[stdout]

starting vdj_asm_asm, mem = 0.01
available mem = 833.14 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_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/chnk07-ucc6a7a72e6 /scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/chnk07-ucc6a7a72e6/files /scratch/etanis/ST-118/multi/dimitri-multi/journal/SC_MULTI_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ.fork0.chnk07.ucc6a7a72e6
n50_n50_rpu = 2159

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

BARCODE 7.0 = ACGATACTCAAGATCC-1

using 100 reads

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

graph has 38 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[100]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.5 = ACGATACTCACATACG-1

using 42 reads

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

graph has 16 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[42]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.6 = ACGATACTCACATGCA-1

using 68 reads

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

graph has 30 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[68]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.11 = ACGATACTCATGCAAC-1

using 112 reads

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

graph has 42 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[112]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.15 = ACGATACTCCTGCTTG-1

using 18 reads

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

graph has 24 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[18]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.19 = ACGATACTCGAGAGCA-1

using 98 reads

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

graph has 118 edges initially, 2 edges after simplification

total ucounts = 7
nonsolo ucounts = 4[2^2, 36, 55]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.22 = ACGATACTCGCATGGC-1

using 94 reads

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

graph has 26 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[94]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.26 = ACGATACTCTCTGAGA-1

using 38 reads

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

graph has 32 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[38]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.27 = ACGATACTCTTAACCT-1

using 77 reads

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

graph has 72 edges initially, 2 edges after simplification

total ucounts = 8
nonsolo ucounts = 6[3, 5, 6, 10, 15, 36]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.33 = ACGATGTAGACAGGCT-1

using 45 reads

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

graph has 28 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[45]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.34 = ACGATGTAGACTACAA-1

using 293 reads

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

graph has 218 edges initially, 14 edges after simplification

total ucounts = 19
nonsolo ucounts = 17[2^3, 3, 5^2, 7, 8^2, 13, 14, 24, 31, 32, 40, 42, 53]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.35 = ACGATGTAGACTAGAT-1

using 38 reads

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

graph has 40 edges initially, 2 edges after simplification

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

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

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

BARCODE 7.39 = ACGATGTAGAGTTGGC-1

using 36 reads

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

graph has 28 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[36]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.42 = ACGATGTAGATGGGTC-1

using 33 reads

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

graph has 32 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 1[32]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.43 = ACGATGTAGCACACAG-1

using 73 reads

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

graph has 48 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 3[6, 10, 57]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.44 = ACGATGTAGCCACGCT-1

using 13624 reads

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

graph has 7671 edges initially, 118 edges after simplification

total ucounts = 765
nonsolo ucounts = 547[2^95, 3^66, 4^54, 5^43, 6^38, 7^42, 8^26, 9^29, 10^17, 11^15, 12^14, 13^15, 14^15, 15^8, 16^9, 17^5, 18^9, 20^4, 21, 22, 23^5, 24, 26^2, 27, 28^3, 31^2, 32, 34^2, 36, 39, 43^2, 44, 46, 47^2, 48^2, 49, 51, 53, 57, 61, 70, 71^2, 88, 185, 646, 1565, 2584, 3598]
surviving nonsolo ucounts = 5[185, 646, 1565, 2584, 3598]
ids = [94, 446, 52, 750, 651]

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

UMI info for barcode ACGATGTAGCCACGCT-1 contig 1 = GTGATTTCTT...
umi ACAACCATAC = 1593 reads: +235 -1XX +158 invalidated
umi ACGCTTTCCA = 185 reads: +394 validated
umi GCATGTGCAA = 645 reads: -7X +387 invalidated

GOOD CONTIGS

TIG 1[bases=488]
0-52 ==> 4-56 on |529|TRAV9-2|5'UTR| [len=56] (mis=0)
52-390 ==> 0-338 on |530|TRAV9-2|L-REGION+V-REGION| [len=338] (mis=2)
389-446 ==> 0-57 on |417|TRAJ31|J-REGION| [len=57] (mis=2)
446-488 ==> 0-42 on |393|TRAC|C-REGION| [len=422] (mis=0)
junction support: 3 umis using 175 reads
cdr3 = CALSGRNNARLMF at 376, score = 9 + 7
umis assigned: [52, 94, 446]
of which 3 are surviving nonsolos
reads assigned: 2340
start codons at 11, 52, 127, 215, 269, 398, 409, 419
confident = true

