Starting /dee2/code/volunteer_pipeline.sh SRR11699517
    current disk space = 2464278712320
    free memory = 1581524896 
SRR11699517 SRAfilesize
89036686bf2737f378f6e234bb3e87ef  SRR11699517.sra
SRR11699517.sra file validated
SRR11699517 is single end
SRR11699517 is conventional basespace
SRR11699517 read1 length is 86 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699517_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	31.37475	32.0	32.0	32.0	32.0	32.0
2	31.43425	32.0	32.0	32.0	32.0	32.0
3	31.59275	32.0	32.0	32.0	32.0	32.0
4	31.511	32.0	32.0	32.0	32.0	32.0
5	31.46625	32.0	32.0	32.0	32.0	32.0
6	35.0535	36.0	36.0	36.0	36.0	36.0
7	35.155	36.0	36.0	36.0	36.0	36.0
8	35.00625	36.0	36.0	36.0	36.0	36.0
9	34.9785	36.0	36.0	36.0	36.0	36.0
10-11	35.044	36.0	36.0	36.0	36.0	36.0
12-13	35.028000000000006	36.0	36.0	36.0	36.0	36.0
14-15	35.084875	36.0	36.0	36.0	36.0	36.0
16-17	35.092625	36.0	36.0	36.0	36.0	36.0
18-19	35.07875	36.0	36.0	36.0	36.0	36.0
20-21	34.949875	36.0	36.0	36.0	36.0	36.0
22-23	34.9815	36.0	36.0	36.0	36.0	36.0
24-25	34.946	36.0	36.0	36.0	36.0	36.0
26-27	34.734375	36.0	36.0	36.0	34.0	36.0
28-29	34.87225	36.0	36.0	36.0	34.0	36.0
30-31	34.910125	36.0	36.0	36.0	36.0	36.0
32-33	34.904875000000004	36.0	36.0	36.0	36.0	36.0
34-35	34.939375	36.0	36.0	36.0	34.0	36.0
36-37	34.899874999999994	36.0	36.0	36.0	36.0	36.0
38-39	34.8785	36.0	36.0	36.0	36.0	36.0
40-41	34.88612500000001	36.0	36.0	36.0	34.0	36.0
42-43	34.74925	36.0	36.0	36.0	32.0	36.0
44-45	34.76625	36.0	36.0	36.0	34.0	36.0
46-47	34.75087499999999	36.0	36.0	36.0	32.0	36.0
48-49	34.82925	36.0	36.0	36.0	34.0	36.0
50-51	34.655249999999995	36.0	36.0	36.0	34.0	36.0
52-53	34.590125	36.0	36.0	36.0	32.0	36.0
54-55	34.075375	36.0	36.0	36.0	32.0	36.0
56-57	33.782125	36.0	36.0	36.0	27.0	36.0
58-59	33.644	36.0	36.0	36.0	27.0	36.0
60-61	33.682	36.0	36.0	36.0	27.0	36.0
62-63	33.454750000000004	36.0	36.0	36.0	27.0	36.0
64-65	33.209	36.0	34.0	36.0	24.0	36.0
66-67	33.451125000000005	36.0	34.0	36.0	27.0	36.0
68-69	33.272625000000005	36.0	32.0	36.0	27.0	36.0
70-71	33.8315	36.0	36.0	36.0	32.0	36.0
72-73	33.517375	36.0	36.0	36.0	27.0	36.0
74-75	33.650625000000005	36.0	36.0	36.0	27.0	36.0
76-77	33.86725	36.0	36.0	36.0	32.0	36.0
78-79	33.92100000000001	36.0	36.0	36.0	32.0	36.0
80-81	33.915125	36.0	36.0	36.0	27.0	36.0
82-83	33.832625	36.0	36.0	36.0	27.0	36.0
84-85	33.855625	36.0	36.0	36.0	27.0	36.0
86	32.467	36.0	32.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
22	1.0
23	2.0
24	10.0
25	20.0
26	31.0
27	34.0
28	57.0
29	84.0
30	118.0
31	144.0
32	219.0
33	325.0
34	842.0
35	2113.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	28.857214303575894	24.20605151287822	23.980995248812203	22.95573893473368
2	26.6	23.625	24.575	25.2
3	29.975	33.125	15.75	21.15
4	25.4	36.75	18.375	19.475
5	20.45	23.974999999999998	26.200000000000003	29.375
6	25.906476619154787	23.63090772693173	30.607651912978245	19.854963740935233
7	36.625	31.175000000000004	17.675	14.524999999999999
8	21.075	26.375	34.849999999999994	17.7
9	22.125	36.375	17.599999999999998	23.9
10-11	33.625	24.5125	25.525	16.3375
12-13	19.6375	21.762500000000003	25.387500000000003	33.2125
14-15	29.9	39.875	15.687499999999998	14.5375
16-17	22.1875	21.7	36.9625	19.15
18-19	40.4625	19.7125	24.3125	15.512500000000001
20-21	21.8625	35.775	24.8	17.5625
22-23	32.4125	38.35	14.1375	15.1
24-25	28.875	38.525	17.7375	14.8625
