Starting /dee2/code/volunteer_pipeline.sh SRR11699506
    current disk space = 2464296366080
    free memory = 1575245900 
SRR11699506 SRAfilesize
1b6f0b48f2babac14dde2855273e784a  SRR11699506.sra
SRR11699506.sra file validated
SRR11699506 is single end
SRR11699506 is conventional basespace
SRR11699506 read1 length is 86 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699506_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	86
%GC	48
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.2915	32.0	32.0	32.0	32.0	32.0
2	31.51175	32.0	32.0	32.0	32.0	32.0
3	31.523	32.0	32.0	32.0	32.0	32.0
4	31.5765	32.0	32.0	32.0	32.0	32.0
5	31.52225	32.0	32.0	32.0	32.0	32.0
6	35.054	36.0	36.0	36.0	36.0	36.0
7	35.1445	36.0	36.0	36.0	36.0	36.0
8	35.12775	36.0	36.0	36.0	36.0	36.0
9	34.939	36.0	36.0	36.0	36.0	36.0
10-11	35.161625	36.0	36.0	36.0	36.0	36.0
12-13	35.085625	36.0	36.0	36.0	36.0	36.0
14-15	35.137375000000006	36.0	36.0	36.0	36.0	36.0
16-17	35.106750000000005	36.0	36.0	36.0	36.0	36.0
18-19	35.215875	36.0	36.0	36.0	36.0	36.0
20-21	35.08125	36.0	36.0	36.0	36.0	36.0
22-23	34.984125	36.0	36.0	36.0	36.0	36.0
24-25	34.959	36.0	36.0	36.0	36.0	36.0
26-27	34.702749999999995	36.0	36.0	36.0	34.0	36.0
28-29	34.96675	36.0	36.0	36.0	36.0	36.0
30-31	35.031125	36.0	36.0	36.0	36.0	36.0
32-33	34.845	36.0	36.0	36.0	36.0	36.0
34-35	34.888125	36.0	36.0	36.0	34.0	36.0
36-37	34.94825	36.0	36.0	36.0	36.0	36.0
38-39	34.961875	36.0	36.0	36.0	36.0	36.0
40-41	34.904375	36.0	36.0	36.0	36.0	36.0
42-43	34.859375	36.0	36.0	36.0	36.0	36.0
44-45	34.883875	36.0	36.0	36.0	36.0	36.0
46-47	35.008250000000004	36.0	36.0	36.0	36.0	36.0
48-49	34.914249999999996	36.0	36.0	36.0	34.0	36.0
50-51	34.712625	36.0	36.0	36.0	32.0	36.0
52-53	34.5865	36.0	36.0	36.0	34.0	36.0
54-55	34.068250000000006	36.0	36.0	36.0	32.0	36.0
56-57	33.792249999999996	36.0	36.0	36.0	27.0	36.0
58-59	33.562375	36.0	36.0	36.0	27.0	36.0
60-61	33.909875	36.0	36.0	36.0	32.0	36.0
62-63	33.628	36.0	36.0	36.0	27.0	36.0
64-65	33.56525	36.0	36.0	36.0	27.0	36.0
66-67	33.592	36.0	34.0	36.0	27.0	36.0
68-69	33.64275	36.0	34.0	36.0	29.5	36.0
70-71	34.076750000000004	36.0	36.0	36.0	32.0	36.0
72-73	33.696625	36.0	36.0	36.0	29.5	36.0
74-75	33.72125	36.0	36.0	36.0	29.5	36.0
76-77	33.87475	36.0	36.0	36.0	32.0	36.0
78-79	33.949625	36.0	36.0	36.0	32.0	36.0
80-81	33.889125	36.0	36.0	36.0	32.0	36.0
82-83	33.577375	36.0	36.0	36.0	27.0	36.0
84-85	33.610125	36.0	36.0	36.0	27.0	36.0
86	32.2745	36.0	32.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	1.0
22	0.0
23	6.0
24	6.0
25	16.0
26	28.0
27	38.0
28	48.0
29	78.0
30	103.0
31	133.0
32	182.0
33	317.0
34	936.0
35	2108.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	30.340170085042523	25.71285642821411	23.58679339669835	20.36018009004502
2	28.425	25.05	21.75	24.775
3	29.775000000000002	30.9	17.125	22.2
4	27.05	37.5	17.375	18.075
5	19.25	25.924999999999997	27.675	27.150000000000002
6	24.6	22.725	31.974999999999998	20.7
7	38.2	30.575000000000003	15.725	15.5
8	19.975	24.775	36.975	18.275
9	22.55	37.65	17.45	22.35
10-11	32.625	24.85	25.974999999999998	16.55
12-13	19.7125	21.475	26.025	32.7875
14-15	30.9375	39.95	15.3375	13.775
16-17	20.7	23.400000000000002	36.0375	19.8625
18-19	41.15	21.7	21.325	15.825
20-21	22.2625	33.1875	25.174999999999997	19.375
22-23	34.625	36.825	14.637500000000001	13.9125
24-25	29.45	39.3125	15.950000000000001	15.287500000000001
26-27	26.275	34.7125	17.224999999999998	21.7875
28-29	28.549999999999997	27.500000000000004	16.4375	27.5125
30-31	34.2125	31.937500000000004	11.4	22.45
32-33	27.975	36.8625	10.9375	24.224999999999998