REJECT CONTIGS

TIG 1[bases=475]
5-81 ==> 49-125 on segment before TRBV15 exon 2 [len=125] (mis=0)
77-376 ==> 45-344 on |579|TRBV15|L-REGION+V-REGION| [len=344] (mis=3)
374-423 ==> 0-49 on |546|TRBJ2-3|J-REGION| [len=49] (mis=1)
423-475 ==> 0-52 on |534|TRBC2|C-REGION| [len=536] (mis=0)
cdr3 = CATSSSADTQYF at 359, score = 6 + 8
umis assigned: [140, 275, 651, 750]
of which 2 are surviving nonsolos
reads assigned: 6087
start codons at 84, 90, 95, 182, 237, 255, 350
confident = false
not full
VJ delta = 18
not full
now this is a cell
NOT paired!

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

BARCODE 7.45 = ACGATGTAGCCGCCTA-1

using 59 reads

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

graph has 58 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 1[55]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.48 = ACGATGTAGCGACGTA-1

using 67 reads

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

graph has 70 edges initially, 2 edges after simplification

total ucounts = 9
nonsolo ucounts = 6[2, 3, 4, 7, 15, 33]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.52 = ACGATGTAGCTAGCCC-1

using 21738 reads

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

graph has 4432 edges initially, 22 edges after simplification

total ucounts = 100
nonsolo ucounts = 58[2^13, 3^6, 4^4, 5^6, 6^3, 7^2, 8^2, 9^3, 13^4, 17, 18^2, 21, 31, 34, 42, 43, 83, 87, 334, 338, 3742, 7732, 8939]
surviving nonsolo ucounts = 5[334, 338, 3742, 7732, 8939]
ids = [69, 88, 47, 3, 57]

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

REJECT CONTIGS

TIG 1[bases=311]
5-82 ==> 723-800 on segment before TRAJ12 exon 1 [len=800] (mis=0)
205-269 ==> 0-64 on |395|TRAJ10|J-REGION| [len=64] (mis=0)
269-311 ==> 0-42 on |393|TRAC|C-REGION| [len=422] (mis=0)
umis assigned: [57]
of which 1 are surviving nonsolos
reads assigned: 8794
start codons at 28, 37, 84
confident = false
did not find CDR3
NOT paired!

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

BARCODE 7.55 = ACGATGTAGGCATGGT-1

using 7497 reads

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

graph has 1638 edges initially, 6 edges after simplification

total ucounts = 11
nonsolo ucounts = 8[2^2, 4, 24, 37, 38, 48, 7339]
surviving nonsolo ucounts = 1[7339]
ids = [4]

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

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

BARCODE 7.56 = ACGATGTAGGCTAGAC-1

using 108 reads

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

graph has 102 edges initially, 2 edges after simplification

total ucounts = 7
nonsolo ucounts = 5[9, 13, 15, 32, 37]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.59 = ACGATGTAGTACGTAA-1

using 57 reads

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

graph has 60 edges initially, 2 edges after simplification

total ucounts = 7
nonsolo ucounts = 3[2, 3, 48]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.60 = ACGATGTAGTATGACA-1

using 39 reads

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

graph has 24 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[39]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.62 = ACGATGTAGTCGATAA-1

using 18 reads

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

graph has 14 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 1[17]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.65 = ACGATGTAGTGGGCTA-1

using 41 reads

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

graph has 48 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 4[2, 5, 6, 27]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.69 = ACGATGTAGTTGAGAT-1

using 64 reads

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

graph has 36 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[64]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.70 = ACGATGTAGTTTAGGA-1

using 128 reads

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

graph has 96 edges initially, 2 edges after simplification

total ucounts = 9
nonsolo ucounts = 5[2, 3, 7, 8, 104]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.73 = ACGATGTCAATCACAC-1

using 69 reads

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

graph has 78 edges initially, 2 edges after simplification

total ucounts = 7
nonsolo ucounts = 5[2, 4, 8, 22, 31]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.74 = ACGATGTCAATCTACG-1

using 205 reads

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

graph has 122 edges initially, 6 edges after simplification

total ucounts = 4
nonsolo ucounts = 3[24, 28, 152]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.81 = ACGATGTCACATTCGA-1

