Starting /dee2/code/volunteer_pipeline.sh SRR11699542
    current disk space = 2462162808832
    free memory = 1581728816 
SRR11699542 SRAfilesize
1bc40aff398e8ec3dc78cf635a27acc2  SRR11699542.sra
SRR11699542.sra file validated
SRR11699542 is single end
SRR11699542 is conventional basespace
SRR11699542 read1 length is 86 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699542_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	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.53625	32.0	32.0	32.0	32.0	32.0
2	31.69725	32.0	32.0	32.0	32.0	32.0
3	31.64725	32.0	32.0	32.0	32.0	32.0
4	31.67225	32.0	32.0	32.0	32.0	32.0
5	31.689	32.0	32.0	32.0	32.0	32.0
6	35.246	36.0	36.0	36.0	36.0	36.0
7	35.312	36.0	36.0	36.0	36.0	36.0
8	35.275	36.0	36.0	36.0	36.0	36.0
9	35.18075	36.0	36.0	36.0	36.0	36.0
10-11	35.322500000000005	36.0	36.0	36.0	36.0	36.0
12-13	35.340875	36.0	36.0	36.0	36.0	36.0
14-15	35.282875000000004	36.0	36.0	36.0	36.0	36.0
16-17	35.334999999999994	36.0	36.0	36.0	36.0	36.0
18-19	35.38775	36.0	36.0	36.0	36.0	36.0
20-21	35.245000000000005	36.0	36.0	36.0	36.0	36.0
22-23	35.314	36.0	36.0	36.0	36.0	36.0
24-25	35.20625	36.0	36.0	36.0	36.0	36.0
26-27	35.159625000000005	36.0	36.0	36.0	36.0	36.0
28-29	35.121125	36.0	36.0	36.0	36.0	36.0
30-31	35.085750000000004	36.0	36.0	36.0	36.0	36.0
32-33	35.213750000000005	36.0	36.0	36.0	36.0	36.0
34-35	35.280874999999995	36.0	36.0	36.0	36.0	36.0
36-37	35.155125	36.0	36.0	36.0	36.0	36.0
38-39	35.179375	36.0	36.0	36.0	36.0	36.0
40-41	35.116125	36.0	36.0	36.0	36.0	36.0
42-43	35.103	36.0	36.0	36.0	36.0	36.0
44-45	35.000375	36.0	36.0	36.0	36.0	36.0
46-47	35.233000000000004	36.0	36.0	36.0	36.0	36.0
48-49	35.111	36.0	36.0	36.0	36.0	36.0
50-51	35.0185	36.0	36.0	36.0	36.0	36.0
52-53	35.016625000000005	36.0	36.0	36.0	36.0	36.0
54-55	34.691874999999996	36.0	36.0	36.0	34.0	36.0
56-57	33.94725	36.0	36.0	36.0	32.0	36.0
58-59	34.058625	36.0	36.0	36.0	32.0	36.0
60-61	33.945125000000004	36.0	36.0	36.0	29.5	36.0
62-63	33.989375	36.0	36.0	36.0	32.0	36.0
64-65	33.84	36.0	36.0	36.0	29.5	36.0
66-67	33.57425	36.0	36.0	36.0	27.0	36.0
68-69	33.64125	36.0	36.0	36.0	27.0	36.0
70-71	33.786375	36.0	36.0	36.0	27.0	36.0
72-73	33.816125	36.0	36.0	36.0	27.0	36.0
74-75	33.708875000000006	36.0	36.0	36.0	27.0	36.0
76-77	33.841625	36.0	36.0	36.0	27.0	36.0
78-79	33.942125000000004	36.0	36.0	36.0	29.5	36.0
80-81	34.072125	36.0	36.0	36.0	32.0	36.0
82-83	34.236374999999995	36.0	36.0	36.0	32.0	36.0
84-85	34.2585	36.0	36.0	36.0	32.0	36.0
86	33.152	36.0	36.0	36.0	21.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
23	6.0
24	7.0
25	11.0
26	23.0
27	21.0
28	41.0
29	73.0
30	87.0
31	114.0
32	162.0
33	293.0
34	697.0
35	2465.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	37.45	20.4	26.125	16.025
2	28.525	19.25	17.075000000000003	35.15
3	34.725	24.4	14.649999999999999	26.224999999999998
4	36.175000000000004	26.3	20.0	17.525
5	18.725	25.624999999999996	26.924999999999997	28.725
6	18.7	20.175	40.875	20.25
7	46.375	23.799999999999997	15.925	13.900000000000002
8	18.425	17.9	49.5	14.174999999999999
9	20.9	45.525	16.625	16.950000000000003
10-11	37.075	18.4375	27.5875	16.900000000000002
12-13	17.275	16.7	29.212500000000002	36.8125
14-15	30.412499999999998	44.35	13.237499999999999	12.0
16-17	24.5375	20.6625	33.3125	21.4875
