[stdout]

starting vdj_asm_asm, mem = 0.01
available mem = 844.35 GB
/scratch/etanis/software/cellranger-6.1.2/lib/bin/cr_vdj martian assembly main /scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/chnk010-ucc6a7a72ce /scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/chnk010-ucc6a7a72ce/files /scratch/etanis/ST-118/multi/dimitri-multi/journal/SC_MULTI_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ.fork0.chnk010.ucc6a7a72ce
n50_n50_rpu = 288

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.0 = AGATTGCGTTGGTAAA-1

using 232 reads

====================================================================================

graph has 72 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 2[2, 229]
surviving nonsolo ucounts = 1[229]
ids = [0]

====================================================================================
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.5 = AGATTGCTCACAGTAC-1

using 217 reads

====================================================================================

graph has 210 edges initially, 2 edges after simplification

total ucounts = 7
nonsolo ucounts = 3[2, 4, 207]
surviving nonsolo ucounts = 1[207]
ids = [1]

====================================================================================

UMI info for barcode AGATTGCTCACAGTAC-1 contig 1 = AGCCCTCAGA...
umi ACGACGGAGG = 206 reads: +430 validated

GOOD CONTIGS

TIG 1[bases=525]
0-79 ==> 0-79 on |141|IGHV3-48|5'UTR| [len=79] (mis=1)
79-432 ==> 0-353 on |142|IGHV3-48|L-REGION+V-REGION| [len=353] (mis=37)
463-509 ==> 0-46 on |54|IGHJ4|J-REGION| [len=46] (mis=5)
junction support: 1 umis using 12 reads
cdr3 = CARESYVGLYSSTSYPDYW at 421, score = 8 + 7
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 200
start codons at 79, 228, 235, 314, 356, 382, 437
confident = false
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.7 = AGATTGCTCACGCATA-1

using 23 reads

====================================================================================

graph has 8 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[23]
surviving nonsolo ucounts = 0[]
ids = []

====================================================================================
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.11 = AGATTGCTCCAAATGC-1

using 12 reads

====================================================================================

graph has 8 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 2[2, 9]
surviving nonsolo ucounts = 1[9]
ids = [2]

====================================================================================
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.20 = AGATTGCTCCGATATG-1

using 315 reads

====================================================================================

graph has 122 edges initially, 2 edges after simplification

total ucounts = 6
nonsolo ucounts = 1[310]
surviving nonsolo ucounts = 1[310]
ids = [1]

====================================================================================

UMI info for barcode AGATTGCTCCGATATG-1 contig 1 = GAATCAGTCC...
umi ATGCGTCACA = 315 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=549]
0-25 ==> 2-27 on |222|IGKV1-17|5'UTR| [len=27] (mis=0)
25-376 ==> 0-351 on |223|IGKV1-17|L-REGION+V-REGION| [len=351] (mis=19)
375-413 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=1)
413-549 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 44 reads
cdr3 = CLQYSSSPWTF at 352, score = 9 + 8
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 309
start codons at 25, 31, 100, 236, 455
confident = false
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.21 = AGATTGCTCCTAAGTG-1

using 30 reads

====================================================================================

graph has 12 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 1[29]
surviving nonsolo ucounts = 0[]
ids = []

====================================================================================
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.30 = AGATTGCTCTTTACGT-1

using 213 reads

====================================================================================

graph has 72 edges initially, 2 edges after simplification

total ucounts = 6
nonsolo ucounts = 2[3, 206]
surviving nonsolo ucounts = 1[206]
ids = [4]

====================================================================================

UMI info for barcode AGATTGCTCTTTACGT-1 contig 1 = GGGGTCTCAG...
umi CCGTTTTGGA = 206 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=528]
0-38 ==> 125-163 on |346|IGLV2-8|5'UTR| [len=163] (mis=0)
38-392 ==> 0-354 on |347|IGLV2-8|L-REGION+V-REGION| [len=354] (mis=13)
388-426 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=5)
426-528 ==> 0-102 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 36 reads
cdr3 = CSSHAGSTRVLF at 362, score = 8 + 8
umis assigned: [4]
of which 1 are surviving nonsolos
reads assigned: 201
start codons at 38, 195, 246, 345, 372
confident = false
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.32 = AGCAGCCAGAAGCCCA-1

using 397 reads

====================================================================================

graph has 150 edges initially, 6 edges after simplification

total ucounts = 7
nonsolo ucounts = 4[2, 4, 150, 238]
surviving nonsolo ucounts = 2[150, 238]
ids = [3, 6]

