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RC dedup entry
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willbradshaw committed Mar 1, 2024
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1 change: 1 addition & 0 deletions data/2024-02-29_dedup/cc-prev/cc-libraries.txt
1 change: 1 addition & 0 deletions data/2024-02-29_dedup/cc-prev/qc_basic_stats.tsv
1 change: 1 addition & 0 deletions data/2024-02-29_dedup/cc-rerun/cc-libraries.txt
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91 changes: 91 additions & 0 deletions data/2024-02-29_dedup/cc-rerun/qc_basic_stats.tsv
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sample percent_gc mean_seq_len n_read_pairs percent_duplicates n_bases_approx per_base_sequence_quality per_sequence_quality_scores per_base_sequence_content per_sequence_gc_content per_base_n_content sequence_length_distribution sequence_duplication_levels overrepresented_sequences adapter_content stage
5_13_A_S1 49 72.40893391071245 38796 46.995824311784716 5600000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn warn/fail warn/warn pass/pass cleaned
5_13_C_S2 49 71.96122250684569 11321 29.926684921826684 1640.7 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/warn warn/warn pass/pass cleaned
5_19_A_S4 48 71.92518301519476 160779 45.273325496488965 23200000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn warn/warn warn/warn pass/pass cleaned
5_19_F_S3 49 72.38420941927836 156891 57.19990311745097 22800000 pass/pass pass/pass fail/fail fail/warn pass/pass warn/warn fail/fail warn/warn pass/pass cleaned
5_28_E 44 70.71878543216337 481554 26.174567048252605 68500000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/warn pass/pass pass/pass cleaned
5_28_I 47 70.3242412233352 585416 36.55298736015812 82900000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/warn warn/warn pass/pass cleaned
630-N 45 74.02278636672565 35640829 27.671176618217842 5200000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass cleaned
630-S1 44 73.60501339368068 38834732 67.33274321744497 5600000000 pass/pass pass/pass fail/fail fail/warn pass/pass warn/warn fail/fail pass/pass pass/pass cleaned
630-S2 41 72.00361437681678 47500028 54.68721043620661 6800000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn fail/fail pass/pass pass/pass cleaned
630-SF1 42 72.13395243183896 46906375 40.792780453633725 6600000000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn warn/warn pass/pass pass/pass cleaned
6_09_N1 48 70.07379049032505 444705 48.04078792202006 62700000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn warn/fail warn/warn pass/pass cleaned
6_09_S1 49 69.62540087357382 446213 57.11891900577148 62500000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn fail/fail warn/warn pass/pass cleaned
MR2 43 72.29250759694028 37682276 68.74551951679672 5400000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn fail/fail pass/pass pass/pass cleaned
MR3 44 72.43900297312246 40340417 56.69898791033769 5800000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn fail/fail pass/pass pass/pass cleaned
MR_1_7_1_MOS 49 72.56278322457946 2592245 57.77182055383652 378800000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn warn/fail pass/pass pass/pass cleaned
S68-1 41 72.46112723723834 44640807 55.84437565466368 6400000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn fail/fail pass/pass pass/pass cleaned
S_3_6_30_COL 49 72.61652125936965 2171372 56.847894154513114 317500000 pass/pass pass/pass fail/fail pass/warn pass/pass warn/warn warn/fail pass/pass pass/pass cleaned
S_3_6_30_MOS 48 72.13298012395909 873514 20.151060340790828 126800000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/pass pass/pass pass/pass cleaned
