Starting /dee2/code/volunteer_pipeline.sh SRR11699454
    current disk space = 2474744455168
    free memory = 1568442100 
SRR11699454 SRAfilesize
fbc6fe07f970c485f27e5f4e8d97d48c  SRR11699454.sra
SRR11699454.sra file validated
SRR11699454 is single end
SRR11699454 is conventional basespace
SRR11699454 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699454_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	31.331	32.0	32.0	32.0	32.0	32.0
2	31.495	32.0	32.0	32.0	32.0	32.0
3	31.4315	32.0	32.0	32.0	32.0	32.0
4	31.43775	32.0	32.0	32.0	32.0	32.0
5	31.599	32.0	32.0	32.0	32.0	32.0
6	35.01875	36.0	36.0	36.0	36.0	36.0
7	35.1785	36.0	36.0	36.0	36.0	36.0
8	35.11825	36.0	36.0	36.0	36.0	36.0
9	34.8895	36.0	36.0	36.0	32.0	36.0
10-11	35.037499999999994	36.0	36.0	36.0	36.0	36.0
12-13	35.130125	36.0	36.0	36.0	36.0	36.0
14-15	35.0505	36.0	36.0	36.0	36.0	36.0
16-17	35.128249999999994	36.0	36.0	36.0	36.0	36.0
18-19	35.146	36.0	36.0	36.0	36.0	36.0
20-21	35.034875	36.0	36.0	36.0	36.0	36.0
22-23	34.945625	36.0	36.0	36.0	36.0	36.0
24-25	34.99575	36.0	36.0	36.0	36.0	36.0
26-27	34.846000000000004	36.0	36.0	36.0	34.0	36.0
28-29	34.952	36.0	36.0	36.0	36.0	36.0
30-31	34.944	36.0	36.0	36.0	36.0	36.0
32-33	34.968125	36.0	36.0	36.0	36.0	36.0
34-35	34.935375	36.0	36.0	36.0	36.0	36.0
36-37	34.960375	36.0	36.0	36.0	36.0	36.0
38-39	34.861625000000004	36.0	36.0	36.0	36.0	36.0
40-41	34.963625	36.0	36.0	36.0	36.0	36.0
42-43	34.76649999999999	36.0	36.0	36.0	34.0	36.0
44-45	34.76675	36.0	36.0	36.0	32.0	36.0
46-47	34.7495	36.0	36.0	36.0	34.0	36.0
48-49	34.587875	36.0	36.0	36.0	32.0	36.0
50-51	34.201750000000004	36.0	36.0	36.0	32.0	36.0
52-53	34.132	36.0	36.0	36.0	32.0	36.0
54-55	33.923249999999996	36.0	36.0	36.0	29.5	36.0
56-57	33.433625	36.0	36.0	36.0	27.0	36.0
58-59	33.146125	36.0	36.0	36.0	24.0	36.0
60-61	33.17	36.0	36.0	36.0	24.0	36.0
62-63	33.041375	36.0	36.0	36.0	21.0	36.0
64-65	32.946124999999995	36.0	34.0	36.0	17.5	36.0
66-67	32.3245	36.0	32.0	36.0	17.5	36.0
68-69	32.5535	36.0	32.0	36.0	14.0	36.0
70-71	32.848375000000004	36.0	34.0	36.0	17.5	36.0
72-73	33.063500000000005	36.0	34.0	36.0	24.0	36.0
74-75	33.348124999999996	36.0	36.0	36.0	27.0	36.0
76	29.83675	36.0	27.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
19	1.0
20	0.0
21	2.0
22	5.0
23	8.0
24	14.0
25	13.0
26	24.0
27	47.0
28	66.0
29	91.0
30	120.0
31	151.0
32	239.0
33	366.0
34	902.0
35	1951.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	21.95	32.625	21.775	23.65
2	22.3	28.95	26.525	22.225
3	24.9	33.2	16.725	25.174999999999997
4	26.125	32.550000000000004	17.675	23.65
5	22.3	27.250000000000004	22.425	28.025
6	26.174999999999997	29.775000000000002	23.225	20.825
7	28.775000000000002	36.275	17.275	17.675
8	22.825	26.8	26.450000000000003	23.925
9	26.950000000000003	30.8	17.424999999999997	24.825
10-11	29.1625	29.562500000000004	22.2	19.075
12-13	23.35	24.0375	23.6125	28.999999999999996
14-15	29.8375	36.3375	18.6	15.225
16-17	24.575	25.7	30.012499999999996	19.7125
18-19	33.2625	27.6125	22.5625	16.5625
20-21	23.549999999999997	35.825	23.75	16.875
22-23	31.75	38.074999999999996	14.05	16.125
24-25	28.237499999999997	39.2	15.024999999999999	17.5375
26-27	31.0625	33.7	15.262500000000001	19.975
28-29	32.125	30.112499999999997	14.8375	22.925
30-31	35.275	35.7875	9.112499999999999	19.825
32-33	28.15	40.2	10.025	21.625
34-35	30.15	32.4	12.2	25.25
36-37	24.6875	33.35	11.15	30.8125
38-39	22.1375	32.824999999999996	14.249999999999998	30.7875
40-41	22.675	28.6375	17.5875	31.1
42-43	25.2125	25.174999999999997	21.4375	28.175
