[stdout]

starting vdj_asm_asm, mem = 0.01
available mem = 844.31 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/chnk024-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/chnk024-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.chnk024.ucc6a7a72ce
n50_n50_rpu = 288

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

BARCODE 24.5 = CATCCACTCTCATTCA-1

using 76 reads

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

graph has 110 edges initially, 2 edges after simplification

total ucounts = 23
nonsolo ucounts = 13[2^2, 3^6, 5^3, 6, 23]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 24.19 = CATCGAAAGAATGTTG-1

using 181 reads

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

graph has 62 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 1[179]
surviving nonsolo ucounts = 1[179]
ids = [1]

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

UMI info for barcode CATCGAAAGAATGTTG-1 contig 1 = GGGCCTAAGG...
umi CTCGGTAGTC = 166 reads: +379 validated

GOOD CONTIGS

TIG 1[bases=558]
0-35 ==> 216-251 on |358|IGLV3-21|5'UTR| [len=251] (mis=0)
35-377 ==> 0-342 on |359|IGLV3-21|L-REGION+V-REGION| [len=351] (mis=0)
376-414 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=0)
414-558 ==> 0-144 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 40 reads
cdr3 = CQVWDSSSDVVF at 350, score = 8 + 8
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 166
start codons at 35, 96, 234, 237, 333, 375
confident = false
NOT paired!

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

BARCODE 24.20 = CATCGAAAGACAAGCC-1

using 271 reads

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

graph has 94 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 1[269]
surviving nonsolo ucounts = 1[269]
ids = [2]

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

UMI info for barcode CATCGAAAGACAAGCC-1 contig 1 = GCTTCAGCTG...
umi GTATCTACAT = 260 reads: +394 validated

GOOD CONTIGS

TIG 1[bases=581]
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)
440-581 ==> 0-141 on |305|IGLC1|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 36 reads
cdr3 = CQSYDSSLSGLYVF at 370, score = 7 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 254
start codons at 46, 200, 203, 254, 353, 380, 404, 572
confident = false
NOT paired!

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

BARCODE 24.26 = CATCGAAAGAGTAATC-1

using 383 reads

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

graph has 132 edges initially, 2 edges after simplification

total ucounts = 7
nonsolo ucounts = 3[2, 6, 371]
surviving nonsolo ucounts = 1[371]
ids = [6]

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

UMI info for barcode CATCGAAAGAGTAATC-1 contig 1 = GGGAGCATCA...
umi TGTTGGCTAG = 344 reads: +424 validated

GOOD CONTIGS

TIG 1[bases=518]
0-64 ==> 0-64 on |66|IGHV1-2|5'UTR| [len=64] (mis=1)
64-417 ==> 0-353 on |67|IGHV1-2|L-REGION+V-REGION| [len=353] (mis=7)
440-488 ==> 0-48 on |55|IGHJ4|J-REGION| [len=48] (mis=6)
488-518 ==> 0-30 on |60|IGHM|C-REGION| [len=1358] (mis=0)
junction support: 1 umis using 31 reads
cdr3 = CARSLVSYSSSWIFDYW at 406, score = 8 + 7
umis assigned: [6]
of which 1 are surviving nonsolos
reads assigned: 340
start codons at 64, 262, 267, 299, 328, 361
confident = false
NOT paired!

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

BARCODE 24.32 = CATCGAAAGCCAGTAG-1

using 282 reads

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

graph has 136 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 2[11, 271]
surviving nonsolo ucounts = 1[271]
ids = [1]

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

UMI info for barcode CATCGAAAGCCAGTAG-1 contig 1 = GGAGTCAGTC...
umi ATTCGAAGCG = 272 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=550]
0-26 ==> 21-47 on |230|IGKV1-39|5'UTR| [len=47] (mis=0)
26-377 ==> 0-351 on |231|IGKV1-39|L-REGION+V-REGION| [len=351] (mis=11)
376-414 ==> 0-38 on |217|IGKJ5|J-REGION| [len=38] (mis=0)
414-550 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 48 reads
cdr3 = CQQSYRRPITF at 353, score = 8 + 8
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 267
start codons at 26, 32, 88, 101, 237, 336, 456
confident = false
NOT paired!