5_13_A_S1 49 72.7806879836955 36309 44.36227932468534 5200000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn warn/warn warn/warn pass/pass dedup
5_13_C_S2 49 72.23984865263935 10836 27.533222591362126 1576.5 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/warn warn/warn pass/pass dedup
5_19_A_S4 48 72.4436590296496 148400 41.907345013477084 21600000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn warn/warn warn/warn pass/pass dedup
5_19_F_S3 49 72.85955475767938 145943 55.09548248288716 21300000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn fail/fail warn/warn pass/pass dedup
5_28_E 43.5 71.08439600387348 453339 21.998171484896382 64800000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass dedup
5_28_I 47 70.95311862645212 536887 36.57863211303854 76700000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/warn warn/warn pass/pass dedup
630-N 45 73.97647498261234 27358492 6.275319386435839 4000000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass dedup
630-S1 46 72.86950492755514 17177890 10.920011758371821 2400000000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/pass pass/pass pass/pass dedup
630-S2 42 72.16248859308982 28343565 16.012697393520916 4000000000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/pass pass/pass pass/pass dedup
630-SF1 42 72.3276227397755 33740509 10.88620256680587 4800000000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/pass pass/pass pass/pass dedup
6_09_N1 48 70.85741120005588 400873 43.909327801533834 57100000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn warn/fail warn/warn pass/pass dedup
6_09_S1 49 70.67850206407483 389763 53.36517912115496 55400000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn warn/fail warn/warn pass/pass dedup
MR2 44 71.67451579969912 17771984 17.39660625946214 2400000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass dedup
MR3 45 71.97208053529302 20717625 14.802622341696349 2800000000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/pass pass/pass pass/pass dedup
MR_1_7_1_MOS 49 72.98671563927397 2402976 52.75468401642968 353200000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn warn/fail pass/pass pass/pass dedup
S68-1 42 72.63264878782599 28247842 16.900351005095835 4000000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass dedup
S_3_6_30_COL 49 73.0040586869408 2021097 50.85723756544867 297100000 pass/pass pass/pass fail/fail pass/warn pass/pass warn/warn warn/fail pass/pass pass/pass dedup
S_3_6_30_MOS 48 72.39377734208361 818107 17.745455687467754 119200000 pass/pass pass/pass fail/fail pass/warn pass/pass warn/warn pass/pass pass/pass pass/pass dedup
5_13_A_S1 49 73.83982768272202 41087 46.52566505220629 6000000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn warn/fail warn/warn pass/pass raw_concat
5_13_C_S2 49 73.9226308813784 12072 30.748840291583832 1784.7 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/warn warn/warn pass/pass raw_concat
5_19_A_S4 48 73.61478447321501 171626 45.24370683023242 25200000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn warn/warn warn/warn pass/pass raw_concat
5_19_F_S3 49 73.76138468340363 167374 55.83155089798893 24600000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn fail/fail warn/warn pass/pass raw_concat
5_28_E 44 72.1761527470328 504599 26.145367328182957 72800000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/warn pass/warn pass/pass raw_concat
5_28_I 47 71.93223093083517 624031 35.49242005747763 89600000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/warn warn/warn pass/pass raw_concat
630-N 45 76 36420649 28.132263492784077 5400000000 pass/pass pass/pass fail/fail fail/fail pass/pass pass/pass pass/pass pass/pass pass/pass raw_concat
630-S1 45 76 39759745 68.13765447137285 6000000000 pass/pass pass/pass fail/fail warn/warn pass/pass pass/pass fail/fail pass/warn pass/pass raw_concat