26-27	26.437500000000004	32.625	18.912499999999998	22.025
28-29	32.087500000000006	27.650000000000002	16.162499999999998	24.099999999999998
30-31	33.25	35.112500000000004	10.362499999999999	21.275
32-33	29.849999999999998	38.6625	10.2875	21.2
34-35	30.375000000000004	32.625	13.5	23.5
36-37	27.55	34.150000000000006	10.8375	27.462500000000002
38-39	25.75	34.275	12.1625	27.8125
40-41	26.3	30.2875	16.3125	27.1
42-43	27.275	28.1	19.175	25.45
44-45	22.925	33.137499999999996	15.187500000000002	28.749999999999996
46-47	19.9375	31.275	15.4875	33.300000000000004
48-49	15.412500000000001	27.0	18.625	38.9625
50-51	16.45	26.6125	21.462500000000002	35.475
52-53	17.625	22.9875	25.9875	33.4
54-55	15.562500000000002	26.150000000000002	23.5625	34.725
56-57	12.2875	22.975	26.35	38.3875
58-59	12.950000000000001	20.849999999999998	32.975	33.225
60-61	14.549999999999999	21.8625	37.025000000000006	26.5625
62-63	14.875	26.787499999999998	32.0125	26.325
64-65	12.675	23.7	31.837500000000002	31.7875
66-67	14.8625	15.662499999999998	36.262499999999996	33.2125
68-69	17.0375	17.0875	38.7125	27.1625
70-71	18.7	17.4	39.775	24.125
72-73	19.575	15.8875	34.862500000000004	29.675
74-75	21.352669083635455	12.301537692211527	35.14189273659207	31.203900487560944
76-77	18.975	10.05	39.550000000000004	31.424999999999997
78-79	15.45	11.125	45.35	28.075
80-81	19.629907476869217	13.3408352088022	40.79769942485621	26.231557889472366
82-83	19.51493936742093	16.777097137142142	34.75434429303663	28.9536192024003
84-85	21.215151893986747	20.31503937992249	35.75446930866358	22.715339417427177
86	20.205051262815704	28.257064266066518	32.53313328332083	19.004751187796952
>>END_MODULE
>>Per sequence GC content	fail
#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	0.0
37	0.0
38	1.0
39	3.5
40	10.0
41	31.5
42	70.5
43	93.0
44	162.0
45	252.0
46	402.5
47	607.0
48	639.5
49	547.5
50	498.0
51	462.0
52	330.5
53	191.0
54	122.5
55	78.5
56	44.0
57	29.0
58	23.0
59	10.0
60	5.0
61	4.5
62	1.0
63	0.5
64	1.0
65	0.5
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	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.025
2	0.0
3	0.0
4	0.0
5	0.0
6	0.025
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	0.0125
76-77	0.0
78-79	0.0
80-81	0.025
82-83	0.0125
84-85	0.0125
86	0.025
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
86	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	63.349999999999994
#Duplication Level	Percentage of deduplicated	Percentage of total
1	87.96369376479873	55.725
2	5.05130228887135	6.4
3	2.131018153117601	4.05
4	1.1444356748224151	2.9000000000000004
5	0.6708760852407262	2.125
6	0.6314127861089187	2.4
7	0.3946329913180742	1.7500000000000002
8	0.35516969218626676	1.7999999999999998
9	0.31570639305445936	1.7999999999999998
>10	1.2628255722178374	14.224999999999998
>50	0.03946329913180742	2.125
>100	0.03946329913180742	4.7
>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	188	4.7	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	85	2.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	38	0.95	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	37	0.9249999999999999	No Hit
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	36	0.8999999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	31	0.775	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	29	0.7250000000000001	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	24	0.6	No Hit
