[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/chnk013-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/chnk013-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.chnk013.ucc6a7a72ce
n50_n50_rpu = 288

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BARCODE 13.0 = AGTGAGGGTTGACGTT-1

using 12523 reads

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

graph has 5170 edges initially, 42 edges after simplification

total ucounts = 772
nonsolo ucounts = 371[2^135, 3^75, 4^53, 5^25, 6^19, 7^11, 8^7, 9^3, 10^2, 12^2, 16^2, 17, 44, 46, 88, 96, 123, 130, 176, 179, 182, 188, 211, 215, 223, 226, 227, 231, 242, 248, 256, 261, 271, 274, 281^2, 293, 311, 313, 318, 339, 340, 343, 362, 571, 708, 883, 1443]
surviving nonsolo ucounts = 36[8, 12, 46, 96, 123, 130, 176, 179, 182, 188, 211, 215, 223, 226, 227, 231, 242, 248, 256, 261, 271, 274, 281^2, 293, 311, 313, 318, 339, 340, 343, 362, 571, 708, 883, 1443]
ids = [584, 463, 22, 413, 583, 542, 639, 246, 102, 578, ...]

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

UMI info for barcode AGTGAGGGTTGACGTT-1 contig 1 = GAGCTACAAC...
umi AATGAGCCAG = 628 reads: -362X +1 -3XX +2 -1XX +6 -2XX +15 -1XX +7 invalidated
umi AGAAACATCG = 340 reads: +400 validated
umi AGAAGCACCA = 182 reads: +400 validated
umi AGTTCCTTGA = 38 reads: -359X +4 -3XX +2 -1XX +6 -2XX +15 -1XX +7 invalidated
umi ATCCCTCGGG = 311 reads: +400 validated
umi ATTGACCCGT = 224 reads: +400 validated
umi CAACCAGCTC = 293 reads: +400 validated
umi CACCAGACAG = 216 reads: +400 validated
umi CAGATCCGGC = 241 reads: +400 validated
umi CCATCACTGT = 181 reads: +400 validated
umi CGAACCGGTA = 231 reads: +400 validated
umi CGTACCAGGC = 338 reads: +400 validated
umi CTCACGCTTG = 228 reads: +400 validated
umi CTCGCACTCT = 344 reads: +400 validated
umi CTCGCGCTCC = 312 reads: +400 validated
umi CTCGGCCGTC = 560 reads: +400 validated
umi CTGATATCGG = 259 reads: +400 validated
umi GACTTGCATA = 621 reads: -358X +1 -3XX +1 -3XX +2 -1XX +6 -2XX +15 -1XX +7 invalidated
umi TAGACTCGGA = 1078 reads: -358 +1 -3XX +1 -3XX +2 -1XX +6 -2XX +15 -1XX +7 invalidated
umi TATATATCTG = 188 reads: +400 validated
umi TATGGATTCG = 110 reads: +400 validated
umi TCATCTTTCA = 242 reads: +400 validated
umi TCCGATGTGA = 267 reads: +400 validated
umi TCCGGATCAC = 282 reads: +400 validated
umi TCGATAGCTT = 360 reads: +400 validated
umi TCTATATCGG = 176 reads: +400 validated
umi TGACACACGG = 285 reads: +400 validated
umi TTGAATAGCG = 321 reads: +400 validated

UMI info for barcode AGTGAGGGTTGACGTT-1 contig 2 = AGGTCTCAGA...
umi AAGAATTCCG = 43 reads: +425 -5 non-validated
umi GATCTCGGCT = 96 reads: -346 +84 non-validated
umi GATTCTCTGT = 204 reads: +97 -1X +332 invalidated