18-19	44.45	17.150000000000002	23.150000000000002	15.25
20-21	24.725	30.4	26.737499999999997	18.1375
22-23	36.987500000000004	39.3375	12.4375	11.2375
24-25	30.775000000000002	39.5625	16.3875	13.275
26-27	24.712500000000002	36.5875	18.4875	20.2125
28-29	26.25	27.8125	19.8	26.137500000000003
30-31	32.92911613951744	30.82885360670084	11.026378297287161	25.21565195649456
32-33	29.6375	34.6875	12.775	22.900000000000002
34-35	30.675	31.65	16.75	20.925
36-37	30.587500000000002	34.075	11.625	23.7125
38-39	27.21590198774847	34.404300537567195	11.988998624828104	26.390798849856235
40-41	23.56544568071009	33.45418177272159	13.30166270783848	29.678709838729837
42-43	28.1	30.7125	15.2	25.9875
44-45	22.625	29.2875	17.0625	31.025000000000002
46-47	19.0625	31.337500000000002	15.312500000000002	34.2875
48-49	16.650000000000002	26.3625	19.3875	37.6
50-51	14.20355088772193	23.718429607401852	23.15578894723681	38.92223055763941
52-53	18.2875	20.25	23.7125	37.75
54-55	15.837499999999999	25.412499999999998	23.3625	35.3875
56-57	12.1625	21.6625	26.6	39.574999999999996
58-59	11.326415801975246	18.277284660582573	26.015751968996128	44.380547568446055
60-61	14.8125	18.2375	26.9625	39.9875
62-63	16.412499999999998	17.349999999999998	30.612499999999997	35.625
64-65	13.9375	18.337500000000002	26.4125	41.3125
66-67	16.652081510188772	11.788973621702713	30.52881610201275	41.030128766095764
68-69	14.5875	12.3875	34.5875	38.4375
70-71	18.05	10.612499999999999	37.55	33.7875
72-73	18.099999999999998	12.737499999999999	34.387499999999996	34.775
74-75	20.5	9.8	34.65	35.05
76-77	21.690211276409553	8.31353919239905	37.554694336792096	32.4415551943993
78-79	18.025	14.249999999999998	38.75	28.975
80-81	19.5125	18.75	37.6125	24.125
82-83	18.212500000000002	21.762500000000003	32.125	27.900000000000002
84-85	19.66495811976497	25.028128516064506	30.97887235904488	24.32804100512564
86	17.75	29.275000000000002	33.425	19.55
>>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	0.5
28	0.5
29	0.0
30	0.0
31	0.0
32	0.5
33	0.5
34	0.0
35	0.0
36	0.0
37	0.0
38	0.5
39	1.5
40	1.5
41	4.0
42	9.5
43	12.0
44	23.0
45	65.0
46	136.0
47	225.0
48	370.5
49	508.5
50	550.0
51	602.5
52	620.0
53	537.5
54	392.5
55	219.0
56	119.0
57	95.0
58	78.0
59	46.0
60	19.5
61	7.0
62	3.5
63	1.0
64	1.0
65	1.5
66	1.0
67	0.0
68	0.5
69	0.5
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	0.5
90	0.5
91	0.0
92	0.0
93	0.0
94	0.0
95	1.0
96	1.0
97	0.0
98	0.0
99	0.5
100	1.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
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	0.0125
32-33	0.0
34-35	0.0
36-37	0.0
38-39	0.0125
40-41	0.0125
42-43	0.0
44-45	0.0
46-47	0.0
48-49	0.0
50-51	0.025
52-53	0.0
54-55	0.0
56-57	0.0
58-59	0.0125
60-61	0.0
62-63	0.0
64-65	0.0
66-67	0.0125
68-69	0.0
70-71	0.0
72-73	0.0
74-75	0.0
76-77	0.0125
78-79	0.0
80-81	0.0
82-83	0.0
84-85	0.0125
86	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
86	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	58.475
#Duplication Level	Percentage of deduplicated	Percentage of total
1	86.31893971782813	50.475
2	5.857203933304831	6.8500000000000005
3	2.2659256092347158	3.975
4	1.1115861479264644	2.6
5	1.1543394613082514	3.375
6	0.42753313381787095	1.5
7	0.470286447199658	1.925
8	0.5557930739632322	2.6
9	0.21376656690893547	1.125
>10	1.453612654980761	16.5