630-S2 41 76 48462833 54.830263399559854 7200000000 pass/pass pass/pass fail/fail fail/fail pass/pass pass/pass fail/fail pass/warn fail/fail raw_concat
630-SF1 42 76 47832942 41.092497875470755 7200000000 pass/pass pass/pass fail/fail warn/warn pass/pass pass/pass warn/warn pass/pass warn/warn raw_concat
6_09_N1 48.5 71.66169728433654 469609 46.403178366678176 67200000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn warn/fail warn/warn pass/pass raw_concat
6_09_S1 49 71.24448535582411 476640 54.89427389041134 67800000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn fail/fail warn/warn pass/pass raw_concat
MR2 44 76 38572859 69.09566041552405 5800000000 pass/pass pass/pass fail/fail fail/fail pass/pass pass/pass fail/fail pass/warn warn/warn raw_concat
MR3 44 76 41207484 56.7984259859093 6200000000 pass/pass pass/pass fail/fail warn/warn pass/pass pass/pass fail/fail pass/pass warn/warn raw_concat
MR_1_7_1_MOS 49 74.3702767452952 2891359 51.91613256423034 430000000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn warn/fail pass/warn pass/pass raw_concat
S68-1 42 76 45434265 55.98895577364665 6800000000 pass/pass pass/pass fail/fail fail/fail pass/pass pass/pass fail/fail pass/pass warn/warn raw_concat
S_3_6_30_COL 48.5 74.44300560137219 2405482 52.10000319708038 358000000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn warn/fail pass/warn pass/pass raw_concat
S_3_6_30_MOS 48 74.14565106533003 953038 20.539526098763844 141200000 pass/pass pass/pass fail/fail pass/pass pass/pass warn/warn pass/pass pass/pass pass/pass raw_concat
5_13_A_S1 47 70.78265858056056 6101 11.973446975905588 869.7 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/pass warn/warn pass/pass ribo_initial
5_13_C_S2 45 70.90974990938746 2759 10.02174700978616 393.9 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass warn/warn pass/pass ribo_initial
5_19_A_S4 43.5 71.73071530843575 67048 16.051187209163587 9600000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/pass pass/pass pass/pass ribo_initial
5_19_F_S3 41 71.98813631296778 37678 30.130314772546313 5400000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/warn pass/pass pass/pass ribo_initial
5_28_E 40 70.87330554988256 313376 10.594305061599044 44700000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/pass pass/pass pass/pass ribo_initial
5_28_I 44 70.43816181479163 290678 13.43229624655676 41100000 pass/pass pass/pass fail/fail pass/pass pass/pass warn/warn pass/pass pass/pass pass/pass ribo_initial
630-N 45 73.97309123580553 27195266 6.203643048336573 4000000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass ribo_initial
630-S1 45.5 72.86411731614744 17026062 10.844570830301741 2400000000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/pass pass/pass pass/pass ribo_initial
630-S2 41 72.06233618574747 26959269 15.376395841034586 3800000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass ribo_initial
630-SF1 42 72.29669292495981 33090752 10.558543414507398 4600000000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/pass pass/pass pass/pass ribo_initial
6_09_N1 44 69.69338544837926 152739 25.2300951069263 21300000 pass/pass pass/pass fail/fail pass/pass pass/pass warn/warn pass/pass pass/pass pass/pass ribo_initial
6_09_S1 44 68.83392964651243 116270 23.090651070783515 16000000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/pass pass/pass pass/pass ribo_initial
MR2 44 71.58459000983962 17051458 16.81036645534479 2400000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass ribo_initial
MR3 44 71.90191333072438 19977414 14.267571185757859 2800000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass ribo_initial
