[stdout]

starting vdj_asm_asm, mem = 0.01
available mem = 844.21 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/chnk049-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/chnk049-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.chnk049.ucc6a7a72ce
n50_n50_rpu = 288

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

BARCODE 49.0 = CTCGAGGAGAGCTATA-1

using 599 reads

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

graph has 150 edges initially, 12 edges after simplification

total ucounts = 8
nonsolo ucounts = 4[3, 4, 216, 372]
surviving nonsolo ucounts = 2[216, 372]
ids = [2, 6]

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

UMI info for barcode CTCGAGGAGAGCTATA-1 contig 1 = GGAGTCAGAC...
umi GCAGTATTGT = 214 reads: +388 validated
umi TCCTCCGGCT = 367 reads: +48 -1XX +7 -2XX +1 -7XX +1 -9XX +1 -286XX +2 -9XX +1 -1XX +1 -3XX +1 -1XX +2 -2XX +1 -1XX invalidated

GOOD CONTIGS

TIG 1[bases=550]
0-26 ==> 21-47 on |218|IGKV1-12|5'UTR| [len=47] (mis=0)
26-377 ==> 0-351 on |219|IGKV1-12|L-REGION+V-REGION| [len=351] (mis=10)
377-414 ==> 0-37 on |216|IGKJ4|J-REGION| [len=37] (mis=0)
414-550 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 21 reads
cdr3 = CQQANSFPLTF at 353, score = 9 + 9
umis assigned: [2, 6]
of which 2 are surviving nonsolos
reads assigned: 574
start codons at 26, 32, 88, 101, 240, 258, 456
confident = false
NOT paired!

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

BARCODE 49.2 = CTCGAGGAGATCCGAG-1

using 48 reads

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

graph has 22 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 1[47]
surviving nonsolo ucounts = 1[47]
ids = [0]

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

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

BARCODE 49.7 = CTCGAGGAGCGTAATA-1

using 606 reads

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

graph has 832 edges initially, 8 edges after simplification

total ucounts = 262
nonsolo ucounts = 99[2^33, 3^22, 4^14, 5^7, 6^7, 7^3, 8^4, 9^3, 10^2, 16^2, 17, 29]
surviving nonsolo ucounts = 1[29]
ids = [18]

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

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

BARCODE 49.11 = CTCGAGGAGCTGAACG-1

using 420 reads

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

graph has 176 edges initially, 4 edges after simplification

total ucounts = 8
nonsolo ucounts = 5[2, 7, 8, 177, 223]
surviving nonsolo ucounts = 2[177, 223]
ids = [7, 3]

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

UMI info for barcode CTCGAGGAGCTGAACG-1 contig 1 = ACCCAAAAAC...
umi CACATAGCAG = 212 reads: +436 validated

GOOD CONTIGS

TIG 1[bases=602]
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)
490-602 ==> 0-112 on |1|IGHA1|C-REGION| [len=1058] (mis=0)
junction support: 1 umis using 20 reads
cdr3 = CARDKHFRDPYYHYSGALDHW at 396, score = 7 + 7
umis assigned: [3]
of which 1 are surviving nonsolos
reads assigned: 209
start codons at 54, 252, 257, 274, 318, 351, 544
confident = false

REJECT CONTIGS

TIG 1[bases=407]
0-342 ==> 3-345 on |281|IGKV3-15|L-REGION+V-REGION| [len=345] (mis=12)
341-379 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=2)
379-407 ==> 0-28 on |212|IGKC|C-REGION| [len=320] (mis=0)
cdr3 = CLQYYNWPRTF at 318, score = 9 + 8
umis assigned: [4, 7]
of which 1 are surviving nonsolos
reads assigned: 150
start codons at 52, 66, 202
confident = false
not full
VJ delta = 14
not full
NOT paired!

