Starting /dee2/code/volunteer_pipeline.sh SRR11699276
    current disk space = 2472639512576
    free memory = 976800696 
SRR11699276 SRAfilesize
25ce863714d55da12e4d260f8dfb45d6  SRR11699276.sra
SRR11699276.sra file validated
SRR11699276 is single end
SRR11699276 is conventional basespace
SRR11699276 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699276_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	76
%GC	52
>>END_MODULE
>>Per base sequence quality	warn
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	30.9975	32.0	32.0	32.0	32.0	32.0
2	31.26375	32.0	32.0	32.0	32.0	32.0
3	31.40625	32.0	32.0	32.0	32.0	32.0
4	31.46	32.0	32.0	32.0	32.0	32.0
5	31.42625	32.0	32.0	32.0	32.0	32.0
6	34.98875	36.0	36.0	36.0	36.0	36.0
7	34.9885	36.0	36.0	36.0	36.0	36.0
8	34.90125	36.0	36.0	36.0	36.0	36.0
9	34.85075	36.0	36.0	36.0	32.0	36.0
10-11	34.961124999999996	36.0	36.0	36.0	34.0	36.0
12-13	35.0	36.0	36.0	36.0	36.0	36.0
14-15	34.965125	36.0	36.0	36.0	36.0	36.0
16-17	35.02825	36.0	36.0	36.0	36.0	36.0
18-19	35.018125	36.0	36.0	36.0	36.0	36.0
20-21	34.77925	36.0	36.0	36.0	34.0	36.0
22-23	34.909625	36.0	36.0	36.0	36.0	36.0
24-25	34.904125	36.0	36.0	36.0	36.0	36.0
26-27	34.670874999999995	36.0	36.0	36.0	34.0	36.0
28-29	34.8235	36.0	36.0	36.0	34.0	36.0
30-31	34.815625	36.0	36.0	36.0	34.0	36.0
32-33	34.738625	36.0	36.0	36.0	34.0	36.0
34-35	34.922625	36.0	36.0	36.0	36.0	36.0
36-37	34.82275	36.0	36.0	36.0	34.0	36.0
38-39	34.818875000000006	36.0	36.0	36.0	34.0	36.0
40-41	34.73375	36.0	36.0	36.0	32.0	36.0
42-43	34.735625	36.0	36.0	36.0	32.0	36.0
44-45	34.6705	36.0	36.0	36.0	32.0	36.0
46-47	34.707	36.0	36.0	36.0	32.0	36.0
48-49	34.60925	36.0	36.0	36.0	32.0	36.0
50-51	34.309625	36.0	36.0	36.0	32.0	36.0
52-53	33.9785	36.0	36.0	36.0	32.0	36.0
54-55	33.45525	36.0	36.0	36.0	24.0	36.0
56-57	32.3985	36.0	32.0	36.0	14.0	36.0
58-59	31.261125	36.0	32.0	36.0	14.0	36.0
60-61	30.143	36.0	27.0	36.0	14.0	36.0
62-63	29.336875	36.0	17.5	36.0	14.0	36.0
64-65	27.789625	32.0	14.0	36.0	14.0	36.0
66-67	25.50475	27.0	14.0	36.0	14.0	36.0
68-69	25.09175	27.0	14.0	36.0	14.0	36.0
70-71	25.402625	27.0	14.0	36.0	14.0	36.0
72-73	25.971	29.5	14.0	36.0	14.0	36.0
74-75	25.791249999999998	32.0	14.0	36.0	14.0	36.0
76	22.86875	21.0	14.0	32.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	2.0
22	7.0
23	11.0
24	25.0
25	38.0
26	61.0
27	98.0
28	127.0
29	197.0
30	313.0
31	404.0
32	569.0
33	828.0
34	936.0
35	384.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	22.475	31.275	21.4	24.85
2	21.275	29.525000000000002	26.775	22.425
3	23.275000000000002	35.725	16.650000000000002	24.349999999999998
4	27.675	35.099999999999994	16.775000000000002	20.45
5	21.25	25.95	25.35	27.450000000000003
6	25.85	26.924999999999997	25.974999999999998	21.25
7	27.675	38.175	17.974999999999998	16.175
8	22.175	28.125	27.474999999999998	22.225
9	25.424999999999997	31.85	17.275	25.45
10-11	29.462500000000002	29.575000000000003	23.9875	16.975
12-13	22.4875	22.525000000000002	25.4625	29.525000000000002
14-15	30.4625	37.45	17.7	14.387500000000001
16-17	21.512500000000003	24.875	33.5	20.1125
18-19	36.225	26.4125	22.237499999999997	15.125
20-21	23.425	36.7875	23.075000000000003	16.7125
22-23	32.875	37.7875	13.450000000000001	15.8875
24-25	28.525	42.075	13.8625	15.537500000000001
26-27	30.887500000000003	33.6	15.1	20.4125
28-29	33.6625	29.6625	13.100000000000001	23.575
30-31	35.362500000000004	37.012499999999996	8.5625	19.0625
32-33	27.200000000000003	41.3	8.450000000000001	23.05
34-35	31.4375	31.25	11.637500000000001	25.674999999999997
36-37	24.725	32.5	11.05	31.724999999999998
38-39	21.8875	32.8375	13.875000000000002	31.4
40-41	21.875	28.199999999999996	18.1875	31.7375
