[stdout]

starting vdj_asm_asm, mem = 0.01
available mem = 828.09 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/chnk91-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/chnk91-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.chnk91.ucc6a7a72e6
n50_n50_rpu = 2159

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

BARCODE 91.0 = TGGCTGGTCTGAGTGT-1

using 12500 reads

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

graph has 6415 edges initially, 188 edges after simplification

total ucounts = 830
nonsolo ucounts = 593[2^98, 3^70, 4^46, 5^41, 6^36, 7^30, 8^31, 9^26, 10^15, 11^18, 12^23, 13^12, 14^13, 15^10, 16^12, 17^4, 18^7, 19^2, 20^10, 21^9, 22^7, 23^6, 24^2, 25^3, 26^3, 27^4, 28^4, 29^4, 30^3, 31^4, 32^2, 33^3, 34^3, 35^2, 37^3, 38, 39^2, 40, 41^2, 45, 46, 47, 48^2, 49, 50, 52, 55^2, 56^3, 65, 73, 81, 89, 93, 377, 907, 4560]
surviving nonsolo ucounts = 3[377, 907, 4560]
ids = [448, 754, 340]

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

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

BARCODE 91.1 = TGGCTGGTCTGATTCT-1

using 96 reads

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

graph has 82 edges initially, 4 edges after simplification

total ucounts = 11
nonsolo ucounts = 7[2, 3^3, 4, 10, 67]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.13 = TGGCTGGTCTTATCTG-1

using 59 reads

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

graph has 36 edges initially, 2 edges after simplification

total ucounts = 4
nonsolo ucounts = 4[4, 6, 13, 36]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.16 = TGGCTGGTCTTCCTTC-1

using 23 reads

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

graph has 12 edges initially, 2 edges after simplification

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

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

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

BARCODE 91.21 = TGGCTGGTCTTGCCGT-1

using 96 reads

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

graph has 30 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 1[95]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.24 = TGGCTGGTCTTGTATC-1

using 94 reads

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

graph has 20 edges initially, 2 edges after simplification

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

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

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

BARCODE 91.25 = TGGCTGGTCTTGTCAT-1

using 32 reads

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

graph has 20 edges initially, 4 edges after simplification

total ucounts = 2
nonsolo ucounts = 2[15, 17]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.26 = TGGCTGGTCTTTACGT-1

using 100 reads

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

graph has 20 edges initially, 2 edges after simplification

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

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

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

BARCODE 91.27 = TGGCTGGTCTTTAGTC-1

using 33 reads

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

graph has 28 edges initially, 2 edges after simplification

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

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

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

BARCODE 91.29 = TGGGAAGAGACAAAGG-1

using 92 reads

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

graph has 30 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[92]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.32 = TGGGAAGAGAGACTAT-1

using 1613 reads

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

graph has 1524 edges initially, 50 edges after simplification

total ucounts = 222
nonsolo ucounts = 133[2^20, 3^20, 4^14, 5^9, 6^7, 7^6, 8^4, 9^3, 10^3, 11^3, 12^2, 13^3, 14^5, 15, 16, 17^3, 18^3, 20^2, 21^4, 22, 23, 24^2, 25, 26^3, 28, 32^2, 35, 37^2, 39^2, 43, 58, 72, 76]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.34 = TGGGAAGAGATACACA-1

using 27 reads

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

graph has 30 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 3[2, 8, 17]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.36 = TGGGAAGAGCCTATGT-1

using 63 reads

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

graph has 58 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 3[12, 13, 38]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.39 = TGGGAAGAGCTCAACT-1

using 20 reads

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

graph has 26 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[20]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.40 = TGGGAAGAGCTTTGGT-1

using 48 reads

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

graph has 22 edges initially, 2 edges after simplification

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

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

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

BARCODE 91.41 = TGGGAAGAGGAACTGC-1

using 5570 reads

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

graph has 1546 edges initially, 2 edges after simplification

total ucounts = 8
nonsolo ucounts = 3[4, 2708, 2853]
surviving nonsolo ucounts = 2[2708, 2853]
ids = [6, 1]

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

UMI info for barcode TGGGAAGAGGAACTGC-1 contig 1 = TGGGGGCCAT...
umi ATATCCTTTT = 2878 reads: +403 validated
umi TGTATAAAGG = 2720 reads: +403 validated

GOOD CONTIGS

TIG 1[bases=463]
8-355 ==> 0-347 on |687|TRBV7-8|L-REGION+V-REGION| [len=347] (mis=4)
367-411 ==> 6-50 on |540|TRBJ1-5|J-REGION| [len=50] (mis=0)
411-463 ==> 0-52 on |531|TRBC1|C-REGION| [len=530] (mis=0)
junction support: 2 umis using 398 reads
cdr3 = CASGVGTGSGQPQHF at 338, score = 8 + 8
umis assigned: [1, 6]
of which 2 are surviving nonsolos
reads assigned: 5497
start codons at 8, 117, 150, 216, 387
confident = false
NOT paired!

