[stdout]

starting vdj_asm_asm, mem = 0.01
available mem = 844.37 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/chnk006-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/chnk006-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.chnk006.ucc6a7a72ce
n50_n50_rpu = 288

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

BARCODE 6.0 = ACCGTAAAGGATGGTC-1

using 13353 reads

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

graph has 4769 edges initially, 56 edges after simplification

total ucounts = 515
nonsolo ucounts = 230[2^69, 3^39, 4^17, 5^18, 6^12, 7^10, 8^3, 9^2, 10^3, 11, 12^4, 13, 14, 16, 17^2, 28, 75, 91, 92, 100, 117, 119, 137, 147, 151, 154, 170, 186, 218, 228, 232, 233, 236, 245, 246, 248, 250, 254, 256, 269, 275, 276, 278, 281^2, 287, 289, 299, 303, 304, 319, 323, 327, 343, 377, 390, 393, 399, 422, 442, 529, 686]
surviving nonsolo ucounts = 42[75, 91, 92, 117, 137, 151, 170, 186, 218, 228, 232, 233, 236, 245, 246, 248, 250, 254, 256, 269, 275, 276, 278, 281^2, 287, 289, 299, 303, 304, 319, 323, 327, 343, 377, 390, 393, 399, 422, 442, 529, 686]
ids = [42, 373, 296, 336, 235, 234, 387, 353, 95, 134, ...]

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

UMI info for barcode ACCGTAAAGGATGGTC-1 contig 1 = ACTTTCTGAG...
umi ACATGACGGC = 67 reads: +434 -1 +1 non-validated
umi AGAAAAACCG = 331 reads: +436 validated
umi AGCATCGCCG = 235 reads: +436 validated
umi ATTTCATATA = 692 reads: -132X +304 invalidated
umi CTAATGTGCA = 140 reads: +436 validated
umi GAAGGTCGCC = 240 reads: +223 -1XX +212 invalidated
umi GCCCTGTCGT = 94 reads: +436 validated
umi GTACGGTGTA = 117 reads: +436 validated
umi GTATCCCTCT = 404 reads: +436 validated
umi TCCAGCATTG = 270 reads: +436 validated
umi TCGAAACCAG = 284 reads: +436 validated
umi TTGAAAATCT = 236 reads: +436 validated

UMI info for barcode ACCGTAAAGGATGGTC-1 contig 2 = GGGGAGGAAC...
umi AATTTTCGCC = 400 reads: +385 validated
umi ACATTACCGG = 389 reads: +385 validated
umi ACTGGGAGTA = 384 reads: +385 validated
umi AGACCGCGTC = 251 reads: +385 validated
umi AGTTTATTCG = 218 reads: +385 validated
umi CATCCAAATG = 304 reads: +385 validated
umi CCAGCACAGG = 389 reads: -313X +2 -2X +1 -1X +1 -5XX +1 -2XX +1 -5XX +1 -3XX +2 -2XX +1 -4XX +38 invalidated
umi GCATGTGATC = 285 reads: +385 validated
umi GCCGTTCTTC = 252 reads: +385 validated
umi GGTACCGGGT = 345 reads: +385 validated
umi GGTTCCATAG = 254 reads: +385 validated
umi GTACGTGTGA = 329 reads: +385 validated
umi GTCGCGATCT = 298 reads: +146 -1XX +238 invalidated
umi GTTAATCAGA = 185 reads: +385 validated
umi GTTCCTCGGT = 266 reads: +385 validated
umi GTTGTGTACA = 339 reads: +92 -1XX +2 -8XX +1 -3XX +1 -5XX +272 invalidated
umi TATCAACGGC = 279 reads: +385 validated
umi TATGAGCCAT = 168 reads: +385 validated
umi TATTTTCGCT = 278 reads: +385 validated
umi TCGTTTCCCC = 301 reads: +385 validated

