips. 23: Pruned 227 tips. 12: Pruned 231 tips. 20: Pruned 227 tips. 13: Pruned 223 tips. 3: Pruned 213 tips. 9: Pruned 206 tips. 6: Pruned 240 tips. 5: Pruned 214 tips. 0: Pruned 232 tips. 11: Pruned 208 tips. 7: Pruned 213 tips. 1: Pruned 202 tips. 10: Pruned 224 tips. 2: Pruned 230 tips. 8: Pruned 239 tips. Pruned 2136499 k-mer in 10490 tips. Pruning tips shorter than 1024 bp... 29: Pruned 71 tips. 37: Pruned 69 tips. 35: Pruned 73 tips. 27: Pruned 76 tips. 26: Pruned 91 tips. 32: Pruned 83 tips. 46: Pruned 74 tips. 24: Pruned 90 tips. 33: Pruned 83 tips. 22: Pruned 87 tips. 43: Pruned 67 tips. 4: Pruned 67 tips. 34: Pruned 74 tips. 44: Pruned 66 tips. 31: Pruned 75 tips. 30: Pruned 83 tips. 38: Pruned 79 tips. 45: Pruned 80 tips. 39: Pruned 83 tips. 25: Pruned 77 tips. 19: Pruned 87 tips. 36: Pruned 86 tips. 40: Pruned 83 tips. 42: Pruned 87 tips. 47: Pruned 81 tips. 21: Pruned 73 tips. 41: Pruned 73 tips. 15: Pruned 79 tips. 28: Pruned 84 tips. 14: Pruned 76 tips. 18: Pruned 73 tips. 23: Pruned 89 tips. 20: Pruned 95 tips. 17: Pruned 93 tips. 3: Pruned 77 tips. 16: Pruned 90 tips. 0: Pruned 92 tips. 6: Pruned 91 tips. 12: Pruned 105 tips. 9: Pruned 85 tips. 11: Pruned 79 tips. 7: Pruned 78 tips. 1: Pruned 102 tips. 5: Pruned 88 tips. 10: Pruned 87 tips. 13: Pruned 100 tips. 2: Pruned 80 tips. 8: Pruned 91 tips. Pruned 1596229 k-mer in 3952 tips. Pruning tips shorter than 2000 bp... 26: Pruned 18 tips. 27: Pruned 30 tips. 24: Pruned 29 tips. 1: Pruned 29 tips. 0: Pruned 21 tips. 33: Pruned 17 tips. 29: Pruned 19 tips. 32: Pruned 30 tips. 9: Pruned 17 tips. 34: Pruned 29 tips. 4: Pruned 25 tips. 31: Pruned 24 tips. 43: Pruned 24 tips. 11: Pruned 20 tips. 46: Pruned 21 tips. 30: Pruned 30 tips. 38: Pruned 22 tips. 35: Pruned 28 tips. 6: Pruned 23 tips. 45: Pruned 30 tips. 15: Pruned 22 tips. 10: Pruned 24 tips. 28: Pruned 30 tips. 3: Pruned 28 tips. 7: Pruned 35 tips. 37: Pruned 20 tips. 42: Pruned 26 tips. 8: Pruned 27 tips. 25: Pruned 37 tips. 36: Pruned 25 tips. 5: Pruned 26 tips. 40: Pruned 25 tips. 2: Pruned 23 tips. 39: Pruned 21 tips. 19: Pruned 22 tips. 44: Pruned 24 tips. 22: Pruned 24 tips. 16: Pruned 29 tips. 47: Pruned 34 tips. 23: Pruned 24 tips. 12: Pruned 22 tips. 21: Pruned 35 tips. 20: Pruned 31 tips. 41: Pruned 32 tips. 13: Pruned 31 tips. 14: Pruned 29 tips. 17: Pruned 29 tips. 18: Pruned 20 tips. Pruned 986338 k-mer in 1241 tips. Pruning tips shorter than 2000 bp... 32: Pruned 0 tips. 27: Pruned 0 tips. 24: Pruned 0 tips. 26: Pruned 0 tips. 34: Pruned 0 tips. 15: Pruned 0 tips. 21: Pruned 0 tips. 16: Pruned 1 tips. 29: Pruned 0 tips. 20: Pruned 0 tips. 22: Pruned 0 tips. 30: Pruned 0 tips. 19: Pruned 0 tips. 1: Pruned 0 tips. 23: Pruned 0 tips. 31: Pruned 0 tips. 13: Pruned 0 tips. 28: Pruned 0 tips. 4: Pruned 1 tips. 33: Pruned 0 tips. 35: Pruned 0 tips. 12: Pruned 1 tips. 14: Pruned 0 tips. 0: Pruned 0 tips. 9: Pruned 0 tips. 25: Pruned 0 tips. 17: Pruned 0 tips. 3: Pruned 0 tips. 11: Pruned 1 tips. 7: Pruned 0 tips. 6: Pruned 0 tips. 18: Pruned 0 tips. 8: Pruned 0 tips. 10: Pruned 0 tips. 5: Pruned 0 tips. 45: Pruned 0 tips. 2: Pruned 0 tips. 43: Pruned 0 tips. 38: Pruned 0 tips. 46: Pruned 0 tips. 42: Pruned 0 tips. 40: Pruned 0 tips. 37: Pruned 0 tips. 36: Pruned 0 tips. 47: Pruned 0 tips. 39: Pruned 0 tips. 41: Pruned 0 tips. 44: Pruned 0 tips. Pruned 