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

BARCODE 49.14 = CTCGAGGAGCTTATCG-1

using 1797 reads

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

graph has 2493 edges initially, 46 edges after simplification

total ucounts = 813
nonsolo ucounts = 370[2^143, 3^99, 4^47, 5^33, 6^16, 7^11, 8^6, 9^4, 10, 11^2, 12^3, 14, 15, 17, 18, 29]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 49.21 = CTCGAGGAGGCATGTG-1

using 704 reads

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

graph has 260 edges initially, 2 edges after simplification

total ucounts = 8
nonsolo ucounts = 3[3, 5, 691]
surviving nonsolo ucounts = 1[691]
ids = [1]

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

REJECT CONTIGS

TIG 1[bases=564]
0-63 ==> 5937-6000 on segment before IGKV2D-40 exon 1 [len=6000] (mis=2)
23-69 ==> 3411-3457 on segment before IGKV2OR2-2 exon 1 [len=3837] (mis=2)
30-390 ==> 0-360 on |275|IGKV2D-29|L-REGION+V-REGION| [len=360] (mis=9)
390-428 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=0)
428-564 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 685
start codons at 30, 63, 99, 187, 250, 349, 369, 470
confident = false
did not find CDR3
NOT paired!

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

BARCODE 49.30 = CTCGAGGAGTGAACGC-1

using 585 reads

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

graph has 222 edges initially, 2 edges after simplification

total ucounts = 4
nonsolo ucounts = 2[164, 419]
surviving nonsolo ucounts = 2[164, 419]
ids = [1, 0]

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

UMI info for barcode CTCGAGGAGTGAACGC-1 contig 1 = GAATCAGTCC...
umi ACTTCTTTCT = 417 reads: +388 validated
umi ATATCTCCAC = 163 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: 2 umis using 103 reads
cdr3 = CLQYSSSPWTF at 352, score = 9 + 8
umis assigned: [0, 1]
of which 2 are surviving nonsolos
reads assigned: 572
start codons at 25, 31, 100, 236, 455
confident = false
NOT paired!

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

BARCODE 49.31 = CTCGAGGAGTGCTGCC-1

using 88 reads

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

graph has 38 edges initially, 2 edges after simplification

total ucounts = 4
nonsolo ucounts = 1[85]
surviving nonsolo ucounts = 1[85]
ids = [2]

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

UMI info for barcode CTCGAGGAGTGCTGCC-1 contig 1 = TGAGCGCAGA...
umi CGATTACCGA = 82 reads: +385 validated

GOOD CONTIGS

TIG 1[bases=501]
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=5)
383-421 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=3)
421-501 ==> 0-80 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 10 reads
cdr3 = CGTWDSSLSALF at 357, score = 7 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 82
start codons at 36, 190, 241, 365
confident = false
NOT paired!

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

BARCODE 49.35 = CTCGAGGAGTTGTCGT-1

using 223 reads

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

graph has 58 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 1[219]
surviving nonsolo ucounts = 1[219]
ids = [3]

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

UMI info for barcode CTCGAGGAGTTGTCGT-1 contig 1 = GGTGATCAGC...
umi GTCACTCGGG = 222 reads: +427 validated

GOOD CONTIGS

TIG 1[bases=529]
0-31 ==> 48-79 on |119|IGHV3-21|5'UTR| [len=79] (mis=0)
31-384 ==> 0-353 on |120|IGHV3-21|L-REGION+V-REGION| [len=353] (mis=4)
411-458 ==> 16-63 on |737|IGHJ6|J-REGION| [len=63] (mis=0)
458-529 ==> 0-71 on |60|IGHM|C-REGION| [len=1358] (mis=0)
junction support: 1 umis using 22 reads
cdr3 = CARDLLRSYGDYGGMDVW at 373, score = 9 + 7
umis assigned: [3]
of which 1 are surviving nonsolos
reads assigned: 219
start codons at 31, 187, 334, 415
confident = false
NOT paired!

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

BARCODE 49.38 = CTCGAGGCAACAACCT-1

using 380 reads

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

graph has 156 edges initially, 4 edges after simplification

total ucounts = 11
nonsolo ucounts = 6[2, 3, 13, 15, 21, 321]
surviving nonsolo ucounts = 3[15, 21, 321]
ids = [6, 5, 1]

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

UMI info for barcode CTCGAGGCAACAACCT-1 contig 1 = GAAGAGCTGC...
umi AATCCAATGG = 321 reads: +385 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=3)
379-418 ==> 0-39 on |214|IGKJ2|J-REGION| [len=39] (mis=5)
418-554 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 46 reads
cdr3 = CQQYGSSPVTF at 357, score = 9 + 8
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 317
start codons at 33, 241, 244, 367, 460
confident = false
NOT paired!

