Starting /dee2/code/volunteer_pipeline.sh SRR11699532
    current disk space = 2462343610368
    free memory = 1579450016 
SRR11699532 SRAfilesize
811f5c1d9aef269650a0254400cc866c  SRR11699532.sra
SRR11699532.sra file validated
SRR11699532 is single end
SRR11699532 is conventional basespace
SRR11699532 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699532_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	49
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.3455	32.0	32.0	32.0	32.0	32.0
2	31.47625	32.0	32.0	32.0	32.0	32.0
3	31.46225	32.0	32.0	32.0	32.0	32.0
4	31.517	32.0	32.0	32.0	32.0	32.0
5	31.62175	32.0	32.0	32.0	32.0	32.0
6	35.08925	36.0	36.0	36.0	36.0	36.0
7	35.0805	36.0	36.0	36.0	36.0	36.0
8	35.15025	36.0	36.0	36.0	36.0	36.0
9	35.00975	36.0	36.0	36.0	36.0	36.0
10-11	35.174625	36.0	36.0	36.0	36.0	36.0
12-13	35.157375	36.0	36.0	36.0	36.0	36.0
14-15	35.074375	36.0	36.0	36.0	36.0	36.0
16-17	35.173375	36.0	36.0	36.0	36.0	36.0
18-19	35.261875	36.0	36.0	36.0	36.0	36.0
20-21	35.080625	36.0	36.0	36.0	36.0	36.0
22-23	34.980125	36.0	36.0	36.0	36.0	36.0
24-25	35.04275	36.0	36.0	36.0	36.0	36.0
26-27	34.951	36.0	36.0	36.0	36.0	36.0
28-29	34.975750000000005	36.0	36.0	36.0	36.0	36.0
30-31	34.97475	36.0	36.0	36.0	36.0	36.0
32-33	34.8905	36.0	36.0	36.0	36.0	36.0
34-35	35.0095	36.0	36.0	36.0	36.0	36.0
36-37	35.046375	36.0	36.0	36.0	36.0	36.0
38-39	34.951	36.0	36.0	36.0	36.0	36.0
40-41	34.915499999999994	36.0	36.0	36.0	36.0	36.0
42-43	34.868875	36.0	36.0	36.0	36.0	36.0
44-45	34.798	36.0	36.0	36.0	34.0	36.0
46-47	34.816	36.0	36.0	36.0	36.0	36.0
48-49	34.641000000000005	36.0	36.0	36.0	32.0	36.0
50-51	34.425375	36.0	36.0	36.0	32.0	36.0
52-53	34.393625	36.0	36.0	36.0	32.0	36.0
54-55	34.170125	36.0	36.0	36.0	32.0	36.0
56-57	33.74575	36.0	36.0	36.0	27.0	36.0
58-59	33.73475	36.0	36.0	36.0	27.0	36.0
60-61	33.69425	36.0	36.0	36.0	27.0	36.0
62-63	33.456375	36.0	36.0	36.0	27.0	36.0
64-65	33.27575	36.0	34.0	36.0	27.0	36.0
66-67	33.03775	36.0	32.0	36.0	27.0	36.0
68-69	32.978750000000005	36.0	32.0	36.0	27.0	36.0
70-71	32.938625	36.0	34.0	36.0	20.5	36.0
72-73	32.649625	36.0	34.0	36.0	17.5	36.0
74-75	33.204	36.0	34.0	36.0	24.0	36.0
76	30.996	36.0	32.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
20	1.0
21	1.0
22	3.0
23	6.0
24	10.0
25	20.0
26	22.0
27	30.0
28	47.0
29	88.0
30	91.0
31	115.0
32	208.0
33	359.0
34	1028.0
35	1971.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	23.150000000000002	28.849999999999998	24.725	23.275000000000002
2	22.3	27.025	25.15	25.525
3	25.3	32.35	18.224999999999998	24.125
4	27.975	32.75	19.05	20.225
5	21.825	25.7	23.549999999999997	28.925
6	28.999999999999996	24.825	26.400000000000002	19.775000000000002
7	33.175	33.0	17.175	16.650000000000002
8	22.425	27.125	30.675	19.775000000000002
9	22.975	32.475	19.075	25.474999999999998
10-11	31.937500000000004	26.737499999999997	23.3125	18.0125
12-13	21.7875	24.0375	23.9125	30.2625
14-15	30.075000000000003	35.925000000000004	17.5875	16.412499999999998
16-17	23.1125	23.6875	32.85	20.349999999999998
18-19	37.0375	23.549999999999997	22.7	16.7125
20-21	22.5875	35.362500000000004	23.799999999999997	18.25
22-23	31.2125	37.3875	14.2125	17.1875
24-25	28.575	38.0625	17.3375	16.025
26-27	27.425	32.025	19.45	21.099999999999998
28-29	31.887500000000003	28.299999999999997	16.625	23.1875