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

BARCODE 24.33 = CATCGAAAGCCCGAAA-1

using 2178 reads

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

graph has 1130 edges initially, 60 edges after simplification

total ucounts = 145
nonsolo ucounts = 49[2^16, 3^9, 4^2, 5, 6^2, 7^2, 8, 9^3, 10^2, 13, 14^4, 32, 250, 341, 379, 382, 476]
surviving nonsolo ucounts = 6[32, 250, 341, 379, 382, 476]
ids = [13, 66, 38, 79, 74, 43]

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

UMI info for barcode CATCGAAAGCCCGAAA-1 contig 1 = GAGGGTCCAG...
umi ACACACCCCC = 29 reads: -381 +3 -3X +15 -1X +27 invalidated
umi CAACTTTACT = 344 reads: +430 validated
umi CTGGCCATCA = 220 reads: +430 validated
umi GCCATTTAGT = 387 reads: +430 validated

UMI info for barcode CATCGAAAGCCCGAAA-1 contig 2 = GAAGAGCTGC...
umi CACCTATAGC = 479 reads: +388 validated

UMI info for barcode CATCGAAAGCCCGAAA-1 contig 3 = GGAGGAACTG...
umi GAATTTCCTA = 382 reads: +382 validated

GOOD CONTIGS

TIG 1[bases=539]
38-409 ==> 0-371 on |186|IGHV4-34|L-REGION+V-REGION| [len=371] (mis=0)
414-468 ==> 7-61 on |58|IGHJ6|J-REGION| [len=61] (mis=0)
468-539 ==> 0-71 on |60|IGHM|C-REGION| [len=1358] (mis=0)
junction support: 3 umis using 82 reads
cdr3 = CARGSHYYYMDVW at 398, score = 9 + 7
umis assigned: [13, 38, 66, 79]
of which 4 are surviving nonsolos
reads assigned: 960
start codons at 15, 38, 59, 103, 189, 425
confident = true

TIG 2[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=1)
382-421 ==> 0-39 on |214|IGKJ2|J-REGION| [len=39] (mis=3)
421-557 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 69 reads
cdr3 = CQQYGSSPGYTF at 357, score = 9 + 8
umis assigned: [43]
of which 1 are surviving nonsolos
reads assigned: 468
start codons at 33, 241, 367, 463
confident = true

TIG 3[bases=552]
0-34 ==> 63-97 on |280|IGKV3-15|5'UTR| [len=97] (mis=0)
34-379 ==> 0-345 on |281|IGKV3-15|L-REGION+V-REGION| [len=345] (mis=0)
378-416 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=3)
416-552 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 58 reads
cdr3 = CQQYNNWPLTF at 355, score = 9 + 9
umis assigned: [74]
of which 1 are surviving nonsolos
reads assigned: 378
start codons at 34, 103, 239, 458
confident = true
now this is a cell
NOT paired!

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

BARCODE 24.35 = CATCGAAAGCTGAACG-1

using 219 reads

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

graph has 86 edges initially, 2 edges after simplification

total ucounts = 4
nonsolo ucounts = 2[3, 214]
surviving nonsolo ucounts = 1[214]
ids = [2]

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

UMI info for barcode CATCGAAAGCTGAACG-1 contig 1 = ATCATCCAAC...
umi GCAACTACAG = 210 reads: +430 validated

GOOD CONTIGS

TIG 1[bases=559]
0-58 ==> 246-304 on |78|IGHV1-46|5'UTR| [len=304] (mis=1)
58-411 ==> 0-353 on |79|IGHV1-46|L-REGION+V-REGION| [len=353] (mis=20)
440-488 ==> 13-61 on |58|IGHJ6|J-REGION| [len=61] (mis=1)
488-559 ==> 0-71 on |1|IGHA1|C-REGION| [len=1058] (mis=0)
junction support: 1 umis using 23 reads
cdr3 = CARGDRRAAAFYYHYMDVW at 400, score = 8 + 7
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 206
start codons at 58, 214, 256, 322, 355, 445, 542
confident = false
NOT paired!