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

BARCODE 49.48 = CTCGAGGCACAGCGTC-1

using 529 reads

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

graph has 210 edges initially, 24 edges after simplification

total ucounts = 11
nonsolo ucounts = 4[2, 9, 238, 273]
surviving nonsolo ucounts = 2[238, 273]
ids = [2, 5]

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

UMI info for barcode CTCGAGGCACAGCGTC-1 contig 1 = AGTCTCAGTC...
umi ATCGCAATTA = 239 reads: +388 validated

UMI info for barcode CTCGAGGCACAGCGTC-1 contig 2 = ATCAGTCCCA...
umi TATTAATCCT = 277 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=544]
0-20 ==> 3-23 on |252|IGKV1D-39|5'UTR| [len=23] (mis=0)
20-373 ==> 0-353 on |253|IGKV1D-39|L-REGION+V-REGION| [len=353] (mis=13)
371-408 ==> 0-37 on |216|IGKJ4|J-REGION| [len=37] (mis=0)
408-544 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 37 reads
cdr3 = CQQSYTTLLTF at 347, score = 9 + 9
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 235
start codons at 20, 26, 82, 95, 231, 450
confident = false

TIG 2[bases=547]
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)
411-547 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 49 reads
cdr3 = CLQYSSSPWTF at 350, score = 9 + 8
umis assigned: [5]
of which 1 are surviving nonsolos
reads assigned: 270
start codons at 23, 29, 98, 234, 453
confident = false
NOT paired!

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

BARCODE 49.56 = CTCGAGGCACTCGACG-1

using 23 reads

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

graph has 22 edges initially, 2 edges after simplification

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

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

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

BARCODE 49.70 = CTCGAGGCATATGGTC-1

using 774 reads

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

graph has 268 edges initially, 4 edges after simplification

total ucounts = 5
nonsolo ucounts = 2[245, 526]
surviving nonsolo ucounts = 2[245, 526]
ids = [2, 3]

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

UMI info for barcode CTCGAGGCATATGGTC-1 contig 1 = TGGGGTCACA...
umi CTAACGATGA = 242 reads: +385 validated

GOOD CONTIGS

TIG 1[bases=571]
0-39 ==> 123-162 on |342|IGLV2-23|5'UTR| [len=162] (mis=0)
39-379 ==> 0-340 on |343|IGLV2-23|L-REGION+V-REGION| [len=340] (mis=11)
386-424 ==> 0-38 on |309|IGLJ1|J-REGION| [len=38] (mis=1)
424-571 ==> 0-147 on |305|IGLC1|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 43 reads
cdr3 = CCSKAGRSYVF at 363, score = 8 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 238
start codons at 39, 178, 247, 388, 556
confident = false

REJECT CONTIGS

TIG 1[bases=374]
0-198 ==> 5531-5729 on rc of segment before IGKV3-7 exon 2 [len=11729] (mis=2)
199-238 ==> 0-39 on |214|IGKJ2|J-REGION| [len=39] (mis=3)
238-374 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
umis assigned: [3]
of which 1 are surviving nonsolos
reads assigned: 520
start codons at 180, 280
confident = false
did not find CDR3
NOT paired!