GOOD CONTIGS

TIG 1[bases=566]
0-30 ==> 145-175 on |295|IGKV4-1|5'UTR| [len=175] (mis=0)
30-393 ==> 0-363 on |296|IGKV4-1|L-REGION+V-REGION| [len=363] (mis=23)
393-430 ==> 0-37 on |216|IGKJ4|J-REGION| [len=37] (mis=0)
430-566 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 24 umis using 810 reads
cdr3 = CQQYFSIPLTF at 369, score = 9 + 9
umis assigned: [38, 101, 102, 131, 150, 171, 184, 204, 211, 246] and 18 others
of which 28 are surviving nonsolos
reads assigned: 8736
start codons at 30, 79, 99, 352, 472
confident = true

TIG 2[bases=691]
0-79 ==> 0-79 on |158|IGHV3-7|5'UTR| [len=79] (mis=1)
79-432 ==> 0-353 on |159|IGHV3-7|L-REGION+V-REGION| [len=353] (mis=30)
471-509 ==> 25-63 on |737|IGHJ6|J-REGION| [len=63] (mis=0)
509-691 ==> 0-182 on |40|IGHG1|C-REGION| [len=884] (mis=1)
junction support: 1 umis using 22 reads
cdr3 = CARDNLAPTVTTAAGLGVW at 421, score = 8 + 7
umis assigned: [22, 413, 414]
of which 3 are surviving nonsolos
reads assigned: 338
start codons at 79, 139, 235, 296, 314, 382
confident = true
now this is a cell
paired!

GCTATCTATTACTGTGCGAGAGACAATTTAGCACCTACGGTGACTACGGCTGCCGGTTTGGGCGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG <==> ATCAGCACCCTGCAGGCTGAAGATGTGGCAGTTTATTTCTGTCAGCAGTATTTTAGTATTCCGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC

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

BARCODE 13.16 = AGTGAGGTCAGGCAAG-1

using 52 reads

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

graph has 68 edges initially, 4 edges after simplification

total ucounts = 14
nonsolo ucounts = 6[2, 3^3, 4, 29]
surviving nonsolo ucounts = 1[29]
ids = [1]

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

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

BARCODE 13.32 = AGTGAGGTCGAATCCA-1

using 264 reads

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

graph has 176 edges initially, 2 edges after simplification

total ucounts = 10
nonsolo ucounts = 5[2, 3, 4, 5, 245]
surviving nonsolo ucounts = 1[245]
ids = [6]

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

UMI info for barcode AGTGAGGTCGAATCCA-1 contig 1 = AAAAACCACA...
umi GCTAATGGCT = 239 reads: +436 validated

GOOD CONTIGS

TIG 1[bases=553]
0-50 ==> 9-59 on |64|IGHV1-18|5'UTR| [len=59] (mis=1)
50-403 ==> 0-353 on |65|IGHV1-18|L-REGION+V-REGION| [len=353] (mis=22)
452-486 ==> 12-46 on |54|IGHJ4|J-REGION| [len=46] (mis=0)
486-553 ==> 0-67 on |1|IGHA1|C-REGION| [len=1058] (mis=0)
junction support: 1 umis using 21 reads
cdr3 = CARDKHFRDPYYHYSGALDHW at 392, score = 7 + 7
umis assigned: [6]
of which 1 are surviving nonsolos
reads assigned: 233
start codons at 50, 248, 253, 270, 314, 347, 540
confident = false
NOT paired!

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

BARCODE 13.33 = AGTGAGGTCGAATGGG-1

using 469 reads

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

graph has 200 edges initially, 4 edges after simplification

total ucounts = 13
nonsolo ucounts = 5[3, 4^2, 218, 232]
surviving nonsolo ucounts = 2[218, 232]
ids = [7, 3]

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

UMI info for barcode AGTGAGGTCGAATGGG-1 contig 1 = ACCCAAAAAC...
umi GCACGGGATA = 210 reads: +436 validated

UMI info for barcode AGTGAGGTCGAATGGG-1 contig 2 = TGGGGGAGGA...
umi AGGTCGGACT = 216 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=537]
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)
490-537 ==> 0-47 on |1|IGHA1|C-REGION| [len=1058] (mis=0)
junction support: 1 umis using 11 reads
cdr3 = CARDKHFRDPYYHYSGALDHW at 396, score = 7 + 7
umis assigned: [7]
of which 1 are surviving nonsolos
reads assigned: 208
start codons at 54, 252, 257, 274, 318, 351
confident = false

TIG 2[bases=516]
33-384 ==> 0-351 on |223|IGKV1-17|L-REGION+V-REGION| [len=351] (mis=19)
383-421 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=1)
421-516 ==> 0-95 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 41 reads
cdr3 = CLQYSSSPWTF at 360, score = 9 + 8
umis assigned: [3]
of which 1 are surviving nonsolos
reads assigned: 212
start codons at 33, 39, 108, 244, 463
confident = false
NOT paired!