====================================================================================

UMI info for barcode AGCAGCCAGAAGCCCA-1 contig 1 = GCTGGGGTCT...
umi CTTCGATCGC = 28 reads: -324X +1 -1XX +1 -1XX +1 -12XX +1 -1XX +1 -1XX +3 -1XX +3 -1XX +21 -1XX +12 -1XX invalidated
umi GGCCAATATG = 236 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=640]
0-41 ==> 0-41 on |338|IGLV2-14|5'UTR| [len=41] (mis=0)
41-389 ==> 0-348 on |339|IGLV2-14|L-REGION+V-REGION| [len=361] (mis=0)
391-429 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=0)
429-640 ==> 0-211 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 34 reads
cdr3 = CSSYTSSSSVVF at 365, score = 8 + 8
umis assigned: [3, 6]
of which 2 are surviving nonsolos
reads assigned: 261
start codons at 41, 198, 242, 249
confident = false
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.36 = AGCAGCCAGACCGGAT-1

using 245 reads

====================================================================================

graph has 64 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 1[244]
surviving nonsolo ucounts = 1[244]
ids = [0]

====================================================================================

UMI info for barcode AGCAGCCAGACCGGAT-1 contig 1 = GGGGAGGAAT...
umi AACATACTGT = 228 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=497]
31-382 ==> 0-351 on |223|IGKV1-17|L-REGION+V-REGION| [len=351] (mis=19)
381-419 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=1)
419-497 ==> 0-78 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 43 reads
cdr3 = CLQYSSSPWTF at 358, score = 9 + 8
umis assigned: [0]
of which 1 are surviving nonsolos
reads assigned: 227
start codons at 31, 37, 106, 242, 461
confident = false
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.50 = AGCAGCCAGCAATCTC-1

using 242 reads

====================================================================================

graph has 88 edges initially, 2 edges after simplification

total ucounts = 4
nonsolo ucounts = 2[5, 235]
surviving nonsolo ucounts = 1[235]
ids = [0]

====================================================================================
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.53 = AGCAGCCAGCCACGTC-1

using 223 reads

====================================================================================

graph has 74 edges initially, 2 edges after simplification

total ucounts = 7
nonsolo ucounts = 2[3, 215]
surviving nonsolo ucounts = 1[215]
ids = [4]

====================================================================================

UMI info for barcode AGCAGCCAGCCACGTC-1 contig 1 = AGTCCCAGTC...
umi GTTTTCGATC = 207 reads: +391 validated

GOOD CONTIGS

TIG 1[bases=488]
0-20 ==> 38-58 on |238|IGKV1-9|5'UTR| [len=58] (mis=0)
20-371 ==> 0-351 on |239|IGKV1-9|L-REGION+V-REGION| [len=351] (mis=15)
372-411 ==> 0-39 on |214|IGKJ2|J-REGION| [len=39] (mis=3)
411-488 ==> 0-77 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 41 reads
cdr3 = CQQLNSYPPYTF at 347, score = 8 + 8
umis assigned: [4]
of which 1 are surviving nonsolos
reads assigned: 205
start codons at 20, 26, 82, 170, 453
confident = false
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.56 = AGCAGCCAGCGACGTA-1

using 127 reads

====================================================================================

graph has 74 edges initially, 10 edges after simplification

total ucounts = 6
nonsolo ucounts = 3[2, 26, 96]
surviving nonsolo ucounts = 2[26, 96]
ids = [2, 5]

====================================================================================

UMI info for barcode AGCAGCCAGCGACGTA-1 contig 1 = GTCAGTCCCA...
umi ATTACTGTTA = 4 reads: -254 +3 -1X +5 -1XX +4 -1XX +6 -1XX +2 -1XX +2 -2XX +20 -1XX +8 -1XX +4 -68 invalidated
umi TTCTGTTTCA = 95 reads: +385 validated