GOOD CONTIGS

TIG 1[bases=542]
0-35 ==> 66-101 on |195|IGHV4-61|5'UTR| [len=101] (mis=0)
35-391 ==> 0-356 on |196|IGHV4-61|L-REGION+V-REGION| [len=356] (mis=16)
408-471 ==> 0-63 on |59|IGHJ6|J-REGION| [len=63] (mis=6)
471-542 ==> 0-71 on |60|IGHM|C-REGION| [len=1358] (mis=0)
junction support: 12 umis using 291 reads
cdr3 = CAGHFYGSESYLNYYCMDVW at 380, score = 9 + 7
umis assigned: [42, 70, 77, 127, 235, 271, 296, 336, 341, 404] and 2 others
of which 12 are surviving nonsolos
reads assigned: 3057
start codons at 35, 79, 396, 428
confident = true

TIG 2[bases=557]
0-36 ==> 61-97 on |280|IGKV3-15|5'UTR| [len=97] (mis=0)
36-381 ==> 0-345 on |281|IGKV3-15|L-REGION+V-REGION| [len=345] (mis=1)
383-421 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=0)
421-557 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 19 umis using 808 reads
cdr3 = CQQYNNWPPWTF at 357, score = 9 + 8
umis assigned: [35, 44, 66, 72, 95, 162, 180, 294, 299, 325] and 10 others
of which 20 are surviving nonsolos
reads assigned: 5778
start codons at 36, 105, 241, 463
confident = true

REJECT CONTIGS

TIG 1[bases=326]
0-92 ==> 0-92 on rc of segment before IGHD7-27 exon 1 [len=92] (mis=1)
92-144 ==> 0-52 on |49|IGHJ1|J-REGION| [len=52] (mis=0)
144-326 ==> 0-182 on |40|IGHG1|C-REGION| [len=884] (mis=1)
umis assigned: [145, 203, 258, 382]
of which 3 are surviving nonsolos
reads assigned: 993
start codons at 28
confident = false
did not find CDR3
now this is a cell
paired!

GTGTACTACTGTGCGGGACATTTCTATGGTTCGGAGAGTTATTTAAACTACTACTGCATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG <==> AGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCCGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC

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

BARCODE 6.7 = ACCGTAAAGGGCATGT-1

using 82 reads

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

graph has 100 edges initially, 6 edges after simplification

total ucounts = 15
nonsolo ucounts = 14[2, 3^4, 4, 5^2, 6, 8^2, 10^2, 11]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 6.11 = ACCGTAAAGTACCGGA-1

using 538 reads

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

graph has 218 edges initially, 4 edges after simplification

total ucounts = 10
nonsolo ucounts = 3[8, 212, 311]
surviving nonsolo ucounts = 2[212, 311]
ids = [8, 6]

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

UMI info for barcode ACCGTAAAGTACCGGA-1 contig 1 = GAATCAGTCC...
umi GAACGGACAG = 312 reads: +388 validated

UMI info for barcode ACCGTAAAGTACCGGA-1 contig 2 = CCAAAAACCA...
umi TGTCTACCTT = 201 reads: +436 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 62 reads
cdr3 = CLQYSSSPWTF at 352, score = 9 + 8
umis assigned: [6]
of which 1 are surviving nonsolos
reads assigned: 305
start codons at 25, 31, 100, 236, 455
confident = false

TIG 2[bases=490]
0-52 ==> 7-59 on |64|IGHV1-18|5'UTR| [len=59] (mis=1)
52-405 ==> 0-353 on |65|IGHV1-18|L-REGION+V-REGION| [len=353] (mis=22)
454-488 ==> 12-46 on |54|IGHJ4|J-REGION| [len=46] (mis=0)
junction support: 1 umis using 18 reads
cdr3 = CARDKHFRDPYYHYSGALDHW at 394, score = 7 + 7
umis assigned: [8]
of which 1 are surviving nonsolos
reads assigned: 196
start codons at 52, 250, 255, 272, 316, 349
confident = false
NOT paired!