44-45	18.3	31.662499999999998	18.075	31.9625
46-47	19.05	31.2125	15.925	33.8125
48-49	12.675	29.6375	16.0625	41.625
50-51	12.55	28.7	17.962500000000002	40.7875
52-53	14.2375	29.262500000000003	16.925	39.574999999999996
54-55	12.712499999999999	30.7625	17.6375	38.8875
56-57	7.2375	31.924999999999997	15.2125	45.625
58-59	8.1125	33.387499999999996	14.0125	44.487500000000004
60-61	7.3	35.275	17.6375	39.787499999999994
62-63	9.8375	35.05	20.837500000000002	34.275
64-65	9.45	29.262500000000003	25.5	35.7875
66-67	13.775	19.6	30.5125	36.1125
68-69	15.375	19.400000000000002	30.875000000000004	34.35
70-71	18.0	19.75	31.6	30.65
72-73	17.974999999999998	18.275	31.0625	32.6875
74-75	20.125	13.700000000000001	31.0125	35.1625
76	15.024999999999999	12.55	37.625	34.8
>>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	0.5
28	0.5
29	0.0
30	0.5
31	1.5
32	1.0
33	0.0
34	0.5
35	0.5
36	1.0
37	2.0
38	2.0
39	3.0
40	4.5
41	10.5
42	16.0
43	37.5
44	74.5
45	134.0
46	178.0
47	335.0
48	747.5
49	776.5
50	550.0
51	529.5
52	468.0
53	358.0
54	289.0
55	212.0
56	119.5
57	91.0
58	78.0
59	56.5
60	21.5
61	6.5
62	5.0
63	3.0
64	0.5
65	0.5
66	0.5
67	0.0
68	0.0
69	0.0
70	0.5
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	0.5
89	0.5
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	62.35000000000001
#Duplication Level	Percentage of deduplicated	Percentage of total
1	88.81315156375301	55.375
2	5.012028869286287	6.25
3	2.0048115477145148	3.75
4	0.8420208500400962	2.1
5	0.8420208500400962	2.625
6	0.40096230954290296	1.5
7	0.32076984763432237	1.4000000000000001
8	0.36086607858861264	1.7999999999999998
9	0.040096230954290296	0.22499999999999998
>10	1.2429831595829992	16.775000000000002
>50	0.08019246190858059	3.925
>100	0.040096230954290296	4.275
>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	171	4.275	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	84	2.1	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	73	1.825	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	49	1.225	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	39	0.975	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	35	0.8750000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	35	0.8750000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCA	34	0.8500000000000001	TruSeq Adapter, Index 2 (97% over 36bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCA	33	0.8250000000000001	TruSeq Adapter, Index 2 (97% over 36bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	32	0.8	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	32	0.8	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCAA	30	0.75	TruSeq Adapter, Index 2 (97% over 36bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	30	0.75	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	23	0.575	No Hit
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCAACAAT	23	0.575	TruSeq Adapter, Index 2 (97% over 36bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	18	0.44999999999999996	No Hit
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCAACA	11	0.27499999999999997	TruSeq Adapter, Index 2 (97% over 36bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCAACAA	10	0.25	TruSeq Adapter, Index 2 (97% over 36bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCAAC	8	0.2	TruSeq Adapter, Index 2 (97% over 36bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCC	8	0.2	TruSeq Adapter, Index 5 (97% over 35bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	8	0.2	No Hit
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	8	0.2	No Hit