GOOD CONTIGS

TIG 1[bases=544]
0-23 ==> 8-31 on |226|IGKV1-33|5'UTR| [len=31] (mis=0)
23-374 ==> 0-351 on |227|IGKV1-33|L-REGION+V-REGION| [len=351] (mis=2)
370-408 ==> 0-38 on |217|IGKJ5|J-REGION| [len=38] (mis=5)
408-544 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 18 reads
cdr3 = CQQYDNLPTF at 350, score = 9 + 8
umis assigned: [2, 5]
of which 2 are surviving nonsolos
reads assigned: 98
start codons at 23, 29, 85, 98, 237, 360, 450
confident = false
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.58 = AGCAGCCAGCGATCCC-1

using 472 reads

====================================================================================

graph has 564 edges initially, 4 edges after simplification

total ucounts = 188
nonsolo ucounts = 56[2^32, 3^5, 4^9, 5^2, 6^2, 7, 8^2, 9, 40, 131]
surviving nonsolo ucounts = 1[131]
ids = [37]

====================================================================================
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.68 = AGCAGCCAGGAGCGAG-1

using 235 reads

====================================================================================

graph has 104 edges initially, 2 edges after simplification

total ucounts = 8
nonsolo ucounts = 3[2, 4, 224]
surviving nonsolo ucounts = 1[224]
ids = [2]

====================================================================================

UMI info for barcode AGCAGCCAGGAGCGAG-1 contig 1 = CCACTCAGGA...
umi ATACTCTGGA = 209 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=424]
16-367 ==> 0-351 on |223|IGKV1-17|L-REGION+V-REGION| [len=351] (mis=19)
366-404 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=1)
404-424 ==> 0-20 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 36 reads
cdr3 = CLQYSSSPWTF at 343, score = 9 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 204
start codons at 16, 22, 91, 227
confident = false
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.82 = AGCAGCCAGTACGCGA-1

using 764 reads

====================================================================================

graph has 302 edges initially, 4 edges after simplification

total ucounts = 12
nonsolo ucounts = 3[187, 245, 323]
surviving nonsolo ucounts = 3[187, 245, 323]
ids = [6, 8, 3]

====================================================================================

UMI info for barcode AGCAGCCAGTACGCGA-1 contig 1 = GGGGGCTTTC...
umi CACTTTGGAT = 187 reads: +460 validated

GOOD CONTIGS

TIG 1[bases=545]
18-389 ==> 0-371 on |186|IGHV4-34|L-REGION+V-REGION| [len=371] (mis=3)
427-478 ==> 0-51 on |57|IGHJ5|J-REGION| [len=51] (mis=4)
478-545 ==> 0-67 on |40|IGHG1|C-REGION| [len=884] (mis=0)
junction support: 1 umis using 29 reads
cdr3 = CARGHFYFASGSRIPGGVWFDPW at 378, score = 9 + 7
umis assigned: [6]
of which 1 are surviving nonsolos
reads assigned: 182
start codons at 18, 39, 83, 169
confident = false

REJECT CONTIGS

TIG 1[bases=553]
0-31 ==> 0-31 on |226|IGKV1-33|5'UTR| [len=31] (mis=2)
20-83 ==> 5678-5741 on segment before IGKV1OR2-6 exon 1 [len=5879] (mis=1)
31-382 ==> 0-351 on |227|IGKV1-33|L-REGION+V-REGION| [len=351] (mis=14)
380-417 ==> 0-37 on |216|IGKJ4|J-REGION| [len=37] (mis=1)
417-553 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
umis assigned: [3, 8]
of which 2 are surviving nonsolos
reads assigned: 559
start codons at 31, 37, 93, 106, 368, 459
confident = false
did not find CDR3
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.83 = AGCAGCCAGTAGCGGT-1

using 257 reads

====================================================================================

graph has 98 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 2[2, 252]
surviving nonsolo ucounts = 1[252]
ids = [3]

====================================================================================

UMI info for barcode AGCAGCCAGTAGCGGT-1 contig 1 = GCTCTGCTTC...
umi TGCATCTTCC = 246 reads: +394 validated

GOOD CONTIGS

TIG 1[bases=560]
0-51 ==> 0-51 on |320|IGLV1-40|5'UTR| [len=51] (mis=0)
51-407 ==> 0-356 on |321|IGLV1-40|L-REGION+V-REGION| [len=356] (mis=4)
407-445 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=0)
445-560 ==> 0-115 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 35 reads
cdr3 = CQSYDSSLSADVVF at 375, score = 8 + 8
umis assigned: [3]
of which 1 are surviving nonsolos
reads assigned: 244
start codons at 51, 205, 208, 259, 358, 385, 406
confident = false
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.94 = AGCAGCCAGTTAGGTA-1

using 885 reads

====================================================================================

graph has 1272 edges initially, 8 edges after simplification

total ucounts = 461
nonsolo ucounts = 186[2^95, 3^39, 4^20, 5^10, 6^10, 7^4, 8^4, 10^2, 11, 22]
surviving nonsolo ucounts = 0[]
ids = []