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

BARCODE 6.15 = ACCGTAAAGTGCCAGA-1

using 573 reads

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

graph has 186 edges initially, 2 edges after simplification

total ucounts = 8
nonsolo ucounts = 5[2^2, 3, 5, 558]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 6.18 = ACCGTAAAGTGTGAAT-1

using 344 reads

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

graph has 136 edges initially, 2 edges after simplification

total ucounts = 7
nonsolo ucounts = 2[4, 335]
surviving nonsolo ucounts = 1[335]
ids = [4]

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

UMI info for barcode ACCGTAAAGTGTGAAT-1 contig 1 = GGTGGTAGCT...
umi CGTAATGCGG = 342 reads: +63 -1XX +327 invalidated

GOOD CONTIGS

TIG 1[bases=562]
0-39 ==> 47-86 on |732|IGLV6-57|5'UTR| [len=86] (mis=0)
39-392 ==> 0-353 on |384|IGLV6-57|L-REGION+V-REGION| [len=353] (mis=17)
392-430 ==> 0-38 on |313|IGLJ3|J-REGION| [len=38] (mis=3)
430-562 ==> 0-132 on |307|IGLC3|C-REGION| [len=317] (mis=1)
junction support: 1 umis using 51 reads
cdr3 = CQSYDGNTKWVF at 366, score = 5 + 8
umis assigned: [4]
of which 1 are surviving nonsolos
reads assigned: 323
start codons at 39, 102, 193, 376, 379, 392
confident = false
NOT paired!

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

BARCODE 6.20 = ACCGTAAAGTTAACGA-1

using 276 reads

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

graph has 94 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 2[5, 270]
surviving nonsolo ucounts = 1[270]
ids = [1]

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

UMI info for barcode ACCGTAAAGTTAACGA-1 contig 1 = ACTGGTTGTT...
umi ATGAGGAACC = 262 reads: +400 validated

GOOD CONTIGS

TIG 1[bases=543]
0-110 ==> 65-175 on |295|IGKV4-1|5'UTR| [len=175] (mis=0)
110-473 ==> 0-363 on |296|IGKV4-1|L-REGION+V-REGION| [len=363] (mis=0)
472-510 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=2)
510-543 ==> 0-33 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 11 reads
cdr3 = CQQYYSTPRTF at 449, score = 9 + 8
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 259
start codons at 110, 179, 432
confident = false
NOT paired!

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

BARCODE 6.33 = ACCGTAACAATGACCT-1

using 248 reads

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

graph has 124 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 3[2, 7, 239]
surviving nonsolo ucounts = 1[239]
ids = [1]

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

UMI info for barcode ACCGTAACAATGACCT-1 contig 1 = GTGGGCTCAG...
umi TAAACCTGAA = 234 reads: +382 validated

GOOD CONTIGS

TIG 1[bases=552]
0-35 ==> 0-35 on |350|IGLV3-10|5'UTR| [len=35] (mis=0)
35-382 ==> 0-347 on |351|IGLV3-10|L-REGION+V-REGION| [len=347] (mis=8)
379-417 ==> 0-38 on |313|IGLJ3|J-REGION| [len=38] (mis=0)
417-552 ==> 0-135 on |307|IGLC3|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 43 reads
cdr3 = CYSADSSGDLWVF at 350, score = 7 + 8
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 229
start codons at 35, 96, 165, 183, 234, 296, 333
confident = false
NOT paired!

