Starting /dee2/code/volunteer_pipeline.sh SRR11699510
    current disk space = 2464477351936
    free memory = 1581305884 
SRR11699510 SRAfilesize
abaa64831c459e5210e4a3e999e7c5c9  SRR11699510.sra
SRR11699510.sra file validated
SRR11699510 is single end
SRR11699510 is conventional basespace
SRR11699510 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699510_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	76
%GC	50
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.28025	32.0	32.0	32.0	32.0	32.0
2	31.42925	32.0	32.0	32.0	32.0	32.0
3	31.527	32.0	32.0	32.0	32.0	32.0
4	31.49325	32.0	32.0	32.0	32.0	32.0
5	31.51925	32.0	32.0	32.0	32.0	32.0
6	35.099	36.0	36.0	36.0	36.0	36.0
7	35.10275	36.0	36.0	36.0	36.0	36.0
8	35.17675	36.0	36.0	36.0	36.0	36.0
9	34.925	36.0	36.0	36.0	36.0	36.0
10-11	35.072	36.0	36.0	36.0	36.0	36.0
12-13	35.161625	36.0	36.0	36.0	36.0	36.0
14-15	35.18025	36.0	36.0	36.0	36.0	36.0
16-17	35.174375	36.0	36.0	36.0	36.0	36.0
18-19	35.182	36.0	36.0	36.0	36.0	36.0
20-21	34.953375	36.0	36.0	36.0	36.0	36.0
22-23	35.04625	36.0	36.0	36.0	36.0	36.0
24-25	35.0605	36.0	36.0	36.0	36.0	36.0
26-27	34.884625	36.0	36.0	36.0	36.0	36.0
28-29	34.99075	36.0	36.0	36.0	36.0	36.0
30-31	34.949875000000006	36.0	36.0	36.0	36.0	36.0
32-33	34.948125000000005	36.0	36.0	36.0	36.0	36.0
34-35	34.99925	36.0	36.0	36.0	36.0	36.0
36-37	35.020125	36.0	36.0	36.0	36.0	36.0
38-39	34.8945	36.0	36.0	36.0	36.0	36.0
40-41	34.855000000000004	36.0	36.0	36.0	36.0	36.0
42-43	34.909125	36.0	36.0	36.0	36.0	36.0
44-45	34.874624999999995	36.0	36.0	36.0	36.0	36.0
46-47	34.915	36.0	36.0	36.0	36.0	36.0
48-49	34.77075	36.0	36.0	36.0	34.0	36.0
50-51	34.537000000000006	36.0	36.0	36.0	32.0	36.0
52-53	34.4125	36.0	36.0	36.0	32.0	36.0
54-55	34.3955	36.0	36.0	36.0	32.0	36.0
56-57	33.781000000000006	36.0	36.0	36.0	29.5	36.0
58-59	33.796125	36.0	36.0	36.0	29.5	36.0
60-61	33.83175	36.0	36.0	36.0	29.5	36.0
62-63	33.670125	36.0	36.0	36.0	27.0	36.0
64-65	33.431375	36.0	36.0	36.0	27.0	36.0
66-67	32.81925	36.0	32.0	36.0	27.0	36.0
68-69	32.81125	36.0	32.0	36.0	27.0	36.0
70-71	33.077375	36.0	34.0	36.0	27.0	36.0
72-73	33.201375	36.0	34.0	36.0	24.0	36.0
74-75	33.64875	36.0	36.0	36.0	29.5	36.0
76	30.143	36.0	27.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	1.0
22	1.0
23	5.0
24	6.0
25	15.0
26	37.0
27	42.0
28	55.0
29	76.0
30	112.0
31	133.0
32	233.0
33	297.0
34	776.0
35	2211.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	24.525	30.65	21.825	23.0
2	23.150000000000002	26.825	26.424999999999997	23.599999999999998
3	26.150000000000002	32.800000000000004	17.775	23.275000000000002
4	26.974999999999998	35.175	17.65	20.200000000000003
5	21.5	27.775	23.425	27.3
6	26.3	26.55	26.85	20.3
7	30.975	33.75	18.075	17.2
8	23.150000000000002	26.55	29.75	20.549999999999997
9	23.9	33.875	19.45	22.775000000000002
10-11	32.4375	27.787499999999998	23.175	16.6
12-13	21.637500000000003	23.599999999999998	24.2375	30.525000000000002
14-15	28.95	37.075	18.512500000000003	15.462500000000002
16-17	23.225	24.3625	33.324999999999996	19.0875
18-19	35.6625	24.4125	22.95	16.975
20-21	24.525	35.6625	23.1125	16.7
22-23	30.95	37.8125	14.249999999999998	16.9875
24-25	29.612500000000004	38.0375	15.412500000000001	16.9375
26-27	29.25	32.4125	17.0625	21.275
28-29	31.7875	29.099999999999998	15.712499999999999	23.400000000000002
30-31	33.7	36.2875	9.6	20.4125
32-33	28.199999999999996	39.3625	10.975	21.462500000000002
34-35	29.325000000000003	30.725	13.5625	26.387500000000003