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

BARCODE 13.37 = AGTGAGGTCGCCAGCA-1

using 655 reads

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

graph has 315 edges initially, 4 edges after simplification

total ucounts = 7
nonsolo ucounts = 2[302, 348]
surviving nonsolo ucounts = 2[302, 348]
ids = [4, 2]

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

UMI info for barcode AGTGAGGTCGCCAGCA-1 contig 1 = GAAGAGCTGC...
umi CAGGCCAGTA = 349 reads: +388 validated

UMI info for barcode AGTGAGGTCGCCAGCA-1 contig 2 = GGGAGGGTCC...
umi GGCCATCTAT = 308 reads: +433 validated

GOOD CONTIGS

TIG 1[bases=557]
0-33 ==> 19-52 on |282|IGKV3-20|5'UTR| [len=52] (mis=0)
33-381 ==> 0-348 on |283|IGKV3-20|L-REGION+V-REGION| [len=348] (mis=13)
384-421 ==> 0-37 on |216|IGKJ4|J-REGION| [len=37] (mis=1)
421-557 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 45 reads
cdr3 = CQQYDSSPALTF at 357, score = 9 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 344
start codons at 33, 228, 241, 367, 408, 463
confident = false

TIG 2[bases=654]
61-409 ==> 0-348 on |740|IGHV4-30-4|L-REGION+V-REGION| [len=348] (mis=20)
446-494 ==> 0-48 on |55|IGHJ4|J-REGION| [len=48] (mis=1)
494-654 ==> 0-160 on |1|IGHA1|C-REGION| [len=1058] (mis=0)
junction support: 1 umis using 37 reads
cdr3 = CARDWGDRSVGSPHYFDYW at 406, score = 9 + 7
umis assigned: [4]
of which 1 are surviving nonsolos
reads assigned: 299
start codons at 17, 61, 105, 261, 340, 548
confident = false
NOT paired!

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

BARCODE 13.44 = AGTGAGGTCTATCCCG-1

using 217 reads

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

graph has 70 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[217]
surviving nonsolo ucounts = 1[217]
ids = [0]

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

UMI info for barcode AGTGAGGTCTATCCCG-1 contig 1 = GGGGTCACAA...
umi TAACCCGGCC = 205 reads: +394 validated

GOOD CONTIGS

TIG 1[bases=518]
0-38 ==> 124-162 on |342|IGLV2-23|5'UTR| [len=162] (mis=0)
38-378 ==> 0-340 on |343|IGLV2-23|L-REGION+V-REGION| [len=340] (mis=29)
394-432 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=6)
432-518 ==> 0-86 on |306|IGLC2|C-REGION| [len=317] (mis=2)
junction support: 1 umis using 36 reads
cdr3 = CCSEAGGGVPGLLF at 362, score = 7 + 9
umis assigned: [0]
of which 1 are surviving nonsolos
reads assigned: 202
start codons at 38, 192
confident = false
NOT paired!

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

BARCODE 13.49 = AGTGAGGTCTGAAAGA-1

using 250 reads

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

graph has 130 edges initially, 2 edges after simplification

total ucounts = 15
nonsolo ucounts = 4[3^2, 6, 227]
surviving nonsolo ucounts = 1[227]
ids = [10]

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

UMI info for barcode AGTGAGGTCTGAAAGA-1 contig 1 = ACCCAAAAAC...
umi GGAACGCAGA = 221 reads: +436 validated

GOOD CONTIGS

TIG 1[bases=529]
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)
490-529 ==> 0-39 on |1|IGHA1|C-REGION| [len=1058] (mis=0)
junction support: 1 umis using 16 reads
cdr3 = CARDKHFRDPYYHYSGALDHW at 396, score = 7 + 7
umis assigned: [10]
of which 1 are surviving nonsolos
reads assigned: 216
start codons at 54, 252, 257, 274, 318, 351
confident = false
NOT paired!