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

BARCODE 49.79 = CTCGAGGCATTAGGCT-1

using 21517 reads

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

graph has 8095 edges initially, 201 edges after simplification

total ucounts = 1092
nonsolo ucounts = 474[2^195, 3^102, 4^44, 5^34, 6^11, 7^9, 8^5, 9^6, 10^4, 11, 12^3, 13^2, 14, 16, 19, 43, 64, 85, 111, 119, 132, 135, 138, 141, 151, 154, 155, 159, 177, 182, 186, 193, 212, 217, 221, 224, 226, 233, 246, 247, 256, 270, 272, 279^2, 290, 299, 301, 312, 315, 325, 326, 327, 341^3, 348, 375, 383, 390, 481, 520, 702, 744, 790, 817, 917, 1017, 1371, 1592]
surviving nonsolo ucounts = 55[3, 16, 19, 43, 64, 85, 111, 119, 132, 138, 141, 151, 155, 177, 182, 186, 193, 212, 217, 221, 224, 226, 233, 246, 247, 256, 270, 272, 279^2, 290, 299, 301, 312, 315, 325, 326, 327, 341^3, 348, 375, 383, 390, 481, 520, 702, 744, 790, 817, 917, 1017, 1371, 1592]
ids = [191, 1087, 559, 894, 587, 269, 447, 18, 318, 10, ...]

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

UMI info for barcode CTCGAGGCATTAGGCT-1 contig 1 = AGAGAGGTGC...
umi AAAGGGAGAT = 9 reads: -409X +2 -2X +1 -10XX +1 -1XX +1 -3XX +1 -5XX +1 -2XX +3 invalidated
umi AAATTTGGCC = 21 reads: -413X +1 -10X +1 -1XX +1 -3XX +1 -5XX +1 -2XX +3 invalidated
umi ATTCTCTGGG = 507 reads: -409 +1 -3XX +3 -2XX +3 -10XX +1 -2XX +1 -2XX +1 -3XX +1 invalidated
umi CATGCCATGG = 131 reads: +442 validated
umi CCACATGCTT = 12 reads: -409 +2 -2X +1 -10X +1 -1XX +1 -3XX +1 -5XX +1 -2XX +3 invalidated
umi CGGTTTATTG = 116 reads: +442 validated
umi CTTTATCCAA = 19 reads: +302 -1 +28 -40 +37 -1 +13 -13 +7 non-validated
umi CTTTCATGGA = 155 reads: +442 validated
umi GAGAAAACGG = 62 reads: +93 -1X +329 -1 +2 -1 +3 -2 +10 invalidated
umi GCTCTATCAT = 155 reads: +407 -15 +20 non-validated
umi GGAACCACTG = 135 reads: -409X +2 -2XX +1 -10XX +1 -1XX +1 -3XX +1 -5XX +1 -2XX +3 invalidated
umi TAATTTGTGT = 177 reads: +442 validated
umi TAGAGATGGT = 142 reads: +413 -29 non-validated
umi TCGGGTTGCC = 2 reads: -442 non-validated
umi TTTTTGGTCT = 16 reads: +49 -51 +109 -4 +7 -1 +2 -1 +3 -1 +68 -79 +1 -1 +56 -9 non-validated

UMI info for barcode CTCGAGGCATTAGGCT-1 contig 2 = GCTCTGCTTC...
umi ACAACTTGTC = 227 reads: +388 validated
umi ACAAGACCTT = 314 reads: +388 validated
umi AGGCGAGGTT = 181 reads: +388 validated
umi CCTCCGAGAA = 289 reads: +388 validated
umi CGTTCCGTTC = 226 reads: +388 validated
umi CTGTCCTTTC = 179 reads: +388 validated
umi TGAACTGTTT = 277 reads: +388 validated
umi TGCGTGCGAT = 255 reads: +388 validated
umi TGTCACGGTC = 246 reads: +388 validated
umi TTATGTCGGT = 221 reads: +388 validated
umi TTTTTTTCAG = 214 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=696]
0-72 ==> 7-79 on |141|IGHV3-48|5'UTR| [len=79] (mis=0)
72-425 ==> 0-353 on |142|IGHV3-48|L-REGION+V-REGION| [len=353] (mis=15)
453-514 ==> 0-61 on |58|IGHJ6|J-REGION| [len=61] (mis=5)
514-696 ==> 0-182 on |40|IGHG1|C-REGION| [len=884] (mis=1)
junction support: 5 umis using 67 reads
cdr3 = CARDFVGYDLLTGADYLYYMDVW at 414, score = 9 + 7
umis assigned: [10, 18, 243, 318, 338, 447, 559, 560, 587, 666] and 5 others
of which 15 are surviving nonsolos
reads assigned: 1621
start codons at 72, 138, 228, 349, 375, 471
confident = true