34-35	31.624999999999996	32.425	13.900000000000002	22.05
36-37	27.037499999999998	33.825	12.125	27.0125
38-39	25.412499999999998	33.95	12.5	28.1375
40-41	25.087500000000002	31.6875	14.6	28.625
42-43	28.849999999999998	27.85	19.037499999999998	24.2625
44-45	21.4375	33.1125	16.925	28.525
46-47	21.625	31.1	16.0125	31.2625
48-49	16.175	30.887500000000003	17.175	35.7625
50-51	18.45	28.1375	20.724999999999998	32.6875
52-53	18.862499999999997	27.3625	21.825	31.95
54-55	16.4625	28.712500000000002	22.912499999999998	31.912499999999998
56-57	12.7625	33.1625	22.0875	31.9875
58-59	16.3	26.424999999999997	25.2125	32.0625
60-61	14.575	24.65	29.4	31.374999999999996
62-63	14.8125	27.237499999999997	29.612500000000004	28.3375
64-65	12.5125	29.4125	27.575	30.5
66-67	15.962499999999999	19.6125	31.162499999999998	33.2625
68-69	15.412500000000001	19.7	34.387499999999996	30.5
70-71	19.475	19.1375	35.55	25.837500000000002
72-73	17.925	18.15	33.175	30.75
74-75	19.787499999999998	14.224999999999998	33.0125	32.975
76-77	19.725	12.475	36.15	31.65
78-79	15.625	13.575000000000001	42.425000000000004	28.375
80-81	18.525	17.9875	38.5625	24.925
82-83	17.575	20.7375	34.4125	27.275
84-85	20.075000000000003	23.4375	32.375	24.1125
86	18.65466366591648	29.08227056764191	32.58314578644661	19.679919979995
>>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	0.5
20	0.5
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	0.5
35	1.0
36	1.0
37	1.0
38	1.0
39	3.0
40	11.0
41	30.5
42	100.0
43	156.0
44	200.5
45	274.0
46	400.5
47	554.0
48	566.5
49	499.0
50	475.0
51	463.0
52	355.0
53	222.5
54	146.5
55	87.0
56	44.5
57	22.0
58	16.5
59	8.0
60	4.5
61	2.5
62	1.5
63	2.5
64	3.0
65	1.5
66	0.0
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	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.5
100	1.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.05
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
76-77	0.0
78-79	0.0
80-81	0.0
82-83	0.0
84-85	0.0
86	0.025
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
86	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	61.475
#Duplication Level	Percentage of deduplicated	Percentage of total
1	87.79991866612444	53.974999999999994
2	5.08336722244815	6.25
3	2.3586823912159414	4.35
4	1.2200081333875559	3.0
5	0.9760065067100446	3.0
6	0.24400162667751116	0.8999999999999999
7	0.32533550223668156	1.4000000000000001
8	0.32533550223668156	1.6
9	0.16266775111834078	0.8999999999999999
>10	1.3826758845058966	17.9
>50	0.08133387555917039	3.05
>100	0.040666937779585195	3.675
>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	147	3.675	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	68	1.7000000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	54	1.35	No Hit
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	43	1.075	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	41	1.0250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	40	1.0	No Hit
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATG	39	0.975	TruSeq Adapter, Index 15 (100% over 36bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	39	0.975	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	35	0.8750000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	34	0.8500000000000001	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	33	0.8250000000000001	No Hit
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATG	32	0.8	TruSeq Adapter, Index 15 (100% over 36bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	25	0.625	No Hit
TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA	23	0.575	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	22	0.5499999999999999	No Hit
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	19	0.475	No Hit
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG	15	0.375	No Hit
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGT	14	0.35000000000000003	TruSeq Adapter, Index 15 (100% over 37bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGAGATCGGAAG	13	0.325	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCAGATCGGAAGAGCACACGTCTGAA	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGGATTGTAGTTCAATCGGAAGAGCACACGTCTGAACTCCAGTCACATGT	13	0.325	TruSeq Adapter, Index 15 (97% over 37bp)
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAGATCGGAAGAGC	11	0.27499999999999997	No Hit
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TGGAACCCTGAACAGACCGCCGGTGTTAAGCCGGAGGAAGGAGATCGGAA	11	0.27499999999999997	No Hit
GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGTAGTTCGACCGTGGATTAGATCGGAAGAGCACACGTCTGAACTCCAGT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TTTGGAACCCTGAACAGACCGCCGGTGTTAAGCCGGAGGAAGGAGATCGG	10	0.25	No Hit
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TTAAATTCAAGTCTCTTGGCTCTTTTCAGATCGGAAGAGCACACGTCTGA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	8	0.2	No Hit
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	8	0.2	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	8	0.2	No Hit
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	8	0.2	No Hit
GGGATTGTAGTTCAATTGGTCAGAAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CATATCGGGTAGGTTGTGGTATTTCATTGCTAGATCGGAAGAGCACACGT	8	0.2	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	8	0.2	No Hit
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT	7	0.17500000000000002	TruSeq Adapter, Index 1 (100% over 35bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCAAAAGAGGAAAGGCTTGCGGTGGATAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
AACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
ATATCGGGTAGGTTGTGGTATTTCATTGCAGATCGGAAGAGCACACGTCT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TCTCATGGAGAGTTCGATCCTGGCAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GACACGACTCTCGGCAACGGATATCTCGGCTCTCAGATCGGAAGAGCACA	6	0.15	No Hit
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	6	0.15	No Hit
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	6	0.15	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGGGATATGGCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGT	5	0.125	TruSeq Adapter, Index 15 (100% over 37bp)
TCAAAAGAGGAAAGGCTTGCGGTGGATAAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	5	0.125	No Hit
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAGATCGGAAGA	5	0.125	No Hit
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT	5	0.125	TruSeq Adapter, Index 1 (100% over 35bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCA	5	0.125	No Hit
TTCGGACCAGGCTTCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TATTCTGGTGTCCTAGGCGTAGAGGAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGACCCCAGGTCAGTCGGGACTACCCGCTGAGTTTAAGCAGATCGGAAG	5	0.125	No Hit
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCCCCCATCGTCTAGTGGTTCAGGACATCAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CGACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGT	5	0.125	No Hit
GCGTTTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	5	0.125	No Hit
GCGACCCCAGGTCAGTCGGGACTACAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
CGACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAG	5	0.125	No Hit