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

BARCODE 13.53 = AGTGAGGTCTGTTTGT-1

using 138 reads

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

graph has 50 edges initially, 2 edges after simplification

total ucounts = 12
nonsolo ucounts = 2[5, 123]
surviving nonsolo ucounts = 1[123]
ids = [8]

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

REJECT CONTIGS

TIG 1[bases=361]
0-326 ==> 25-351 on |223|IGKV1-17|L-REGION+V-REGION| [len=351] (mis=18)
325-361 ==> 0-36 on |213|IGKJ1|J-REGION| [len=38] (mis=1)
cdr3 = CLQYSSSPWTF at 302, score = 9 + 8
umis assigned: [8]
of which 1 are surviving nonsolos
reads assigned: 103
start codons at 50, 186
confident = false
not full
VJ delta = 14
not full
NOT paired!

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

BARCODE 13.55 = AGTGAGGTCTTACCGC-1

using 266 reads

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

graph has 122 edges initially, 2 edges after simplification

total ucounts = 11
nonsolo ucounts = 6[2^3, 3, 12, 240]
surviving nonsolo ucounts = 1[240]
ids = [0]

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

UMI info for barcode AGTGAGGTCTTACCGC-1 contig 1 = AGCTGTGGGC...
umi AACACAGGAT = 232 reads: +382 validated

GOOD CONTIGS

TIG 1[bases=513]
0-40 ==> 0-40 on |356|IGLV3-19|5'UTR| [len=40] (mis=0)
40-377 ==> 0-337 on |357|IGLV3-19|L-REGION+V-REGION| [len=337] (mis=0)
384-422 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=1)
422-513 ==> 0-91 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 35 reads
cdr3 = CNSRDSSGNHLVF at 355, score = 8 + 9
umis assigned: [0]
of which 1 are surviving nonsolos
reads assigned: 229
start codons at 40, 159, 188, 239, 338
confident = false
NOT paired!

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

BARCODE 13.57 = AGTGAGGTCTTTAGGG-1

using 11641 reads

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

graph has 6588 edges initially, 104 edges after simplification

total ucounts = 1754
nonsolo ucounts = 862[2^316, 3^181, 4^127, 5^80, 6^36, 7^24, 8^17, 9^9, 10^8, 11^7, 12^7, 13^4, 14, 15, 16, 24^2, 25, 46, 47^2, 61, 66, 81, 84, 94, 102, 111, 116, 117, 122, 132, 141, 144, 175, 178, 179, 190, 195^3, 198, 201, 205, 213, 219, 223^2, 226, 236, 248, 258, 270, 274, 287, 288, 384, 883]
surviving nonsolo ucounts = 40[24, 46, 47^2, 66, 81, 84, 94, 102, 111, 116, 117, 122, 132, 141, 144, 175, 178, 179, 190, 195^3, 198, 201, 205, 213, 219, 223^2, 226, 236, 248, 258, 270, 274, 287, 288, 384, 883]
ids = [837, 370, 286, 294, 678, 468, 1570, 1231, 987, 1035, ...]

