[stdout]

starting vdj_asm_asm, mem = 0.01
available mem = 844.32 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/chnk021-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/chnk021-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.chnk021.ucc6a7a72ce
n50_n50_rpu = 288

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

BARCODE 21.0 = CACCTTGTCCAATGGT-1

using 274 reads

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

graph has 100 edges initially, 6 edges after simplification

total ucounts = 12
nonsolo ucounts = 4[2^2, 9, 253]
surviving nonsolo ucounts = 1[253]
ids = [8]

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

UMI info for barcode CACCTTGTCCAATGGT-1 contig 1 = AGGAGTCAGA...
umi CCTCCTTCGT = 1 reads: -388 non-validated
umi TCATGCCATG = 253 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=551]
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)
415-551 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 38 reads
cdr3 = CQQYDSFSWTF at 354, score = 8 + 8
umis assigned: [3, 8]
of which 1 are surviving nonsolos
reads assigned: 252
start codons at 27, 33, 89, 102, 238, 241, 334, 364, 457
confident = false
NOT paired!

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

BARCODE 21.11 = CACCTTGTCCGTTGTC-1

using 14 reads

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

graph has 10 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[14]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 21.43 = CACCTTGTCTTGTATC-1

using 19 reads

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

graph has 16 edges initially, 4 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[19]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 21.47 = CACTCCAAGAAGGGTA-1

using 166 reads

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

graph has 200 edges initially, 2 edges after simplification

total ucounts = 21
nonsolo ucounts = 17[2^2, 3^2, 6^2, 7, 8, 10, 13^3, 14^2, 15^2, 18]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 21.53 = CACTCCAAGAGTTGGC-1

using 2965 reads

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

graph has 3730 edges initially, 66 edges after simplification

total ucounts = 980
nonsolo ucounts = 540[2^163, 3^101, 4^75, 5^50, 6^43, 7^28, 8^19, 9^16, 10^11, 11^7, 12^8, 13, 14^6, 15^4, 16^2, 17, 19^3, 22, 28]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 21.57 = CACTCCAAGATCCGAG-1

using 158 reads

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

graph has 64 edges initially, 2 edges after simplification

total ucounts = 9
nonsolo ucounts = 2[3, 148]
surviving nonsolo ucounts = 1[148]
ids = [6]

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

UMI info for barcode CACTCCAAGATCCGAG-1 contig 1 = AGTGACTCCT...
umi TAGGTCACTG = 139 reads: +433 validated

GOOD CONTIGS

TIG 1[bases=454]
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=19)
403-453 ==> 0-50 on |53|IGHJ3|J-REGION| [len=50] (mis=4)
junction support: 1 umis using 20 reads
cdr3 = CAHQLAIVTGYYENAFDIW at 365, score = 8 + 8
umis assigned: [6]
of which 1 are surviving nonsolos
reads assigned: 137
start codons at 20, 64, 243, 246, 249, 335, 405
confident = false
NOT paired!

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

BARCODE 21.63 = CACTCCAAGCAGGCTA-1

using 409 reads

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

graph has 178 edges initially, 2 edges after simplification

total ucounts = 9
nonsolo ucounts = 4[2, 4, 6, 392]
surviving nonsolo ucounts = 1[392]
ids = [0]

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

UMI info for barcode CACTCCAAGCAGGCTA-1 contig 1 = AGTCTCAGTC...
umi ACTAACTCAG = 372 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=470]
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=24)
370-408 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=2)
408-470 ==> 0-62 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 70 reads
cdr3 = CQQSYRTPLTF at 347, score = 9 + 9
umis assigned: [0]
of which 1 are surviving nonsolos
reads assigned: 367
start codons at 20, 26, 82, 95, 218, 231, 450
confident = false
NOT paired!