36-37	26.8375	33.2	10.674999999999999	29.2875
38-39	22.287499999999998	33.125	14.4625	30.125
40-41	24.2875	29.275000000000002	18.0625	28.375
42-43	26.5125	26.2875	20.674999999999997	26.525
44-45	19.9375	31.900000000000002	17.549999999999997	30.612499999999997
46-47	20.9125	31.374999999999996	14.3375	33.375
48-49	16.725	27.8875	16.9625	38.425
50-51	15.85	27.6	18.575	37.974999999999994
52-53	18.637500000000003	26.787499999999998	19.225	35.35
54-55	17.6625	29.299999999999997	18.425	34.612500000000004
56-57	16.3375	25.85	18.6625	39.15
58-59	14.924999999999999	27.075	17.224999999999998	40.775
60-61	11.450000000000001	30.4625	24.15	33.9375
62-63	12.025	31.974999999999998	27.0125	28.9875
64-65	13.65	22.975	30.275000000000002	33.1
66-67	15.625	16.85	31.724999999999998	35.8
68-69	17.1125	19.0	32.3125	31.574999999999996
70-71	19.412499999999998	18.3	33.900000000000006	28.3875
72-73	18.075	17.2375	31.5625	33.125
74-75	21.0125	12.85	32.275	33.862500000000004
76	15.325	11.125	40.9	32.65
>>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	0.5
32	0.5
33	0.0
34	0.0
35	0.0
36	2.5
37	5.0
38	4.0
39	6.0
40	8.0
41	18.0
42	29.0
43	41.5
44	75.0
45	145.0
46	194.0
47	297.5
48	701.5
49	792.5
50	583.0
51	555.0
52	478.5
53	357.0
54	284.0
55	212.0
56	114.5
57	87.5
58	86.0
59	58.0
60	20.5
61	8.5
62	6.0
63	4.5
64	3.5
65	3.0
66	2.0
67	2.0
68	1.0
69	0.5
70	1.0
71	1.0
72	0.5
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	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10-11	0.0
12-13	0.0
14-15	0.0
16-17	0.0
18-19	0.0
20-21	0.0
22-23	0.0
24-25	0.0
26-27	0.0
28-29	0.0
30-31	0.0
32-33	0.0
34-35	0.0
36-37	0.0
38-39	0.0
40-41	0.0
42-43	0.0
44-45	0.0
46-47	0.0
48-49	0.0
50-51	0.0
52-53	0.0
54-55	0.0
56-57	0.0
58-59	0.0
60-61	0.0
62-63	0.0
64-65	0.0
66-67	0.0
68-69	0.0
70-71	0.0
72-73	0.0
74-75	0.0
76	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
76	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	63.7
#Duplication Level	Percentage of deduplicated	Percentage of total
1	89.1287284144427	56.775
2	4.866562009419153	6.2
3	1.9623233908948194	3.75
4	0.6671899529042387	1.7000000000000002
5	0.9811616954474097	3.125
6	0.4317111459968602	1.6500000000000001
7	0.47095761381475665	2.1
8	0.11773940345368916	0.6
9	0.11773940345368916	0.675
>10	1.1381475667189953	14.85
>50	0.07849293563579278	3.125
>100	0.03924646781789639	5.45
>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	218	5.45	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	63	1.575	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	62	1.55	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	45	1.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	37	0.9249999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	33	0.8250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	32	0.8	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	28	0.7000000000000001	No Hit
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGC	27	0.675	TruSeq Adapter, Index 5 (97% over 35bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCC	26	0.65	TruSeq Adapter, Index 6 (100% over 36bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCA	26	0.65	TruSeq Adapter, Index 6 (100% over 37bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	25	0.625	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCC	24	0.6	TruSeq Adapter, Index 6 (100% over 36bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATAT	20	0.5	TruSeq Adapter, Index 6 (100% over 41bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	18	0.44999999999999996	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	17	0.42500000000000004	No Hit