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

BARCODE 24.52 = CATCGAAAGTATGACA-1

using 461 reads

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

graph has 166 edges initially, 4 edges after simplification

total ucounts = 5
nonsolo ucounts = 3[4, 178, 277]
surviving nonsolo ucounts = 2[178, 277]
ids = [2, 4]

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

UMI info for barcode CATCGAAAGTATGACA-1 contig 1 = ATCAGTCCCA...
umi GATGTTTTAT = 158 reads: +388 validated

UMI info for barcode CATCGAAAGTATGACA-1 contig 2 = GTCTGGGAGA...
umi TTCGACCGGC = 253 reads: +406 validated

GOOD CONTIGS

TIG 1[bases=497]
0-23 ==> 4-27 on |222|IGKV1-17|5'UTR| [len=27] (mis=0)
23-374 ==> 0-351 on |223|IGKV1-17|L-REGION+V-REGION| [len=351] (mis=19)
373-411 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=1)
411-497 ==> 0-86 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 27 reads
cdr3 = CLQYSSSPWTF at 350, score = 9 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 157
start codons at 23, 29, 98, 234, 453
confident = false

TIG 2[bases=494]
77-430 ==> 0-353 on |128|IGHV3-33|L-REGION+V-REGION| [len=353] (mis=28)
433-483 ==> 0-50 on |53|IGHJ3|J-REGION| [len=50] (mis=2)
junction support: 1 umis using 18 reads
cdr3 = CARENDAFDIW at 419, score = 8 + 8
umis assigned: [4]
of which 1 are surviving nonsolos
reads assigned: 247
start codons at 77, 137, 228, 233, 291, 294, 380, 464
confident = false
NOT paired!

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

BARCODE 24.60 = CATCGAACAAAGTCAA-1

using 313 reads

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

graph has 156 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 2[6, 304]
surviving nonsolo ucounts = 1[304]
ids = [4]

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

UMI info for barcode CATCGAACAAAGTCAA-1 contig 1 = TTTTCAGGTG...
umi TGATAGTCCC = 303 reads: +433 validated

GOOD CONTIGS

TIG 1[bases=554]
0-50 ==> 29-79 on |121|IGHV3-23|5'UTR| [len=79] (mis=0)
50-403 ==> 0-353 on |122|IGHV3-23|L-REGION+V-REGION| [len=353] (mis=1)
409-438 ==> 0-29 on |19|IGHD3-16|D-REGION| [len=37] (mis=5)
450-483 ==> 13-46 on |54|IGHJ4|J-REGION| [len=46] (mis=0)
483-554 ==> 0-71 on |60|IGHM|C-REGION| [len=1358] (mis=0)
junction support: 1 umis using 25 reads
cdr3 = CAKDEIGYDYIWGSYPPGFR at 392, score = 9 + 6
umis assigned: [4]
of which 1 are surviving nonsolos
reads assigned: 298
start codons at 50, 201, 206, 353, 402, 414
confident = false
NOT paired!

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

BARCODE 24.61 = CATCGAACAACACCCG-1

using 190 reads

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

graph has 54 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 1[189]
surviving nonsolo ucounts = 1[189]
ids = [1]

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

UMI info for barcode CATCGAACAACACCCG-1 contig 1 = ATCATCCAAC...
umi TCGGCGCGAT = 173 reads: +430 validated

GOOD CONTIGS

TIG 1[bases=529]
0-58 ==> 246-304 on |78|IGHV1-46|5'UTR| [len=304] (mis=0)
58-411 ==> 0-353 on |79|IGHV1-46|L-REGION+V-REGION| [len=353] (mis=33)
435-488 ==> 0-53 on |51|IGHJ2|J-REGION| [len=53] (mis=7)
488-529 ==> 0-41 on |1|IGHA1|C-REGION| [len=1058] (mis=0)
junction support: 1 umis using 20 reads
cdr3 = CARNPGDNSWDSYFHLDLW at 400, score = 8 + 7
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 173
start codons at 58, 212, 252, 256, 322, 355
confident = false
NOT paired!