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

BARCODE 21.68 = CACTCCAAGCCCGAAA-1

using 340 reads

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

graph has 132 edges initially, 2 edges after simplification

total ucounts = 4
nonsolo ucounts = 2[2, 336]
surviving nonsolo ucounts = 1[336]
ids = [3]

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

UMI info for barcode CACTCCAAGCCCGAAA-1 contig 1 = ATCAGTCCCA...
umi TACGGCAGCA = 342 reads: +388 validated

GOOD CONTIGS

TIG 1[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 55 reads
cdr3 = CLQYSSSPWTF at 350, score = 9 + 8
umis assigned: [3]
of which 1 are surviving nonsolos
reads assigned: 334
start codons at 23, 29, 98, 234, 453
confident = false
NOT paired!

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

BARCODE 21.75 = CACTCCAAGCTGAACG-1

using 17341 reads

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

graph has 10060 edges initially, 102 edges after simplification

total ucounts = 1797
nonsolo ucounts = 1004[2^318, 3^184, 4^127, 5^99, 6^56, 7^36, 8^42, 9^32, 10^13, 11^11, 12^8, 13^7, 14^8, 15^3, 16^4, 17^2, 19, 20, 26, 42, 58, 71, 80, 84, 110, 112, 137^2, 155, 156, 159^2, 190^2, 201, 207, 208, 218, 227, 229, 230, 234^2, 237, 245, 246, 250, 257, 276, 278, 279, 284, 286, 289, 291, 298, 300, 302, 306^2, 308, 329, 344, 346, 360, 363, 366, 370, 387, 656]
surviving nonsolo ucounts = 48[58, 80, 84, 110, 112, 137^2, 155, 159^2, 190^2, 201, 207, 208, 218, 227, 229, 230, 234^2, 237, 245, 246, 250, 257, 276, 278, 279, 284, 286, 289, 291, 298, 300, 302, 306^2, 308, 329, 344, 346, 360, 363, 366, 370, 387, 656]
ids = [1353, 222, 1789, 253, 4, 399, 496, 1020, 1184, 1614, ...]

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

UMI info for barcode CACTCCAAGCTGAACG-1 contig 1 = AGCTCTGAGA...
umi AAATGCCTGT = 281 reads: +427 validated
umi ACGGATTGCT = 79 reads: +424 -3 non-validated
umi CAAACGGCGA = 193 reads: +427 validated
umi CAAATACCAA = 139 reads: +427 validated
umi CATTTACCCG = 191 reads: +427 validated
umi CATTTGGTCA = 230 reads: +391 -36 non-validated
umi GGGATATCGT = 231 reads: +427 validated
umi GGTCCTAGTT = 149 reads: +418 -9 non-validated
umi TAGATACTCA = 56 reads: +367 -60 non-validated
umi TGTGCGGTAC = 210 reads: +421 -6 non-validated

UMI info for barcode CACTCCAAGCTGAACG-1 contig 2 = GATCAGGACT...
umi AAAACCGTTA = 115 reads: +397 validated
umi AAGAGTCCAC = 220 reads: +397 validated
umi AATCTTCCTC = 345 reads: +397 validated
umi ACTTAATGCA = 111 reads: +397 validated
umi AGCTCTTGTT = 235 reads: +397 validated
umi AGGTCTCTTT = 290 reads: +397 validated
umi ATCGGCACCA = 139 reads: +31 -1XX +365 invalidated
umi ATGAAGGGCT = 254 reads: +112 -1XX +284 invalidated
umi CACACTAGCT = 222 reads: +397 validated
umi CACACTCGTC = 332 reads: +397 validated
umi CAGATGTCGG = 229 reads: +397 validated
umi CATCCTCTTA = 390 reads: +397 validated
umi CATGGTTTTA = 346 reads: +397 validated
umi CCATTACTGT = 306 reads: +397 validated
umi CCCCCCGTAA = 308 reads: +397 validated
umi CCCCTTCACT = 240 reads: +397 validated
umi CCTGAAGGGG = 275 reads: +397 validated
umi CCTGGTCCAG = 246 reads: +397 validated
umi CTATATTCGG = 292 reads: +397 validated
umi CTCAATGCTT = 287 reads: +397 validated
umi GACAAGGTCC = 227 reads: +397 validated
umi GACTCATTAT = 368 reads: +397 validated
umi GAGTTATTGG = 370 reads: +397 validated
umi GATACGAGCC = 156 reads: +397 validated
umi GATTACGAGT = 299 reads: +397 validated
umi GCATGTTCTT = 260 reads: +397 validated
umi GGAGACCACT = 368 reads: +397 validated
umi GGATAAAGTA = 294 reads: +397 validated
umi GGCATCGTCT = 204 reads: +397 validated
umi GTTCTCGGAT = 279 reads: +397 validated
umi TAACTATGGT = 366 reads: +397 validated
umi TAGCGCCGGG = 210 reads: +397 validated
umi TATGCGAGCA = 287 reads: +397 validated
umi TGTGTGGTCA = 157 reads: +397 validated
umi TTAAATTATG = 288 reads: +397 validated
umi TTATACGCAG = 307 reads: +397 validated
umi TTTTCACTGC = 86 reads: +397 validated