42-43	24.0375	24.4875	23.724999999999998	27.750000000000004
44-45	19.2	31.137500000000003	17.6625	32.0
46-47	20.1125	29.825000000000003	16.5875	33.475
48-49	14.512500000000001	28.262500000000003	16.475	40.75
50-51	16.162499999999998	28.5875	17.25	38.0
52-53	22.35	23.674999999999997	17.349999999999998	36.625
54-55	21.925	25.162499999999998	16.8375	36.075
56-57	20.925	29.75	12.875	36.449999999999996
58-59	25.7875	22.3	14.499999999999998	37.4125
60-61	30.7375	16.85	17.2	35.212500000000006
62-63	27.875	20.5625	21.3125	30.25
64-65	22.875	19.6	26.437500000000004	31.087500000000002
66-67	19.925	12.775	31.887500000000003	35.4125
68-69	20.837500000000002	14.774999999999999	33.4375	30.95
70-71	22.7125	14.0875	34.6875	28.512500000000003
72-73	22.175	12.425	32.337500000000006	33.0625
74-75	24.375	9.125	32.85	33.650000000000006
76	12.925	9.049999999999999	43.15	34.875
>>END_MODULE
>>Per sequence GC content	warn
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.5
37	1.0
38	0.5
39	1.5
40	4.0
41	5.0
42	5.0
43	9.5
44	25.0
45	47.0
46	58.0
47	102.0
48	216.5
49	447.5
50	608.0
51	776.0
52	732.5
53	481.0
54	441.0
55	413.0
56	303.5
57	183.5
58	145.0
59	111.0
60	71.0
61	41.5
62	18.0
63	11.0
64	5.0
65	6.0
66	3.0
67	0.0
68	0.0
69	0.0
70	0.0
71	0.0
72	0.0
73	0.0
74	0.0
75	0.0
76	0.0
77	0.0
78	0.0
79	0.0
80	0.0
81	0.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.5
94	0.5
95	0.0
96	0.0
97	0.0
98	1.0
99	1.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10-11	0.0
12-13	0.0
14-15	0.0
16-17	0.0
18-19	0.0
20-21	0.0
22-23	0.0
24-25	0.0
26-27	0.0
28-29	0.0
30-31	0.0
32-33	0.0
34-35	0.0
36-37	0.0
38-39	0.0
40-41	0.0
42-43	0.0
44-45	0.0
46-47	0.0
48-49	0.0
50-51	0.0
52-53	0.0
54-55	0.0
56-57	0.0
58-59	0.0
60-61	0.0
62-63	0.0
64-65	0.0
66-67	0.0
68-69	0.0
70-71	0.0
72-73	0.0
74-75	0.0
76	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
76	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	58.12500000000001
#Duplication Level	Percentage of deduplicated	Percentage of total
1	89.11827956989248	51.800000000000004
2	4.688172043010753	5.45
3	2.064516129032258	3.5999999999999996
4	0.7311827956989247	1.7000000000000002
5	0.7741935483870968	2.25
6	0.5161290322580645	1.7999999999999998
7	0.34408602150537637	1.4000000000000001
8	0.25806451612903225	1.2
9	0.12903225806451613	0.675
>10	1.1612903225806452	16.325
>50	0.12903225806451613	5.4
>100	0.08602150537634409	8.4
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC	233	5.825	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	103	2.5749999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	81	2.025	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	73	1.825	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	62	1.55	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	42	1.05	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	41	1.0250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACG	41	1.0250000000000001	TruSeq Adapter, Index 15 (97% over 36bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	39	0.975	No Hit
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	38	0.95	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	37	0.9249999999999999	No Hit
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	35	0.8750000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	32	0.8	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	30	0.75	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	29	0.7250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACGC	26	0.65	TruSeq Adapter, Index 15 (97% over 36bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACG	25	0.625	TruSeq Adapter, Index 15 (97% over 36bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACGCGGA	24	0.6	TruSeq Adapter, Index 15 (97% over 36bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGTAGTTCGACCGTGGATTAGATCGGAAGAGCACACGTCTGAACTCCAGT	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACGCGGAT	14	0.35000000000000003	TruSeq Adapter, Index 15 (97% over 36bp)