TIG 2[bases=650]
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=6)
401-439 ==> 0-38 on |309|IGLJ1|J-REGION| [len=38] (mis=0)
439-650 ==> 0-211 on |305|IGLC1|C-REGION| [len=317] (mis=1)
junction support: 11 umis using 460 reads
cdr3 = CQSYDSSLCYVF at 375, score = 8 + 8
umis assigned: [62, 63, 154, 391, 462, 529, 929, 949, 966, 995] and 1 others
of which 11 are surviving nonsolos
reads assigned: 2588
start codons at 51, 205, 208, 259, 358, 385, 403
confident = true

REJECT CONTIGS

TIG 1[bases=568]
1-48 ==> 5953-6000 on rc of segment after IGKV1-16 exon 1 [len=6000] (mis=1)
31-95 ==> 5672-5736 on segment before IGKV1OR2-6 exon 1 [len=5879] (mis=3)
48-399 ==> 0-351 on |221|IGKV1-16|L-REGION+V-REGION| [len=351] (mis=7)
395-432 ==> 0-37 on |216|IGKJ4|J-REGION| [len=37] (mis=5)
432-568 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
umis assigned: [12, 120, 269, 316, 379, 400, 414, 547, 616, 642] and 9 others
of which 19 are surviving nonsolos
reads assigned: 5659
start codons at 48, 54, 110, 123, 238, 259, 474
confident = false
did not find CDR3

TIG 2[bases=306]
11-64 ==> 2883-2936 on segment before IGLVV-58 exon 1 [len=3104] (mis=3)
62-88 ==> 2937-2963 on segment before IGLVV-58 exon 1 [len=3104] (mis=1)
95-306 ==> 0-211 on |306|IGLC2|C-REGION| [len=317] (mis=1)
umis assigned: [16, 84, 98, 117, 174, 357, 564, 764, 919]
of which 9 are surviving nonsolos
reads assigned: 8195
start codons at 46
confident = false
did not find CDR3
now this is a cell
paired!

TGTGCGAGAGATTTCGTGGGTTACGATCTTTTGACTGGTGCCGACTACCTCTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG <==> ACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGTGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG

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

BARCODE 49.90 = CTCGAGGGTCAGTGGA-1

using 577 reads

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

graph has 218 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 3[8^2, 561]
surviving nonsolo ucounts = 1[561]
ids = [0]

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

REJECT CONTIGS

TIG 1[bases=334]
3-161 ==> 202-360 on |265|IGKV2-28|L-REGION+V-REGION| [len=360] (mis=1)
161-198 ==> 0-37 on |216|IGKJ4|J-REGION| [len=37] (mis=0)
198-334 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
cdr3 = CMQALQTPLTF at 137, score = 9 + 9
umis assigned: [0]
of which 1 are surviving nonsolos
reads assigned: 550
start codons at 120, 140, 240
confident = false
not full
VJ delta = 13
not full
NOT paired!

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

BARCODE 49.91 = CTCGAGGGTCATCCCT-1

using 288 reads

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

graph has 130 edges initially, 2 edges after simplification

total ucounts = 4
nonsolo ucounts = 3[3, 4, 280]
surviving nonsolo ucounts = 1[280]
ids = [2]

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

UMI info for barcode CTCGAGGGTCATCCCT-1 contig 1 = GCCTGGGCCT...
umi GCTTGCCCTG = 274 reads: +379 validated

GOOD CONTIGS

TIG 1[bases=582]
0-39 ==> 13-52 on |348|IGLV3-1|5'UTR| [len=52] (mis=0)
39-373 ==> 0-334 on |349|IGLV3-1|L-REGION+V-REGION| [len=346] (mis=11)
380-418 ==> 0-38 on |313|IGLJ3|J-REGION| [len=38] (mis=1)
418-582 ==> 0-164 on |306|IGLC2|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 55 reads
cdr3 = CQAWDSTTDWVF at 354, score = 6 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 268
start codons at 39, 44, 100, 187, 333, 337
confident = false
NOT paired!