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTT	19	0.475	TruSeq Adapter, Index 12 (100% over 36bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	18	0.44999999999999996	No Hit
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTT	17	0.42500000000000004	TruSeq Adapter, Index 12 (100% over 36bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG	14	0.35000000000000003	No Hit
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	13	0.325	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	13	0.325	No Hit
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	12	0.3	No Hit
GCGTTTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	12	0.3	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCAGATCGGAAGAGCACACGTCTGAA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	10	0.25	No Hit
GGGATTGTAGTTCAATTGGTCAGAAGATCGGAAGAGCACACGTCTGAACT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCT	10	0.25	TruSeq Adapter, Index 1 (97% over 35bp)
CGACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGT	10	0.25	No Hit
CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGAGC	10	0.25	No Hit
GGTAGTTCGACCGTGGATAGATCGGAAGAGCACACGTCTGAACTCCAGTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
TCTCATGGAGAGTTCGATCCTGGCAGATCGGAAGAGCACACGTCTGAACT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
ACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	9	0.22499999999999998	No Hit
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	9	0.22499999999999998	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCAGATCGGAAGAGCACACGTC	8	0.2	No Hit
CTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	8	0.2	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCAAGATCGGAAGAGCACACGTCTGA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	8	0.2	No Hit
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	8	0.2	No Hit
GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGA	8	0.2	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCAGATCGGAAGAGCACACGTCT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCAAAAGAGGAAAGGCTTGCGGTGGATAAGATCGGAAGAGCACACGTCTG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GCGACCCCAGGTCAGTCGGGAAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	7	0.17500000000000002	No Hit
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTG	7	0.17500000000000002	TruSeq Adapter, Index 12 (100% over 37bp)
GGGTGTTTGGTCTAGTGGTATGATTCTCAGATCGGAAGAGCACACGTCTG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCACCAGTGGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCACCAGTGGTCTAGTGGTAGAATAGTACCCAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCT	6	0.15	TruSeq Adapter, Index 1 (97% over 35bp)
GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAGATCGGAAGAGC	6	0.15	No Hit
CAGCTGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACA	6	0.15	No Hit
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGAGATCGGAAG	6	0.15	No Hit
AGGGATATAACTCAGCGGTAGAGTAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGACCCCAGGTCAGTCGGGAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	6	0.15	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	6	0.15	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	6	0.15	No Hit
GGTAGTTCGACCGTGGATTAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAAAGATCGGAAGAGCA	5	0.125	No Hit