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	14	0.35000000000000003	No Hit
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATA	13	0.325	TruSeq Adapter, Index 6 (100% over 40bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGC	10	0.25	TruSeq Adapter, Index 5 (97% over 35bp)
AAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAG	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	10	0.25	No Hit
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	9	0.22499999999999998	No Hit
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	8	0.2	No Hit
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGC	7	0.17500000000000002	TruSeq Adapter, Index 5 (97% over 35bp)
CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
AAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
ACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCACCAGTGGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	6	0.15	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATACTGTAGGGGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATC	6	0.15	No Hit
TAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCA	6	0.15	No Hit
ATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	6	0.15	No Hit
AGTTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGAGC	6	0.15	No Hit
GGTAGTTCGACCGTGGATTAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCA	5	0.125	TruSeq Adapter, Index 6 (97% over 37bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG	5	0.125	No Hit
ACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA	5	0.125	No Hit
GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	5	0.125	No Hit
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAAT	5	0.125	TruSeq Adapter, Index 6 (100% over 39bp)
GGGGACGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGC	5	0.125	TruSeq Adapter, Index 5 (97% over 35bp)
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCAGATCGGAAGAGCACAC	5	0.125	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CGACACGACTCTCGGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
ACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCAGATCGGAAGA	5	0.125	No Hit
AACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGACCCCAGGTCAGTCGGGACTACCCGCTAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACAGATCGGAAGAGCACACGT	5	0.125	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	5	0.125	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	5	0.125	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	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	0.075	0.0	0.0	0.0	0.0
3	0.1	0.0	0.0	0.0	0.0
4	0.1	0.0	0.0	0.0	0.0
5	0.125	0.0	0.0	0.0	0.0
6	0.2	0.0	0.0	0.0	0.0
7	0.275	0.0	0.0	0.0	0.0
8	0.5	0.0	0.0	0.0	0.0
9	1.175	0.0	0.0	0.0	0.0
10	1.65	0.0	0.0	0.0	0.0
11	2.15	0.0	0.0	0.0	0.0
12	2.65	0.0	0.0	0.0	0.0
13	4.0	0.0	0.0	0.0	0.0
14	6.525	0.0	0.0	0.0	0.0
15	8.7	0.0	0.0	0.0	0.0
16	10.125	0.0	0.0	0.0	0.0
17	13.175	0.0	0.0	0.0	0.0
18	16.5	0.0	0.0	0.0	0.0
19	19.075	0.0	0.0	0.0	0.0
20	23.525	0.0	0.0	0.0	0.0
21	27.3	0.0	0.0	0.0	0.0
22	33.2	0.0	0.0	0.0	0.0
23	43.075	0.0	0.0	0.0	0.0
24	46.25	0.0	0.0	0.0	0.0
25	54.825	0.0	0.0	0.0	0.0
26	58.975	0.0	0.0	0.0	0.0
27	61.3	0.0	0.0	0.0	0.0
28	63.925	0.0	0.0	0.0	0.0
29	65.625	0.0	0.0	0.0	0.0
30	68.3	0.0	0.0	0.0	0.0