using 45 reads

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

graph has 56 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 2[3, 39]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.82 = ACGATGTCACGAAGCA-1

using 140 reads

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

graph has 62 edges initially, 4 edges after simplification

total ucounts = 8
nonsolo ucounts = 5[3, 6, 8, 12, 108]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.83 = ACGATGTCACGACTCG-1

using 488 reads

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

graph has 618 edges initially, 20 edges after simplification

total ucounts = 18
nonsolo ucounts = 16[3, 5, 6, 7, 8, 9, 18, 19, 24^2, 26, 45, 46, 62, 79, 105]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.85 = ACGATGTCACTTACGA-1

using 49 reads

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

graph has 16 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[49]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.90 = ACGATGTCAGCCTATA-1

using 18 reads

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

graph has 12 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[18]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.91 = ACGATGTCAGCCTTGG-1

using 8751 reads

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

graph has 5228 edges initially, 124 edges after simplification

total ucounts = 629
nonsolo ucounts = 414[2^66, 3^52, 4^29, 5^30, 6^27, 7^14, 8^22, 9^23, 10^18, 11^11, 12^18, 13^9, 14^9, 15^5, 16^6, 17^4, 18^3, 19^6, 20^2, 21^7, 22^4, 23^2, 24^5, 25^4, 26^2, 27^4, 29, 30^2, 31, 32, 33, 34^2, 35^2, 36^2, 38^2, 40^3, 41, 43, 44, 47, 48, 50, 51^2, 64, 79, 105, 259, 280, 366, 3352]
surviving nonsolo ucounts = 4[259, 280, 366, 3352]
ids = [416, 590, 130, 135]

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

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

BARCODE 7.94 = ACGATGTCAGGTCTCG-1

using 55 reads

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

graph has 24 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 1[53]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.95 = ACGATGTCAGTACACT-1

using 2626 reads

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

graph has 2542 edges initially, 70 edges after simplification

total ucounts = 260
nonsolo ucounts = 198[2^25, 3^24, 4^9, 5^9, 6^6, 7^6, 8^11, 9^7, 10^8, 11^6, 12^6, 13^5, 14^4, 15^11, 16^4, 17^4, 18^5, 19^3, 20^5, 21^7, 22^6, 23, 24, 25^4, 26^2, 27^4, 28^3, 29, 31^2, 34^2, 40, 44, 51, 59, 64, 69, 93]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.99 = ACGATGTCATACCATG-1

using 84 reads

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

graph has 48 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[84]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.100 = ACGATGTCATACTACG-1

using 819 reads

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

graph has 322 edges initially, 4 edges after simplification

total ucounts = 12
nonsolo ucounts = 8[2, 3^2, 8, 11, 12, 17, 759]
surviving nonsolo ucounts = 1[759]
ids = [10]

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

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

BARCODE 7.105 = ACGATGTCATCTACGA-1

using 162 reads

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

graph has 120 edges initially, 4 edges after simplification

total ucounts = 3
nonsolo ucounts = 3[13, 40, 109]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.106 = ACGATGTCATCTCCCA-1

using 38 reads

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

graph has 60 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 3[2^2, 32]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.107 = ACGATGTCATGATCCA-1

using 84 reads

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

graph has 24 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[84]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.111 = ACGATGTCATTGCGGC-1

using 101 reads

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

graph has 72 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[101]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.114 = ACGATGTGTAAGGGCT-1

using 190 reads

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

graph has 130 edges initially, 4 edges after simplification

total ucounts = 12
nonsolo ucounts = 6[3, 11, 13, 18, 19, 120]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.118 = ACGATGTGTAGCCTCG-1

using 52 reads

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

graph has 58 edges initially, 2 edges after simplification

total ucounts = 8
nonsolo ucounts = 6[2, 4, 7, 8, 9, 20]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.122 = ACGATGTGTCAGTGGA-1

using 89 reads

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

graph has 36 edges initially, 2 edges after simplification

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

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

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

BARCODE 7.125 = ACGATGTGTCCGTTAA-1

using 25 reads

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

graph has 26 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[25]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.127 = ACGATGTGTCGGCTCA-1