MR_1_7_1_MOS 47.5 71.07757173850752 488580 14.036266467797873 69900000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/pass pass/pass pass/pass ribo_initial
S68-1 41 72.53683327442295 26695916 16.481096655028743 3800000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass ribo_initial
S_3_6_30_COL 48 71.4235470788118 456150 14.046460175435435 65600000 pass/pass pass/pass fail/fail pass/pass pass/pass warn/warn pass/pass pass/pass pass/pass ribo_initial
S_3_6_30_MOS 48 72.24016412956713 714070 13.28773197021718 103800000 pass/pass pass/pass fail/fail warn/fail pass/pass warn/warn pass/pass pass/pass pass/pass ribo_initial
5_13_A_S1_2 45 71.65598411798072 3526 15.51332955190017 508.9 pass/pass pass/pass fail/fail fail/warn pass/pass warn/warn pass/pass warn/warn pass/pass ribo_secondary
5_13_C_S2_2 44 71.78205128205127 2106 11.44349477682811 304.3 pass/pass pass/pass fail/fail warn/fail pass/pass warn/warn pass/pass warn/warn pass/pass ribo_secondary
5_19_A_S4_2 43 72.23265703619542 61610 16.85278363901964 8900000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/pass pass/pass pass/pass ribo_secondary
5_19_F_S3_2 39 73.11725656336525 29977 35.66901290989759 4300000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn warn/warn pass/pass pass/pass ribo_secondary
5_28_E_2 40 71.09521020020821 298739 11.033446953708356 42700000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/pass pass/pass pass/pass ribo_secondary
5_28_I_2 44 70.91519856338502 267295 14.045350295567282 38100000 pass/pass pass/pass fail/fail pass/pass pass/pass warn/warn pass/pass pass/pass pass/pass ribo_secondary
630-N_2 45 73.99315787932923 27156785 6.206919533344951 4000000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass ribo_secondary
630-S1_2 45.5 72.92916671847523 16969523 10.842794657546342 2400000000 pass/pass pass/pass fail/fail fail/warn pass/pass warn/warn pass/pass pass/pass pass/pass ribo_secondary
630-S2_2 41 72.21737261030705 26665089 15.399771930088654 3800000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass ribo_secondary
630-SF1_2 42 72.37061678529662 32809310 10.529577769101657 4600000000 pass/pass pass/pass fail/fail warn/warn pass/pass warn/warn pass/pass pass/pass pass/pass ribo_secondary
6_09_N1_2 42 70.5117646117918 125036 25.327105793531466 17700000 pass/pass pass/pass fail/fail pass/warn pass/pass warn/warn pass/pass pass/pass pass/pass ribo_secondary
6_09_S1_2 42 70.33516034709315 84473 24.841665384205598 11800000 pass/pass pass/pass fail/fail pass/pass pass/pass warn/warn pass/pass pass/pass pass/pass ribo_secondary
MR2_2 44 71.73186767454337 16858676 16.831094187685586 2400000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass ribo_secondary
MR3_2 44 72.0337523143047 19775918 14.299665535599182 2800000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass ribo_secondary
MR_1_7_1_MOS_2 46 71.43422337491896 256018 11.580337715970536 36800000 pass/pass pass/pass fail/fail pass/pass pass/pass warn/warn pass/pass pass/pass pass/pass ribo_secondary
S68-1_2 41 72.66267382896984 26403611 16.53822322947083 3800000000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass ribo_secondary
S_3_6_30_COL_2 48 71.93711482350648 287206 12.131438799151738 41500000 pass/pass pass/pass fail/fail pass/pass pass/pass warn/warn pass/pass pass/pass pass/pass ribo_secondary
S_3_6_30_MOS_2 48 72.2749768575047 704332 13.337724649398282 102400000 pass/pass pass/pass fail/fail fail/fail pass/pass warn/warn pass/pass pass/pass pass/pass ribo_secondary
19 changes: 19 additions & 0 deletions data/2024-02-29_dedup/multiqc/multiqc_clumpify_fastqc.txt