30-31	32.0125	36.425000000000004	10.95	20.6125
32-33	29.799999999999997	37.9125	12.45	19.8375
34-35	29.725	31.424999999999997	14.4875	24.3625
36-37	26.325	34.625	11.3	27.750000000000004
38-39	24.8625	34.925	12.2	28.012500000000003
40-41	25.2625	29.7875	16.662499999999998	28.287499999999998
42-43	26.5	26.275	19.287499999999998	27.9375
44-45	21.512500000000003	35.1625	15.1	28.225
46-47	19.0	32.324999999999996	15.4	33.275
48-49	15.387500000000001	28.6875	17.75	38.175
50-51	14.7375	29.7125	18.05	37.5
52-53	16.675	29.45	20.9375	32.9375
54-55	12.937499999999998	30.7125	19.675	36.675000000000004
56-57	9.325	31.374999999999996	18.85	40.45
58-59	9.65	34.8125	17.974999999999998	37.5625
60-61	9.2875	32.125	25.2625	33.324999999999996
62-63	9.5875	33.275	25.2375	31.900000000000002
64-65	8.9625	28.249999999999996	26.8375	35.949999999999996
66-67	12.712499999999999	23.625	28.599999999999998	35.0625
68-69	13.7625	22.3125	31.7625	32.1625
70-71	14.7	24.762500000000003	32.9375	27.6
72-73	16.2625	19.650000000000002	30.612499999999997	33.475
74-75	18.575	15.837499999999999	32.4625	33.125
76	16.6	15.0	37.05	31.35
>>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	0.5
29	1.0
30	0.5
31	0.5
32	0.5
33	0.0
34	1.0
35	1.0
36	1.0
37	2.0
38	2.0
39	7.0
40	18.0
41	48.5
42	73.0
43	86.0
44	140.5
45	266.0
46	350.0
47	667.5
48	793.5
49	591.0
50	580.0
51	481.0
52	326.0
53	221.5
54	173.0
55	145.5
56	100.5
57	54.5
58	26.0
59	17.5
60	8.0
61	6.0
62	5.0
63	3.5
64	2.0
65	2.5
66	1.5
67	0.0
68	0.5
69	1.0
70	1.0
71	1.0
72	1.0
73	0.5
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	0.5
98	0.5
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	65.55
#Duplication Level	Percentage of deduplicated	Percentage of total
1	89.58810068649885	58.72500000000001
2	4.195270785659801	5.5
3	2.2883295194508007	4.5
4	0.7627765064836003	2.0
5	0.8771929824561403	2.875
6	0.5339435545385203	2.1
7	0.15255530129672007	0.7000000000000001
8	0.19069412662090007	1.0
9	0.19069412662090007	1.125
>10	1.1441647597254003	13.8
>50	0.0	0.0
>100	0.07627765064836003	7.675
>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	206	5.1499999999999995	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	101	2.5250000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	40	1.0	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	35	0.8750000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	27	0.675	No Hit
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAA	24	0.6	TruSeq Adapter, Index 2 (97% over 36bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAC	23	0.575	TruSeq Adapter, Index 23 (97% over 37bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	22	0.5499999999999999	No Hit
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	19	0.475	No Hit
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACTAAT	18	0.44999999999999996	TruSeq Adapter, Index 23 (97% over 38bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACTAA	18	0.44999999999999996	TruSeq Adapter, Index 23 (97% over 38bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	13	0.325	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	13	0.325	No Hit
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAA	13	0.325	TruSeq Adapter, Index 2 (97% over 36bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	12	0.3	TruSeq Adapter, Index 7 (100% over 35bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	11	0.27499999999999997	No Hit