using 228 reads

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

graph has 128 edges initially, 12 edges after simplification

total ucounts = 13
nonsolo ucounts = 12[2, 6, 9, 13^2, 15, 20, 22, 26, 27, 35, 39]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.129 = ACGATGTGTCTCTCTG-1

using 212 reads

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

graph has 124 edges initially, 6 edges after simplification

total ucounts = 9
nonsolo ucounts = 9[2^2, 3, 4, 5, 6, 46, 61, 83]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.130 = ACGATGTGTCTGGAGA-1

using 13 reads

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

graph has 2 edges initially, 2 edges after simplification

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

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

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

BARCODE 7.133 = ACGATGTGTGCCTGCA-1

using 79 reads

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

graph has 80 edges initially, 4 edges after simplification

total ucounts = 7
nonsolo ucounts = 5[2^2, 5, 31, 37]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.140 = ACGATGTGTTCACGGC-1

using 1658 reads

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

graph has 472 edges initially, 2 edges after simplification

total ucounts = 6
nonsolo ucounts = 5[2, 4, 5, 19, 1627]
surviving nonsolo ucounts = 1[1627]
ids = [2]

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

UMI info for barcode ACGATGTGTTCACGGC-1 contig 1 = AAGCACTCTT...
umi GCCACTCGCA = 1640 reads: +391 validated

GOOD CONTIGS

TIG 1[bases=530]
0-97 ==> 0-97 on |492|TRAV27|5'UTR| [len=97] (mis=0)
97-425 ==> 0-328 on |493|TRAV27|L-REGION+V-REGION| [len=328] (mis=3)
425-488 ==> 0-63 on |407|TRAJ22|J-REGION| [len=63] (mis=1)
488-530 ==> 0-42 on |393|TRAC|C-REGION| [len=422] (mis=0)
junction support: 1 umis using 93 reads
cdr3 = CAGPSSGSARQLTF at 415, score = 10 + 9
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 1615
start codons at 70, 79, 97, 141, 249, 350
confident = false
NOT paired!

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

BARCODE 7.142 = ACGATGTTCAACACAC-1

using 39 reads

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

graph has 46 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[39]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.144 = ACGATGTTCACCGGGT-1

using 1051 reads

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

graph has 380 edges initially, 2 edges after simplification

total ucounts = 6
nonsolo ucounts = 3[5, 8, 1035]
surviving nonsolo ucounts = 1[1035]
ids = [2]

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

UMI info for barcode ACGATGTTCACCGGGT-1 contig 1 = TGGGGGCTTT...
umi CTACGCGTAT = 1031 reads: +427 validated

GOOD CONTIGS

TIG 1[bases=523]
44-418 ==> 0-374 on |575|TRBV13|L-REGION+V-REGION| [len=374] (mis=4)
421-471 ==> 0-50 on |543|TRBJ2-1|J-REGION| [len=50] (mis=5)
471-523 ==> 0-52 on |534|TRBC2|C-REGION| [len=536] (mis=0)
junction support: 1 umis using 56 reads
cdr3 = CASRFLDRGNEQFF at 401, score = 9 + 8
umis assigned: [2]
of which 1 are surviving nonsolos
reads assigned: 1020
start codons at 44, 101, 196, 279, 287, 362, 429
confident = false
NOT paired!

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

BARCODE 7.146 = ACGATGTTCAGAGCTT-1

using 66 reads

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

graph has 56 edges initially, 2 edges after simplification

total ucounts = 9
nonsolo ucounts = 6[2^3, 3, 4, 50]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.148 = ACGATGTTCATAGCAC-1

using 76 reads

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

graph has 38 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[76]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.149 = ACGATGTTCATGGTCA-1

using 140 reads

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

graph has 34 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[140]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.150 = ACGATGTTCATGTCCC-1

using 439 reads

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

graph has 178 edges initially, 4 edges after simplification

total ucounts = 10
nonsolo ucounts = 8[2^2, 3, 6, 8, 12, 74, 330]
surviving nonsolo ucounts = 1[330]
ids = [8]

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

UMI info for barcode ACGATGTTCATGTCCC-1 contig 1 = AGTGCCTTTT...
umi TGATAAATCA = 330 reads: +388 validated