GOOD CONTIGS

TIG 1[bases=577]
0-79 ==> 0-79 on |119|IGHV3-21|5'UTR| [len=79] (mis=0)
79-432 ==> 0-353 on |120|IGHV3-21|L-REGION+V-REGION| [len=353] (mis=17)
428-455 ==> 10-37 on |19|IGHD3-16|D-REGION| [len=37] (mis=4)
470-506 ==> 10-46 on |54|IGHJ4|J-REGION| [len=46] (mis=1)
506-577 ==> 0-71 on |60|IGHM|C-REGION| [len=1358] (mis=0)
junction support: 5 umis using 73 reads
cdr3 = CALRLGEVSSNRELSSNW at 421, score = 9 + 6
umis assigned: [36, 222, 494, 496, 632, 637, 1159, 1184, 1353, 1611]
of which 10 are surviving nonsolos
reads assigned: 1724
start codons at 79, 235, 382
confident = true

TIG 2[bases=563]
0-30 ==> 0-30 on |264|IGKV2-28|5'UTR| [len=30] (mis=0)
30-353 ==> 0-323 on |265|IGKV2-28|L-REGION+V-REGION| [len=360] (mis=3)
390-427 ==> 0-37 on |216|IGKJ4|J-REGION| [len=37] (mis=0)
427-563 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 37 umis using 1336 reads
cdr3 = CMQALQTRLTF at 366, score = 8 + 9
umis assigned: [4, 85, 123, 253, 303, 320, 399, 413, 526, 527] and 27 others
of which 37 are surviving nonsolos
reads assigned: 9529
start codons at 30, 63, 99, 187, 349, 369, 469
confident = true
now this is a cell
paired!

ACGGCTGTCTATTACTGTGCCCTACGTTTGGGGGAGGTATCGTCCAACCGGGAATTATCGTCCAACTGGGGCCAGGGAACCCTGGTCATCGTCTCCTCAG <==> ATCAGCAGAGTGGAGGCTGACGATGTAGGCGTTTATTACTGTATGCAAGCTCTGCAAACTCGCCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC

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

BARCODE 21.88 = CACTCCAAGGTGACCA-1

using 2600 reads

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

graph has 3516 edges initially, 40 edges after simplification

total ucounts = 848
nonsolo ucounts = 482[2^143, 3^84, 4^82, 5^55, 6^30, 7^20, 8^15, 9^14, 10^11, 11^5, 12^4, 13^5, 14^4, 15^2, 16, 17^3, 19^2, 24, 34]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 21.92 = CACTCCAAGTACGATA-1

using 129 reads

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

graph has 60 edges initially, 2 edges after simplification

total ucounts = 6
nonsolo ucounts = 1[124]
surviving nonsolo ucounts = 1[124]
ids = [5]

