Analysis date: Fri Jul 28 14:51:01 CEST 2023
Input file(s): /Users/alegac/Documents/bulk_tcr/D1454T05/D1454T05_trimmed_R1.fastq.gz,/Users/alegac/Documents/bulk_tcr/D1454T05/D1454T05_trimmed_R2.fastq.gz
Output file(s): /Users/alegac/Documents/bulk_tcr/D1454T05/results_05.vdjca
Version: 4.4.1; built=Thu Jul 06 19:36:41 CEST 2023; rev=f7cd556c6c; lib=repseqio.v3.0.1
Command line arguments: align --report /Users/alegac/Documents/bulk_tcr/D1454T05/results_05.align.report.txt --json-report /Users/alegac/Documents/bulk_tcr/D1454T05/results_05.align.report.json --preset milab-human-rna-tcr-umi-multiplex /Users/alegac/Documents/bulk_tcr/D1454T05/D1454T05_trimmed_R1.fastq.gz /Users/alegac/Documents/bulk_tcr/D1454T05/D1454T05_trimmed_R2.fastq.gz /Users/alegac/Documents/bulk_tcr/D1454T05/results_05.vdjca
Analysis time: 30,28m
Total sequencing reads: 47533850
Successfully aligned reads: 42366412 (89,13%)
Coverage (percent of successfully aligned):
  CDR3: 99,83%
  FR3_TO_FR4: 0%
  CDR2_TO_FR4: 0%
  FR2_TO_FR4: 0%
  CDR1_TO_FR4: 0%
  VDJRegion: 0%
Alignment failed: no hits (not TCR/IG?): 1281908 (2,7%)
Alignment failed: absence of V hits: 99369 (0,21%)
Alignment failed: absence of J hits: 1806961 (3,8%)
Alignment failed: no target with both V and J alignments: 94595 (0,2%)
Alignment failed: absent barcode: 1884605 (3,96%)
Overlapped: 43573480 (91,67%)
Overlapped and aligned: 41802849 (87,94%)
Overlapped and not aligned: 1770631 (3,72%)
Alignment-aided overlaps, percent of overlapped and aligned: 25463 (0,06%)
No CDR3 parts alignments, percent of successfully aligned: 121 (0%)
Partial aligned reads, percent of successfully aligned: 73705 (0,17%)
Chimeras: 6 (0%)
V gene chimeras: 29420 (0,06%)
J gene chimeras: 11600 (0,02%)
Paired-end alignment conflicts eliminated: 8973 (0,02%)
Realigned with forced non-floating bound: 4202456 (8,84%)
Realigned with forced non-floating right bound in left read: 11464 (0,02%)
Realigned with forced non-floating left bound in right read: 11464 (0,02%)
TRA chains: 42366405 (100%)
TRA non-functional: 4892213 (11,55%)
TRD chains: 1 (0%)
TRD non-functional: 1 (100%)
Trimming report:
  R1 reads trimmed left: 10193 (0,02%)
  R1 reads trimmed right: 5950 (0,01%)
  Average R1 nucleotides trimmed left: 4.2188882238657294E-4
  Average R1 nucleotides trimmed right: 1.9775381123136458E-4
  R2 reads trimmed left: 2589 (0,01%)
  R2 reads trimmed right: 2319 (0%)
  Average R2 nucleotides trimmed left: 0.001425447339106763
  Average R2 nucleotides trimmed right: 2.482651836533334E-4
Tag parsing report:
  Execution time: 0ns
  Total reads: 47533850
  Matched reads: 45649245 (96,04%)
  Projection +R1 +R2: 45649245 (96,04%)
  For variant 0:
    For projection +R1 +R2:
      UMI:Left position:
        17: + 20048776 (43,92%) = 20048776 (43,92%)
        18: + 13945293 (30,55%) = 33994069 (74,47%)
        19: + 11655176 (25,53%) = 45649245 (100%)
      UMI:Right position:
        31: + 20048776 (43,92%) = 20048776 (43,92%)
        32: + 13945293 (30,55%) = 33994069 (74,47%)
        33: + 11655176 (25,53%) = 45649245 (100%)
      R1:Left position:
        52: + 20048776 (43,92%) = 20048776 (43,92%)
        53: + 13945293 (30,55%) = 33994069 (74,47%)
        54: + 11655176 (25,53%) = 45649245 (100%)
      R1:Right position:
        52~148: + 7040661 (15,42%) = 7040661 (15,42%)
        149: + 3275704 (7,18%) = 10316365 (22,6%)
        150: + 9262741 (20,29%) = 19579106 (42,89%)
        151: + 26070139 (57,11%) = 45649245 (100%)
      R2:Left position: 20
      Variants: 0
      Cost:
        0: + 43339848 (94,94%) = 43339848 (94,94%)
        5~10: + 2309397 (5,06%) = 45649245 (100%)
      UMI length: 14
      R1 length:
        0~95: + 7552570 (16,54%) = 7552570 (16,54%)
        96: + 2369978 (5,19%) = 9922548 (21,74%)
        97: + 10642103 (23,31%) = 20564651 (45,05%)
        98: + 12264201 (26,87%) = 32828852 (71,92%)
        99: + 12820393 (28,08%) = 45649245 (100%)
      R2 length:
        0~129: + 5733452 (12,56%) = 5733452 (12,56%)
        130: + 20690033 (45,32%) = 26423485 (57,88%)
        131: + 19225760 (42,12%) = 45649245 (100%)
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