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CACGACTCTCGGCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ATATCGGGTAGGTTGTGGTATTTCATTGCAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GGGCATTTGGTCTAGTGGTATGATTCTCGCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	5	0.125	No Hit
ACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGAG	5	0.125	No Hit
CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ATATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCAC	5	0.125	No Hit
TGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAGATCGGAAGAGCACA	5	0.125	No Hit
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTAGATCGGAAGAGC	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	0.0	0.0	0.0	0.0	0.0
2	0.0	0.0	0.0	0.0	0.0
3	0.0	0.0	0.0	0.0	0.0
4	0.0	0.0	0.0	0.0	0.0
5	0.05	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	0.15	0.0	0.0	0.0	0.0
9	0.3	0.0	0.0	0.0	0.0
10	0.425	0.0	0.0	0.0	0.0
11	0.65	0.0	0.0	0.0	0.0
12	0.925	0.0	0.0	0.0	0.0
13	1.45	0.0	0.0	0.0	0.0
14	2.95	0.0	0.0	0.0	0.0
15	4.425	0.0	0.0	0.0	0.0
16	5.6	0.0	0.0	0.0	0.0
17	7.95	0.0	0.0	0.0	0.0
18	10.275	0.0	0.0	0.0	0.0
19	12.25	0.0	0.0	0.0	0.0
20	15.275	0.0	0.0	0.0	0.0
21	19.075	0.0	0.0	0.0	0.0
22	25.5	0.0	0.0	0.0	0.0
23	34.825	0.0	0.0	0.0	0.0
24	38.125	0.0	0.0	0.0	0.0
25	45.75	0.0	0.0	0.0	0.0
26	49.375	0.0	0.0	0.0	0.0
27	52.45	0.0	0.0	0.0	0.0
28	56.275	0.0	0.0	0.0	0.0
29	58.9	0.0	0.0	0.0	0.0
30	61.875	0.0	0.0	0.0	0.0
31	66.275	0.0	0.0	0.0	0.0
32	69.45	0.0	0.0	0.0	0.0
33	73.5	0.0	0.0	0.0	0.0
34	76.45	0.0	0.0	0.0	0.0
35	79.65	0.0	0.0	0.0	0.0
36	83.6	0.0	0.0	0.0	0.0
37	85.775	0.0	0.0	0.0	0.0
38	87.25	0.0	0.0	0.0	0.0
39	88.375	0.0	0.0	0.0	0.0
40	89.85	0.0	0.0	0.0	0.0
41	90.6	0.0	0.0	0.0	0.0
42	91.425	0.0	0.0	0.0	0.0
43	91.9	0.0	0.0	0.0	0.0
44	92.225	0.0	0.0	0.0	0.0
45	92.45	0.0	0.0	0.0	0.0
46	92.725	0.0	0.0	0.0	0.0
47	92.8	0.0	0.0	0.0	0.0
48	92.925	0.0	0.0	0.0	0.0
49	93.1	0.0	0.0	0.0	0.0
50	93.2	0.0	0.0	0.0	0.0
51	93.2	0.0	0.0	0.0	0.0
52	93.225	0.0	0.0	0.0	0.0
53	93.275	0.0	0.0	0.0	0.0
54	93.3	0.0	0.0	0.0	0.0
55	93.325	0.0	0.0	0.0	0.0
56	93.325	0.0	0.0	0.0	0.0
57	93.325	0.0	0.0	0.0	0.0
58	93.35	0.0	0.0	0.0	0.0
59	93.375	0.0	0.0	0.0	0.0
60	93.4	0.0	0.0	0.0	0.0
61	93.4	0.0	0.0	0.0	0.0
62	93.4	0.0	0.0	0.0	0.0
63	93.4	0.0	0.0	0.0	0.0
64	93.4	0.0	0.0	0.0	0.0
65	93.4	0.0	0.0	0.0	0.0
66	93.4	0.0	0.0	0.0	0.0
67	93.4	0.0	0.0	0.0	0.0
68	93.4	0.0	0.0	0.0	0.0
69	93.4	0.0	0.0	0.0	0.0
70	93.4	0.0	0.0	0.0	0.0
71	93.4	0.0	0.0	0.0	0.0
72	93.4	0.0	0.0	0.0	0.0
73	93.4	0.0	0.0	0.0	0.0
74	93.4	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GGCATTT	15	0.0012159165	80.00001	2
GGGCATT	15	0.0012159165	80.00001	1
GGATTGT	30	3.1202944E-8	80.00001	2
CATTTGG	15	0.0012159165	80.00001	4
GATTGTA	30	3.1202944E-8	80.00001	3
TAGTTCA	40	2.5465852E-11	80.00001	8
ATTGTAG	30	3.1202944E-8	80.00001	4
GGGATTG	30	3.1202944E-8	80.00001	1
ATTTGGT	15	0.0012159165	80.00001	5
TTTGGTC	20	3.6123936E-5	80.00001	6
TTGGTCT	20	3.6123936E-5	80.00001	7
GCATTTG	15	0.0012159165	80.00001	3
GTAGTTC	40	2.5465852E-11	80.00001	7
TGGTCTA	25	1.0653384E-6	80.0	8
TTGTAGT	55	0.0	80.0	5
GGTCTAG	25	1.0653384E-6	80.0	9
CCGTTGT	25	1.0653384E-6	80.0	2
TAGTCTA	25	1.0653384E-6	80.0	8
TGTAGTC	25	1.0653384E-6	80.0	6
TCCGTTG	25	1.0653384E-6	80.0	1
>>END_MODULE
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291986 READS because READLEN < 1
Read 291986 spots for SRR11699517.sra
Written 291986 spots for SRR11699517.sra
Rejected 291999 READS because READLEN < 1
Read 291999 spots for SRR11699517.sra