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	10	0.25	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	10	0.25	No Hit
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	9	0.22499999999999998	No Hit
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
TCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	8	0.2	TruSeq Adapter, Index 7 (100% over 35bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	8	0.2	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	6	0.15	No Hit
GCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	6	0.15	TruSeq Adapter, Index 7 (100% over 35bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GATCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACT	6	0.15	TruSeq Adapter, Index 23 (97% over 38bp)
TGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTC	6	0.15	No Hit
ACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTAGATCGGAAGAGC	6	0.15	No Hit
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	6	0.15	No Hit
CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGAGC	6	0.15	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CCTGCGGCAAAATAGCTCGATGCCAGAATAAGATCGGAAGAGCACACGTC	5	0.125	No Hit
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	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)
GCGGCAAAATAGCTCGATGCCAGAATAAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
AGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACA	5	0.125	No Hit
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACTA	5	0.125	TruSeq Adapter, Index 23 (97% over 38bp)
GGGGACGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	5	0.125	TruSeq Adapter, Index 7 (100% over 35bp)
TAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCA	5	0.125	No Hit
CAGCTGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACA	5	0.125	No Hit
AAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATTGGTCAGAAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCTGCGGCAAAATAGCTCGATGCCAGAATAAGATCGGAAGAGCACACGT	5	0.125	No Hit
ACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AAAATAGCTCGATGCCAGAATAAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	5	0.125	No Hit
GGGTGTTTGGTCTAGTGGTATGATTCTCAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
ATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAG	5	0.125	No Hit
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTAGATCGGAAGAGCACA	5	0.125	No Hit
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	5	0.125	No Hit
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
>>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	0.15	0.0	0.0	0.0	0.0
4	0.25	0.0	0.0	0.0	0.0
5	0.3	0.0	0.0	0.0	0.0
6	0.375	0.0	0.0	0.0	0.0
7	0.525	0.0	0.0	0.0	0.0
8	0.65	0.0	0.0	0.0	0.0
9	1.375	0.0	0.0	0.0	0.0
10	2.05	0.0	0.0	0.0	0.0
11	2.425	0.0	0.0	0.0	0.0
12	3.1	0.0	0.0	0.0	0.0
13	4.35	0.0	0.0	0.0	0.0
14	6.45	0.0	0.0	0.0	0.0
15	8.0	0.0	0.0	0.0	0.0
16	9.6	0.0	0.0	0.0	0.0
17	12.45	0.0	0.0	0.0	0.0
18	14.75	0.0	0.0	0.0	0.0
19	16.575	0.0	0.0	0.0	0.0
20	19.25	0.0	0.0	0.0	0.0
21	22.45	0.0	0.0	0.0	0.0
22	28.975	0.0	0.0	0.0	0.0
23	37.8	0.0	0.0	0.0	0.0
24	42.05	0.0	0.0	0.0	0.0
25	48.7	0.0	0.0	0.0	0.0
26	52.375	0.0	0.0	0.0	0.0
27	55.25	0.0	0.0	0.0	0.0
28	58.65	0.0	0.0	0.0	0.0
29	61.4	0.0	0.0	0.0	0.0
30	64.225	0.0	0.0	0.0	0.0
31	69.5	0.0	0.0	0.0	0.0