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGATCGGAAGAG	5	0.125	No Hit
AGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCGACCCCAGGTCAGTCGGGAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAAAAGGACTTTGAAAAGAGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGG	5	0.125	No Hit
>>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	0.025	0.0	0.0	0.0	0.0
2	0.05	0.0	0.0	0.0	0.0
3	0.05	0.0	0.0	0.0	0.0
4	0.05	0.0	0.0	0.0	0.0
5	0.075	0.0	0.0	0.0	0.0
6	0.1	0.0	0.0	0.0	0.0
7	0.125	0.0	0.0	0.0	0.0
8	0.2	0.0	0.0	0.0	0.0
9	0.375	0.0	0.0	0.0	0.0
10	0.5	0.0	0.0	0.0	0.0
11	0.65	0.0	0.0	0.0	0.0
12	1.175	0.0	0.0	0.0	0.0
13	2.05	0.0	0.0	0.0	0.0
14	4.65	0.0	0.0	0.0	0.0
15	5.725	0.0	0.0	0.0	0.0
16	7.575	0.0	0.0	0.0	0.0
17	10.85	0.0	0.0	0.0	0.0
18	12.625	0.0	0.0	0.0	0.0
19	14.35	0.0	0.0	0.0	0.0
20	16.9	0.0	0.0	0.0	0.0
21	20.4	0.0	0.0	0.0	0.0
22	26.175	0.0	0.0	0.0	0.0
23	32.975	0.0	0.0	0.0	0.0
24	36.3	0.0	0.0	0.0	0.0
25	45.0	0.0	0.0	0.0	0.0
26	48.525	0.0	0.0	0.0	0.0
27	51.575	0.0	0.0	0.0	0.0
28	55.1	0.0	0.0	0.0	0.0
29	57.45	0.0	0.0	0.0	0.0
30	60.2	0.0	0.0	0.0	0.0
31	64.175	0.0	0.0	0.0	0.0
32	66.7	0.0	0.0	0.0	0.0
33	70.25	0.0	0.0	0.0	0.0
34	73.675	0.0	0.0	0.0	0.0
35	76.75	0.0	0.0	0.0	0.0
36	79.775	0.0	0.0	0.0	0.0
37	81.85	0.0	0.0	0.0	0.0
38	83.425	0.0	0.0	0.0	0.0
39	84.325	0.0	0.0	0.0	0.0
40	85.625	0.0	0.0	0.0	0.0
41	87.025	0.0	0.0	0.0	0.0
42	89.35	0.0	0.0	0.0	0.0
43	89.95	0.0	0.0	0.0	0.0
44	91.1	0.0	0.0	0.0	0.0
45	91.825	0.0	0.0	0.0	0.0
46	92.2	0.0	0.0	0.0	0.0
47	92.55	0.0	0.0	0.0	0.0
48	92.875	0.0	0.0	0.0	0.0
49	93.375	0.0	0.0	0.0	0.0
50	93.525	0.0	0.0	0.0	0.0
51	93.675	0.0	0.0	0.0	0.0
52	93.8	0.0	0.0	0.0	0.0
53	93.8	0.0	0.0	0.0	0.0
54	93.9	0.0	0.0	0.0	0.0
55	93.9	0.0	0.0	0.0	0.0
56	94.025	0.0	0.0	0.0	0.0
57	94.075	0.0	0.0	0.0	0.0
58	94.1	0.0	0.0	0.0	0.0
59	94.1	0.0	0.0	0.0	0.0
60	94.125	0.0	0.0	0.0	0.0
61	94.125	0.0	0.0	0.0	0.0
62	94.125	0.0	0.0	0.0	0.0
63	94.125	0.0	0.0	0.0	0.0
64	94.125	0.0	0.0	0.0	0.0
65	94.125	0.0	0.0	0.0	0.0
66	94.125	0.0	0.0	0.0	0.0
67	94.125	0.0	0.0	0.0	0.0
68	94.125	0.0	0.0	0.0	0.0
69	94.125	0.0	0.0	0.0	0.0
70	94.125	0.0	0.0	0.0	0.0
71	94.125	0.0	0.0	0.0	0.0
72	94.125	0.0	0.0	0.0	0.0
73	94.125	0.0	0.0	0.0	0.0
74	94.125	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CGACACG	15	0.0012159165	80.00001	1
AGCTCAG	15	0.0012159165	80.00001	9
TAGCTCA	15	0.0012159165	80.00001	8
CCGTTGT	20	3.6123936E-5	80.00001	2
TAGTCTA	20	3.6123936E-5	80.00001	8
TAGTCCA	15	0.0012159165	80.00001	8
TCCGTTG	20	3.6123936E-5	80.00001	1
AGTCCAA	15	0.0012159165	80.00001	9
AGTCTAG	20	3.6123936E-5	80.00001	9
GTAGTCT	20	3.6123936E-5	80.00001	7
GTAGTCC	15	0.0012159165	80.00001	7
GATTGTA	25	1.0653384E-6	80.0	3
TAGTTCA	25	1.0653384E-6	80.0	8
ATTGTAG	25	1.0653384E-6	80.0	4
TGTAGTT	25	1.0653384E-6	80.0	6
TGTAGTC	35	9.076757E-10	80.0	6
GGGATTG	25	1.0653384E-6	80.0	1
AGTTCAA	25	1.0653384E-6	80.0	9
TTGTAGT	55	0.0	72.72727	5
GGATTGT	30	3.1497257E-6	66.66667	2
>>END_MODULE
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
Rejected 248447 READS because READLEN < 1
Read 248447 spots for SRR11699506.sra
Written 248447 spots for SRR11699506.sra
Rejected 248433 READS because READLEN < 1
Read 248433 spots for SRR11699506.sra
Written 248433 spots for SRR11699506.sra
SRR ids: ['SRR11699506.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ab9yt37p
SRR11699506.sra spots: 4968674
blocks: [[1, 248433], [248434, 496866], [496867, 745299], [745300, 993732], [993733, 1242165], [1242166, 1490598], [1490599, 1739031], [1739032, 1987464], [1987465, 2235897], [2235898, 2484330], [2484331, 2732763], [2732764, 2981196], [2981197, 3229629], [3229630, 3478062], [3478063, 3726495], [3726496, 3974928], [3974929, 4223361], [4223362, 4471794], [4471795, 4720227], [4720228, 4968674]]