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

BARCODE 6.42 = ACCGTAACACCTGGTG-1

using 639 reads

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

graph has 248 edges initially, 2 edges after simplification

total ucounts = 10
nonsolo ucounts = 4[2, 4, 296, 331]
surviving nonsolo ucounts = 2[296, 331]
ids = [4, 5]

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

UMI info for barcode ACCGTAACACCTGGTG-1 contig 1 = GGGAATCAGT...
umi CGGCGTTCCC = 300 reads: +388 validated
umi CTCGCAGTAC = 329 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=551]
0-27 ==> 0-27 on |222|IGKV1-17|5'UTR| [len=27] (mis=1)
27-378 ==> 0-351 on |223|IGKV1-17|L-REGION+V-REGION| [len=351] (mis=19)
377-415 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=1)
415-551 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 2 umis using 97 reads
cdr3 = CLQYSSSPWTF at 354, score = 9 + 8
umis assigned: [4, 5]
of which 2 are surviving nonsolos
reads assigned: 617
start codons at 27, 33, 102, 238, 457
confident = false
NOT paired!

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

BARCODE 6.46 = ACCGTAACAGACTCGC-1

using 264 reads

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

graph has 58 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[264]
surviving nonsolo ucounts = 1[264]
ids = [0]

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

UMI info for barcode ACCGTAACAGACTCGC-1 contig 1 = CTGGGCCTCA...
umi AAGTCAAGCG = 266 reads: +376 validated

GOOD CONTIGS

TIG 1[bases=624]
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)
413-624 ==> 0-211 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 31 reads
cdr3 = CQAWDSTEVVF at 352, score = 6 + 8
umis assigned: [0]
of which 1 are surviving nonsolos
reads assigned: 263
start codons at 37, 42, 331, 335
confident = false
NOT paired!

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

BARCODE 6.50 = ACCGTAACAGCAGTTT-1

using 204 reads

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

graph has 118 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 2[3, 200]
surviving nonsolo ucounts = 1[200]
ids = [1]

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

UMI info for barcode ACCGTAACAGCAGTTT-1 contig 1 = ATAAAATCTG...
umi GACCTAAGCG = 194 reads: +382 validated

GOOD CONTIGS

TIG 1[bases=503]
0-63 ==> 0-63 on |297|IGKV5-2|5'UTR| [len=63] (mis=0)
63-408 ==> 0-345 on |298|IGKV5-2|L-REGION+V-REGION| [len=345] (mis=1)
406-445 ==> 0-39 on |214|IGKJ2|J-REGION| [len=39] (mis=3)
445-503 ==> 0-58 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 33 reads
cdr3 = CLQHDNFPYTF at 384, score = 8 + 8
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 192
start codons at 63, 153, 211, 214, 219, 322, 367, 394, 487
confident = false
NOT paired!

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

BARCODE 6.56 = ACCGTAACAGGAATGC-1

using 665 reads

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

graph has 180 edges initially, 6 edges after simplification

total ucounts = 8
nonsolo ucounts = 5[3, 4, 7, 272, 376]
surviving nonsolo ucounts = 2[272, 376]
ids = [2, 7]

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

UMI info for barcode ACCGTAACAGGAATGC-1 contig 1 = AGCTTCAGCT...
umi ATATTGCTCA = 270 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=646]
0-47 ==> 67-114 on |322|IGLV1-44|5'UTR| [len=114] (mis=0)
47-400 ==> 0-353 on |323|IGLV1-44|L-REGION+V-REGION| [len=353] (mis=19)
397-435 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=0)
435-646 ==> 0-211 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 43 reads
cdr3 = CAAWDDSLNGVVF at 368, score = 8 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 266
start codons at 47, 252, 351, 376, 381, 393
confident = false

REJECT CONTIGS

TIG 1[bases=379]
0-118 ==> 214-332 on |359|IGLV3-21|L-REGION+V-REGION| [len=351] (mis=7)
0-133 ==> 214-347 on |353|IGLV3-12|L-REGION+V-REGION| [len=347] (mis=20)
130-168 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=1)
168-379 ==> 0-211 on |306|IGLC2|C-REGION| [len=317] (mis=0)
cdr3 = CQVWDRSRDHVVF at 101, score = 6 + 8
umis assigned: [7]
of which 1 are surviving nonsolos
reads assigned: 373
start codons at 84, 129
confident = false
not full
VJ delta = 26
not full
NOT paired!