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	8	0.2	No Hit
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCC	7	0.17500000000000002	TruSeq Adapter, Index 5 (97% over 35bp)
AGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	7	0.17500000000000002	No Hit
CCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGACCCCAGGTCAGTCGGGAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	6	0.15	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	6	0.15	No Hit
TGAAGCTGCCAGCATGATCTGAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
AGCGGAGTAGAGCAGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
ACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTAGATCGGAAGAGCACA	6	0.15	No Hit
CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGTAGTTCGACCGTGGATTAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAAAGATCGGAAGAGCA	5	0.125	No Hit
GAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	5	0.125	No Hit
CGACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	5	0.125	No Hit
TCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	5	0.125	No Hit
ACACGACTCTCGGCAACGGATATCTCGGCTAGATCGGAAGAGCACACGTC	5	0.125	No Hit
CGACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCA	5	0.125	No Hit
GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	5	0.125	No Hit
TCAAAAGAGGAAAGGCTTGCGGTGGATAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GCACCAGTGGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCA	5	0.125	TruSeq Adapter, Index 2 (97% over 36bp)
CATATCGGGTAGGTTGTGGTATTTCATTGCTAGATCGGAAGAGCACACGT	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	0.075	0.0	0.0	0.0	0.0
2	0.1	0.0	0.0	0.0	0.0
3	0.175	0.0	0.0	0.0	0.0
4	0.25	0.0	0.0	0.0	0.0
5	0.35	0.0	0.0	0.0	0.0
6	0.425	0.0	0.0	0.0	0.0
7	0.55	0.0	0.0	0.0	0.0
8	0.8	0.0	0.0	0.0	0.0
9	1.625	0.0	0.0	0.0	0.0
10	2.275	0.0	0.0	0.0	0.0
11	3.075	0.0	0.0	0.0	0.0
12	3.825	0.0	0.0	0.0	0.0
13	5.275	0.0	0.0	0.0	0.0
14	8.55	0.0	0.0	0.0	0.0
15	9.875	0.0	0.0	0.0	0.0
16	12.025	0.0	0.0	0.0	0.0
17	15.825	0.0	0.0	0.0	0.0
18	19.375	0.0	0.0	0.0	0.0
19	21.975	0.0	0.0	0.0	0.0
20	26.25	0.0	0.0	0.0	0.0
21	31.15	0.0	0.0	0.0	0.0
22	37.675	0.0	0.0	0.0	0.0
23	46.875	0.0	0.0	0.0	0.0
24	51.425	0.0	0.0	0.0	0.0
25	60.8	0.0	0.0	0.0	0.0
26	65.525	0.0	0.0	0.0	0.0
27	68.0	0.0	0.0	0.0	0.0
28	70.675	0.0	0.0	0.0	0.0
29	72.675	0.0	0.0	0.0	0.0
30	74.975	0.0	0.0	0.0	0.0
31	77.875	0.0	0.0	0.0	0.0
32	80.375	0.0	0.0	0.0	0.0
33	81.85	0.0	0.0	0.0	0.0
34	84.15	0.0	0.0	0.0	0.0
35	86.4	0.0	0.0	0.0	0.0
36	88.475	0.0	0.0	0.0	0.0
37	90.225	0.0	0.0	0.0	0.0
38	91.425	0.0	0.0	0.0	0.0
39	92.2	0.0	0.0	0.0	0.0
40	92.8	0.0	0.0	0.0	0.0
41	93.525	0.0	0.0	0.0	0.0
42	94.2	0.0	0.0	0.0	0.0
43	94.675	0.0	0.0	0.0	0.0
44	95.075	0.0	0.0	0.0	0.0
45	95.325	0.0	0.0	0.0	0.0
46	95.55	0.0	0.0	0.0	0.0
47	95.875	0.0	0.0	0.0	0.0
48	95.95	0.0	0.0	0.0	0.0
49	96.05	0.0	0.0	0.0	0.0
50	96.05	0.0	0.0	0.0	0.0
51	96.05	0.0	0.0	0.0	0.0
52	96.05	0.0	0.0	0.0	0.0
53	96.075	0.0	0.0	0.0	0.0
54	96.075	0.0	0.0	0.0	0.0
55	96.075	0.0	0.0	0.0	0.0
56	96.075	0.0	0.0	0.0	0.0
57	96.1	0.0	0.0	0.0	0.0
58	96.1	0.0	0.0	0.0	0.0
59	96.1	0.0	0.0	0.0	0.0
60	96.1	0.0	0.0	0.0	0.0
61	96.1	0.0	0.0	0.0	0.0
62	96.1	0.0	0.0	0.0	0.0
63	96.1	0.0	0.0	0.0	0.0
64	96.1	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ATCCTAA	40	3.822406E-5	43.75	1
TCCTAAC	40	3.822406E-5	43.75	2
CCTAACG	45	7.661899E-5	38.88889	3
CTTCTGC	45	7.661899E-5	38.88889	70
TTTGAAC	75	4.3394008E-5	28.0	16
TTGAACA	75	4.3394008E-5	28.0	17
TGAACAG	75	4.3394008E-5	28.0	18
CTAACGA	90	4.4050794E-6	27.222223	1