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

BARCODE 24.66 = CATCGAACAAGGGTCA-1

using 332 reads

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

graph has 124 edges initially, 2 edges after simplification

total ucounts = 6
nonsolo ucounts = 4[2, 3, 10, 315]
surviving nonsolo ucounts = 1[315]
ids = [5]

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

UMI info for barcode CATCGAACAAGGGTCA-1 contig 1 = GAGTCAGTCC...
umi TGTGCTCCGT = 286 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=500]
0-25 ==> 6-31 on |226|IGKV1-33|5'UTR| [len=31] (mis=0)
25-376 ==> 0-351 on |227|IGKV1-33|L-REGION+V-REGION| [len=351] (mis=16)
374-413 ==> 0-39 on |214|IGKJ2|J-REGION| [len=39] (mis=6)
413-500 ==> 0-87 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 53 reads
cdr3 = CQQYEDLPYTF at 352, score = 9 + 7
umis assigned: [5]
of which 1 are surviving nonsolos
reads assigned: 282
start codons at 25, 31, 87, 100, 362, 406, 455
confident = false
NOT paired!

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

BARCODE 24.74 = CATCGAACACGCGAAA-1

using 367 reads

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

graph has 112 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 1[363]
surviving nonsolo ucounts = 1[363]
ids = [2]

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

UMI info for barcode CATCGAACACGCGAAA-1 contig 1 = GGAGTCAGAC...
umi GCTAACGCTC = 364 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=550]
0-26 ==> 155-181 on |232|IGKV1-5|5'UTR| [len=181] (mis=1)
26-377 ==> 0-351 on |233|IGKV1-5|L-REGION+V-REGION| [len=351] (mis=10)
376-414 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=2)
414-550 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 49 reads
cdr3 = CQQYDSFSWTF at 353, score = 8 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 359
start codons at 26, 32, 88, 101, 237, 240, 333, 363, 456
confident = false
NOT paired!

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

BARCODE 24.78 = CATCGAACACTTGGAT-1

using 265 reads

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

graph has 102 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 1[263]
surviving nonsolo ucounts = 1[263]
ids = [2]

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

UMI info for barcode CATCGAACACTTGGAT-1 contig 1 = GAGTCAGTCC...
umi TGCACACTGC = 263 reads: +382 validated

GOOD CONTIGS

TIG 1[bases=549]
31-279 ==> 0-248 on |237|IGKV1-8|L-REGION+V-REGION| [len=345] (mis=34)
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 45 reads
cdr3 = CLHYDNRRRTF at 352, score = 9 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 259
start codons at 31, 87, 100, 239, 362, 455
confident = false
NOT paired!

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

BARCODE 24.86 = CATCGAACAGGCGATA-1

using 488 reads

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

graph has 147 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[488]
surviving nonsolo ucounts = 1[488]
ids = [0]

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

REJECT CONTIGS

TIG 1[bases=496]
0-243 ==> 91-334 on |349|IGLV3-1|L-REGION+V-REGION| [len=346] (mis=15)
247-285 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=4)
285-496 ==> 0-211 on |306|IGLC2|C-REGION| [len=317] (mis=0)
cdr3 = CQAWDSTEVVF at 224, score = 6 + 8
umis assigned: [0]
of which 1 are surviving nonsolos
reads assigned: 482
start codons at 203, 207
confident = false
not full
VJ delta = 21
not full
NOT paired!

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

BARCODE 24.88 = CATCGAACAGTCAGAG-1

using 413 reads

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

graph has 110 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 1[412]
surviving nonsolo ucounts = 1[412]
ids = [0]

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

UMI info for barcode CATCGAACAGTCAGAG-1 contig 1 = AGGAACTGCT...
umi CAACTTGAGG = 365 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=503]
0-32 ==> 65-97 on |280|IGKV3-15|5'UTR| [len=97] (mis=0)
32-377 ==> 0-345 on |281|IGKV3-15|L-REGION+V-REGION| [len=345] (mis=1)
382-420 ==> 0-38 on |217|IGKJ5|J-REGION| [len=38] (mis=1)
420-503 ==> 0-83 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 74 reads
cdr3 = CQQYNNWPPAITF at 353, score = 9 + 8
umis assigned: [0]
of which 1 are surviving nonsolos
reads assigned: 364
start codons at 32, 101, 237, 462
confident = false
NOT paired!