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

BARCODE 6.59 = ACCGTAACAGTCGTGC-1

using 1213 reads

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

graph has 1754 edges initially, 18 edges after simplification

total ucounts = 548
nonsolo ucounts = 223[2^80, 3^47, 4^30, 5^23, 6^9, 7^14, 8^7, 9^3, 10^4, 12^3, 13, 14^2]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 6.60 = ACCGTAACAGTCTTCC-1

using 89 reads

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

graph has 58 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[89]
surviving nonsolo ucounts = 0[]
ids = []

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

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BARCODE 6.63 = ACCGTAACATACAGCT-1

using 98 reads

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

graph has 46 edges initially, 2 edges after simplification

total ucounts = 10
nonsolo ucounts = 5[2^2, 3^2, 83]
surviving nonsolo ucounts = 1[83]
ids = [5]

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

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BARCODE 6.66 = ACCGTAACATGTCGAT-1

using 385 reads

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

graph has 238 edges initially, 2 edges after simplification

total ucounts = 7
nonsolo ucounts = 3[2, 4, 375]
surviving nonsolo ucounts = 1[375]
ids = [0]

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

UMI info for barcode ACCGTAACATGTCGAT-1 contig 1 = GAGTCAGACT...
umi CACTCGCCGT = 380 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=549]
0-25 ==> 156-181 on |232|IGKV1-5|5'UTR| [len=181] (mis=1)
25-376 ==> 0-351 on |233|IGKV1-5|L-REGION+V-REGION| [len=351] (mis=5)
375-413 ==> 0-38 on |217|IGKJ5|J-REGION| [len=38] (mis=3)
413-549 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 65 reads
cdr3 = CQQYNSYSLTF at 352, score = 8 + 9
umis assigned: [0]
of which 1 are surviving nonsolos
reads assigned: 371
start codons at 25, 31, 87, 100, 236, 239, 332, 455
confident = false
NOT paired!

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BARCODE 6.72 = ACCGTAAGTAGCTCCG-1

using 305 reads

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

graph has 118 edges initially, 2 edges after simplification

total ucounts = 6
nonsolo ucounts = 3[2^2, 298]
surviving nonsolo ucounts = 1[298]
ids = [0]

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

UMI info for barcode ACCGTAAGTAGCTCCG-1 contig 1 = TTTCTTCCGA...
umi CACGTCCCTC = 302 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=576]
52-403 ==> 0-351 on |235|IGKV1-6|L-REGION+V-REGION| [len=351] (mis=2)
402-440 ==> 0-38 on |217|IGKJ5|J-REGION| [len=38] (mis=0)
440-576 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 42 reads
cdr3 = CLQDYNYPITF at 379, score = 9 + 8
umis assigned: [0]
of which 1 are surviving nonsolos
reads assigned: 297
start codons at 26, 52, 58, 114, 127, 209, 263, 482
confident = false
NOT paired!

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BARCODE 6.77 = ACCGTAAGTCAGGACA-1

using 48 reads

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

graph has 8 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[48]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 6.97 = ACCGTAAGTTCCATGA-1

using 640 reads

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

graph has 308 edges initially, 2 edges after simplification

total ucounts = 6
nonsolo ucounts = 4[2, 5, 281, 350]
surviving nonsolo ucounts = 2[281, 350]
ids = [2, 0]

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

UMI info for barcode ACCGTAAGTTCCATGA-1 contig 1 = TGGGGGGACA...
umi AGGAGTACTG = 335 reads: +388 validated
umi CATACGTCCG = 268 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=502]
47-398 ==> 0-351 on |223|IGKV1-17|L-REGION+V-REGION| [len=351] (mis=10)
396-435 ==> 0-39 on |214|IGKJ2|J-REGION| [len=39] (mis=3)
435-502 ==> 0-67 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 2 umis using 82 reads
cdr3 = CQQHNSFPYTF at 374, score = 9 + 8
umis assigned: [0, 2]
of which 2 are surviving nonsolos
reads assigned: 588
start codons at 16, 47, 53, 122, 204, 477
confident = false
NOT paired!