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Sample Filename File type Encoding Total Sequences Total Bases Sequences flagged as poor quality Sequence length %GC total_deduplicated_percentage avg_sequence_length median_sequence_length basic_statistics per_base_sequence_quality per_sequence_quality_scores per_base_sequence_content per_sequence_gc_content per_base_n_content sequence_length_distribution sequence_duplication_levels overrepresented_sequences adapter_content
5_13_A_S1 5_13_A_S1.fastq.gz Conventional base calls Sanger / Illumina 1.9 566.0 77.5 kbp 0.0 51-152 38.0 86.74911660777384 137.01766784452298 147 pass pass pass fail fail warn warn pass warn pass
5_13_C_S2 5_13_C_S2.fastq.gz Conventional base calls Sanger / Illumina 1.9 822.0 117.6 kbp 0.0 65-152 38.0 95.1338199513382 142.61557177615572 150 pass pass pass fail warn warn warn pass warn pass
5_19_A_S4 5_19_A_S4.fastq.gz Conventional base calls Sanger / Illumina 1.9 9398.0 1.3 Mbp 0.0 37-152 40.0 77.13343264524367 143.35007448393276 151 pass pass pass fail warn warn warn pass warn pass
5_19_F_S3 5_19_F_S3.fastq.gz Conventional base calls Sanger / Illumina 1.9 23773.0 3.4 Mbp 0.0 38-152 38.0 60.86316409371977 146.7604004542969 151 pass pass pass fail pass warn warn warn pass pass
5_28_E 5_28_E.fastq.gz Conventional base calls Sanger / Illumina 1.9 3498.0 478.9 kbp 0.0 39-149 39.0 86.39222412807318 136.62978845054317 147 pass pass pass fail warn warn warn pass warn pass
5_28_I 5_28_I.fastq.gz Conventional base calls Sanger / Illumina 1.9 15063.0 2.1 Mbp 0.0 35-149 40.0 64.98705437163912 140.15076677952598 147 pass pass pass fail warn warn warn warn warn pass
630-N 630-N.fastq.gz Conventional base calls Sanger / Illumina 1.9 90544.0 12.8 Mbp 0.0 31-153 39.0 94.9924898391942 141.4655637038346 152 pass pass pass fail fail warn warn pass pass pass
630-S1 630-S1.fastq.gz Conventional base calls Sanger / Illumina 1.9 52024.0 7.2 Mbp 0.0 31-153 39.0 90.74657850222974 137.75724665538982 152 pass pass pass fail fail warn warn pass pass pass
630-S2 630-S2.fastq.gz Conventional base calls Sanger / Illumina 1.9 77972.0 10.4 Mbp 0.0 31-153 35.0 80.91109629097625 133.4868157800236 152 pass pass pass fail fail warn warn pass warn pass
630-SF1 630-SF1.fastq.gz Conventional base calls Sanger / Illumina 1.9 111713.0 15 Mbp 0.0 31-153 36.0 83.8174608147664 134.40101868180068 152 pass pass pass fail fail warn warn pass warn pass
6_09_N1 6_09_N1.fastq.gz Conventional base calls Sanger / Illumina 1.9 1383.0 184 kbp 0.0 39-149 40.0 89.08170643528561 132.93275488069415 147 pass pass pass fail fail warn warn pass warn pass
6_09_S1 6_09_S1.fastq.gz Conventional base calls Sanger / Illumina 1.9 8558.0 1.1 Mbp 0.0 40-149 40.0 73.87240009347978 138.17609254498714 147 pass pass pass fail warn warn warn pass warn pass
MR2 MR2.fastq.gz Conventional base calls Sanger / Illumina 1.9 44905.0 5.8 Mbp 0.0 31-153 37.0 83.0620198196192 129.78487918939985 147 pass pass pass fail fail warn warn pass warn pass
MR3 MR3.fastq.gz Conventional base calls Sanger / Illumina 1.9 53932.0 7 Mbp 0.0 31-153 37.0 85.54661425498776 129.9765259956983 147 pass pass pass fail fail warn warn pass warn pass
MR_1_7_1_MOS MR_1_7_1_MOS.fastq.gz Conventional base calls Sanger / Illumina 1.9 21572.0 3.1 Mbp 0.0 37-153 38.0 69.29816428703876 146.23720563693678 152 pass pass pass fail warn warn warn warn pass pass
S68-1 S68-1.fastq.gz Conventional base calls Sanger / Illumina 1.9 83500.0 11.2 Mbp 0.0 31-153 35.0 78.02994011976048 133.9025748502994 152 pass pass pass fail fail warn warn pass warn pass
S_3_6_30_COL S_3_6_30_COL.fastq.gz Conventional base calls Sanger / Illumina 1.9 15736.0 2.2 Mbp 0.0 38-153 40.0 75.8960345704118 145.6559481443823 152 pass pass pass fail warn warn warn pass warn pass
S_3_6_30_MOS S_3_6_30_MOS.fastq.gz Conventional base calls Sanger / Illumina 1.9 12274.0 1.7 Mbp 0.0 36-153 40.0 83.50985823692358 144.10933680951604 152 pass pass pass fail fail warn warn pass warn pass
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