1126 k-mer in 4 tips. Pruning tips shorter than 2000 bp... 32: Pruned 0 tips. 27: Pruned 0 tips. 24: Pruned 0 tips. 26: Pruned 0 tips. 21: Pruned 0 tips. 15: Pruned 0 tips. 34: Pruned 0 tips. 1: Pruned 0 tips. 22: Pruned 0 tips. 16: Pruned 0 tips. 29: Pruned 0 tips. 20: Pruned 0 tips. 19: Pruned 0 tips. 30: Pruned 0 tips. 31: Pruned 0 tips. 23: Pruned 0 tips. 4: Pruned 0 tips. 28: Pruned 0 tips. 12: Pruned 0 tips. 0: Pruned 0 tips. 33: Pruned 0 tips. 35: Pruned 0 tips. 13: Pruned 0 tips. 3: Pruned 0 tips. 14: Pruned 0 tips. 6: Pruned 0 tips. 9: Pruned 0 tips. 7: Pruned 0 tips. 17: Pruned 0 tips. 11: Pruned 0 tips. 25: Pruned 0 tips. 18: Pruned 0 tips. 8: Pruned 0 tips. 5: Pruned 0 tips. 10: Pruned 0 tips. 45: Pruned 0 tips. 43: Pruned 0 tips. 38: Pruned 0 tips. 2: Pruned 0 tips. 46: Pruned 0 tips. 42: Pruned 0 tips. 37: Pruned 0 tips. 47: Pruned 0 tips. 36: Pruned 0 tips. 40: Pruned 0 tips. 39: Pruned 0 tips. 44: Pruned 0 tips. 41: Pruned 0 tips. Pruned 402891 tips in 13 rounds. Popping bubbles... 0: Removed 7220 bubbles. 1: Removed 7039 bubbles. 2: Removed 6983 bubbles. 3: Removed 6836 bubbles. 4: Removed 6581 bubbles. 5: Removed 6419 bubbles. 6: Removed 6216 bubbles. 7: Removed 6174 bubbles. 8: Removed 5951 bubbles. 9: Removed 5729 bubbles. 10: Removed 5621 bubbles. 11: Removed 5537 bubbles. 12: Removed 5353 bubbles. 13: Removed 5394 bubbles. 14: Removed 5168 bubbles. 15: Removed 4818 bubbles. 16: Removed 4848 bubbles. 17: Removed 4466 bubbles. 18: Removed 4485 bubbles. 19: Removed 4320 bubbles. 20: Removed 4190 bubbles. 21: Removed 4061 bubbles. 22: Removed 3846 bubbles. 23: Removed 3798 bubbles. 24: Removed 3503 bubbles. 25: Removed 3458 bubbles. 26: Removed 3256 bubbles. 27: Removed 3195 bubbles. 28: Removed 2903 bubbles. 29: Removed 2856 bubbles. 30: Removed 2537 bubbles. 31: Removed 2477 bubbles. 32: Removed 2344 bubbles. 33: Removed 2264 bubbles. 34: Removed 2096 bubbles. 35: Removed 1972 bubbles. 36: Removed 1736 bubbles. 37: Removed 1640 bubbles. 38: Removed 1449 bubbles. 39: Removed 1276 bubbles. 40: Removed 1138 bubbles. 41: Removed 1022 bubbles. 42: Removed 869 bubbles. 43: Removed 705 bubbles. 44: Removed 506 bubbles. 45: Removed 378 bubbles. 46: Removed 255 bubbles. 47: Removed 84 bubbles. Removed 174972 bubbles. Removed 174972 bubbles. Marking ambiguous branches... 22: Marked 58464 edges of 25354 ambiguous vertices. 10: Marked 58383 edges of 25357 ambiguous vertices. 35: Marked 55098 edges of 24117 ambiguous vertices. 1: Marked 57966 edges of 25073 ambiguous vertices. 47: Marked 57685 edges of 25059 ambiguous vertices. 34: Marked 57279 edges of 24851 ambiguous vertices. 13: Marked 57025 edges of 24717 ambiguous vertices. 2: Marked 57533 edges of 24899 ambiguous vertices. 21: Marked 57709 edges of 25111 ambiguous vertices. 24: Marked 58802 edges of 25383 ambiguous vertices. 23: Marked 57037 edges of 24734 ambiguous vertices. 0: Marked 58202 edges of 25233 ambiguous vertices. 14: Marked 56507 edges of 24698 ambiguous vertices. 11: Marked 55352 edges of 24159 ambiguous vertices. 28: Marked 57409 edges of 24892 ambiguous vertices. 37: Marked 58161 edges of 25241 ambiguous vertices. 26: Marked 58354 edges of 25178 ambiguous vertices. 18: Marked 57250 edges of 24821 ambiguous vertices. 30: Marked 56309 edges of 24567 ambiguous vertices. 