31	72.3	0.0	0.0	0.0	0.0
32	74.425	0.0	0.0	0.0	0.0
33	76.5	0.0	0.0	0.0	0.0
34	78.6	0.0	0.0	0.0	0.0
35	81.15	0.0	0.0	0.0	0.0
36	83.925	0.0	0.0	0.0	0.0
37	85.85	0.0	0.0	0.0	0.0
38	87.3	0.0	0.0	0.0	0.0
39	88.25	0.0	0.0	0.0	0.0
40	89.225	0.0	0.0	0.0	0.0
41	90.125	0.0	0.0	0.0	0.0
42	91.45	0.0	0.0	0.0	0.0
43	92.025	0.0	0.0	0.0	0.0
44	92.6	0.0	0.0	0.0	0.0
45	93.25	0.0	0.0	0.0	0.0
46	93.65	0.0	0.0	0.0	0.0
47	94.05	0.0	0.0	0.0	0.0
48	94.35	0.0	0.0	0.0	0.0
49	94.825	0.0	0.0	0.0	0.0
50	94.9	0.0	0.0	0.0	0.0
51	94.975	0.0	0.0	0.0	0.0
52	94.975	0.0	0.0	0.0	0.0
53	95.075	0.0	0.0	0.0	0.0
54	95.125	0.0	0.0	0.0	0.0
55	95.125	0.0	0.0	0.0	0.0
56	95.125	0.0	0.0	0.0	0.0
57	95.15	0.0	0.0	0.0	0.0
58	95.15	0.0	0.0	0.0	0.0
59	95.15	0.0	0.0	0.0	0.0
60	95.15	0.0	0.0	0.0	0.0
61	95.15	0.0	0.0	0.0	0.0
62	95.15	0.0	0.0	0.0	0.0
63	95.15	0.0	0.0	0.0	0.0
64	95.15	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	0.0020658788	70.00001	8
GGATGTA	15	0.0020658788	70.00001	3
TGGTCAG	15	0.0020658788	70.00001	17
GGTCTAG	15	0.0020658788	70.00001	9
AGTGGTA	15	0.0020658788	70.00001	14
GATGTAG	15	0.0020658788	70.00001	4
GAGCACC	15	0.0020658788	70.00001	23
TGTAGTC	15	0.0020658788	70.00001	6
TGTAGCT	15	0.0020658788	70.00001	6
GGGATGT	15	0.0020658788	70.00001	2
GTCTAGC	15	0.0020658788	70.00001	10
ATGTAGC	15	0.0020658788	70.00001	5
CGGTTAG	15	0.0020658788	70.00001	16
GGGGATG	15	0.0020658788	70.00001	1
TTGTAGT	25	2.3570374E-6	70.0	5
TAGCTCA	20	7.003785E-5	70.0	8
TAGTTCA	20	7.003785E-5	70.0	8
GTAGCTC	20	7.003785E-5	70.0	7
GTAGTTC	25	2.1136815E-4	55.999996	7
GGTTAGG	20	0.0064587677	52.5	17
>>END_MODULE
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385109 READS because READLEN < 1
Read 385109 spots for SRR11699510.sra
Written 385109 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
Rejected 385093 READS because READLEN < 1
Read 385093 spots for SRR11699510.sra
Written 385093 spots for SRR11699510.sra
SRR ids: ['SRR11699510.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_32kdk5i5
SRR11699510.sra spots: 7701876
blocks: [[1, 385093], [385094, 770186], [770187, 1155279], [1155280, 1540372], [1540373, 1925465], [1925466, 2310558], [2310559, 2695651], [2695652, 3080744], [3080745, 3465837], [3465838, 3850930], [3850931, 4236023], [4236024, 4621116], [4621117, 5006209], [5006210, 5391302], [5391303, 5776395], [5776396, 6161488], [6161489, 6546581], [6546582, 6931674], [6931675, 7316767], [7316768, 7701876]]
SRR11699510 file size 1464496
SRR11699510 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 SRR11699510 SRR11699510_1.fastq
Input file:	SRR11699510_1.fastq
trimmed:	SRR11699510-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 13:28:01 2025 >> started

Fri Jun 20 13:28:04 2025 >> done (3.053s)
7701876 reads processed; of these:
1448102 (18.80%) short reads filtered out after trimming by size control
   2304 ( 0.03%) empty reads filtered out after trimming by size control
6251470 (81.17%) reads available; of these:
6061925 (96.97%) trimmed reads available after processing
 189545 ( 3.03%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 176755	  2.83%
 19	 276101	  4.42%
 20	 321661	  5.15%
 21	 445690	  7.13%
 22	 824703	 13.19%
 23	 260811	  4.17%
 24	 677793	 10.84%
 25	 295668	  4.73%
 26	 199695	  3.19%
 27	 196731	  3.15%
 28	 162808	  2.60%
 29	 182650	  2.92%
 30	 329452	  5.27%
 31	 184768	  2.96%
 32	 184381	  2.95%
 33	 191490	  3.06%
 34	 176236	  2.82%
 35	 226331	  3.62%