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	11	0.27499999999999997	No Hit
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCGACCCCAGGTCAGTCGGGAGATCGGAAGAGCACACGTCTGAACTCCAG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	8	0.2	No Hit
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	8	0.2	No Hit
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAATTCATGATCTGGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
CCTTATCGGATTGGACGTGCTTCGAAACAGATCGGAAGAGCACACGTCTG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACG	7	0.17500000000000002	TruSeq Adapter, Index 15 (97% over 36bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACGCGG	7	0.17500000000000002	TruSeq Adapter, Index 15 (97% over 36bp)
CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
ATCCTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
CGACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACGCG	6	0.15	TruSeq Adapter, Index 15 (97% over 36bp)
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAC	6	0.15	TruSeq Adapter, Index 5 (100% over 35bp)
CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTC	6	0.15	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	6	0.15	No Hit
CGACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	6	0.15	No Hit
CGACACGACTCTCGGCAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGTAGTTCGACCGTGGATAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	5	0.125	No Hit
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAC	5	0.125	TruSeq Adapter, Index 5 (100% over 35bp)
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GGGCCTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACG	5	0.125	TruSeq Adapter, Index 15 (97% over 36bp)
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
AGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACGCG	5	0.125	TruSeq Adapter, Index 15 (97% over 36bp)
ACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTAGATCGGAAGAGCACA	5	0.125	No Hit
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.125	0.0	0.0	0.0	0.0
2	0.15	0.0	0.0	0.0	0.0
3	0.175	0.0	0.0	0.0	0.0
4	0.2	0.0	0.0	0.0	0.0
5	0.275	0.0	0.0	0.0	0.0
6	0.35	0.0	0.0	0.0	0.0
7	0.45	0.0	0.0	0.0	0.0
8	0.575	0.0	0.0	0.0	0.0
9	1.05	0.0	0.0	0.0	0.0
10	1.975	0.0	0.0	0.0	0.0
11	2.55	0.0	0.0	0.0	0.0
12	3.4	0.0	0.0	0.0	0.0
13	4.8	0.0	0.0	0.0	0.0
14	7.95	0.0	0.0	0.0	0.0
15	9.175	0.0	0.0	0.0	0.0
16	11.725	0.0	0.0	0.0	0.0
17	16.25	0.0	0.0	0.0	0.0
18	20.25	0.0	0.0	0.0	0.0
19	22.825	0.0	0.0	0.0	0.0
20	27.55	0.0	0.0	0.0	0.0
21	31.7	0.0	0.0	0.0	0.0
22	39.225	0.0	0.0	0.0	0.0
23	49.725	0.0	0.0	0.0	0.0
24	53.3	0.0	0.0	0.0	0.0
25	64.25	0.0	0.0	0.0	0.0
26	68.375	0.0	0.0	0.0	0.0
27	70.225	0.0	0.0	0.0	0.0
28	74.375	0.0	0.0	0.0	0.0
29	76.15	0.0	0.0	0.0	0.0
30	78.2	0.0	0.0	0.0	0.0
31	80.275	0.0	0.0	0.0	0.0
32	82.05	0.0	0.0	0.0	0.0
33	83.5	0.0	0.0	0.0	0.0
34	85.675	0.0	0.0	0.0	0.0
35	87.375	0.0	0.0	0.0	0.0
36	90.225	0.0	0.0	0.0	0.0
37	91.1	0.0	0.0	0.0	0.0
38	91.8	0.0	0.0	0.0	0.0
39	92.25	0.0	0.0	0.0	0.0
40	92.95	0.0	0.0	0.0	0.0
41	93.225	0.0	0.0	0.0	0.0
42	93.85	0.0	0.0	0.0	0.0
43	94.2	0.0	0.0	0.0	0.0
44	94.525	0.0	0.0	0.0	0.0
45	94.675	0.0	0.0	0.0	0.0
46	94.7	0.0	0.0	0.0	0.0
47	94.9	0.0	0.0	0.0	0.0
48	95.025	0.0	0.0	0.0	0.0
49	95.125	0.0	0.0	0.0	0.0
50	95.125	0.0	0.0	0.0	0.0
51	95.125	0.0	0.0	0.0	0.0
52	95.175	0.0	0.0	0.0	0.0
53	95.175	0.0	0.0	0.0	0.0
54	95.175	0.0	0.0	0.0	0.0