3: Marked 56310 edges of 24498 ambiguous vertices. 27: Marked 55811 edges of 24270 ambiguous vertices. 36: Marked 59113 edges of 25496 ambiguous vertices. 38: Marked 57956 edges of 25186 ambiguous vertices. 6: Marked 58563 edges of 25365 ambiguous vertices. 8: Marked 58466 edges of 25177 ambiguous vertices. 16: Marked 58009 edges of 25278 ambiguous vertices. 33: Marked 57091 edges of 24699 ambiguous vertices. 17: Marked 58089 edges of 25197 ambiguous vertices. 5: Marked 57373 edges of 24923 ambiguous vertices. 42: Marked 58813 edges of 25452 ambiguous vertices. 19: Marked 56477 edges of 24541 ambiguous vertices. 4: Marked 60686 edges of 26187 ambiguous vertices. 15: Marked 57789 edges of 25142 ambiguous vertices. 45: Marked 57479 edges of 25004 ambiguous vertices. 29: Marked 56823 edges of 24663 ambiguous vertices. 25: Marked 58016 edges of 25165 ambiguous vertices. 43: Marked 56377 edges of 24538 ambiguous vertices. 39: Marked 57664 edges of 24904 ambiguous vertices. 41: Marked 56857 edges of 24690 ambiguous vertices. 9: Marked 58025 edges of 25108 ambiguous vertices. 40: Marked 59698 edges of 25733 ambiguous vertices. 31: Marked 57563 edges of 25014 ambiguous vertices. 44: Marked 57017 edges of 24717 ambiguous vertices. 32: Marked 58430 edges of 25315 ambiguous vertices. 12: Marked 58107 edges of 25151 ambiguous vertices. 46: Marked 56053 edges of 24509 ambiguous vertices. 7: Marked 57218 edges of 24839 ambiguous vertices. 20: Marked 60868 edges of 26044 ambiguous vertices. Marked 1200249 ambiguous branches. Assembling... 22: Assembled 1068135 k-mer in 28073 contigs. 32: Assembled 1098547 k-mer in 28100 contigs. 35: Assembled 1078607 k-mer in 27191 contigs. 27: Assembled 1067489 k-mer in 27535 contigs. 33: Assembled 1082954 k-mer in 27380 contigs. 28: Assembled 1117364 k-mer in 27995 contigs. 29: Assembled 1083064 k-mer in 27466 contigs. 15: Assembled 1067893 k-mer in 27458 contigs. 16: Assembled 1088783 k-mer in 27974 contigs. 34: Assembled 1126828 k-mer in 27732 contigs. 23: Assembled 1033567 k-mer in 27323 contigs. 19: Assembled 1071773 k-mer in 27109 contigs. 31: Assembled 1148590 k-mer in 27808 contigs. 9: Assembled 1094352 k-mer in 27973 contigs. 17: Assembled 1061976 k-mer in 27988 contigs. 25: Assembled 1096744 k-mer in 27884 contigs. 13: Assembled 1100302 k-mer in 27628 contigs. 26: Assembled 1130819 k-mer in 27786 contigs. 21: Assembled 1127958 k-mer in 27793 contigs. 24: Assembled 1061795 k-mer in 27758 contigs. 7: Assembled 1053590 k-mer in 27492 contigs. 1: Assembled 1056772 k-mer in 27826 contigs. 30: Assembled 1128467 k-mer in 27490 contigs. 12: Assembled 1110418 k-mer in 27761 contigs. 20: Assembled 1123690 k-mer in 28704 contigs. 14: Assembled 1131163 k-mer in 27576 contigs. 5: Assembled 1119658 k-mer in 27655 contigs. 46: Assembled 1039097 k-mer in 27222 contigs. 6: Assembled 1079134 k-mer in 27812 contigs. 18: Assembled 1116069 k-mer in 27765 contigs. 41: Assembled 1101558 k-mer in 27675 contigs. 2: Assembled 1116656 k-mer in 27755 contigs. 8: Assembled 1091952 k-mer in 27818 contigs. 37: Assembled 1040096 k-mer in 27617 contigs. 3: Assembled 1070818 k-mer in 27621 contigs. 10: Assembled 1104121 k-mer in 28194 contigs. 11: Assembled 1120966 k-mer in 27344 contigs. 0: Assembled 1049558 k-mer in 27669 contigs. 38: Assembled 1100863 k-mer in 27776 contigs. 