TCTTCTG	65	6.650945E-4	26.923077	69
GAACAGA	80	6.740297E-5	26.25	19
GTCTTCT	70	0.0010258359	25.000002	68
AACAGAT	85	1.01866215E-4	24.705881	20
TAACGAA	100	1.0001939E-5	24.499998	2
GAACGAA	100	1.0001939E-5	24.499998	6
AACGATT	115	9.717205E-7	24.347826	11
GAACGAT	115	9.717205E-7	24.347826	10
GATTTGA	115	9.717205E-7	24.347826	14
ACGATTT	115	9.717205E-7	24.347826	12
CGATTTG	115	9.717205E-7	24.347826	13
ACAGATC	90	1.5026014E-4	23.333334	21
>>END_MODULE
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211057 READS because READLEN < 1
Read 211057 spots for SRR11699454.sra
Written 211057 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
Rejected 211044 READS because READLEN < 1
Read 211044 spots for SRR11699454.sra
Written 211044 spots for SRR11699454.sra
SRR ids: ['SRR11699454.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_rk59nau3
SRR11699454.sra spots: 4220893
blocks: [[1, 211044], [211045, 422088], [422089, 633132], [633133, 844176], [844177, 1055220], [1055221, 1266264], [1266265, 1477308], [1477309, 1688352], [1688353, 1899396], [1899397, 2110440], [2110441, 2321484], [2321485, 2532528], [2532529, 2743572], [2743573, 2954616], [2954617, 3165660], [3165661, 3376704], [3376705, 3587748], [3587749, 3798792], [3798793, 4009836], [4009837, 4220893]]
SRR11699454 file size 801614
SRR11699454 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 SRR11699454 SRR11699454_1.fastq
Input file:	SRR11699454_1.fastq
trimmed:	SRR11699454-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 03:23:11 2025 >> started

Fri Jun 20 03:29:10 2025 >> done (359.234s)
4220893 reads processed; of these:
 889133 (21.07%) short reads filtered out after trimming by size control
   2590 ( 0.06%) empty reads filtered out after trimming by size control
3329170 (78.87%) reads available; of these:
3282493 (98.60%) trimmed reads available after processing
  46677 ( 1.40%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 120435	  3.62%
 19	 180959	  5.44%
 20	 200773	  6.03%
 21	 291770	  8.76%
 22	 423765	 12.73%
 23	 173401	  5.21%
 24	 417648	 12.55%
 25	 200590	  6.03%
 26	 109542	  3.29%
 27	 121650	  3.65%
 28	  91577	  2.75%
 29	  99705	  2.99%
 30	 108890	  3.27%
 31	  97752	  2.94%
 32	  80869	  2.43%
 33	  99604	  2.99%
 34	  89392	  2.69%
 35	  96023	  2.88%
 36	  64197	  1.93%
 37	  47811	  1.44%
 38	  35778	  1.07%
 39	  32419	  0.97%
 40	  23361	  0.70%
 41	  33814	  1.02%
 42	  18229	  0.55%
 43	  13791	  0.41%
 44	   8746	  0.26%
 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	      0	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      2	  0.00%
 76	  46677	  1.40%
3329170 reads passed initial QC


criterion=sequence-density
sequence-density=2.28
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGG


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=39
fanout-score=92.00
fanout-score-rank=1
prefix-density=0.49
prefix-fanout=1.0
sequence=CCTCGTGTTTAGTTGCCACTATGAGTTTGGAACCCTGAACAGACCGCCGGTGTTAAGCCGGAGGAAGGAGA
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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGG -o SRR11699454 -
Input file:	STDIN
trimmed:	SRR11699454-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGG
-- 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 03:29:28 2025 >> started

Fri Jun 20 03:29:31 2025 >> done (3.324s)
1109723 reads processed; of these:
   3904 ( 0.35%) short reads filtered out after trimming by size control
  25629 ( 2.31%) empty reads filtered out after trimming by size control