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

BARCODE 49.103 = CTCGAGGGTGTTGAGG-1

using 312 reads

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

graph has 124 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 3[2^2, 306]
surviving nonsolo ucounts = 1[306]
ids = [2]

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

UMI info for barcode CTCGAGGGTGTTGAGG-1 contig 1 = GGGGAGGAAT...
umi CGCATAACCT = 305 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=555]
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)
419-555 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 50 reads
cdr3 = CLQYSSSPWTF at 358, score = 9 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 301
start codons at 31, 37, 106, 242, 461
confident = false
NOT paired!

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

BARCODE 49.104 = CTCGAGGGTTAAAGAC-1

using 240 reads

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

graph has 100 edges initially, 2 edges after simplification

total ucounts = 7
nonsolo ucounts = 5[2, 3, 5, 6, 222]
surviving nonsolo ucounts = 1[222]
ids = [6]

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

UMI info for barcode CTCGAGGGTTAAAGAC-1 contig 1 = GGCTGGGATC...
umi TTGTGCTGGC = 218 reads: +391 validated

GOOD CONTIGS

TIG 1[bases=529]
42-380 ==> 0-338 on |341|IGLV2-18|L-REGION+V-REGION| [len=354] (mis=16)
395-433 ==> 0-38 on |309|IGLJ1|J-REGION| [len=38] (mis=5)
433-529 ==> 0-96 on |305|IGLC1|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 29 reads
cdr3 = CSSYTNSTTPGVF at 366, score = 8 + 8
umis assigned: [6]
of which 1 are surviving nonsolos
reads assigned: 214
start codons at 42, 178, 250
confident = false
NOT paired!

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

BARCODE 49.110 = CTCGAGGGTTCCCTTG-1

using 178 reads

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

graph has 30 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[178]
surviving nonsolo ucounts = 1[178]
ids = [0]

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

UMI info for barcode CTCGAGGGTTCCCTTG-1 contig 1 = ACCCAAAAAC...
umi TTCGTGGCTC = 177 reads: +409 validated

GOOD CONTIGS

TIG 1[bases=545]
0-54 ==> 5-59 on |64|IGHV1-18|5'UTR| [len=59] (mis=0)
54-407 ==> 0-353 on |65|IGHV1-18|L-REGION+V-REGION| [len=353] (mis=23)
412-463 ==> 0-51 on |57|IGHJ5|J-REGION| [len=51] (mis=5)
463-545 ==> 0-82 on |40|IGHG1|C-REGION| [len=884] (mis=1)
junction support: 1 umis using 16 reads
cdr3 = CARGSTSWYDYW at 396, score = 8 + 7
umis assigned: [0]
of which 1 are surviving nonsolos
reads assigned: 176
start codons at 54, 205, 252, 257, 289, 351
confident = false
NOT paired!

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

BARCODE 49.121 = CTCGAGGTCACGCATA-1

using 22768 reads

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

graph has 16241 edges initially, 378 edges after simplification

total ucounts = 3572
nonsolo ucounts = 2555[2^474, 3^353, 4^292, 5^252, 6^214, 7^165, 8^162, 9^138, 10^96, 11^92, 12^73, 13^69, 14^49, 15^26, 16^30, 17^11, 18^14, 19^2, 20^6, 21^6, 22^3, 27^2, 28, 32, 34, 36, 48, 57, 90, 105, 124, 164, 174, 182, 271, 276, 295, 300, 318, 327, 331, 342, 347, 362, 364, 369, 422, 796]
surviving nonsolo ucounts = 21[15, 48, 90, 105, 124, 164, 174, 271, 276, 295, 300, 318, 327, 331, 342, 347, 362, 364, 369, 422, 796]
ids = [3436, 2256, 807, 3077, 2853, 2916, 2075, 863, 487, 405, ...]