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

BARCODE 6.98 = ACCGTAAGTTCGCGAC-1

using 324 reads

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

graph has 138 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 3[2, 5, 315]
surviving nonsolo ucounts = 1[315]
ids = [4]

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

REJECT CONTIGS

TIG 1[bases=548]
0-26 ==> 5-31 on |224|IGKV1-27|5'UTR| [len=31] (mis=0)
0-26 ==> 7774-7800 on rc of segment before IGKV2-28 exon 2 [len=7800] (mis=0)
11-81 ==> 8895-8965 on segment before IGKV1OR2-3 exon 1 [len=9099] (mis=7)
11-81 ==> 8904-8974 on rc of segment before IGKV2OR2-10 exon 1 [len=9109] (mis=7)
11-81 ==> 8903-8973 on segment before IGKV1OR2-11 exon 1 [len=9108] (mis=7)
26-377 ==> 0-351 on |225|IGKV1-27|L-REGION+V-REGION| [len=351] (mis=0)
375-412 ==> 0-37 on |216|IGKJ4|J-REGION| [len=37] (mis=0)
412-548 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
umis assigned: [4]
of which 1 are surviving nonsolos
reads assigned: 306
start codons at 26, 32, 88, 101, 237, 336, 454
confident = false
did not find CDR3
NOT paired!

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

BARCODE 6.107 = ACCGTAATCAATCACG-1

using 5808 reads

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

graph has 6076 edges initially, 102 edges after simplification

total ucounts = 1552
nonsolo ucounts = 770[2^296, 3^174, 4^120, 5^63, 6^42, 7^27, 8^13, 9^7, 10^5, 11^4, 12^3, 13, 14^2, 15^2, 18, 19, 20, 28, 64, 89, 192, 226, 336, 506, 810]
surviving nonsolo ucounts = 7[28, 64, 89, 226, 336, 506, 810]
ids = [953, 196, 214, 197, 27, 787, 421]

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

UMI info for barcode ACCGTAATCAATCACG-1 contig 1 = GATGGCCTGG...
umi ACTAGCCATT = 229 reads: +391 validated
umi CAAATATTTA = 818 reads: -354X +1 -1XX +35 invalidated
umi CTTTAGCCAC = 506 reads: -347 +1 -1 +1 -1 +2 -1 +3 -2 +32 non-validated
umi GGCCCTTAAC = 19 reads: -11 +2 -3X +1 -5X +1 -2XX +2 -1X +1 -7X +1 -6XX +222 -58 +29 -1 +26 -12 invalidated

GOOD CONTIGS

TIG 1[bases=603]
1-357 ==> 0-356 on |321|IGLV1-40|L-REGION+V-REGION| [len=356] (mis=11)
354-392 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=6)
392-603 ==> 0-211 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 37 reads
cdr3 = CQSYDSSLSGEIF at 325, score = 7 + 9
umis assigned: [197, 421, 787, 953]
of which 4 are surviving nonsolos
reads assigned: 1546
start codons at 1, 155, 158, 308, 335
confident = true
NOT paired!

