Megachile rotundata

Data

Original Traces

• 8 pairs of data files (paired ends)

 cat trace.count | grep _1_ | sed 's/_sequence.txt//' | perl -ane 'print "  ",$F[1],"\t",$F[0]/4,"\t",$F[0]/2,"\n";'

 lib        insert   mates           reads        readLen   ~coverage(500M genome)  reverse  adaptors            comments
 s_2_3kbp   3000     21,563,283      43,126,566   124       11                      ?        circularizarion
 #s_2_5kbp  5000/300 36218589        72,437,178   35        5                       yes      ?                   insert size is << 5kbp
 s_2_8kbp   8000     198377          396,754      124       0.1                     ?        ?
 s_3        475      35548153        71,096,306   124       18
 s_4        475      35471044        70,942,088   124       18
 s_5        475      35616846        71,233,692   124       18
 s_6        475      35303840        70,607,680   124       18
 s_7        475      34893313        69,786,626   124       18
 total      .        198,594,856     397,189,712

Corrected Traces

• Mated ones

 lib        insert   mates           reads
 s_2_3kb    3000     4,823,235       9,646,470   
 s_2_8kb    8000     111,267         222,534    
 s_3        475      33,024,597      66,049,194  
 s_4        475      33,237,593      66,475,186  
 s_5        475      33,150,790      66,301,580  
 s_6        475      33,223,371      66,446,742  
 s_7        475      32,647,890      65,295,780
 total      .        170,218,743     340,437,486

Adaptors

 >circularizarion
 CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA
 >circularizarion.revcomp
 TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG 

Location

 /fs/szattic-asmg5/Bees/Megachile_rotundata/error_correction/large_libs/s_?_?_?kb.sequence.cor.all.txt
 /fs/szattic-asmg5/Bees/Megachile_rotundata/error_free/s_?_?_sequence.cor.txt
 /fs/szattic-asmg5/Bees/Megachile_rotundata/frg/  # frg files to assemble

Assemblies

• CA Version: 6.1 (09/01/2010) /fs/szdevel/dpuiu/SourceForge/wgs-6.1/Linux-amd64/bin/runCA
• SOAP version 1.04: /nfshomes/dpuiu/szdevel/SOAPdenovo_Release1.04/

CA noOBT partial

• Data : 3 libraries

 LibraryName           numActiveFRG  numDeletedFRG  numMatedFRG  readLength  clearLength  
 GLOBAL                72995448      0              70632632     8307194830  8278360381   
 LegacyUnmatedReads    0             0              0            0           0            
 s_2_3kb               9166343       0              8736228      942501164   914798596    
 s_2_8kb               210266        0              199620       21669112    20742291     
 s_3                   63618839      0              61696784     7343024554  7342819494   

• Stats

 .       elem       min    q1     q2     q3     max        mean       n50        sum            
 utg     1437146    64     123    143    195    67048      308.78     870        443759899      
 ctg     37494      65     2185   3998   7706   191323     6380.39    10151      239226293      
 deg     1136469    64     123    143    184    5031       160.11     164        181954480      
 scf     20827      122    3228   6374   13700  202495     11508.95   20462      239696810      

• Locations

 ginkgo:/scratch1/dpuiu/Megachile_rotundata/Assembly/wgs-noOBT-partial/

 Moved  from
 mulberry:/scratch2/dpuiu/Megachile_rotundata/Assembly/wgs-noOBT-partial/

CA noOBT

Gatekeeper

• ~ 74X cvg

 LOAD                  STATS          
 7                     libInput       
 7                     libLoaded      
 0                     libErrors      
 5                     libWarnings    
 
 326,236,387           frgLoaded        
 326236387             numRandom      
 326236387             numPacked       

 LibraryName           numActiveFRG  numDelFRG  numMatedFRG  readLength   clearLength    #AATCATACAATCACAATCATAC|GTATGATTGTGATTGTATGATT   #AATCATACAATCAC|GTGATTGTATGATT   #AATCATACAATCAC|GTGATTGTATGATT(1mutation)
                                                                                                                                                             
 GLOBAL                326,236,387   0          315518526    37451489553  37418130441  
 LegacyUnmatedReads    0             0          0            0            0            
 s_2_3kb               9107424       0          9107424      942165284    910444046      #1125738  12%                                    1366161
 s_2_8kb               209336        0          209336       21814418     20787384       #46762    22%                                    55736(26%)                          68729(32%)
 s_3                   63618839      0          61696784     7343024554   7342819494     #         11%
 s_4                   63544688      0          61255960     7291557748   7291478152     #6804757  11%
 s_5                   63370860      0          61084368     7271218123   7271051639     #         11%
 s_6                   63780887      0          61685156     7359094156   7359012512     #         11%
 s_7                   62604353      0          60479498     7222615270   7222537214     #         11%