SRR11699506 file size 1041058
SRR11699506 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 SRR11699506 SRR11699506_1.fastq
Input file:	SRR11699506_1.fastq
trimmed:	SRR11699506-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
Fri Jun 20 12:34:15 2025 >> started

Fri Jun 20 12:34:18 2025 >> done (2.854s)
4968674 reads processed; of these:
 770500 (15.51%) short reads filtered out after trimming by size control
   1168 ( 0.02%) empty reads filtered out after trimming by size control
4197006 (84.47%) reads available; of these:
4171450 (99.39%) trimmed reads available after processing
  25556 ( 0.61%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  91857	  2.19%
 19	 141314	  3.37%
 20	 188625	  4.49%
 21	 301372	  7.18%
 22	 397912	  9.48%
 23	 172828	  4.12%
 24	 443692	 10.57%
 25	 174671	  4.16%
 26	 147423	  3.51%
 27	 174463	  4.16%
 28	 112866	  2.69%
 29	 142185	  3.39%
 30	 231328	  5.51%
 31	 136806	  3.26%
 32	 177023	  4.22%
 33	 143075	  3.41%
 34	 160657	  3.83%
 35	 165390	  3.94%
 36	  84087	  2.00%
 37	  80922	  1.93%
 38	  57375	  1.37%
 39	  58642	  1.40%
 40	  54162	  1.29%
 41	 116972	  2.79%
 42	  38090	  0.91%
 43	  43072	  1.03%
 44	  26919	  0.64%
 45	  24491	  0.58%
 46	  18489	  0.44%
 47	  16667	  0.40%
 48	  21721	  0.52%
 49	   9218	  0.22%
 50	   6249	  0.15%
 51	   4620	  0.11%
 52	   2662	  0.06%
 53	   2254	  0.05%
 54	   1342	  0.03%
 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	      2	  0.00%
 72	      0	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      0	  0.00%
 76	      0	  0.00%
 77	      0	  0.00%
 78	      1	  0.00%
 79	      0	  0.00%
 80	      0	  0.00%
 81	      0	  0.00%
 82	      1	  0.00%
 83	      0	  0.00%
 84	      0	  0.00%
 85	      4	  0.00%
 86	  25556	  0.61%
4197006 reads passed initial QC


criterion=sequence-density
sequence-density=7.13
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGGAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGCCA


criterion=fanout-score
sequence-density=0.16
sequence-density-rank=25
fanout-score=16.44
fanout-score-rank=1
prefix-density=0.51
prefix-fanout=5.1
sequence=ATAGCTCAGTGGTAGAGCAATTGA
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:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -f sanger -l 18 -t 20 -x GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGGAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGCCA -o SRR11699506 -
Input file:	STDIN
trimmed:	SRR11699506-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGGAAGCTGCGGGTTCGAGCCCC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ 
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	20
Fri Jun 20 12:34:26 2025 >> started

Fri Jun 20 12:34:29 2025 >> done (2.726s)
3147755 reads processed; of these:
   9278 ( 0.29%) short reads filtered out after trimming by size control
 227496 ( 7.23%) empty reads filtered out after trimming by size control
2910981 (92.48%) reads available; of these:
  22229 ( 0.76%) trimmed reads available after processing
2888752 (99.24%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  69935	  2.40%
 19	 106733	  3.67%
 20	 138693	  4.76%
 21	 223700	  7.68%
 22	 297283	 10.21%
 23	 128124	  4.40%
 24	 320752	 11.02%
 25	 130137	  4.47%
 26	  95139	  3.27%
 27	 124736	  4.29%
 28	  83937	  2.88%
 29	  90339	  3.10%
 30	 172566	  5.93%
 31	 101446	  3.48%