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

BARCODE 6.109 = ACCGTAATCACATAGC-1

using 19441 reads

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

graph has 7857 edges initially, 50 edges after simplification

total ucounts = 1121
nonsolo ucounts = 550[2^182, 3^117, 4^75, 5^38, 6^27, 7^18, 8^6, 9^8, 10, 11, 12^2, 16, 18, 25, 28, 32, 34, 39, 46, 57, 59, 68, 71, 84, 90, 101, 114, 118, 123^2, 152^2, 153, 161, 164, 170, 172, 191, 193, 195, 196, 199, 211, 213^2, 220, 234, 240, 250, 257^2, 266, 270, 271, 274^2, 276, 287, 288, 291^2, 295^2, 297, 300, 309, 311^2, 319, 321^2, 322, 324, 329, 330, 342, 352, 356, 359, 370, 373, 380, 385, 493, 517, 674]
surviving nonsolo ucounts = 63[34, 39, 46, 59, 68, 71, 90, 101, 114, 118, 123^2, 152^2, 153, 172, 191, 193, 195, 196, 199, 213, 220, 234, 240, 250, 257^2, 266, 270, 271, 274^2, 276, 287, 288, 291^2, 295^2, 297, 300, 309, 311^2, 319, 321^2, 322, 324, 329, 330, 342, 352, 356, 359, 370, 373, 380, 385, 493, 517, 674]
ids = [596, 665, 473, 182, 548, 751, 346, 2, 1055, 678, ...]

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

UMI info for barcode ACCGTAATCACATAGC-1 contig 1 = TGGGAGGAGT...
umi AAAATGCACG = 149 reads: +388 validated
umi AATAGAACCC = 212 reads: +388 validated
umi AATCAATCTC = 329 reads: +388 validated
umi AATTGACCCA = 237 reads: +388 validated
umi ACAATACATC = 12 reads: -340 +2 -2XX +1 -5XX +1 -2XX +6 -1XX +3 -3XX +9 -1XX +12 invalidated
umi ACGTTGGTAG = 319 reads: +388 validated
umi ACTCACCTTC = 278 reads: +388 validated
umi AGAATTATGG = 310 reads: +388 validated
umi AGTTGTTAAA = 366 reads: +388 validated
umi AGTTTATCCT = 351 reads: +388 validated
umi ATACTAATCG = 311 reads: +388 validated
umi ATCCCTACAC = 676 reads: +388 validated
umi ATTTTAATTC = 323 reads: +388 validated
umi ATTTTTTTGG = 384 reads: +388 validated
umi CAAGTTGGAG = 142 reads: +41 -1XX +6 -1XX +3 -1XX +4 -1XX +7 -1XX +26 -1XX +2 -2XX +37 -1XX +5 -1XX +6 -3XX +10 -2XX +3 -3XX +10 -1XX +22 -1XX +9 -1XX +2 -1XX +9 -1XX +7 -1XX +21 -1XX +32 -1XX +8 -1XX +5 -1XX +33 -2XX +1 -1XX +5 -2XX +3 -1XX +37 invalidated
umi CATACTTTAT = 270 reads: +388 validated
umi CATTTGGGAA = 199 reads: +388 validated
umi CGCCCAAGTT = 301 reads: +388 validated
umi GCCAAGTAAA = 327 reads: +388 validated
umi GCCACAGTCA = 258 reads: +388 validated
umi GCGGCCCAGA = 247 reads: +388 validated
umi GCGGTCTAGC = 257 reads: +388 validated
umi GCTCCGCACT = 291 reads: +388 validated
umi GGAACACCTC = 298 reads: +388 validated
umi GGTAATATCC = 324 reads: +388 validated
umi GGTCGACGCC = 235 reads: +388 validated
umi GTAGAACGGG = 151 reads: +388 validated
umi GTCCTCTGGT = 283 reads: +388 validated
umi GTCGCAACGA = 170 reads: +388 validated
umi GTGACACTAT = 494 reads: +388 validated
umi TACGACCCTA = 124 reads: +388 validated
umi TCAAGCTTCC = 355 reads: +388 validated
umi TCACTGTATA = 299 reads: +388 validated
umi TCCGAGTATC = 307 reads: +388 validated
umi TCGGTGGTCA = 264 reads: +388 validated
umi TCGTATCGGT = 195 reads: +388 validated
umi TCTACGACTA = 151 reads: +388 validated
umi TGTAGCAACA = 346 reads: +388 validated
umi TTAATCCCAC = 291 reads: +388 validated
umi TTCCGTCTGC = 362 reads: +37 -1XX +1 -4XX +1 -5XX +2 -2XX +335 invalidated
umi TTCCTAGGTT = 290 reads: +388 validated
umi TTCCTGGGTG = 276 reads: +388 validated
umi TTTTCAGGGA = 290 reads: +388 validated