====================================================================================
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.103 = AGCAGCCCAAGCGCTC-1

using 269 reads

====================================================================================

graph has 146 edges initially, 10 edges after simplification

total ucounts = 9
nonsolo ucounts = 4[2, 3, 11, 248]
surviving nonsolo ucounts = 2[11, 248]
ids = [2, 5]

====================================================================================

UMI info for barcode AGCAGCCCAAGCGCTC-1 contig 1 = ACCCAAAAAC...
umi ATGTCATCAC = 3 reads: -69 +2 -1XX +8 -1XX +24 -1XX +10 -1XX +10 -35X +14 -1X +6 -1X +20 -4X +1 -5X +2 -220X invalidated
umi GTAAACGGAA = 241 reads: +427 -1 +8 non-validated

GOOD CONTIGS

TIG 1[bases=495]
0-54 ==> 5-59 on |64|IGHV1-18|5'UTR| [len=59] (mis=1)
54-407 ==> 0-353 on |65|IGHV1-18|L-REGION+V-REGION| [len=353] (mis=22)
456-490 ==> 12-46 on |54|IGHJ4|J-REGION| [len=46] (mis=0)
junction support: 1 umis using 15 reads
cdr3 = CARDKHFRDPYYHYSGALDHW at 396, score = 7 + 7
umis assigned: [2, 5]
of which 2 are surviving nonsolos
reads assigned: 240
start codons at 54, 252, 257, 274, 318, 351
confident = false
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.106 = AGCAGCCCAAGGCTCC-1

using 104 reads

====================================================================================

graph has 58 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 4[2^3, 97]
surviving nonsolo ucounts = 1[97]
ids = [2]

====================================================================================

REJECT CONTIGS

TIG 1[bases=415]
0-337 ==> 21-358 on |98|IGHV2-5|L-REGION+V-REGION| [len=358] (mis=20)
367-415 ==> 0-48 on |55|IGHJ4|J-REGION| [len=48] (mis=1)
cdr3 = CAHIVGFYFPNSGYYYFDSW at 324, score = 7 + 7
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 86
start codons at 23, 202, 205, 294
confident = false
VJ delta = 10
not full
not full
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.111 = AGCAGCCCACACAGAG-1

using 141 reads

====================================================================================

graph has 38 edges initially, 2 edges after simplification

total ucounts = 4
nonsolo ucounts = 3[2^2, 136]
surviving nonsolo ucounts = 1[136]
ids = [1]

====================================================================================
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.112 = AGCAGCCCACACCGAC-1

using 39 reads

====================================================================================

graph has 22 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 1[35]
surviving nonsolo ucounts = 0[]
ids = []

====================================================================================
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.115 = AGCAGCCCACATGTGT-1

using 231 reads

====================================================================================

graph has 88 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 1[229]
surviving nonsolo ucounts = 1[229]
ids = [2]

====================================================================================

UMI info for barcode AGCAGCCCACATGTGT-1 contig 1 = GCTTCAGCTG...
umi TCATGGGAGT = 228 reads: +394 validated

GOOD CONTIGS

TIG 1[bases=475]
0-46 ==> 5-51 on |320|IGLV1-40|5'UTR| [len=51] (mis=0)
46-402 ==> 0-356 on |321|IGLV1-40|L-REGION+V-REGION| [len=356] (mis=12)
402-440 ==> 0-38 on |309|IGLJ1|J-REGION| [len=38] (mis=1)
440-475 ==> 0-35 on |305|IGLC1|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 35 reads
cdr3 = CQSYDSSLSGLYVF at 370, score = 7 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 223
start codons at 46, 200, 203, 254, 353, 380, 404
confident = false
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.116 = AGCAGCCCACCATGTA-1

using 273 reads

====================================================================================

graph has 130 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 1[269]
surviving nonsolo ucounts = 1[269]
ids = [0]

====================================================================================