1080190 (97.34%) reads available; of these:
   7909 ( 0.73%) trimmed reads available after processing
1072281 (99.27%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  40673	  3.77%
 19	  60667	  5.62%
 20	  65804	  6.09%
 21	  96818	  8.96%
 22	 140782	 13.03%
 23	  57493	  5.32%
 24	 137535	 12.73%
 25	  66787	  6.18%
 26	  36286	  3.36%
 27	  40330	  3.73%
 28	  30274	  2.80%
 29	  33055	  3.06%
 30	  36128	  3.34%
 31	  32510	  3.01%
 32	  25470	  2.36%
 33	  23336	  2.16%
 34	  24695	  2.29%
 35	  24725	  2.29%
 36	  20591	  1.91%
 37	  15827	  1.47%
 38	  11801	  1.09%
 39	  10713	  0.99%
 40	   7770	  0.72%
 41	  11109	  1.03%
 42	   6003	  0.56%
 43	   4513	  0.42%
 44	   2897	  0.27%
 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	      0	  0.00%
 73	    785	  0.07%
 74	      0	  0.00%
 75	      2	  0.00%
 76	  14811	  1.37%


criterion=sequence-density
sequence-density=1.56
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=11
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAAGACCCGGGTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=38
fanout-score=88.22
fanout-score-rank=1
prefix-density=0.50
prefix-fanout=1.0
sequence=CCTCGTGTTTAGTTGCCACTATGAGTTTGGAACCCTGAACAGACCGCCGGTGTTAAGCCGGAGGAAGGAGA
                                 Started job on |	Jun 20 03:39:44
                             Started mapping on |	Jun 20 03:41:43
                                    Finished on |	Jun 20 03:42:42
       Mapping speed, Million of reads per hour |	201.33

                          Number of input reads |	3299637
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	331509
                        Uniquely mapped reads % |	10.05%
                          Average mapped length |	23.68
                       Number of splices: Total |	6470
            Number of splices: Annotated (sjdb) |	2562
                       Number of splices: GT/AG |	5856
                       Number of splices: GC/AG |	458
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	153
                      Mismatch rate per base, % |	0.99%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.40
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	324829
             % of reads mapped to multiple loci |	9.84%
        Number of reads mapped to too many loci |	574119
             % of reads mapped to too many loci |	17.40%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.40%
                     % of reads unmapped: other |	57.31%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2643299	2643299	2643299
N_multimapping	324829	324829	324829
N_noFeature	280852	291883	318986
N_ambiguous	1537	27	24
UnstrandedReadsAssigned:49120 PositiveStrandReadsAssigned:39599 NegativeStrandReadsAssigned:12499
Dataset is classified unstranded
MeadianReadLen=24 20thPercentileLength=21 echo kmer=19
SRR11699454 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: SRR11699454-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,299,637 reads, 540,137 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 900 rounds

  72540 SRR11699454.ke.tsv
  44303 SRR11699454.se.tsv
 116843 total
==> SRR11699454.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	1	0.966566
Zm00001eb321680_T001	3417	3318	3	1.71989
Zm00001eb323640_T001	3273	3174	1	0.599308
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

==> SRR11699454.se.tsv <==
Zm00001eb015280	1
Zm00001eb000610	0
Zm00001eb033210	1
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699454 completed mapping pipeline successfully