Written 291999 spots for SRR11699517.sra
SRR ids: ['SRR11699517.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_p52455vt
SRR11699517.sra spots: 5839733
blocks: [[1, 291986], [291987, 583972], [583973, 875958], [875959, 1167944], [1167945, 1459930], [1459931, 1751916], [1751917, 2043902], [2043903, 2335888], [2335889, 2627874], [2627875, 2919860], [2919861, 3211846], [3211847, 3503832], [3503833, 3795818], [3795819, 4087804], [4087805, 4379790], [4379791, 4671776], [4671777, 4963762], [4963763, 5255748], [5255749, 5547734], [5547735, 5839733]]
SRR11699517 file size 1223946
SRR11699517 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 SRR11699517 SRR11699517_1.fastq
Input file:	SRR11699517_1.fastq
trimmed:	SRR11699517-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 15:47:10 2025 >> started

Fri Jun 20 15:47:14 2025 >> done (3.806s)
5839733 reads processed; of these:
 684656 (11.72%) short reads filtered out after trimming by size control
   1187 ( 0.02%) empty reads filtered out after trimming by size control
5153890 (88.26%) reads available; of these:
5123020 (99.40%) trimmed reads available after processing
  30870 ( 0.60%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 127130	  2.47%
 19	 174362	  3.38%
 20	 239074	  4.64%
 21	 393343	  7.63%
 22	 534234	 10.37%
 23	 210566	  4.09%
 24	 501560	  9.73%
 25	 241220	  4.68%
 26	 207707	  4.03%
 27	 238847	  4.63%
 28	 169344	  3.29%
 29	 200362	  3.89%
 30	 267694	  5.19%
 31	 208058	  4.04%
 32	 249775	  4.85%
 33	 181098	  3.51%
 34	 212676	  4.13%
 35	 199468	  3.87%
 36	 129846	  2.52%
 37	  96672	  1.88%
 38	  61740	  1.20%
 39	  55251	  1.07%
 40	  47388	  0.92%
 41	  56629	  1.10%
 42	  27005	  0.52%
 43	  23175	  0.45%
 44	  16515	  0.32%
 45	  14987	  0.29%
 46	   9892	  0.19%
 47	   7848	  0.15%
 48	   8929	  0.17%
 49	   3918	  0.08%
 50	   2451	  0.05%
 51	   1738	  0.03%
 52	   1051	  0.02%
 53	    884	  0.02%
 54	    573	  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	      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	      0	  0.00%
 83	      3	  0.00%
 84	      0	  0.00%
 85	      4	  0.00%
 86	  30870	  0.60%
5153890 reads passed initial QC


criterion=sequence-density
sequence-density=5.44
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGG


criterion=fanout-score
sequence-density=0.22
sequence-density-rank=21
fanout-score=24.31
fanout-score-rank=1
prefix-density=0.90
prefix-fanout=6.1
sequence=TAGCTCAGTGGTAGAGC
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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGG -o SRR11699517 -
Input file:	STDIN
trimmed:	SRR11699517-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGG
-- 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 15:47:21 2025 >> started

Fri Jun 20 15:47:23 2025 >> done (2.275s)
3435927 reads processed; of these:
  11668 ( 0.34%) short reads filtered out after trimming by size control
 188189 ( 5.48%) empty reads filtered out after trimming by size control
3236070 (94.18%) reads available; of these:
  21832 ( 0.67%) trimmed reads available after processing
3214238 (99.33%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  85466	  2.64%
 19	 117283	  3.62%
 20	 155744	  4.81%
 21	 259349	  8.01%
 22	 355240	 10.98%
 23	 139062	  4.30%
 24	 320971	  9.92%
 25	 159590	  4.93%
 26	 122961	  3.80%
 27	 153240	  4.74%