UMI info for barcode AGCAGCCCACCATGTA-1 contig 1 = GATCAGGACT...
umi ATCGTTAATA = 277 reads: +400 validated

GOOD CONTIGS

TIG 1[bases=566]
0-30 ==> 0-30 on |264|IGKV2-28|5'UTR| [len=30] (mis=0)
30-390 ==> 0-360 on |265|IGKV2-28|L-REGION+V-REGION| [len=360] (mis=1)
392-430 ==> 0-38 on |215|IGKJ3|J-REGION| [len=38] (mis=0)
430-566 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 42 reads
cdr3 = CMQALQTPLFTF at 366, score = 9 + 8
umis assigned: [0]
of which 1 are surviving nonsolos
reads assigned: 265
start codons at 30, 63, 99, 187, 349, 369, 472
confident = false
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.123 = AGCAGCCCACGCGAAA-1

using 12481 reads

====================================================================================

graph has 3556 edges initially, 30 edges after simplification

total ucounts = 425
nonsolo ucounts = 167[2^56, 3^26, 4^19, 5^11, 6^3, 7, 8^4, 9, 10^2, 11, 12, 13, 16, 102, 114, 116, 155, 156, 172, 200, 213, 222, 233, 237, 240, 251, 269^2, 270, 283, 297, 298, 302, 305, 307, 311, 314, 322, 325^2, 329^2, 331, 332, 346, 350^2, 360^2, 384, 388, 624, 673]
surviving nonsolo ucounts = 39[102, 116, 155, 156, 172, 200, 213, 222, 233, 237, 240, 251, 269^2, 270, 283, 297, 298, 302, 305, 307, 311, 314, 322, 325^2, 329^2, 331, 332, 346, 350^2, 360^2, 384, 388, 624, 673]
ids = [198, 53, 229, 414, 396, 365, 330, 57, 325, 33, ...]

====================================================================================

UMI info for barcode AGCAGCCCACGCGAAA-1 contig 1 = GGGAGAGCCC...
umi AAACACCGGC = 325 reads: +382 validated
umi ACACCGTGAT = 239 reads: +382 validated
umi AGAATCCGCT = 113 reads: -382 non-validated
umi AGAGCGCCCC = 220 reads: +382 validated
umi AGGATCAGCG = 265 reads: +382 validated
umi AGTGACCAAA = 326 reads: +382 validated
umi ATCAATTGGG = 358 reads: +382 validated
umi ATCATCCGTC = 628 reads: +382 validated
umi ATTAATACTT = 691 reads: -140 +242 non-validated
umi CACTTATCTC = 343 reads: +382 validated
umi CCCGCTATGT = 302 reads: +382 validated
umi CGATCTACTA = 355 reads: +382 validated
umi CGCCAGTTCC = 328 reads: +382 validated
umi CTATTACACG = 297 reads: +382 validated
umi GAAAGTGGCG = 392 reads: +382 validated
umi GAAGAATGTT = 153 reads: +382 validated
umi GACCATCCCT = 271 reads: +382 validated
umi GACTCTTTAT = 332 reads: +382 validated
umi GCCTTCAATG = 270 reads: +382 validated
umi GTGATACGTT = 335 reads: +382 validated
umi TACACACCAT = 385 reads: +382 validated
umi TACTTCTGAT = 309 reads: +382 validated
umi TATCGGTACA = 234 reads: +382 validated
umi TATGGGGTTC = 216 reads: +382 validated
umi TCACGTATAC = 254 reads: +382 validated
umi TCCCTTTTTC = 305 reads: +382 validated
umi TCCTGCCTGC = 337 reads: +382 validated
umi TCTACGTCGC = 201 reads: +382 validated
umi TGACTGTTGT = 300 reads: +382 validated
umi TGATCCAGCC = 287 reads: +382 validated
umi TGTGGGACGA = 351 reads: +382 validated
umi TTAAAACCAT = 177 reads: +382 validated
umi TTCAATCGCT = 343 reads: +382 validated
umi TTCCAATCGT = 310 reads: +382 validated
umi TTCGCTTGAG = 313 reads: +382 validated
umi TTGCGCTAGA = 156 reads: +382 validated

UMI info for barcode AGCAGCCCACGCGAAA-1 contig 2 = GAGGGTCCTG...
umi ATGCTTCGGG = 324 reads: +441 -1 +3 non-validated
umi CACCATATGT = 242 reads: +445 validated