>50	0.17101325352714836	9.075
>100	0.0	0.0
>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
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	100	2.5	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	97	2.4250000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC	94	2.35	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCC	72	1.7999999999999998	TruSeq Adapter, Index 6 (97% over 36bp)
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTC	48	1.2	TruSeq Adapter, Index 5 (97% over 35bp)
GGGGACGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTC	44	1.0999999999999999	TruSeq Adapter, Index 5 (97% over 35bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	40	1.0	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	37	0.9249999999999999	No Hit
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	35	0.8750000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCAGATCGGAAGAGCACAC	30	0.75	No Hit
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCC	27	0.675	TruSeq Adapter, Index 6 (97% over 36bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGAGATCGGAAGAGCACACGT	22	0.5499999999999999	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	22	0.5499999999999999	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	20	0.5	No Hit
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCT	16	0.4	TruSeq Adapter, Index 6 (97% over 36bp)
GGGTGTTTGGTCTAGTGGTATGATTCTCAGATCGGAAGAGCACACGTCTG	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	14	0.35000000000000003	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	13	0.325	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAGATCGGAAGAGCACACGTCTGAAC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	13	0.325	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCTAGATCGGAAGAGCACACG	13	0.325	No Hit
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	11	0.27499999999999997	No Hit
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	11	0.27499999999999997	No Hit
GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGAGATCGGAAGAGCA	11	0.27499999999999997	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GCACCAGTGGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GCACCAGTGGTCTAGTGGTAGAATAGATCGGAAGAGCACACGTCTGAACT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA	9	0.22499999999999998	No Hit
ACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTCT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGCATTTGGTCTAGTGGTATGATTCTCGCAGATCGGAAGAGCACACGTC	8	0.2	No Hit
TCTCATGGAGAGTTCGATCCTGGCAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGAGATCGGAAGAGCAC	8	0.2	No Hit
GCGTTTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	8	0.2	No Hit
GCGTTTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	8	0.2	No Hit
TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTGAGATCGGAAGAGCACAC	8	0.2	No Hit
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	8	0.2	No Hit
GCCCCCATCGTCTAGTGGTTCAGGACATCTCAGATCGGAAGAGCACACGT	8	0.2	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	8	0.2	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	8	0.2	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
TCCGTTGTAGTCTAGCTGGTGAGGATACTCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
GCACCAGTAGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CCGACCTTAGCTCAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCACCAGTGGTCTAGTGGTAGAATAGTACCCAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
GCCCCCATCGTCTAGTGGTTCAGGACAAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGGGATGTAGTTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTC	6	0.15	TruSeq Adapter, Index 5 (97% over 35bp)
GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CGACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGGGATATAGCTCAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGAGATCGGAAGAGCACACGTC	6	0.15	No Hit
GCACCAGTAGTCTAGTGGTAGAATAGTACCCAGATCGGAAGAGCACACGT	6	0.15	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATACTCGAGATCGGAAGAGCACACGT	6	0.15	No Hit
GGGGATATGGCGAAATCGGTAGACGCTAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AGGGCTATAGCTCAGTTCGGTAGAGCAAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCACCAGTGGTCTAGTGGTAGAATAGTACCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CGACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCGACCCCAGGTCAGTCGGGACTACCAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	5	0.125	No Hit
GGTCCTGTAGTTCAGTTGGTCAGAACAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TAGTGGTGAGAATTCCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
AGGGATATAACTCAGCGGTAGAGTAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TCTCATGGAGAGTTCGATCCTGGCTCAGGAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GGGCATTTGGTCTAGTGGTATGATTCTCGAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCACCAGTGGTCTAGTGGTAGAATAGTACCTAGATCGGAAGAGCACACGT	5	0.125	No Hit
GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GTCGTTGTAGTATAGTGGTGAGTATTCCCGCCAGATCGGAAGAGCACACG	5	0.125	No Hit
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTAGATCGGAAGAGC	5	0.125	No Hit
TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCAGATCGGAAGAGCAC	5	0.125	No Hit
CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	5	0.125	No Hit
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGTTGGTCAGGATAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
>>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	0.05	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	0.05	0.0	0.0	0.0	0.0
6	0.05	0.0	0.0	0.0	0.0
7	0.05	0.0	0.0	0.0	0.0
8	0.3	0.0	0.0	0.0	0.0
9	0.425	0.0	0.0	0.0	0.0
10	0.525	0.0	0.0	0.0	0.0
11	0.7	0.0	0.0	0.0	0.0
12	0.975	0.0	0.0	0.0	0.0
13	1.85	0.0	0.0	0.0	0.0
14	5.5	0.0	0.0	0.0	0.0
15	9.475	0.0	0.0	0.0	0.0
16	11.05	0.0	0.0	0.0	0.0
17	14.05	0.0	0.0	0.0	0.0
18	16.3	0.0	0.0	0.0	0.0
19	18.25	0.0	0.0	0.0	0.0
20	21.275	0.0	0.0	0.0	0.0
21	23.725	0.0	0.0	0.0	0.0
22	27.975	0.0	0.0	0.0	0.0
23	33.4	0.0	0.0	0.0	0.0
24	36.125	0.0	0.0	0.0	0.0
25	43.825	0.0	0.0	0.0	0.0
26	47.325	0.0	0.0	0.0	0.0
27	51.3	0.0	0.0	0.0	0.0
28	56.725	0.0	0.0	0.0	0.0
29	59.4	0.0	0.0	0.0	0.0
30	62.325	0.0	0.0	0.0	0.0
31	67.575	0.0	0.0	0.0	0.0
32	72.05	0.0	0.0	0.0	0.0
33	77.4	0.0	0.0	0.0	0.0
34	81.025	0.0	0.0	0.0	0.0
35	83.675	0.0	0.0	0.0	0.0
36	87.575	0.0	0.0	0.0	0.0
37	90.15	0.0	0.0	0.0	0.0
38	91.375	0.0	0.0	0.0	0.0
39	92.225	0.0	0.0	0.0	0.0
40	93.025	0.0	0.0	0.0	0.0
41	93.7	0.0	0.0	0.0	0.0
42	94.475	0.0	0.0	0.0	0.0
43	94.9	0.0	0.0	0.0	0.0
44	95.125	0.0	0.0	0.0	0.0
45	95.4	0.0	0.0	0.0	0.0
46	95.65	0.0	0.0	0.0	0.0
47	95.75	0.0	0.0	0.0	0.0
48	95.8	0.0	0.0	0.0	0.0
49	95.95	0.0	0.0	0.0	0.0
50	96.025	0.0	0.0	0.0	0.0