 28	 112123	  3.46%
 29	 116923	  3.61%
 30	 177433	  5.48%
 31	 137601	  4.25%
 32	 153626	  4.75%
 33	  90808	  2.81%
 34	 103798	  3.21%
 35	 105476	  3.26%
 36	  78379	  2.42%
 37	  56802	  1.76%
 38	  38165	  1.18%
 39	  34758	  1.07%
 40	  25864	  0.80%
 41	  37156	  1.15%
 42	  17562	  0.54%
 43	  15015	  0.46%
 44	  10782	  0.33%
 45	   9823	  0.30%
 46	   6499	  0.20%
 47	   5177	  0.16%
 48	   5881	  0.18%
 49	   2595	  0.08%
 50	   1635	  0.05%
 51	   1109	  0.03%
 52	    674	  0.02%
 53	    567	  0.02%
 54	    369	  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	      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	      1	  0.00%
 81	      1	  0.00%
 82	     14	  0.00%
 83	   1288	  0.04%
 84	      0	  0.00%
 85	      4	  0.00%
 86	  19254	  0.59%


criterion=sequence-density
sequence-density=4.25
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=17
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAAGACCCGGGT


criterion=fanout-score
sequence-density=0.18
sequence-density-rank=25
fanout-score=24.37
fanout-score-rank=1
prefix-density=4.35
prefix-fanout=1.0
sequence=TTGTAGTCTAGGTGGTTAGGATACTCG
                                 Started job on |	Jun 20 15:48:24
                             Started mapping on |	Jun 20 15:48:24
                                    Finished on |	Jun 20 15:48:44
       Mapping speed, Million of reads per hour |	891.73

                          Number of input reads |	4954033
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	464384
                        Uniquely mapped reads % |	9.37%
                          Average mapped length |	24.74
                       Number of splices: Total |	11278
            Number of splices: Annotated (sjdb) |	5250
                       Number of splices: GT/AG |	10101
                       Number of splices: GC/AG |	943
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	232
                      Mismatch rate per base, % |	1.04%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.42
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.23
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	671740
             % of reads mapped to multiple loci |	13.56%
        Number of reads mapped to too many loci |	1150536
             % of reads mapped to too many loci |	23.22%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.30%
                     % of reads unmapped: other |	48.55%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3817909	3817909	3817909
N_multimapping	671740	671740	671740
N_noFeature	371730	389173	444093
N_ambiguous	2910	39	36
UnstrandedReadsAssigned:89744 PositiveStrandReadsAssigned:75172 NegativeStrandReadsAssigned:20255
Dataset is classified unstranded
MeadianReadLen=26 20thPercentileLength=22 echo kmer=19
SRR11699517 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: SRR11699517-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,954,033 reads, 1,011,981 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 889 rounds

  72540 SRR11699517.ke.tsv
  44303 SRR11699517.se.tsv
 116843 total
==> SRR11699517.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	6	1.94721
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

==> SRR11699517.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	2
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699517 completed mapping pipeline successfully