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

BARCODE 24.106 = CATCGAAGTATTCGTG-1

using 384 reads

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

graph has 154 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 2[2, 379]
surviving nonsolo ucounts = 1[379]
ids = [1]

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

UMI info for barcode CATCGAAGTATTCGTG-1 contig 1 = GGGACTGATC...
umi ACGTTCCTGC = 381 reads: +397 validated

GOOD CONTIGS

TIG 1[bases=569]
0-36 ==> 0-36 on |272|IGKV2D-28|5'UTR| [len=36] (mis=2)
36-396 ==> 0-360 on |273|IGKV2D-28|L-REGION+V-REGION| [len=360] (mis=7)
394-433 ==> 0-39 on |214|IGKJ2|J-REGION| [len=39] (mis=3)
433-569 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 56 reads
cdr3 = CMQALQTPYTF at 372, score = 9 + 8
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 372
start codons at 36, 69, 105, 193, 355, 375, 475
confident = false
NOT paired!

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

BARCODE 24.107 = CATCGAAGTCCCTACT-1

using 561 reads

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

graph has 214 edges initially, 4 edges after simplification

total ucounts = 4
nonsolo ucounts = 2[229, 330]
surviving nonsolo ucounts = 2[229, 330]
ids = [1, 2]

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

UMI info for barcode CATCGAAGTCCCTACT-1 contig 1 = AGCTTCAGCT...
umi ATCACTTCAT = 227 reads: +388 validated

UMI info for barcode CATCGAAGTCCCTACT-1 contig 2 = AGGAGTCAGA...
umi CAGTTCCTTT = 312 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=524]
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=15)
397-435 ==> 0-38 on |313|IGLJ3|J-REGION| [len=38] (mis=3)
435-524 ==> 0-89 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 35 reads
cdr3 = CASWDDSLRGRVF at 368, score = 8 + 8
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 223
start codons at 47, 201, 351, 376, 381
confident = false

TIG 2[bases=494]
0-27 ==> 154-181 on |232|IGKV1-5|5'UTR| [len=181] (mis=1)
27-378 ==> 0-351 on |233|IGKV1-5|L-REGION+V-REGION| [len=351] (mis=10)
377-415 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=2)
415-494 ==> 0-79 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 62 reads
cdr3 = CQQYDSFSWTF at 354, score = 8 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 306
start codons at 27, 33, 89, 102, 238, 241, 334, 364, 457
confident = false
NOT paired!

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

BARCODE 24.114 = CATCGAAGTGAGGGAG-1

using 497 reads

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

graph has 202 edges initially, 4 edges after simplification

total ucounts = 7
nonsolo ucounts = 2[215, 277]
surviving nonsolo ucounts = 2[215, 277]
ids = [2, 4]

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

UMI info for barcode CATCGAAGTGAGGGAG-1 contig 1 = TGAGCGCAGA...
umi ATGCCCTCCT = 217 reads: +397 validated

UMI info for barcode CATCGAAGTGAGGGAG-1 contig 2 = GGGAATCAGT...
umi GTTACTTTTA = 259 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=597]
0-36 ==> 0-36 on |330|IGLV1-51|5'UTR| [len=36] (mis=0)
36-389 ==> 0-353 on |331|IGLV1-51|L-REGION+V-REGION| [len=353] (mis=3)
395-433 ==> 0-38 on |313|IGLJ3|J-REGION| [len=38] (mis=0)
433-597 ==> 0-164 on |307|IGLC3|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 38 reads
cdr3 = CGTWDSSLSAGAFWVF at 357, score = 7 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 209
start codons at 36, 190, 241, 365
confident = false

TIG 2[bases=500]
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)
415-500 ==> 0-85 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 40 reads
cdr3 = CLQYSSSPWTF at 354, score = 9 + 8
umis assigned: [4]
of which 1 are surviving nonsolos
reads assigned: 256
start codons at 27, 33, 102, 238, 457
confident = false
NOT paired!

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

BARCODE 24.117 = CATCGAAGTGGTAACG-1

using 1356 reads

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

graph has 1263 edges initially, 10 edges after simplification

total ucounts = 361
nonsolo ucounts = 149[2^59, 3^24, 4^20, 5^18, 6^10, 7^5, 8^5, 9^2, 10^2, 17^2, 259, 318]
surviving nonsolo ucounts = 2[259, 318]
ids = [100, 42]

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

UMI info for barcode CATCGAAGTGGTAACG-1 contig 1 = AATACTTTCT...
umi ACGGCTTGGT = 317 reads: +424 validated
umi CAAGCTAGGT = 255 reads: +424 validated

GOOD CONTIGS

TIG 1[bases=575]
0-38 ==> 26-64 on |191|IGHV4-4|5'UTR| [len=64] (mis=1)
38-391 ==> 0-353 on |192|IGHV4-4|L-REGION+V-REGION| [len=353] (mis=9)
414-462 ==> 0-48 on |55|IGHJ4|J-REGION| [len=48] (mis=0)
462-575 ==> 0-113 on |40|IGHG1|C-REGION| [len=884] (mis=1)
junction support: 2 umis using 57 reads
cdr3 = CARGAGITTRAYYFDYW at 380, score = 9 + 7
umis assigned: [42, 100]
of which 2 are surviving nonsolos
reads assigned: 567
start codons at 17, 38, 82
confident = false
NOT paired!