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

UMI info for barcode CTCGAGGTCACGCATA-1 contig 1 = AGTGACTCCT...
umi ACCTCAAGAC = 296 reads: +436 validated
umi ATAATCTCCT = 327 reads: +436 validated
umi ATGGCTGCTT = 271 reads: +434 -1X +1 invalidated
umi GCATCGTCAC = 44 reads: +436 validated
umi TATAAGCCTT = 127 reads: +421 -15 non-validated
umi TCGTCACAGG = 106 reads: +436 validated

UMI info for barcode CTCGAGGTCACGCATA-1 contig 2 = GGAGGAGTCA...
umi ACCAGCCCCC = 368 reads: +388 validated
umi ACTAATACTC = 273 reads: +388 validated
umi ATACCTCTAG = 346 reads: -358X +2 -3XX +2 -3XX +1 -3XX +1 -1XX +1 -1XX +1 -3XX +1 -1XX +2 -4XX invalidated
umi ATCGGAATTC = 91 reads: +388 validated
umi ATCTTAGACA = 305 reads: +388 validated
umi GACAACCGCG = 178 reads: +388 validated
umi GGAGATTGTT = 330 reads: +388 validated
umi GTAAATGCTC = 345 reads: -358X +2 -3XX +2 -3XX +1 -3XX +1 -1XX +1 -1XX +1 -3XX +1 -1XX +2 -4XX invalidated
umi TACACTGGCG = 344 reads: +388 validated
umi TAGCGGACTC = 316 reads: +388 validated
umi TCACACTGTC = 155 reads: -358X +2 -3XX +2 -3XX +1 -3XX +1 -1XX +1 -1XX +1 -3XX +1 -1XX +2 -4XX invalidated
umi TGGCCTCTAG = 408 reads: -363X +2 -3XX +1 -3XX +1 -1XX +1 -1XX +1 -3XX +1 -1XX +2 -4XX invalidated
umi TTTGCAATTT = 341 reads: -358X +2 -3X +2 -3XX +1 -3XX +1 -1XX +1 -1XX +1 -3XX +1 -1XX +2 -4XX invalidated

GOOD CONTIGS

TIG 1[bases=527]
0-20 ==> 0-20 on |97|IGHV2-5|5'UTR| [len=20] (mis=0)
20-378 ==> 0-358 on |98|IGHV2-5|L-REGION+V-REGION| [len=358] (mis=16)
436-456 ==> 32-52 on |49|IGHJ1|J-REGION| [len=52] (mis=1)
456-527 ==> 0-71 on |60|IGHM|C-REGION| [len=1358] (mis=0)
junction support: 5 umis using 92 reads
cdr3 = CAHISTLFRSAYYRPYLDFW at 365, score = 7 + 6
umis assigned: [405, 710, 863, 2256, 2853, 3077]
of which 6 are surviving nonsolos
reads assigned: 1154
start codons at 20, 64, 243, 246, 326, 335
confident = true

TIG 2[bases=553]
29-382 ==> 0-353 on |253|IGKV1D-39|L-REGION+V-REGION| [len=353] (mis=12)
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)
junction support: 8 umis using 355 reads
cdr3 = CQQGYTTPLSF at 356, score = 9 + 8
umis assigned: [345, 487, 714, 807, 831, 2075, 2429, 2567, 2781, 2836] and 3 others
of which 13 are surviving nonsolos
reads assigned: 3716
start codons at 29, 35, 91, 104, 240, 459
confident = true
now this is a cell
paired!

ACATATTACTGTGCGCACATCTCCACTCTTTTCCGGAGTGCTTATTATCGGCCCTACTTAGATTTTTGGGGCCAGGGAGTCCTGGTCTCCGTCTCCTCAG <==> ATCAACTGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGGGTTACACTACCCCTCTCTCTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC

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

BARCODE 49.124 = CTCGAGGTCAGTACGT-1

using 70 reads

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

graph has 106 edges initially, 2 edges after simplification

total ucounts = 23
nonsolo ucounts = 13[2^2, 3^3, 4^2, 5^2, 6^2, 7, 10]
surviving nonsolo ucounts = 0[]
ids = []

====================================================================================
NOT paired!
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/chnk049-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/chnk049-ucc6a7a72ce/files/contig_bam.bam

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

9.255 seconds used processing barcodes, peak mem = 0.23