51	96.05	0.0	0.0	0.0	0.0
52	96.1	0.0	0.0	0.0	0.0
53	96.1	0.0	0.0	0.0	0.0
54	96.1	0.0	0.0	0.0	0.0
55	96.125	0.0	0.0	0.0	0.0
56	96.125	0.0	0.0	0.0	0.0
57	96.15	0.0	0.0	0.0	0.0
58	96.15	0.0	0.0	0.0	0.0
59	96.175	0.0	0.0	0.0	0.0
60	96.175	0.0	0.0	0.0	0.0
61	96.175	0.0	0.0	0.0	0.0
62	96.175	0.0	0.0	0.0	0.0
63	96.175	0.0	0.0	0.0	0.0
64	96.175	0.0	0.0	0.0	0.0
65	96.175	0.0	0.0	0.0	0.0
66	96.175	0.0	0.0	0.0	0.0
67	96.175	0.0	0.0	0.0	0.0
68	96.175	0.0	0.0	0.0	0.0
69	96.175	0.0	0.0	0.0	0.0
70	96.175	0.0	0.0	0.0	0.0
71	96.175	0.0	0.0	0.0	0.0
72	96.175	0.0	0.0	0.0	0.0
73	96.175	0.0	0.0	0.0	0.0
74	96.175	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGGTCTA	15	0.0012159165	80.00001	8
GGATGTA	15	0.0012159165	80.00001	3
AGCTCAG	20	3.6123936E-5	80.00001	9
AGCTCAA	30	3.1202944E-8	80.00001	9
GGTCTAG	15	0.0012159165	80.00001	9
GATGTAG	15	0.0012159165	80.00001	4
GGATTGT	15	0.0012159165	80.00001	2
GTCTGTA	30	3.1202944E-8	80.00001	3
ACGTAGC	20	3.6123936E-5	80.00001	5
CCGTTGT	20	3.6123936E-5	80.00001	2
CGTAGCT	20	3.6123936E-5	80.00001	6
TAGTCCA	30	3.1202944E-8	80.00001	8
TAGTTCA	15	0.0012159165	80.00001	8
ATAGCTC	15	0.0012159165	80.00001	7
TCTGTAG	30	3.1202944E-8	80.00001	4
GACGTAG	20	3.6123936E-5	80.00001	4
GCGTCTG	30	3.1202944E-8	80.00001	1
GGGATTG	15	0.0012159165	80.00001	1
GGGACGT	20	3.6123936E-5	80.00001	2
GGGATGT	15	0.0012159165	80.00001	2
>>END_MODULE
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213485 READS because READLEN < 1
Read 213485 spots for SRR11699542.sra
Written 213485 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
Rejected 213470 READS because READLEN < 1
Read 213470 spots for SRR11699542.sra
Written 213470 spots for SRR11699542.sra
SRR ids: ['SRR11699542.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_w4tww7aw
SRR11699542.sra spots: 4269415
blocks: [[1, 213470], [213471, 426940], [426941, 640410], [640411, 853880], [853881, 1067350], [1067351, 1280820], [1280821, 1494290], [1494291, 1707760], [1707761, 1921230], [1921231, 2134700], [2134701, 2348170], [2348171, 2561640], [2561641, 2775110], [2775111, 2988580], [2988581, 3202050], [3202051, 3415520], [3415521, 3628990], [3628991, 3842460], [3842461, 4055930], [4055931, 4269415]]
SRR11699542 file size 894241
SRR11699542 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 SRR11699542 SRR11699542_1.fastq
Input file:	SRR11699542_1.fastq
trimmed:	SRR11699542-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 20:48:15 2025 >> started

Fri Jun 20 20:48:28 2025 >> done (13.547s)
4269415 reads processed; of these:
 711089 (16.66%) short reads filtered out after trimming by size control
   1519 ( 0.04%) empty reads filtered out after trimming by size control
3556807 (83.31%) reads available; of these:
3544796 (99.66%) trimmed reads available after processing
  12011 ( 0.34%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  89347	  2.51%
 19	 118351	  3.33%
 20	 119489	  3.36%
 21	 197941	  5.57%
 22	 289354	  8.14%
 23	 131345	  3.69%
 24	 312716	  8.79%
 25	 176117	  4.95%
 26	 174316	  4.90%
 27	 249081	  7.00%
 28	 101767	  2.86%
 29	 128299	  3.61%
 30	 245614	  6.91%
 31	 202853	  5.70%
 32	 252830	  7.11%
 33	 156706	  4.41%
 34	 106904	  3.01%
 35	 164424	  4.62%
 36	 103332	  2.91%
 37	  50187	  1.41%
 38	  32200	  0.91%
 39	  28078	  0.79%