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

BARCODE 24.130 = CATCGAATCAACACCA-1

using 964 reads

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

graph has 240 edges initially, 4 edges after simplification

total ucounts = 7
nonsolo ucounts = 5[2^3, 415, 541]
surviving nonsolo ucounts = 2[415, 541]
ids = [3, 5]

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

UMI info for barcode CATCGAATCAACACCA-1 contig 1 = GAAGAGCTGC...
umi CCGTTCGACT = 417 reads: +385 validated

UMI info for barcode CATCGAATCAACACCA-1 contig 2 = GCTCTGCTTC...
umi TGAGGAGGAA = 518 reads: +391 validated

GOOD CONTIGS

TIG 1[bases=554]
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=1)
380-418 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=0)
418-554 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 51 reads
cdr3 = CQQYGSSPWTF at 357, score = 9 + 8
umis assigned: [3]
of which 1 are surviving nonsolos
reads assigned: 414
start codons at 33, 241, 367, 460
confident = false

TIG 2[bases=557]
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=12)
404-442 ==> 0-38 on |313|IGLJ3|J-REGION| [len=38] (mis=3)
442-557 ==> 0-115 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 87 reads
cdr3 = CQSYDTSLSGSVF at 375, score = 8 + 8
umis assigned: [5]
of which 1 are surviving nonsolos
reads assigned: 516
start codons at 51, 205, 208, 259, 358, 385
confident = false
NOT paired!

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

BARCODE 24.131 = CATCGAATCACAAACC-1

using 263 reads

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

graph has 104 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 3[4, 5, 252]
surviving nonsolo ucounts = 1[252]
ids = [4]

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

UMI info for barcode CATCGAATCACAAACC-1 contig 1 = TGAGCGCAGA...
umi TCCGCTAGTG = 242 reads: +385 validated

GOOD CONTIGS

TIG 1[bases=519]
0-36 ==> 0-36 on |330|IGLV1-51|5'UTR| [len=36] (mis=0)
36-389 ==> 0-353 on |331|IGLV1-51|L-REGION+V-REGION| [len=353] (mis=6)
383-421 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=2)
421-519 ==> 0-98 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 39 reads
cdr3 = CGTWDSSLRGVF at 357, score = 7 + 8
umis assigned: [4]
of which 1 are surviving nonsolos
reads assigned: 238
start codons at 36, 190, 241, 365
confident = false
NOT paired!

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

BARCODE 24.143 = CATCGAATCATGCAAC-1

using 328 reads

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

graph has 130 edges initially, 2 edges after simplification

total ucounts = 8
nonsolo ucounts = 4[4^3, 312]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 24.144 = CATCGAATCCAAAGTC-1

using 1043 reads

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

graph has 1562 edges initially, 10 edges after simplification

total ucounts = 475
nonsolo ucounts = 210[2^89, 3^49, 4^22, 5^17, 6^11, 7^10, 8^5, 9, 10, 13, 15, 18, 19, 20]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 24.146 = CATCGAATCCTCGCAT-1

using 370 reads

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

graph has 523 edges initially, 6 edges after simplification

total ucounts = 147
nonsolo ucounts = 76[2^26, 3^19, 4^8, 5^8, 6^4, 7^7, 8, 11, 12, 13]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 24.155 = CATCGAATCGTTTATC-1

using 16 reads

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

graph has 6 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[16]
surviving nonsolo ucounts = 0[]
ids = []

====================================================================================
NOT paired!
sorting bam, mem = 0.03
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/chnk024-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/chnk024-ucc6a7a72ce/files/contig_bam.bam

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

3.361 seconds used processing barcodes, peak mem = 0.23