55	95.175	0.0	0.0	0.0	0.0
56	95.175	0.0	0.0	0.0	0.0
57	95.175	0.0	0.0	0.0	0.0
58	95.175	0.0	0.0	0.0	0.0
59	95.175	0.0	0.0	0.0	0.0
60	95.175	0.0	0.0	0.0	0.0
61	95.175	0.0	0.0	0.0	0.0
62	95.175	0.0	0.0	0.0	0.0
63	95.175	0.0	0.0	0.0	0.0
64	95.175	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TCTAGCT	15	0.0020658788	70.00001	11
TCAGGAT	15	0.0020658788	70.00001	20
GCTGGTC	15	0.0020658788	70.00001	15
TAGCTGG	15	0.0020658788	70.00001	13
CCGTTGT	15	0.0020658788	70.00001	2
TAGTCTA	15	0.0020658788	70.00001	8
GGTCAGG	15	0.0020658788	70.00001	18
CTGGTCA	15	0.0020658788	70.00001	16
CTAGCTG	15	0.0020658788	70.00001	12
GTCTAGC	15	0.0020658788	70.00001	10
TCCGTTG	15	0.0020658788	70.00001	1
CGTTGTA	15	0.0020658788	70.00001	3
AGTCTAG	15	0.0020658788	70.00001	9
CAGGATA	15	0.0020658788	70.00001	21
GTCAGGA	15	0.0020658788	70.00001	19
AGCTGGT	15	0.0020658788	70.00001	14
GTAGTCT	15	0.0020658788	70.00001	7
GTTGTAG	15	0.0020658788	70.00001	4
TGGTCAG	20	7.003785E-5	70.0	17
TTGTAGT	25	2.1136815E-4	55.999996	5
>>END_MODULE
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369932 READS because READLEN < 1
Read 369932 spots for SRR11699276.sra
Written 369932 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
Rejected 369920 READS because READLEN < 1
Read 369920 spots for SRR11699276.sra
Written 369920 spots for SRR11699276.sra
SRR ids: ['SRR11699276.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_s5nxnn81
SRR11699276.sra spots: 7398412
blocks: [[1, 369920], [369921, 739840], [739841, 1109760], [1109761, 1479680], [1479681, 1849600], [1849601, 2219520], [2219521, 2589440], [2589441, 2959360], [2959361, 3329280], [3329281, 3699200], [3699201, 4069120], [4069121, 4439040], [4439041, 4808960], [4808961, 5178880], [5178881, 5548800], [5548801, 5918720], [5918721, 6288640], [6288641, 6658560], [6658561, 7028480], [7028481, 7398412]]
SRR11699276 file size 1406708
SRR11699276 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -f sanger -l 18 -q 10 -k inf -t 20 -o SRR11699276 SRR11699276_1.fastq
Input file:	SRR11699276_1.fastq
trimmed:	SRR11699276-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- end quality threshold (-q):		10
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ 
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	20
Wed Jun 18 05:52:23 2025 >> started

Wed Jun 18 05:52:26 2025 >> done (3.048s)
7398412 reads processed; of these:
1924850 (26.02%) short reads filtered out after trimming by size control
  12355 ( 0.17%) empty reads filtered out after trimming by size control
5461207 (73.82%) reads available; of these:
5399023 (98.86%) trimmed reads available after processing
  62184 ( 1.14%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 222565	  4.08%
 19	 349720	  6.40%
 20	 327379	  5.99%
 21	 574300	 10.52%
 22	 712649	 13.05%
 23	 268727	  4.92%
 24	 767350	 14.05%
 25	 272340	  4.99%
 26	 166410	  3.05%
 27	 263993	  4.83%
 28	 137916	  2.53%
 29	 140438	  2.57%
 30	 147121	  2.69%
 31	 118082	  2.16%
 32	 104268	  1.91%
 33	 151217	  2.77%
 34	 129253	  2.37%
 35	 173588	  3.18%
 36	  90520	  1.66%
 37	  59720	  1.09%
 38	  45927	  0.84%
 39	  41865	  0.77%
 40	  29746	  0.54%
 41	  53643	  0.98%
 42	  21918	  0.40%
 43	  17096	  0.31%
 44	  11268	  0.21%
 45	      0	  0.00%
 46	      0	  0.00%
 47	      0	  0.00%
 48	      0	  0.00%
 49	      0	  0.00%
 50	      0	  0.00%
 51	      0	  0.00%
 52	      0	  0.00%
 53	      0	  0.00%
 54	      0	  0.00%
 55	      0	  0.00%
 56	      0	  0.00%
 57	      0	  0.00%
 58	      0	  0.00%
 59	      0	  0.00%
 60	      0	  0.00%
 61	      0	  0.00%
 62	      0	  0.00%
 63	      0	  0.00%
 64	      0	  0.00%