UMI info for barcode ACCGTAATCACATAGC-1 contig 2 = TGGGGACCCA...
umi AGTATAAGTT = 60 reads: +360 -1 +2 -70 non-validated
umi AGTTTTTACT = 272 reads: +433 validated
umi ATCGTCAGGT = 196 reads: +433 validated
umi CATGTCACGC = 89 reads: +433 validated
umi CTACCAGTAA = 46 reads: +392 -1 +40 non-validated
umi CTTTTGAGCC = 71 reads: +32 -1 +385 -3 +12 non-validated
umi GATGCACTCC = 34 reads: +4 -4 +299 -1 +74 -51 non-validated
umi GCTTGGGCCC = 182 reads: +433 validated
umi GGGATTCCGT = 118 reads: +433 validated
umi GGTACTTTCA = 183 reads: +433 validated
umi GTAAGGTCGG = 369 reads: +433 validated
umi GTGTTGTGCA = 322 reads: +433 validated
umi GTTGGGCCGT = 68 reads: +433 validated
umi TATACATACA = 302 reads: +421 -12 non-validated
umi TATTGTCCCG = 222 reads: -18X +415 invalidated
umi TCCTGGGCCA = 261 reads: +420 -1 +1 -1 +1 -1 +2 -6 non-validated
umi TTCGTGAATC = 114 reads: +392 -8X +3 -1XX +1 -2XX +2 -1X +1 -1 +2 -1 +18 invalidated

GOOD CONTIGS

TIG 1[bases=555]
31-384 ==> 0-353 on |253|IGKV1D-39|L-REGION+V-REGION| [len=353] (mis=2)
382-419 ==> 0-37 on |216|IGKJ4|J-REGION| [len=37] (mis=0)
419-555 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 41 umis using 1931 reads
cdr3 = CQQSYSTPLTF at 358, score = 9 + 9
umis assigned: [6, 46, 49, 62, 72, 124, 132, 148, 193, 194] and 33 others
of which 42 are surviving nonsolos
reads assigned: 11876
start codons at 31, 37, 93, 106, 242, 461
confident = true

TIG 2[bases=563]
0-59 ==> 0-59 on |64|IGHV1-18|5'UTR| [len=59] (mis=5)
59-412 ==> 0-353 on |65|IGHV1-18|L-REGION+V-REGION| [len=353] (mis=5)
444-492 ==> 0-48 on |55|IGHJ4|J-REGION| [len=48] (mis=3)
492-563 ==> 0-71 on |60|IGHM|C-REGION| [len=1358] (mis=0)
junction support: 12 umis using 158 reads
cdr3 = CARILYTSSGYDNPPSFDYW at 401, score = 8 + 7
umis assigned: [182, 196, 234, 346, 473, 548, 596, 655, 678, 683] and 7 others
of which 17 are surviving nonsolos
reads assigned: 2864
start codons at 59, 210, 257, 262, 279, 294, 323, 356
confident = true
now this is a cell
paired!

GTGTATTACTGTGCGAGAATACTCTACACCTCCAGTGGCTACGATAACCCCCCTTCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG <==> ATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC
sorting bam, mem = 0.07
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/chnk006-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/chnk006-ucc6a7a72ce/files/contig_bam.bam

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8.968 seconds used processing barcodes, peak mem = 0.23