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

BARCODE 91.42 = TGGGAAGAGGAATCGC-1

using 166 reads

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

graph has 200 edges initially, 4 edges after simplification

total ucounts = 13
nonsolo ucounts = 9[2, 3, 5, 8, 9, 11, 23, 29, 72]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.45 = TGGGAAGAGGATGGTC-1

using 2233 reads

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

graph has 1870 edges initially, 50 edges after simplification

total ucounts = 325
nonsolo ucounts = 196[2^29, 3^20, 4^15, 5^19, 6^13, 7^11, 8^11, 9^9, 10^9, 11^9, 12, 13^3, 14^2, 15^6, 16^6, 17^4, 18, 20^2, 21, 24, 25^3, 26, 27, 28^3, 29^3, 31, 32, 33, 38, 39, 42^2, 44, 45, 52, 56, 60, 69]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.46 = TGGGAAGAGGCGACAT-1

using 69 reads

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

graph has 78 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[69]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.50 = TGGGAAGAGTCCAGGA-1

using 17 reads

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

graph has 10 edges initially, 2 edges after simplification

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

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

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

BARCODE 91.66 = TGGGAAGCAATTCCTT-1

using 53 reads

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

graph has 24 edges initially, 2 edges after simplification

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

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

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

BARCODE 91.69 = TGGGAAGCACATGGGA-1

using 67 reads

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

graph has 57 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[67]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.73 = TGGGAAGCAGAGCCAA-1

using 60 reads

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

graph has 50 edges initially, 2 edges after simplification

total ucounts = 4
nonsolo ucounts = 2[13, 45]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.77 = TGGGAAGCAGGTCTCG-1

using 784 reads

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

graph has 320 edges initially, 2 edges after simplification

total ucounts = 3
nonsolo ucounts = 1[782]
surviving nonsolo ucounts = 1[782]
ids = [0]

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

UMI info for barcode TGGGAAGCAGGTCTCG-1 contig 1 = GGGGGACAGA...
umi AATTACCCCG = 814 reads: +391 validated

GOOD CONTIGS

TIG 1[bases=447]
14-350 ==> 0-336 on |481|TRAV21|L-REGION+V-REGION| [len=336] (mis=4)
347-405 ==> 0-58 on |420|TRAJ34|J-REGION| [len=58] (mis=2)
405-447 ==> 0-42 on |393|TRAC|C-REGION| [len=422] (mis=0)
junction support: 1 umis using 76 reads
cdr3 = CAVFYNTDKLIF at 338, score = 9 + 9
umis assigned: [0]
of which 1 are surviving nonsolos
reads assigned: 772
start codons at 14, 58, 258
confident = false
NOT paired!

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

BARCODE 91.82 = TGGGAAGCATATGGTC-1

using 38 reads

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

graph has 14 edges initially, 2 edges after simplification

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

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

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

BARCODE 91.85 = TGGGAAGCATGTTGAC-1

using 25 reads

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

graph has 18 edges initially, 2 edges after simplification

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

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

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

BARCODE 91.86 = TGGGAAGGTACGACCC-1

using 2936 reads

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

graph has 2725 edges initially, 82 edges after simplification

total ucounts = 356
nonsolo ucounts = 242[2^44, 3^29, 4^14, 5^24, 6^24, 7^13, 8^11, 9^5, 10^6, 11^6, 12^8, 13^2, 14^2, 15^3, 16^3, 18^2, 19, 20^2, 21, 22^3, 23^2, 24^3, 25^3, 26, 27^4, 28, 29^3, 31, 32^2, 37^2, 38^2, 39^3, 40, 42, 44, 47^2, 53, 64, 68, 80, 81, 88, 94]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.87 = TGGGAAGGTACGCACC-1

using 20 reads

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

graph has 10 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[20]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.88 = TGGGAAGGTACTTCTT-1