 65	      0	  0.00%
 66	      0	  0.00%
 67	      0	  0.00%
 68	      1	  0.00%
 69	      0	  0.00%
 70	      0	  0.00%
 71	      0	  0.00%
 72	      0	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      3	  0.00%
 76	  62184	  1.14%
5461207 reads passed initial QC


criterion=sequence-density
sequence-density=3.28
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=12
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAAGACC


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=38
fanout-score=67.14
fanout-score-rank=1
prefix-density=0.36
prefix-fanout=1.0
sequence=CCTCGTGTTTAGTTGCCACTATGAGTTTGGAACCCTGAACAGACCGCCGGTGTTAAGCCGGAGGAAGGAGA
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    1 (100.00%) aligned >1 times
100.00% overall alignment rate
Potential adapter found in reference sequence. Continuing without clipping.
                                 Started job on |	Jun 18 05:52:49
                             Started mapping on |	Jun 18 05:52:49
                                    Finished on |	Jun 18 05:53:02
       Mapping speed, Million of reads per hour |	1512.33

                          Number of input reads |	5461207
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	575196
                        Uniquely mapped reads % |	10.53%
                          Average mapped length |	22.94
                       Number of splices: Total |	11567
            Number of splices: Annotated (sjdb) |	3417
                       Number of splices: GT/AG |	10764
                       Number of splices: GC/AG |	624
                       Number of splices: AT/AC |	5
               Number of splices: Non-canonical |	174
                      Mismatch rate per base, % |	1.22%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.31
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.25
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	623642
             % of reads mapped to multiple loci |	11.42%
        Number of reads mapped to too many loci |	1093557
             % of reads mapped to too many loci |	20.02%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.31%
                     % of reads unmapped: other |	52.71%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	4262369	4262369	4262369
N_multimapping	623642	623642	623642
N_noFeature	493881	516664	550060
N_ambiguous	2422	37	45
UnstrandedReadsAssigned:78893 PositiveStrandReadsAssigned:58495 NegativeStrandReadsAssigned:25091
Dataset is classified unstranded
MeadianReadLen=24 20thPercentileLength=21 echo kmer=19
SRR11699276 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19

[quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20
[index] k-mer length: 19
[index] number of targets: 72,539
[index] number of k-mers: 56,563,136
[index] number of equivalence classes: 414,827
[quant] running in single-end mode
[quant] will process file 1: SRR11699276-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 5,461,207 reads, 905,687 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 930 rounds

  72540 SRR11699276.ke.tsv
  44303 SRR11699276.se.tsv
 116843 total
==> SRR11699276.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	1	0.589983
Zm00001eb321680_T001	3417	3318	4	1.39974
Zm00001eb323640_T001	3273	3174	0	0
Zm00001eb314140_T001	893	794	1	1.46233
Zm00001eb080260_T001	3529	3430	0	0
Zm00001eb026490_T001	2433	2334	0	0
Zm00001eb026490_T002	2229	2130	0	0
Zm00001eb026490_T003	2220	2121	0	0
Zm00001eb281360_T001	2412	2313	1	0.501983

==> SRR11699276.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	1
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699276 completed mapping pipeline successfully