 32	 117364	  4.03%
 33	  70276	  2.41%
 34	  78233	  2.69%
 35	  74671	  2.57%
 36	  57517	  1.98%
 37	  51874	  1.78%
 38	  38756	  1.33%
 39	  40978	  1.41%
 40	  32320	  1.11%
 41	  87134	  2.99%
 42	  27978	  0.96%
 43	  31434	  1.08%
 44	  19944	  0.69%
 45	  18152	  0.62%
 46	  13711	  0.47%
 47	  12395	  0.43%
 48	  16224	  0.56%
 49	   6740	  0.23%
 50	   4680	  0.16%
 51	   3387	  0.12%
 52	   1909	  0.07%
 53	   1671	  0.06%
 54	    995	  0.03%
 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	      1	  0.00%
 72	      0	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      0	  0.00%
 76	      0	  0.00%
 77	      0	  0.00%
 78	      1	  0.00%
 79	      0	  0.00%
 80	      0	  0.00%
 81	      0	  0.00%
 82	      1	  0.00%
 83	   1013	  0.03%
 84	      0	  0.00%
 85	      3	  0.00%
 86	  18098	  0.62%


criterion=sequence-density
sequence-density=4.77
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=15
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATA


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=41
fanout-score=43.45
fanout-score-rank=1
prefix-density=0.25
prefix-fanout=1.0
sequence=AGCCAAGTGTGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTCCGACTTCC
                                 Started job on |	Jun 20 12:34:55
                             Started mapping on |	Jun 20 12:34:55
                                    Finished on |	Jun 20 12:35:12
       Mapping speed, Million of reads per hour |	838.64

                          Number of input reads |	3960232
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	366649
                        Uniquely mapped reads % |	9.26%
                          Average mapped length |	24.59
                       Number of splices: Total |	8724
            Number of splices: Annotated (sjdb) |	3877
                       Number of splices: GT/AG |	8079
                       Number of splices: GC/AG |	439
                       Number of splices: AT/AC |	8
               Number of splices: Non-canonical |	198
                      Mismatch rate per base, % |	1.02%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.43
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.16
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	553106
             % of reads mapped to multiple loci |	13.97%
        Number of reads mapped to too many loci |	799904
             % of reads mapped to too many loci |	20.20%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.14%
                     % of reads unmapped: other |	51.44%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3040477	3040477	3040477
N_multimapping	553106	553106	553106
N_noFeature	300561	312036	352959
N_ambiguous	2265	31	31
UnstrandedReadsAssigned:63823 PositiveStrandReadsAssigned:54582 NegativeStrandReadsAssigned:13659
Dataset is classified unstranded
MeadianReadLen=26 20thPercentileLength=22 echo kmer=19
SRR11699506 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: SRR11699506-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,960,232 reads, 733,090 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 911 rounds

  72540 SRR11699506.ke.tsv
  44303 SRR11699506.se.tsv
 116843 total
==> SRR11699506.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	4	1.76084
Zm00001eb323640_T001	3273	3174	0	0
Zm00001eb314140_T001	893	794	1	1.83956
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	0	0

==> SRR11699506.se.tsv <==
Zm00001eb015280	1
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699506 completed mapping pipeline successfully