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

UMI info for barcode CACTCCAAGTACGATA-1 contig 1 = ATCACATAAC...
umi ATTCACTACC = 1 reads: +2 -2 +3 -1 +2 -1X +3 -1 +1 -1 +14 -1 +1 -1 +13 -1 +1 -369 invalidated
umi CTTCACGACC = 108 reads: +418 validated

GOOD CONTIGS

TIG 1[bases=490]
0-58 ==> 0-58 on |87|IGHV1-69D|5'UTR| [len=58] (mis=0)
58-411 ==> 0-353 on |88|IGHV1-69D|L-REGION+V-REGION| [len=353] (mis=0)
425-476 ==> 0-51 on |57|IGHJ5|J-REGION| [len=51] (mis=3)
junction support: 1 umis using 15 reads
cdr3 = CARDKGSVEGWFDPW at 400, score = 9 + 7
umis assigned: [1, 5]
of which 1 are surviving nonsolos
reads assigned: 108
start codons at 58, 209, 256, 355
confident = false
NOT paired!

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

BARCODE 21.99 = CACTCCAAGTCGTTTG-1

using 844 reads

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

graph has 220 edges initially, 2 edges after simplification

total ucounts = 9
nonsolo ucounts = 3[2, 6, 830]
surviving nonsolo ucounts = 1[830]
ids = [6]

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

REJECT CONTIGS

TIG 1[bases=365]
4-103 ==> 241-340 on |339|IGLV2-14|L-REGION+V-REGION| [len=361] (mis=5)
116-154 ==> 0-38 on |311|IGLJ2|J-REGION| [len=38] (mis=4)
154-365 ==> 0-211 on |306|IGLC2|C-REGION| [len=317] (mis=0)
cdr3 = CSSYTTRGTFVLF at 87, score = 7 + 8
umis assigned: [6]
of which 1 are surviving nonsolos
reads assigned: 819
start codons at 
confident = false
not full
VJ delta = 27
not full
NOT paired!

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

BARCODE 21.112 = CACTCCACAAACTGCT-1

using 24 reads

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

graph has 24 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[24]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 21.114 = CACTCCACAACCGCCA-1

using 19 reads

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

graph has 12 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 2[3, 16]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 21.119 = CACTCCACAAGCCGTC-1

using 6581 reads

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

graph has 3984 edges initially, 32 edges after simplification

total ucounts = 745
nonsolo ucounts = 336[2^122, 3^63, 4^39, 5^28, 6^22, 7^16, 8^11, 9^4, 10^7, 12, 14^2, 15, 16^2, 18, 23, 102, 191, 207, 211, 228, 249, 251, 255, 262, 266, 277, 305, 330, 364, 688, 691]
surviving nonsolo ucounts = 16[102, 191, 207, 211, 228, 249, 251, 255, 262, 266, 277, 305, 330, 364, 688, 691]
ids = [520, 434, 391, 500, 215, 18, 695, 78, 561, 486, ...]

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

UMI info for barcode CACTCCACAAGCCGTC-1 contig 1 = GAAGAGCTGC...
umi ACATAAGCAT = 260 reads: +388 validated
umi ATTTAACCAT = 235 reads: +388 validated
umi CACCGACTAT = 360 reads: +388 validated
umi CTCAGGAGAA = 328 reads: +388 validated
umi GATCCCACAG = 194 reads: +388 validated
umi GGTAATACCT = 270 reads: +388 validated
umi GTCAAATGTC = 211 reads: +388 validated
umi TAGCTGTTCC = 259 reads: +388 validated
umi TCTTTCCCCT = 300 reads: +388 validated
umi TGATATTCCC = 700 reads: +388 validated
umi TTCCCCTACT = 275 reads: +388 validated

UMI info for barcode CACTCCACAAGCCGTC-1 contig 2 = GATCAGGACT...
umi AACATTAAAC = 238 reads: +442 validated
umi TCGACTTCCT = 487 reads: -385X +1 -16X +1 -6XX +6 -1XX +26 invalidated
umi TTATATACCG = 240 reads: +442 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=8)
384-421 ==> 0-37 on |216|IGKJ4|J-REGION| [len=37] (mis=0)
421-557 ==> 0-136 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 11 umis using 519 reads
cdr3 = CQQYGSSPPLTF at 357, score = 9 + 9
umis assigned: [78, 215, 241, 370, 434, 486, 500, 561, 645, 655] and 1 others
of which 11 are surviving nonsolos
reads assigned: 3332
start codons at 33, 241, 367, 463
confident = true