GOOD CONTIGS

TIG 1[bases=476]
0-36 ==> 31-67 on |614|TRBV29-1|5'UTR| [len=67] (mis=0)
36-371 ==> 0-335 on |615|TRBV29-1|L-REGION+V-REGION| [len=335] (mis=2)
373-424 ==> 0-51 on |544|TRBJ2-2|J-REGION| [len=51] (mis=3)
424-476 ==> 0-52 on |534|TRBC2|C-REGION| [len=536] (mis=0)
junction support: 1 umis using 20 reads
cdr3 = CSVNEGGTGELFF at 357, score = 7 + 9
umis assigned: [8]
of which 1 are surviving nonsolos
reads assigned: 327
start codons at 36, 171, 174, 250, 327
confident = false
NOT paired!

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

BARCODE 7.151 = ACGATGTTCATTGCGA-1

using 73 reads

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

graph has 76 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 3[3, 17, 51]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.154 = ACGATGTTCCACGTTC-1

using 73 reads

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

graph has 42 edges initially, 2 edges after simplification

total ucounts = 4
nonsolo ucounts = 2[15, 56]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.156 = ACGATGTTCCAGTATG-1

using 140 reads

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

graph has 156 edges initially, 2 edges after simplification

total ucounts = 9
nonsolo ucounts = 5[2^2, 4, 49, 79]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.159 = ACGATGTTCCGTCAAA-1

using 25 reads

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

graph has 22 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[25]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.162 = ACGATGTTCCTGTACC-1

using 78 reads

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

graph has 68 edges initially, 2 edges after simplification

total ucounts = 11
nonsolo ucounts = 5[2, 3, 4, 7, 56]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.164 = ACGATGTTCCTTAATC-1

using 69 reads

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

graph has 60 edges initially, 4 edges after simplification

total ucounts = 7
nonsolo ucounts = 7[3^2, 6, 10, 13^2, 21]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.165 = ACGATGTTCCTTGACC-1

using 53 reads

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

graph has 20 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[53]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.168 = ACGATGTTCGACAGCC-1

using 80 reads

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

graph has 52 edges initially, 2 edges after simplification

total ucounts = 4
nonsolo ucounts = 3[3, 17, 59]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.170 = ACGATGTTCGGACAAG-1

using 370 reads

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

graph has 358 edges initially, 28 edges after simplification

total ucounts = 21
nonsolo ucounts = 19[2^2, 3, 4, 5, 6, 8, 11^2, 12^2, 16, 21, 22, 24, 25, 44, 67, 73]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.171 = ACGATGTTCGTATCAG-1

using 72 reads

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

graph has 74 edges initially, 4 edges after simplification

total ucounts = 2
nonsolo ucounts = 2[35, 37]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.176 = ACGATGTTCTTACCGC-1

using 94 reads

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

graph has 72 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 4[2, 7, 10, 74]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.178 = ACGATGTTCTTGGGTA-1

using 22 reads

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

graph has 16 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[22]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.179 = ACGCAGCAGAACAATC-1

using 189 reads

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

graph has 140 edges initially, 10 edges after simplification

total ucounts = 11
nonsolo ucounts = 9[7, 9, 13, 15, 18, 21, 26^2, 52]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.180 = ACGCAGCAGAAGGCCT-1

using 14478 reads

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

graph has 4263 edges initially, 30 edges after simplification

total ucounts = 221
nonsolo ucounts = 137[2^25, 3^22, 4^11, 5^13, 6^9, 7^7, 8^5, 9^9, 10^2, 11^2, 12^4, 13, 14^5, 15, 16, 17, 18, 20^3, 21, 24, 25, 28, 30, 43, 47, 49, 63, 305, 1264, 1713, 1762, 1777, 6495]
surviving nonsolo ucounts = 6[305, 1264, 1713, 1762, 1777, 6495]
ids = [68, 3, 105, 80, 179, 182]

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

UMI info for barcode ACGCAGCAGAAGGCCT-1 contig 1 = AGATCAGAAG...
umi CACGTCTGGG = 300 reads: +415 validated
umi CATCGATAAG = 1760 reads: +415 validated
umi TATACTTGTC = 1777 reads: +415 validated