Meryl

 meryl -Dh -s 0-mercounts/asm-C-ms22-cm0 
 Found 30570218845 mers.
 Found 271464470 distinct mers.
 Found 11164787 unique mers.
 Largest mercount is 87984949; 1896 mers are too big for histogram.
 1       11164787        0.0411  0.0004
 2       9376915         0.0757  0.0010
 3       3714582         0.0894  0.0013
 ...
 54      5344148         0.6573  0.1788
 ... 

 fasta2tab.pl 0-mercounts/asm.nmers.ovl.fasta | sort -n -r | head -5
 87,908,217        AATCATACAATCACAATCATAC
 84,450,288        CAATCATACAATCACAATCATA
 ...
 74,975,282        AATAATATGAGTTAGATTGATA

 egrep -c 'AATCATACAATCACAATCATAC|GTATGATTGTGATTGTATGATT' *fastq *txt > egrep.count
 mulberry:/scratch2/dpuiu/Megachile_rotundata/Data/error_free/egrep.count

 meryl -Dh -s 0-mercounts/asm-C-ms15-cm0 | head
 Found 32850820919 mers.
 Found 142500876 distinct mers.
 Found 2381895 unique mers.
 Largest mercount is 125816941; 2023 mers are too big for histogram.
 1       2381895 0.0167  0.0001
 2       2325770 0.0330  0.0002
 3       708786  0.0380  0.0003
 ...
 54      1851586 0.4894  0.0671
...

Overlap

• job count :

 cat 1-overlapper/ovlopts.pl | grep ^\"h | wc -l
 924

• Failures: 709 jobs failed; runCA 6.1 could not restart overlap properly !!!

 cat 1-overlap/overlap*out | grep "^Could not" | sort -u
 Could not malloc memory (1305184948 bytes)

 cat 1-overlapper/*pl | grep ^\"0 | sed 's/"//' | sed 's/\",//' >! 1-overlapper/ovlopts.pl.0
 cat 1-overlapper/*pl | grep ^\"h | sed 's/"//' | sed 's/\",//' >! 1-overlapper/ovlopts.pl.h
 cat 1-overlapper/*pl | grep ^\"-h | sed 's/"//' | sed 's/\",//' >! 1-overlapper/ovlopts.pl.-h

 paste 1-overlapper/ovlopts.pl.* | p 'print "overlap -M 8GB --hashload 0.8 -t 1 -h $F[3]  -r $F[5] -k 22 -k  \
       ./0-mercounts/asm.nmers.ovl.fasta  -o ./1-overlapper/$F[0]/$F[1].ovb.gz ./asm.gkpStore > \
       ./1-overlapper/overlap.0$..out \n";' | tail -709 > overlap.sh

• Stats

 overlapStore -d asm.ovlStore | awk '{print $1}' | uniq -c | awk '{print $1}' | count.pl | getSummary.pl -i 0 -j 1
 overlapStats -G asm.gkpStore -O asm.ovlStore -o asm

Location

 mulberry:/scratch2/dpuiu/Megachile_rotundata/Assembly/wgs-noOBT

SOAPdenovo (Tanja)

 cat *.ContigIndex | grep -v ^E | grep -v ^i | count.pl -i 1 | getSummary.pl -j 1 -t "contigs"
 cat *.ContigIndex | grep -v ^E | grep -v ^i | count.pl -i 1 | getSummary.pl -j 1 -min 100 -t "contigs(>100bp)"
 grep "^>" *.scaf | getSummary.pl -i 2 -t scaf

• Stats

 .                    elem       min    q1     q2     q3     max        mean       n50        sum            
 contigs              9742349    31     32     33     37     114832     60.09      44         585430821      
 contigs(>100bp)      177327     100    131    261    1398   114832     1333.68    3897       236496823     # N50 for Bee was 7K
 scaf                 7863       102    903    3272   17692  2338728    37825.70   240706     297423517     # N50 for Bee was 1.17M

• Location

 /fs/szattic-asmg5/Bees/Megachile_rotundata/Assembly/assembly5kbForAll

SOAPdenovo (Daniela)

• Stats

 cat asm.K31.contig | grep "^>" | awk '{print $3}' | uniq -c | awk '{print $2,$1}'  > asm.K31.contigLen.count

 .                    elem       min    q1     q2     q3     max        mean       n50        sum            
 contigs(all)         6,917,796  31     32     34     40     121554     70.46      73         487,401,812      
 contigs(>100bp)      210,666    100    124    222    1174   121554     1108.69    3138       233,563,401
 scaff                25,119     351    1896   4444   10914  1102803    11041.00   26876      277,338,897

 reads                340,437,486
 readsOnContigs       171,212,613 

• Location

 mulberry:/scratch2/dpuiu/Megachile_rotundata/Assembly/SOAPdenovo-redo