TIG 2[bases=541]
0-28 ==> 52-80 on |111|IGHV3-15|5'UTR| [len=80] (mis=0)
28-387 ==> 0-359 on |112|IGHV3-15|L-REGION+V-REGION| [len=359] (mis=19)
387-418 ==> 0-31 on |21|IGHD3-3|D-REGION| [len=31] (mis=4)
422-470 ==> 0-48 on |55|IGHJ4|J-REGION| [len=48] (mis=0)
470-541 ==> 0-71 on |60|IGHM|C-REGION| [len=1358] (mis=0)
junction support: 2 umis using 45 reads
cdr3 = CTTGDYDVWSGYYPAYYFDYW at 376, score = 8 + 7
umis assigned: [18, 622, 695]
of which 3 are surviving nonsolos
reads assigned: 954
start codons at 28, 184, 251, 308, 337, 395
confident = true
now this is a cell
paired!

TATTACTGTACCACAGGGGACTACGATGTTTGGAGTGGTTATTATCCCGCATACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG <==> AGCAGACTGGAGCCTGAAGATTTTGCAGTGTATTACTGTCAGCAGTATGGTAGTTCACCCCCGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC

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BARCODE 21.124 = CACTCCACAAGTTAAG-1

using 13 reads

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

graph has 10 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[13]
surviving nonsolo ucounts = 0[]
ids = []

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

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BARCODE 21.129 = CACTCCACAATGGACG-1

using 1523 reads

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

graph has 2059 edges initially, 63 edges after simplification

total ucounts = 610
nonsolo ucounts = 320[2^108, 3^79, 4^48, 5^22, 6^27, 7^14, 8^6, 9^6, 10^3, 11^2, 12^3, 13, 15]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 21.130 = CACTCCACAATTGCTG-1

using 214 reads

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

graph has 108 edges initially, 4 edges after simplification

total ucounts = 12
nonsolo ucounts = 6[2^2, 3, 4, 68, 129]
surviving nonsolo ucounts = 2[68, 129]
ids = [1, 2]

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

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

BARCODE 21.133 = CACTCCACACAGACAG-1

using 347 reads

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

graph has 118 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 4[2, 3, 4, 337]
surviving nonsolo ucounts = 1[337]
ids = [2]

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

UMI info for barcode CACTCCACACAGACAG-1 contig 1 = GGGGGCTGGG...
umi GTATTGGTCC = 331 reads: +391 validated

GOOD CONTIGS

TIG 1[bases=530]
45-383 ==> 0-338 on |341|IGLV2-18|L-REGION+V-REGION| [len=354] (mis=16)
398-436 ==> 0-38 on |309|IGLJ1|J-REGION| [len=38] (mis=5)
436-530 ==> 0-94 on |305|IGLC1|C-REGION| [len=317] (mis=0)
junction support: 1 umis using 57 reads
cdr3 = CSSYTNSTTPGVF at 369, score = 8 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 327
start codons at 45, 181, 253
confident = false
NOT paired!

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BARCODE 21.136 = CACTCCACACCCTATC-1

using 230 reads

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

graph has 96 edges initially, 2 edges after simplification

total ucounts = 6
nonsolo ucounts = 1[225]
surviving nonsolo ucounts = 1[225]
ids = [3]

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

UMI info for barcode CACTCCACACCCTATC-1 contig 1 = GGAATCAGTC...
umi CTAATATGGC = 214 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=467]
0-26 ==> 1-27 on |222|IGKV1-17|5'UTR| [len=27] (mis=0)
26-377 ==> 0-351 on |223|IGKV1-17|L-REGION+V-REGION| [len=351] (mis=19)
376-414 ==> 0-38 on |213|IGKJ1|J-REGION| [len=38] (mis=1)
414-467 ==> 0-53 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 38 reads
cdr3 = CLQYSSSPWTF at 353, score = 9 + 8
umis assigned: [3]
of which 1 are surviving nonsolos
reads assigned: 210
start codons at 26, 32, 101, 237, 456
confident = false
NOT paired!