GOOD CONTIGS

TIG 1[bases=565]
0-47 ==> 0-47 on |278|IGKV3-11|5'UTR| [len=47] (mis=2)
47-392 ==> 0-345 on |279|IGKV3-11|L-REGION+V-REGION| [len=345] (mis=2)
391-429 ==> 0-38 on |215|IGKJ3|J-REGION| [len=38] (mis=4)
429-565 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 35 umis using 1812 reads
cdr3 = CQQRSNWPPTF at 368, score = 9 + 8
umis assigned: [2, 33, 53, 57, 65, 73, 87, 92, 105, 126] and 26 others
of which 36 are surviving nonsolos
reads assigned: 10839
start codons at 47, 252, 255, 471
confident = true

TIG 2[bases=575]
59-407 ==> 0-348 on |740|IGHV4-30-4|L-REGION+V-REGION| [len=348] (mis=10)
405-429 ==> 0-24 on |14|IGHD2-2|D-REGION| [len=31] (mis=4)
441-504 ==> 0-63 on |737|IGHJ6|J-REGION| [len=63] (mis=6)
504-575 ==> 0-71 on |60|IGHM|C-REGION| [len=1358] (mis=0)
junction support: 1 umis using 19 reads
cdr3 = CHIVVVPAVHDRPIHYYYGMDLW at 404, score = 9 + 6
umis assigned: [101, 122]
of which 2 are surviving nonsolos
reads assigned: 557
start codons at 15, 59, 103, 432, 461
confident = true
now this is a cell
paired!

TGTCATATTGTAGTAGTCCCAGCTGTCCATGACCGTCCTATCCACTACTACTACGGTATGGACCTCTGGGGCCAAGGGGCCACGGTCACCGTCTCCTCAG <==> ATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCCAACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.129 = AGCAGCCCACTGCCAG-1

using 170 reads

====================================================================================

graph has 48 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 1[169]
surviving nonsolo ucounts = 1[169]
ids = [1]

====================================================================================

UMI info for barcode AGCAGCCCACTGCCAG-1 contig 1 = AGAGCTGCTC...
umi GACCATTGAG = 168 reads: +385 validated

GOOD CONTIGS

TIG 1[bases=552]
0-31 ==> 21-52 on |282|IGKV3-20|5'UTR| [len=52] (mis=0)
31-379 ==> 0-348 on |283|IGKV3-20|L-REGION+V-REGION| [len=348] (mis=3)
378-416 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=2)
416-552 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 24 reads
cdr3 = CQQYGSSPRTF at 355, score = 9 + 8
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 167
start codons at 31, 239, 365, 458
confident = false
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.137 = AGCAGCCCAGCTATTG-1

using 257 reads

====================================================================================

graph has 98 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 1[256]
surviving nonsolo ucounts = 1[256]
ids = [0]

====================================================================================

UMI info for barcode AGCAGCCCAGCTATTG-1 contig 1 = CTGGGCCTCA...
umi GGACGATGTG = 244 reads: +376 validated

GOOD CONTIGS

TIG 1[bases=554]
0-37 ==> 15-52 on |348|IGLV3-1|5'UTR| [len=52] (mis=0)
37-371 ==> 0-334 on |349|IGLV3-1|L-REGION+V-REGION| [len=346] (mis=18)
375-413 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=4)
413-554 ==> 0-141 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 49 reads
cdr3 = CQAWDSTEVVF at 352, score = 6 + 8
umis assigned: [0]
of which 1 are surviving nonsolos
reads assigned: 241
start codons at 37, 42, 331, 335
confident = false
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.140 = AGCAGCCCAGCTGTTA-1

using 836 reads

====================================================================================

graph has 194 edges initially, 2 edges after simplification

total ucounts = 7
nonsolo ucounts = 2[7, 824]
surviving nonsolo ucounts = 0[]
ids = []

====================================================================================
NOT paired!

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.141 = AGCAGCCCAGCTTAAC-1

using 4448 reads

====================================================================================

graph has 1720 edges initially, 18 edges after simplification

total ucounts = 196
nonsolo ucounts = 69[2^29, 3^13, 4^5, 6, 7^2, 8, 27, 65, 93, 108, 118, 124, 146, 197, 212, 232, 253, 271, 276, 280, 307, 339, 372, 756]
surviving nonsolo ucounts = 16[27, 93, 108, 118, 124, 197, 212, 232, 253, 271, 276, 280, 307, 339, 372, 756]
ids = [27, 34, 19, 1, 141, 156, 23, 140, 103, 96, ...]