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

UMI info for barcode AGTGAGGTCTTTAGGG-1 contig 1 = CTCCCTCACT...
umi ATCTTATGAC = 47 reads: -15 +337 -1 +1 -2 +59 -18 non-validated
umi ATGCCAGCCA = 46 reads: +379 -54 non-validated
umi CACCTGCGAC = 47 reads: +382 -27 +24 non-validated
umi CTCTCGAGGG = 484 reads: -400X +1 -5XX +1 -2XX +3 -10XX +1 -2XX +1 -2XX +1 -3XX +1 invalidated
umi GAATTGGATC = 21 reads: -433 non-validated
umi GCTAACATCG = 103 reads: +433 validated
umi GGTCTTAGTA = 185 reads: +423 -10 non-validated

UMI info for barcode AGTGAGGTCTTTAGGG-1 contig 2 = AGCTTCAGCT...
umi ACATATCGCT = 136 reads: +388 validated
umi ACCATGACCG = 120 reads: +388 validated
umi ACCGGTTCCG = 195 reads: +388 validated
umi ACCTTTTAGT = 141 reads: +388 validated
umi ACGGTTGAGC = 117 reads: +388 validated
umi AGAAACCTAA = 197 reads: +388 validated
umi AGCAGTTAGG = 289 reads: +388 validated
umi AGTGTTGGCC = 275 reads: +388 validated
umi ATGAATATCC = 227 reads: +388 validated
umi CAGCCATAGC = 239 reads: +388 validated
umi CAGTATAAGG = 207 reads: +388 validated
umi CATGTATCCT = 211 reads: +388 validated
umi CCACTGTACG = 80 reads: +388 validated
umi CCGTCATACA = 284 reads: +388 validated
umi CCTCCACGGC = 148 reads: +388 validated
umi CGTCTCGACG = 67 reads: +384 -1 +3 non-validated
umi GAACGGTCTC = 219 reads: +388 validated
umi GCAACCTACG = 190 reads: +388 validated
umi GGACTCATTC = 115 reads: +388 validated
umi GGGCCTATGC = 178 reads: +388 validated
umi GGGGTCCCCT = 210 reads: -17X +1 -2X +2 -3XX +2 -3XX +1 -1XX +1 -3XX +2 -3XX +1 -2XX +344 invalidated
umi GGTACTATCG = 203 reads: +388 validated
umi GTTCGATAGG = 224 reads: +388 validated
umi TAAGCTCTAT = 82 reads: +361 -2 +3 -1 +3 -1 +3 -1X +2 -1 +1 -9 invalidated
umi TACCCTATGG = 772 reads: -352 +2 -1XX +1 -4XX +2 -5XX +2 -3XX +1 -1XX +2 -5XX +1 -6XX invalidated
umi TCATTACTCT = 281 reads: +388 validated
umi TGCCTCCTTC = 243 reads: +388 validated
umi TGCCTTTGCC = 198 reads: +388 validated
umi TGTGATCTCC = 75 reads: +327 -61 non-validated
umi TTTGAATTCG = 196 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=669]
0-54 ==> 5-59 on |202|IGHV5-51|5'UTR| [len=59] (mis=2)
54-407 ==> 0-353 on |203|IGHV5-51|L-REGION+V-REGION| [len=353] (mis=16)
443-487 ==> 19-63 on |737|IGHJ6|J-REGION| [len=63] (mis=1)
487-669 ==> 0-182 on |43|IGHG2|C-REGION| [len=977] (mis=0)
junction support: 1 umis using 12 reads
cdr3 = CARHGYGDLGFYLFNYMDVW at 396, score = 8 + 6
umis assigned: [286, 294, 370, 748, 837, 987, 1100]
of which 7 are surviving nonsolos
reads assigned: 756
start codons at 54, 228, 252, 387, 406, 412, 444
confident = true

TIG 2[bases=646]
0-47 ==> 67-114 on |322|IGLV1-44|5'UTR| [len=114] (mis=1)
47-400 ==> 0-353 on |323|IGLV1-44|L-REGION+V-REGION| [len=353] (mis=21)
397-435 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=1)
435-646 ==> 0-211 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 27 umis using 794 reads
cdr3 = CAVWDDSQNGVVF at 368, score = 8 + 8
umis assigned: [73, 87, 106, 121, 130, 164, 182, 224, 288, 397] and 20 others
of which 30 are surviving nonsolos
reads assigned: 6012
start codons at 47, 198, 261, 351, 376, 381, 393
confident = true