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

BARCODE 21.137 = CACTCCACACCGAAAG-1

using 290 reads

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

graph has 94 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 1[288]
surviving nonsolo ucounts = 1[288]
ids = [1]

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

UMI info for barcode CACTCCACACCGAAAG-1 contig 1 = GAGCTGCTCA...
umi GGCTTTTGTT = 272 reads: +382 validated

GOOD CONTIGS

TIG 1[bases=498]
0-30 ==> 22-52 on |282|IGKV3-20|5'UTR| [len=52] (mis=0)
30-366 ==> 0-336 on |283|IGKV3-20|L-REGION+V-REGION| [len=348] (mis=17)
375-412 ==> 0-37 on |216|IGKJ4|J-REGION| [len=37] (mis=1)
412-498 ==> 0-86 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 45 reads
cdr3 = CQQYRNSITF at 354, score = 9 + 8
umis assigned: [1]
of which 1 are surviving nonsolos
reads assigned: 269
start codons at 30, 454
confident = false
NOT paired!

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

BARCODE 21.138 = CACTCCACACCTGGTG-1

using 17 reads

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

graph has 8 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[17]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 21.141 = CACTCCACACTCAGGC-1

using 342 reads

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

graph has 164 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 4[4^2, 10, 323]
surviving nonsolo ucounts = 1[323]
ids = [3]

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

UMI info for barcode CACTCCACACTCAGGC-1 contig 1 = GCTTTCTGAG...
umi TTCTCTTAAT = 314 reads: +451 validated

GOOD CONTIGS

TIG 1[bases=515]
14-385 ==> 0-371 on |186|IGHV4-34|L-REGION+V-REGION| [len=371] (mis=11)
417-465 ==> 0-48 on |55|IGHJ4|J-REGION| [len=48] (mis=1)
465-515 ==> 0-50 on |1|IGHA1|C-REGION| [len=1058] (mis=0)
junction support: 1 umis using 39 reads
cdr3 = CARGSGILVIAIEDYYFDHW at 374, score = 9 + 7
umis assigned: [3]
of which 1 are surviving nonsolos
reads assigned: 311
start codons at 14, 35, 79, 165, 252
confident = false
NOT paired!

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

BARCODE 21.143 = CACTCCACAGACAAAT-1

using 271 reads

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

graph has 137 edges initially, 2 edges after simplification

total ucounts = 7
nonsolo ucounts = 2[2, 264]
surviving nonsolo ucounts = 1[264]
ids = [2]

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

UMI info for barcode CACTCCACAGACAAAT-1 contig 1 = AGGAGTCAGA...
umi CCTCACAAAT = 245 reads: +382 validated

GOOD CONTIGS

TIG 1[bases=454]
0-33 ==> 20-53 on |236|IGKV1-8|5'UTR| [len=53] (mis=0)
33-378 ==> 0-345 on |237|IGKV1-8|L-REGION+V-REGION| [len=345] (mis=0)
377-415 ==> 0-38 on |215|IGKJ3|J-REGION| [len=38] (mis=2)
415-454 ==> 0-39 on |212|IGKC|C-REGION| [len=320] (mis=0)
junction support: 1 umis using 43 reads
cdr3 = CQQYYSYPLTF at 354, score = 9 + 9
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 241
start codons at 33, 89, 102, 238
confident = false
NOT paired!
sorting bam, mem = 0.08
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/chnk021-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/chnk021-ucc6a7a72ce/files/contig_bam.bam

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6.494 seconds used processing barcodes, peak mem = 0.23