====================================================================================

UMI info for barcode AGCAGCCCAGCTTAAC-1 contig 1 = TGGGGAGTCA...
umi AAAGGCGGCA = 118 reads: +388 validated
umi AGGTCGCTCA = 28 reads: +45 -1 +233 -13 +96 non-validated
umi ATAATAGGGC = 340 reads: +388 validated
umi ATAGTAACAT = 92 reads: +388 validated
umi CTTTAATCTA = 268 reads: +388 validated
umi GAGTACCGTG = 255 reads: +388 validated
umi GCCACTCAAG = 283 reads: +388 validated
umi GTCCAGGCTC = 376 reads: +388 validated
umi GTTGAATGGC = 233 reads: +388 validated
umi GTTTATATAG = 125 reads: +388 validated
umi TCACAAATCG = 197 reads: +388 validated
umi TGTAACCGTC = 277 reads: +388 validated

UMI info for barcode AGCAGCCCAGCTTAAC-1 contig 2 = CGAGCCCAGC...
umi ACCTCTCCAC = 111 reads: +368 -18 +56 non-validated
umi AGAGGGCGAC = 212 reads: +442 validated
umi GCTTGTGTAC = 9 reads: -365X +1 -4X +3 -2XX +1 -7XX +1 -1XX +1 -5XX +2 -1XX +2 -2XX +1 -1XX +40 -1 +1 invalidated
umi TCGACGGCAC = 771 reads: -317 +125 non-validated

GOOD CONTIGS

TIG 1[bases=553]
29-382 ==> 0-353 on |253|IGKV1D-39|L-REGION+V-REGION| [len=353] (mis=16)
379-417 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=3)
417-553 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 11 umis using 386 reads
cdr3 = CQQSFSTPLTF at 356, score = 9 + 9
umis assigned: [1, 27, 30, 34, 96, 103, 110, 132, 140, 141] and 2 others
of which 12 are surviving nonsolos
reads assigned: 2550
start codons at 29, 35, 91, 104, 236, 459
confident = true

TIG 2[bases=669]
0-67 ==> 0-67 on |127|IGHV3-33|5'UTR| [len=67] (mis=0)
67-420 ==> 0-353 on |128|IGHV3-33|L-REGION+V-REGION| [len=353] (mis=17)
423-454 ==> 0-31 on |13|IGHD2-15|D-REGION| [len=31] (mis=6)
461-509 ==> 0-48 on |55|IGHJ4|J-REGION| [len=48] (mis=1)
509-669 ==> 0-160 on |3|IGHA2|C-REGION| [len=1019] (mis=0)
junction support: 2 umis using 90 reads
cdr3 = CARDVQYCSGGNCYGPGDHFDYW at 409, score = 7 + 7
umis assigned: [19, 23, 116, 162]
of which 4 are surviving nonsolos
reads assigned: 1076
start codons at 67, 186, 218, 223, 284, 302, 370, 400, 419, 563, 582
confident = true
now this is a cell
paired!

TGTGCGAGAGATGTACAATATTGTAGTGGTGGTAACTGCTACGGGCCTGGGGACCACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG <==> ATCAACAGTCTGCAACCTGAAGATTTTGCAACTTACTATTGTCAACAGAGTTTCAGTACCCCTCTGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

BARCODE 10.142 = AGCAGCCCAGGATCGA-1

using 47 reads

====================================================================================

graph has 34 edges initially, 2 edges after simplification

total ucounts = 7
nonsolo ucounts = 1[41]
surviving nonsolo ucounts = 1[41]
ids = [1]

====================================================================================

REJECT CONTIGS

TIG 1[bases=360]
2-335 ==> 0-333 on |359|IGLV3-21|L-REGION+V-REGION| [len=351] (mis=29)
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 36
start codons at 2, 63, 132, 300, 336, 345
confident = false
did not find CDR3
NOT paired!
sorting bam, mem = 0.05
running samtools sort -l 8G -o /scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/chnk010-ucc6a7a72ce/files/contig_bam_sorted.bam /scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/chnk010-ucc6a7a72ce/files/contig_bam.bam

▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓

5.184 seconds used processing barcodes, peak mem = 0.23