REJECT CONTIGS

TIG 1[bases=551]
25-100 ==> 5925-6000 on rc of segment after IGHV7-40 exon 1 [len=6000] (mis=3)
177-196 ==> 0-19 on segment before IGLV7-35 exon 1 [len=6000] (mis=1)
430-480 ==> 0-50 on |53|IGHJ3|J-REGION| [len=50] (mis=1)
480-551 ==> 0-71 on |60|IGHM|C-REGION| [len=1358] (mis=0)
umis assigned: [242, 1649]
of which 2 are surviving nonsolos
reads assigned: 286
start codons at 36, 65, 82, 146, 161, 177, 187, 198, 203, 245, 250, 278, 317, 335, 384, 392, 432, 461
confident = false
did not find CDR3
now this is a cell
paired!

ATGTATTTCTGTGCGAGACATGGCTATGGTGACTTGGGCTTCTACCTCTTCAACTATATGGACGTCTGGGGCCAAGGGACCACGGTCATCGTCTCCTCAG <==> GGTCTCCAGTCTGAGGATGAGGCTCATTATTACTGTGCAGTATGGGATGACAGCCAGAATGGTGTGGTATTCGGCGGAGGGACCAAGGTGACCGTCCTAG

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

BARCODE 13.72 = AGTGGGAAGCGACGTA-1

using 267 reads

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

graph has 66 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 2[4, 262]
surviving nonsolo ucounts = 1[262]
ids = [2]

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

UMI info for barcode AGTGGGAAGCGACGTA-1 contig 1 = GGGAGGAATC...
umi TCCTGTGGTC = 264 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=554]
30-381 ==> 0-351 on |223|IGKV1-17|L-REGION+V-REGION| [len=351] (mis=19)
380-418 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=1)
418-554 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 40 reads
cdr3 = CLQYSSSPWTF at 357, score = 9 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 261
start codons at 30, 36, 105, 241, 460
confident = false
NOT paired!

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

BARCODE 13.75 = AGTGGGAAGCTAACTC-1

using 2425 reads

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

graph has 1552 edges initially, 10 edges after simplification

total ucounts = 317
nonsolo ucounts = 126[2^43, 3^26, 4^20, 5^17, 6^4, 7^4, 8^3, 9^2, 11, 13, 97, 194, 294, 337, 865]
surviving nonsolo ucounts = 5[97, 194, 294, 337, 865]
ids = [259, 66, 86, 198, 289]

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

UMI info for barcode AGTGGGAAGCTAACTC-1 contig 1 = AGCCTGGGCC...
umi ATGGATTACA = 190 reads: +379 validated
umi CACTTTGCCT = 293 reads: +379 validated
umi GGATGCTTCA = 338 reads: +379 validated
umi TCGACCTTTG = 98 reads: +379 validated
umi TTACCTTTTG = 870 reads: -369 +9 -1XX invalidated

GOOD CONTIGS

TIG 1[bases=630]
0-40 ==> 12-52 on |348|IGLV3-1|5'UTR| [len=52] (mis=0)
40-386 ==> 0-346 on |349|IGLV3-1|L-REGION+V-REGION| [len=346] (mis=5)
381-419 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=1)
419-630 ==> 0-211 on |306|IGLC2|C-REGION| [len=317] (mis=2)
junction support: 4 umis using 152 reads
cdr3 = CQAWDSSTAVVF at 355, score = 6 + 8
umis assigned: [66, 86, 198, 259, 289]
of which 5 are surviving nonsolos
reads assigned: 1730
start codons at 40, 45, 101, 188, 334, 338
confident = true
now this is a cell
NOT paired!