32	72.475	0.0	0.0	0.0	0.0
33	75.35	0.0	0.0	0.0	0.0
34	78.2	0.0	0.0	0.0	0.0
35	81.025	0.0	0.0	0.0	0.0
36	83.65	0.0	0.0	0.0	0.0
37	86.3	0.0	0.0	0.0	0.0
38	88.1	0.0	0.0	0.0	0.0
39	89.4	0.0	0.0	0.0	0.0
40	90.6	0.0	0.0	0.0	0.0
41	91.475	0.0	0.0	0.0	0.0
42	92.75	0.0	0.0	0.0	0.0
43	93.125	0.0	0.0	0.0	0.0
44	93.8	0.0	0.0	0.0	0.0
45	94.25	0.0	0.0	0.0	0.0
46	94.45	0.0	0.0	0.0	0.0
47	94.775	0.0	0.0	0.0	0.0
48	94.975	0.0	0.0	0.0	0.0
49	95.325	0.0	0.0	0.0	0.0
50	95.425	0.0	0.0	0.0	0.0
51	95.625	0.0	0.0	0.0	0.0
52	95.675	0.0	0.0	0.0	0.0
53	95.725	0.0	0.0	0.0	0.0
54	95.725	0.0	0.0	0.0	0.0
55	95.75	0.0	0.0	0.0	0.0
56	95.775	0.0	0.0	0.0	0.0
57	95.8	0.0	0.0	0.0	0.0
58	95.8	0.0	0.0	0.0	0.0
59	95.8	0.0	0.0	0.0	0.0
60	95.8	0.0	0.0	0.0	0.0
61	95.825	0.0	0.0	0.0	0.0
62	95.825	0.0	0.0	0.0	0.0
63	95.825	0.0	0.0	0.0	0.0
64	95.825	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ATCCTGC	15	0.0020658788	70.00001	11
GTTGATC	15	0.0020658788	70.00001	7
TGGTTGA	15	0.0020658788	70.00001	5
GGTTGAT	15	0.0020658788	70.00001	6
CCTGCCA	15	0.0020658788	70.00001	13
TGATCCT	15	0.0020658788	70.00001	9
CTGGTTG	15	0.0020658788	70.00001	4
ACCTGGT	15	0.0020658788	70.00001	2
GATCCTG	15	0.0020658788	70.00001	10
TTGATCC	15	0.0020658788	70.00001	8
CTGCCAG	15	0.0020658788	70.00001	14
TACCTGG	15	0.0020658788	70.00001	1
TCCTGCC	15	0.0020658788	70.00001	12
CCTGGTT	15	0.0020658788	70.00001	3
TTGTAGT	35	2.2913628E-7	60.000004	5
TGTAGTC	30	6.9588386E-6	58.333336	6
CGTTGTA	30	6.9588386E-6	58.333336	3
GTTGTAG	30	6.9588386E-6	58.333336	4
TCTAGCT	25	2.1136815E-4	55.999996	11
GCTGGTC	25	2.1136815E-4	55.999996	15
>>END_MODULE
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500661 READS because READLEN < 1
Read 500661 spots for SRR11699532.sra
Written 500661 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
Rejected 500653 READS because READLEN < 1
Read 500653 spots for SRR11699532.sra
Written 500653 spots for SRR11699532.sra
SRR ids: ['SRR11699532.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_kpcbzfu7
SRR11699532.sra spots: 10013068
blocks: [[1, 500653], [500654, 1001306], [1001307, 1501959], [1501960, 2002612], [2002613, 2503265], [2503266, 3003918], [3003919, 3504571], [3504572, 4005224], [4005225, 4505877], [4505878, 5006530], [5006531, 5507183], [5507184, 6007836], [6007837, 6508489], [6508490, 7009142], [7009143, 7509795], [7509796, 8010448], [8010449, 8511101], [8511102, 9011754], [9011755, 9512407], [9512408, 10013068]]
SRR11699532 file size 1904641
SRR11699532 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 SRR11699532 SRR11699532_1.fastq
Input file:	SRR11699532_1.fastq
trimmed:	SRR11699532-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 18:31:40 2025 >> started

Fri Jun 20 18:31:46 2025 >> done (5.096s)
10013068 reads processed; of these:
 1645810 (16.44%) short reads filtered out after trimming by size control
    6836 ( 0.07%) empty reads filtered out after trimming by size control
 8360422 (83.50%) reads available; of these:
 8169274 (97.71%) trimmed reads available after processing
  191148 ( 2.29%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 235208	  2.81%
 19	 342916	  4.10%
 20	 344510	  4.12%
 21	 669357	  8.01%
 22	 892510	 10.68%
 23	 345603	  4.13%
 24	 717674	  8.58%
 25	 362419	  4.33%
 26	 296452	  3.55%
 27	 349237	  4.18%
 28	 267058	  3.19%