UMI info for barcode ACGCAGCAGAAGGCCT-1 contig 2 = ATCAATGCAC...
umi AAAGTTGGGG = 1268 reads: +397 validated
umi CGATAATTGG = 1702 reads: +397 validated
umi TATGTGTCCT = 6514 reads: -153X +2 -2XX +2 -1XX +237 invalidated

GOOD CONTIGS

TIG 1[bases=503]
0-46 ==> 0-46 on |506|TRAV38-2/DV8|5'UTR| [len=46] (mis=0)
46-395 ==> 0-349 on |507|TRAV38-2/DV8|L-REGION+V-REGION| [len=349] (mis=3)
392-461 ==> 0-69 on |439|TRAJ52|J-REGION| [len=69] (mis=4)
461-503 ==> 0-42 on |393|TRAC|C-REGION| [len=422] (mis=0)
junction support: 2 umis using 195 reads
cdr3 = CAYRVLAGGTSYGKLTF at 379, score = 7 + 9
umis assigned: [68, 80, 179]
of which 3 are surviving nonsolos
reads assigned: 3781
start codons at 46, 51, 103, 136, 179, 238, 278, 362, 370, 413
confident = true

TIG 2[bases=495]
0-46 ==> 0-46 on |661|TRBV6-6|5'UTR| [len=46] (mis=0)
46-390 ==> 0-344 on |662|TRBV6-6|L-REGION+V-REGION| [len=344] (mis=4)
395-443 ==> 0-48 on |536|TRBJ1-1|J-REGION| [len=48] (mis=4)
443-495 ==> 0-52 on |531|TRBC1|C-REGION| [len=530] (mis=0)
junction support: 3 umis using 923 reads
cdr3 = CASSYKGGSTEAFF at 373, score = 9 + 8
umis assigned: [3, 105, 182]
of which 3 are surviving nonsolos
reads assigned: 9332
start codons at 4, 46, 104, 157, 181, 196, 223, 287
confident = true
now this is a cell
paired!

GATGCCGCGATGTATTTCTGTGCTTATAGGGTCCTTGCTGGTGGTACTAGCTATGGAAAGCTGACATTTGGACAAGGGACCATCTTGACTGTCCATCCAA <==> GCTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAGTTACAAAGGGGGCTCCACTGAAGCTTTCTTTGGACAAGGCACCAGACTCACAGTTGTAG

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

BARCODE 7.184 = ACGCAGCAGACTGGGT-1

using 79 reads

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

graph has 38 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 3[2, 3, 74]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.188 = ACGCAGCAGAGTAATC-1

using 52 reads

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

graph has 74 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[52]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.191 = ACGCAGCAGATCGATA-1

using 38 reads

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

graph has 12 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[38]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.195 = ACGCAGCAGCACCGTC-1

using 33 reads

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

graph has 22 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[33]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.196 = ACGCAGCAGCAGGCTA-1

using 42 reads

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

graph has 18 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 2[2, 40]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.204 = ACGCAGCAGCGGCTTC-1

using 249 reads

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

graph has 178 edges initially, 6 edges after simplification

total ucounts = 12
nonsolo ucounts = 8[2^2, 12, 22, 28, 30, 66, 83]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.207 = ACGCAGCAGCTAGTGG-1

using 57 reads

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

graph has 46 edges initially, 2 edges after simplification

total ucounts = 6
nonsolo ucounts = 3[2, 8, 44]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 7.209 = ACGCAGCAGCTGGAAC-1

using 26 reads

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

graph has 48 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[26]
surviving nonsolo ucounts = 0[]
ids = []

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

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BARCODE 7.212 = ACGCAGCAGGAATTAC-1

using 625 reads

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

graph has 469 edges initially, 24 edges after simplification

total ucounts = 27
nonsolo ucounts = 24[2^2, 3^4, 4^2, 6, 9, 10, 11, 12, 16, 21, 23, 31, 32, 52, 53, 54, 84, 87, 97]
surviving nonsolo ucounts = 0[]
ids = []

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

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BARCODE 7.216 = ACGCAGCAGGATCGCA-1

using 94 reads

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

graph has 44 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[94]
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_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/chnk07-ucc6a7a72e6/files/contig_bam_sorted.bam /scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/chnk07-ucc6a7a72e6/files/contig_bam.bam

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10.214 seconds used processing barcodes, peak mem = 0.23