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

BARCODE 13.77 = AGTGGGAAGCTATGCT-1

using 456 reads

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

graph has 144 edges initially, 2 edges after simplification

total ucounts = 8
nonsolo ucounts = 4[2^2, 8, 440]
surviving nonsolo ucounts = 1[440]
ids = [7]

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

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

BARCODE 13.84 = AGTGGGAAGGCCGAAT-1

using 262 reads

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

graph has 126 edges initially, 2 edges after simplification

total ucounts = 7
nonsolo ucounts = 3[4, 5, 249]
surviving nonsolo ucounts = 1[249]
ids = [5]

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

UMI info for barcode AGTGGGAAGGCCGAAT-1 contig 1 = GGCTTTCTGA...
umi TGATACGCCT = 245 reads: +460 validated

GOOD CONTIGS

TIG 1[bases=576]
15-386 ==> 0-371 on |186|IGHV4-34|L-REGION+V-REGION| [len=371] (mis=3)
424-475 ==> 0-51 on |57|IGHJ5|J-REGION| [len=51] (mis=4)
475-576 ==> 0-101 on |40|IGHG1|C-REGION| [len=884] (mis=1)
junction support: 1 umis using 29 reads
cdr3 = CARGHFYFASGSRIPGGVWFDPW at 375, score = 9 + 7
umis assigned: [5]
of which 1 are surviving nonsolos
reads assigned: 241
start codons at 15, 36, 80, 166
confident = false
NOT paired!

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

BARCODE 13.87 = AGTGGGAAGGGTGTTG-1

using 327 reads

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

graph has 130 edges initially, 2 edges after simplification

total ucounts = 4
nonsolo ucounts = 1[324]
surviving nonsolo ucounts = 1[324]
ids = [1]

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

UMI info for barcode AGTGGGAAGGGTGTTG-1 contig 1 = GATCAGGACT...
umi ATCTTGGTTT = 327 reads: +397 validated

GOOD CONTIGS

TIG 1[bases=563]
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=2)
389-427 ==> 0-38 on |217|IGKJ5|J-REGION| [len=38] (mis=3)
427-563 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 28 reads
cdr3 = CMQALQTRETF at 366, score = 9 + 8
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 322
start codons at 30, 63, 99, 187, 349, 369, 469
confident = false
NOT paired!

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

BARCODE 13.88 = AGTGGGAAGGTAGCCA-1

using 544 reads

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

graph has 268 edges initially, 2 edges after simplification

total ucounts = 9
nonsolo ucounts = 5[3^2, 5, 245, 284]
surviving nonsolo ucounts = 2[245, 284]
ids = [1, 5]

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

UMI info for barcode AGTGGGAAGGTAGCCA-1 contig 1 = GCTCTGCTTC...
umi AACATTACTC = 249 reads: +394 validated
umi ATCTAGCGTT = 284 reads: +394 validated

GOOD CONTIGS

TIG 1[bases=656]
0-51 ==> 0-51 on |320|IGLV1-40|5'UTR| [len=51] (mis=0)
51-390 ==> 0-339 on |321|IGLV1-40|L-REGION+V-REGION| [len=356] (mis=12)
407-445 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=3)
445-656 ==> 0-211 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 2 umis using 72 reads
cdr3 = CQSYDGGQSASAVF at 375, score = 7 + 8
umis assigned: [1, 5]
of which 2 are surviving nonsolos
reads assigned: 519
start codons at 51, 205, 208, 259, 358, 385
confident = false
NOT paired!

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

BARCODE 13.93 = AGTGGGAAGTCCAGGA-1

using 275 reads

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

graph has 110 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 1[273]
surviving nonsolo ucounts = 1[273]
ids = [0]

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

UMI info for barcode AGTGGGAAGTCCAGGA-1 contig 1 = GAGTCAGTCT...
umi CCCCAGTTCC = 269 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=549]
25-378 ==> 0-353 on |253|IGKV1D-39|L-REGION+V-REGION| [len=353] (mis=0)
375-413 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=3)
413-549 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 48 reads
cdr3 = CQQSYSTPPTF at 352, score = 9 + 8
umis assigned: [0]
of which 1 are surviving nonsolos
reads assigned: 266
start codons at 25, 31, 87, 100, 236, 455
confident = false
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/chnk013-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/chnk013-ucc6a7a72ce/files/contig_bam.bam

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6.278 seconds used processing barcodes, peak mem = 0.23