 40	  22770	  0.64%
 41	  38502	  1.08%
 42	  13383	  0.38%
 43	  10131	  0.28%
 44	   7024	  0.20%
 45	   6116	  0.17%
 46	   3991	  0.11%
 47	   3061	  0.09%
 48	   3806	  0.11%
 49	   1626	  0.05%
 50	    977	  0.03%
 51	    856	  0.02%
 52	    529	  0.01%
 53	    435	  0.01%
 54	    336	  0.01%
 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	      0	  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	      0	  0.00%
 76	      0	  0.00%
 77	      0	  0.00%
 78	      0	  0.00%
 79	      0	  0.00%
 80	      0	  0.00%
 81	      0	  0.00%
 82	      0	  0.00%
 83	      0	  0.00%
 84	      0	  0.00%
 85	      2	  0.00%
 86	  12011	  0.34%
3556807 reads passed initial QC


criterion=sequence-density
sequence-density=11.24
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=16
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAAGACCCGGGTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=41
fanout-score=109.10
fanout-score-rank=1
prefix-density=0.58
prefix-fanout=1.0
sequence=AGCCAAGTGTGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTCCGACTTCC
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 20 20:49:26
                             Started mapping on |	Jun 20 20:49:26
                                    Finished on |	Jun 20 20:49:53
       Mapping speed, Million of reads per hour |	474.24

                          Number of input reads |	3556807
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	292745
                        Uniquely mapped reads % |	8.23%
                          Average mapped length |	24.84
                       Number of splices: Total |	6657
            Number of splices: Annotated (sjdb) |	2909
                       Number of splices: GT/AG |	6116
                       Number of splices: GC/AG |	462
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	76
                      Mismatch rate per base, % |	1.13%
                         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 |	731461
             % of reads mapped to multiple loci |	20.57%
        Number of reads mapped to too many loci |	1125311
             % of reads mapped to too many loci |	31.64%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	4.07%
                     % of reads unmapped: other |	35.50%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2532601	2532601	2532601
N_multimapping	731461	731461	731461
N_noFeature	241246	248759	283395
N_ambiguous	1873	27	14
UnstrandedReadsAssigned:49626 PositiveStrandReadsAssigned:43959 NegativeStrandReadsAssigned:9336
Dataset is classified unstranded
MeadianReadLen=27 20thPercentileLength=22 echo kmer=19
SRR11699542 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: SRR11699542-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,556,807 reads, 955,244 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 815 rounds

  72540 SRR11699542.ke.tsv
  44303 SRR11699542.se.tsv
 116843 total
==> SRR11699542.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	2	0.747382
Zm00001eb323640_T001	3273	3174	0	0
Zm00001eb314140_T001	893	794	0	0
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

==> SRR11699542.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	1
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699542 completed mapping pipeline successfully