 29	 287597	  3.44%
 30	 518719	  6.20%
 31	 304665	  3.64%
 32	 314970	  3.77%
 33	 288476	  3.45%
 34	 296880	  3.55%
 35	 310271	  3.71%
 36	 249729	  2.99%
 37	 170597	  2.04%
 38	 129801	  1.55%
 39	 119186	  1.43%
 40	  91614	  1.10%
 41	 106445	  1.27%
 42	  66038	  0.79%
 43	  51852	  0.62%
 44	  39483	  0.47%
 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	      2	  0.00%
 73	      0	  0.00%
 74	      1	  0.00%
 75	      4	  0.00%
 76	 191148	  2.29%
8360422 reads passed initial QC


criterion=sequence-density
sequence-density=4.87
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=17
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATA


criterion=fanout-score
sequence-density=0.18
sequence-density-rank=20
fanout-score=27.87
fanout-score-rank=1
prefix-density=3.66
prefix-fanout=1.4
sequence=GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTG
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 18:32:22
                             Started mapping on |	Jun 20 18:32:23
                                    Finished on |	Jun 20 18:32:47
       Mapping speed, Million of reads per hour |	1254.06

                          Number of input reads |	8360422
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	688403
                        Uniquely mapped reads % |	8.23%
                          Average mapped length |	24.96
                       Number of splices: Total |	19234
            Number of splices: Annotated (sjdb) |	9786
                       Number of splices: GT/AG |	17770
                       Number of splices: GC/AG |	902
                       Number of splices: AT/AC |	11
               Number of splices: Non-canonical |	551
                      Mismatch rate per base, % |	1.10%
                         Deletion rate per base |	0.02%
                        Deletion average length |	1.29
                        Insertion rate per base |	0.01%
                       Insertion average length |	1.42
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	974659
             % of reads mapped to multiple loci |	11.66%
        Number of reads mapped to too many loci |	1856426
             % of reads mapped to too many loci |	22.20%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.28%
                     % of reads unmapped: other |	50.63%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	6697360	6697360	6697360
N_multimapping	974659	974659	974659
N_noFeature	537008	556478	663900
N_ambiguous	5138	61	57
UnstrandedReadsAssigned:146257 PositiveStrandReadsAssigned:131864 NegativeStrandReadsAssigned:24446
Dataset is classified positive stranded
MeadianReadLen=26 20thPercentileLength=22 echo kmer=19
SRR11699532 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: SRR11699532-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 8,360,422 reads, 1,029,974 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 957 rounds

  72540 SRR11699532.ke.tsv
  44303 SRR11699532.se.tsv
 116843 total
==> SRR11699532.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	9	2.40663
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

==> SRR11699532.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	1
Zm00001eb021860	0
Zm00001eb011690	2
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699532 completed mapping pipeline successfully