4: Assembled 1120696 k-mer in 28445 contigs. 45: Assembled 1108323 k-mer in 27604 contigs. 42: Assembled 1118559 k-mer in 28106 contigs. 39: Assembled 1112391 k-mer in 27599 contigs. 47: Assembled 1110299 k-mer in 27691 contigs. 43: Assembled 1092431 k-mer in 27457 contigs. 36: Assembled 1114400 k-mer in 27946 contigs. 40: Assembled 1080011 k-mer in 28049 contigs. 44: Assembled 1107643 k-mer in 27536 contigs. Assembled 52526939 k-mer in 1331159 contigs. Concatenating to assembly-1.fa Concatenating to assembly-bubbles.fa Done. AdjList -k25 -m30 assembly-1.fa >assembly-1.adj abyss-filtergraph -k25 -g assembly-2.adj assembly-1.adj >assembly-1.path PopBubbles -j2 -k25 -b10000 -p0.9 -g assembly-3.adj assembly-1.fa assembly-2.adj >assembly-2.path MergeContigs -k25 -o assembly-3.fa assembly-1.fa assembly-2.adj assembly-2.path awk '!/^>/ {x[">" $1]=1; next} {getline s} $1 in x {print $0 "\n" s}' \ assembly-2.path assembly-1.fa >assembly-indel.fa ln -sf assembly-3.fa assembly-unitigs.fa abyss-bwa -j2 -l25 filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz assembly-3.fa \ |abyss-fixmate -h lib1-3.hist \ |sort -snk3 -k4 \ |DistanceEst -j2 -k25 -l25 -s200 -n10 -o lib1-3.dist lib1-3.hist {"status":"success","message":"","result":{"id":6353,"name":"Abyss_fish546_PE-2013-01-24-11-50-07.639","owner":"sr320","system":"lonestar4.tacc.teragrid.org","software":"abyss-lonestar-1.3.3u1","processors":48,"requestedTime":"08:00:00","memory":2,"callbackUrl":null,"archive":true,"archivePath":"/sr320/analyses/Abyss_fish546_PE-2013-01-24-11-50-07.639","outputPath":null,"outputUrl":"https://foundation.iplantcollaborative.org/io-v1/io/list//sr320/analyses/Abyss_fish546_PE-2013-01-24-11-50-07.639","status":"FINISHED","submitTime":1359028240000,"startTime":1359028272000,"endTime":1359030145085,"inputs":[{"lib2":"/sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz"},{"lib1":"/sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz"}],"parameters":[{"littleE":""},{"minOver":"30"},{"minUnitig":"200"},{"cov":""},{"maxBranch":"2"},{"scaffPairs":""},{"minAlign":""},{"maxBubble":"10000"},{"aligner":"bwa"},{"distErr":"6"},{"contigPairs":"10"},{"minContig":""},{"kmer":"25"},{"name":"assembly"},{"minTip":"2000"},{"qual":"3"},{"bigE":"0"},{"seqidBubble":"0.9"}],"permissions":[]}}{"status":"success","message":"","result":{"id":6353,"name":"Abyss_fish546_PE-2013-01-24-11-50-07.639","owner":"sr320","system":"lonestar4.tacc.teragrid.org","software":"abyss-lonestar-1.3.3u1","processors":48,"requestedTime":"08:00:00","memory":2,"callbackUrl":null,"archive":true,"archivePath":"/sr320/analyses/Abyss_fish546_PE-2013-01-24-11-50-07.639","outputPath":null,"outputUrl":"https://foundation.iplantcollaborative.org/apps-v1/job/6353/output/list","status":"ARCHIVING","submitTime":1359028240000,"startTime":1359028272000,"endTime":1359030145085,"inputs":[{"lib2":"/sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz"},{"lib1":"/sr320/fish546/filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz"}],"parameters":[{"littleE":""},{"minOver":"30"},{"minUnitig":"200"},{"cov":""},{"maxBranch":"2"},{"scaffPairs":""},{"minAlign":""},{"maxBubble":"10000"},{"aligner":"bwa"},{"distErr":"6"},{"contigPairs":"10"},{"minContig":""},{"kmer":"25"},{"name":"assembly"},{"minTip":"2000"},{"qual":"3"},{"bigE":"0"},{"seqidBubble":"0.9"}],"permissions":[]}}