using 90 reads

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

graph has 80 edges initially, 2 edges after simplification

total ucounts = 10
nonsolo ucounts = 8[2, 3, 4, 5^2, 6, 7, 56]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.93 = TGGGAAGGTATGAAAC-1

using 118 reads

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

graph has 28 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[118]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.94 = TGGGAAGGTATTACCG-1

using 593 reads

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

graph has 394 edges initially, 22 edges after simplification

total ucounts = 26
nonsolo ucounts = 24[2, 3, 4, 6, 7, 8^2, 9, 10, 11, 12, 15^2, 19, 20, 21, 23, 28, 32, 36, 45, 62, 88, 107]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.95 = TGGGAAGGTCAAACTC-1

using 33 reads

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

graph has 16 edges initially, 2 edges after simplification

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

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

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

BARCODE 91.96 = TGGGAAGGTCAACATC-1

using 41 reads

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

graph has 30 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 2[9, 32]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.97 = TGGGAAGGTCACTTCC-1

using 47 reads

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

graph has 44 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 5[2, 3, 6, 10, 26]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.102 = TGGGAAGGTCTTCAAG-1

using 11 reads

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

graph has 8 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[11]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.103 = TGGGAAGGTCTTGCGG-1

using 62 reads

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

graph has 18 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[62]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.106 = TGGGAAGGTGAGTATA-1

using 415 reads

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

graph has 276 edges initially, 10 edges after simplification

total ucounts = 23
nonsolo ucounts = 17[2^3, 9, 10^2, 11^2, 16, 17, 18, 24, 32, 34, 36, 80, 95]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.114 = TGGGAAGGTGTTTGTG-1

using 3982 reads

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

graph has 2868 edges initially, 108 edges after simplification

total ucounts = 347
nonsolo ucounts = 240[2^32, 3^18, 4^21, 5^11, 6^12, 7^13, 8^14, 9^5, 10^9, 11^7, 12^4, 13^6, 14^9, 15^9, 16^7, 17^6, 18^5, 19, 20^2, 21^8, 22, 23^2, 24^2, 25^2, 26^2, 27, 28^2, 30^5, 31, 32, 33^2, 34, 35^2, 37, 38, 42, 43^2, 44, 53, 55, 61, 64, 66, 71, 76, 79, 86, 100, 571]
surviving nonsolo ucounts = 2[18, 571]
ids = [108, 303]

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

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

BARCODE 91.116 = TGGGAAGGTTATCACG-1

using 35 reads

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

graph has 20 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[35]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.117 = TGGGAAGGTTCCCTTG-1

using 48 reads

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

graph has 60 edges initially, 2 edges after simplification

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

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

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

BARCODE 91.120 = TGGGAAGTCAAACAAG-1

using 37 reads

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

graph has 58 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 3[8, 12, 15]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.121 = TGGGAAGTCAATAAGG-1

using 42 reads

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

graph has 65 edges initially, 2 edges after simplification

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

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

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

BARCODE 91.122 = TGGGAAGTCACAATGC-1

using 335 reads

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

graph has 198 edges initially, 10 edges after simplification

total ucounts = 13
nonsolo ucounts = 12[2, 4, 5, 7, 11, 12, 25, 27, 34, 42, 54, 111]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.124 = TGGGAAGTCAGAAATG-1

using 34 reads

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

graph has 44 edges initially, 2 edges after simplification

total ucounts = 5
nonsolo ucounts = 4[2, 3, 5, 23]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.125 = TGGGAAGTCAGGCGAA-1

using 67 reads

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

graph has 22 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[67]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.126 = TGGGAAGTCAGTCAGT-1

using 62 reads

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

graph has 24 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[62]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.131 = TGGGAAGTCCACGTGG-1

using 10546 reads

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

graph has 2120 edges initially, 8 edges after simplification

total ucounts = 17
nonsolo ucounts = 5[2, 10, 952, 2247, 7323]
surviving nonsolo ucounts = 3[952, 2247, 7323]
ids = [14, 10, 5]

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

UMI info for barcode TGGGAAGTCCACGTGG-1 contig 1 = GGGGGTGATT...
umi GGTTTATTAG = 2255 reads: +391 validated
umi TACCAGGGAA = 899 reads: -363X +2 -1XX +7 -3XX +1 -3XX +3 -4XX +1 -1XX +1 -1XX invalidated