 36	 157723	  2.52%
 37	 121627	  1.95%
 38	  86942	  1.39%
 39	  86465	  1.38%
 40	  68713	  1.10%
 41	  90069	  1.44%
 42	  56054	  0.90%
 43	  45716	  0.73%
 44	  34886	  0.56%
 45	      0	  0.00%
 46	      0	  0.00%
 47	      0	  0.00%
 48	      0	  0.00%
 49	      0	  0.00%
 50	      0	  0.00%
 51	      0	  0.00%
 52	      0	  0.00%
 53	      0	  0.00%
 54	      0	  0.00%
 55	      0	  0.00%
 56	      0	  0.00%
 57	      0	  0.00%
 58	      0	  0.00%
 59	      0	  0.00%
 60	      0	  0.00%
 61	      0	  0.00%
 62	      0	  0.00%
 63	      0	  0.00%
 64	      0	  0.00%
 65	      0	  0.00%
 66	      0	  0.00%
 67	      0	  0.00%
 68	      0	  0.00%
 69	      0	  0.00%
 70	      0	  0.00%
 71	      0	  0.00%
 72	      1	  0.00%
 73	      0	  0.00%
 74	      1	  0.00%
 75	      4	  0.00%
 76	 189545	  3.03%
6251470 reads passed initial QC


criterion=sequence-density
sequence-density=3.33
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=2.48
sequence-density-rank=3
fanout-score=14.11
fanout-score-rank=1
prefix-density=2.54
prefix-fanout=13.8
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTGA
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 13:28:39
                             Started mapping on |	Jun 20 13:28:39
                                    Finished on |	Jun 20 13:29:04
       Mapping speed, Million of reads per hour |	900.21

                          Number of input reads |	6251470
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	594077
                        Uniquely mapped reads % |	9.50%
                          Average mapped length |	24.31
                       Number of splices: Total |	12435
            Number of splices: Annotated (sjdb) |	5037
                       Number of splices: GT/AG |	11431
                       Number of splices: GC/AG |	630
                       Number of splices: AT/AC |	8
               Number of splices: Non-canonical |	366
                      Mismatch rate per base, % |	1.29%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.50
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.15
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	733689
             % of reads mapped to multiple loci |	11.74%
        Number of reads mapped to too many loci |	1255934
             % of reads mapped to too many loci |	20.09%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.48%
                     % of reads unmapped: other |	51.19%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	4923704	4923704	4923704
N_multimapping	733689	733689	733689
N_noFeature	507654	523100	576204
N_ambiguous	2490	40	35
UnstrandedReadsAssigned:83933 PositiveStrandReadsAssigned:70937 NegativeStrandReadsAssigned:17838
Dataset is classified unstranded
MeadianReadLen=25 20thPercentileLength=22 echo kmer=19
SRR11699510 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: SRR11699510-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 6,251,470 reads, 1,165,440 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 923 rounds

  72540 SRR11699510.ke.tsv
  44303 SRR11699510.se.tsv
 116843 total
==> SRR11699510.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	4	1.10914
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

==> SRR11699510.se.tsv <==
Zm00001eb015280	1
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	1
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699510 completed mapping pipeline successfully