GOOD CONTIGS

TIG 1[bases=489]
0-56 ==> 0-56 on |529|TRAV9-2|5'UTR| [len=56] (mis=4)
56-394 ==> 0-338 on |530|TRAV9-2|L-REGION+V-REGION| [len=338] (mis=6)
387-447 ==> 0-60 on |400|TRAJ16|J-REGION| [len=60] (mis=3)
447-489 ==> 0-42 on |393|TRAC|C-REGION| [len=422] (mis=0)
junction support: 1 umis using 121 reads
cdr3 = CALVSDGQKLLF at 380, score = 9 + 6
umis assigned: [10, 14]
of which 2 are surviving nonsolos
reads assigned: 3120
start codons at 15, 56, 131, 219, 273, 396, 428
confident = false
NOT paired!

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

BARCODE 91.134 = TGGGAAGTCCCATTTA-1

using 56 reads

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

graph has 46 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[56]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.139 = TGGGAAGTCGCAGGCT-1

using 26 reads

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

graph has 24 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 2[13^2]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.141 = TGGGAAGTCGGTTAAC-1

using 479 reads

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

graph has 452 edges initially, 10 edges after simplification

total ucounts = 34
nonsolo ucounts = 27[2^2, 3^3, 4^2, 5^2, 6^2, 7, 11^2, 13^2, 14^3, 23, 27^2, 32, 44, 46, 64, 69]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.145 = TGGGAAGTCTAGCACA-1

using 54 reads

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

graph has 16 edges initially, 2 edges after simplification

total ucounts = 1
nonsolo ucounts = 1[54]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.148 = TGGGAAGTCTGCCAGG-1

using 146 reads

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

graph has 78 edges initially, 4 edges after simplification

total ucounts = 3
nonsolo ucounts = 2[72, 73]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.149 = TGGGAAGTCTGTGCAA-1

using 58 reads

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

graph has 42 edges initially, 2 edges after simplification

total ucounts = 2
nonsolo ucounts = 2[8, 50]
surviving nonsolo ucounts = 0[]
ids = []

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

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

BARCODE 91.154 = TGGGCGTAGAAACGAG-1

using 3013 reads

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

graph has 1742 edges initially, 34 edges after simplification

total ucounts = 260
nonsolo ucounts = 160[2^38, 3^27, 4^17, 5^14, 6^10, 7^9, 8^6, 9^2, 10^4, 11^4, 12^4, 14^2, 15^3, 16^2, 17^5, 19, 20^2, 21, 23, 25^2, 27, 34, 43, 47, 50, 1753]
surviving nonsolo ucounts = 1[1753]
ids = [173]

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

UMI info for barcode TGGGCGTAGAAACGAG-1 contig 1 = AGTCAACTTC...
umi GCCAACATCT = 1772 reads: +415 validated

GOOD CONTIGS

TIG 1[bases=493]
0-36 ==> 0-36 on |455|TRAV10|5'UTR| [len=36] (mis=0)
36-379 ==> 0-343 on |456|TRAV10|L-REGION+V-REGION| [len=343] (mis=1)
388-451 ==> 0-63 on |401|TRAJ17|J-REGION| [len=63] (mis=1)
451-493 ==> 0-42 on |393|TRAC|C-REGION| [len=422] (mis=0)
junction support: 1 umis using 94 reads
cdr3 = CVVSARETIKAAGNKLTF at 366, score = 6 + 9
umis assigned: [173]
of which 1 are surviving nonsolos
reads assigned: 1732
start codons at 36, 94, 164, 246, 298
confident = false
NOT paired!

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BARCODE 91.156 = TGGGCGTAGAATTCCC-1

using 280 reads

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

graph has 248 edges initially, 10 edges after simplification

total ucounts = 19
nonsolo ucounts = 13[2, 4^3, 7^2, 8, 25, 26, 32, 38, 42, 75]
surviving nonsolo ucounts = 0[]
ids = []

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

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BARCODE 91.158 = TGGGCGTAGACAGGCT-1

using 22 reads

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

graph has 18 edges initially, 2 edges after simplification

total ucounts = 4
nonsolo ucounts = 1[19]
surviving nonsolo ucounts = 0[]
ids = []

====================================================================================
NOT paired!
sorting bam, mem = 0.06
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/chnk91-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/chnk91-ucc6a7a72e6/files/contig_bam.bam

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5.303 seconds used processing barcodes, peak mem = 0.23
