Starting /dee2/code/volunteer_pipeline.sh SRR11699362
    current disk space = 2462134059008
    free memory = 1575195808 
SRR11699362 SRAfilesize
08f27bbe227e821e7f14665d2f209fd6  SRR11699362.sra
SRR11699362.sra file validated
SRR11699362 is single end
SRR11699362 is conventional basespace
SRR11699362 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699362_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	45
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.16625	32.0	32.0	32.0	32.0	32.0
2	31.33075	32.0	32.0	32.0	32.0	32.0
3	31.395	32.0	32.0	32.0	32.0	32.0
4	31.475	32.0	32.0	32.0	32.0	32.0
5	31.4865	32.0	32.0	32.0	32.0	32.0
6	34.91575	36.0	36.0	36.0	36.0	36.0
7	34.9175	36.0	36.0	36.0	36.0	36.0
8	35.03875	36.0	36.0	36.0	36.0	36.0
9	34.848	36.0	36.0	36.0	32.0	36.0
10-11	35.102625	36.0	36.0	36.0	36.0	36.0
12-13	35.1155	36.0	36.0	36.0	36.0	36.0
14-15	34.946875	36.0	36.0	36.0	36.0	36.0
16-17	35.07225	36.0	36.0	36.0	36.0	36.0
18-19	35.10925	36.0	36.0	36.0	36.0	36.0
20-21	34.960875	36.0	36.0	36.0	36.0	36.0
22-23	34.798875	36.0	36.0	36.0	34.0	36.0
24-25	34.838625	36.0	36.0	36.0	34.0	36.0
26-27	34.792125	36.0	36.0	36.0	34.0	36.0
28-29	34.850125000000006	36.0	36.0	36.0	36.0	36.0
30-31	34.696749999999994	36.0	36.0	36.0	32.0	36.0
32-33	34.669375	36.0	36.0	36.0	34.0	36.0
34-35	34.839124999999996	36.0	36.0	36.0	36.0	36.0
36-37	34.7965	36.0	36.0	36.0	34.0	36.0
38-39	34.804625	36.0	36.0	36.0	34.0	36.0
40-41	34.676125	36.0	36.0	36.0	32.0	36.0
42-43	34.688625	36.0	36.0	36.0	32.0	36.0
44-45	34.56575	36.0	36.0	36.0	32.0	36.0
46-47	34.2095	36.0	36.0	36.0	32.0	36.0
48-49	33.746875	36.0	36.0	36.0	29.5	36.0
50-51	33.171499999999995	36.0	34.0	36.0	20.5	36.0
52-53	32.967749999999995	36.0	34.0	36.0	17.5	36.0
54-55	32.901125	36.0	36.0	36.0	14.0	36.0
56-57	32.76225	36.0	32.0	36.0	17.5	36.0
58-59	32.685249999999996	36.0	32.0	36.0	14.0	36.0
60-61	32.640375	36.0	32.0	36.0	14.0	36.0
62-63	32.516625000000005	36.0	32.0	36.0	14.0	36.0
64-65	32.55	36.0	32.0	36.0	14.0	36.0
66-67	31.9225	36.0	32.0	36.0	14.0	36.0
68-69	32.409	36.0	32.0	36.0	17.5	36.0
70-71	33.267125	36.0	34.0	36.0	27.0	36.0
72-73	33.264875	36.0	34.0	36.0	27.0	36.0
74-75	33.547250000000005	36.0	36.0	36.0	27.0	36.0
76	30.24325	36.0	27.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
18	1.0
19	0.0
20	0.0
21	3.0
22	7.0
23	4.0
24	8.0
25	22.0
26	39.0
27	63.0
28	88.0
29	105.0
30	138.0
31	167.0
32	272.0
33	455.0
34	957.0
35	1671.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	21.224999999999998	39.2	17.599999999999998	21.975
2	24.575	32.025	24.975	18.425
3	29.125	31.025000000000002	20.3	19.55
4	32.525	29.325000000000003	20.849999999999998	17.299999999999997
5	24.05	31.05	20.025000000000002	24.875
6	23.674999999999997	30.625000000000004	29.375	16.325
7	27.0	38.800000000000004	18.45	15.75
8	20.05	27.725	30.775000000000002	21.45
9	26.525	35.825	16.775000000000002	20.875
10-11	29.6875	32.2125	20.0375	18.0625
12-13	21.45	27.3125	25.137500000000003	26.1
14-15	34.925	36.075	15.875	13.125
16-17	23.5125	33.375	24.65	18.462500000000002
18-19	37.824999999999996	32.737500000000004	14.249999999999998	15.187500000000002
20-21	29.5375	41.2375	13.237499999999999	15.987499999999999
22-23	34.8	38.45	7.375	19.375
24-25	29.675	40.875	7.9625	21.4875
26-27	29.5	33.5625	10.8375	26.1
28-29	27.900000000000002	31.424999999999997	11.700000000000001	28.975
30-31	28.512500000000003	32.887499999999996	12.775	25.825
32-33	20.6125	32.775	15.962499999999999	30.65
34-35	25.525	25.674999999999997	18.775	30.025000000000002
36-37	14.099999999999998	31.7875	16.975	37.1375
38-39	17.974999999999998	25.324999999999996	22.725	33.975
40-41	13.6375	28.9375	20.6125	36.8125
42-43	16.412499999999998	24.1625	27.950000000000003	31.474999999999998
44-45	10.025	32.05	24.3125	33.6125
46-47	10.95	34.375	25.7	28.975
48-49	5.375	35.4	32.05	27.175
50-51	6.675000000000001	36.65	32.025	24.65
52-53	7.2124999999999995	33.9875	37.225	21.575
54-55	9.700000000000001	32.45	35.275	22.575
56-57	7.449999999999999	27.8375	40.0375	24.675
58-59	15.325	24.425	37.2875	22.9625
60-61	13.15	26.9625	36.6125	23.275000000000002
62-63	19.8625	17.675	35.949999999999996	26.5125
64-65	15.6375	13.362499999999999	38.7875	32.2125
66-67	19.7625	8.0	40.425	31.8125
68-69	19.6875	8.674999999999999	40.375	31.2625
70-71	17.8875	10.2	43.987500000000004	27.925
72-73	22.4875	13.3	36.825	27.3875
74-75	17.6625	19.650000000000002	36.625	26.0625
76	15.725	25.974999999999998	40.150000000000006	18.15
>>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	1.0
36	2.0
37	2.0
38	7.5
39	27.0
40	83.0
41	257.5
42	390.0
43	420.5
44	780.5
45	848.5
46	587.0
47	570.5
48	456.5
49	280.0
50	201.0
51	133.0
52	54.0
53	41.0
54	39.0
55	25.5
56	6.0
57	0.0
58	0.0
59	0.0
60	0.0
61	0.0
62	0.0
63	0.0
64	0.0
65	0.0
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	0.5
75	1.0
76	0.5
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	0.5
94	0.5
95	0.0
96	0.0
97	0.0
98	0.0
99	1.0
100	2.0
>>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	52.25
#Duplication Level	Percentage of deduplicated	Percentage of total
1	88.37320574162679	46.175
2	5.4066985645933014	5.65
3	1.8181818181818181	2.85
4	0.7177033492822966	1.5
5	0.5263157894736842	1.375
6	0.7177033492822966	2.25
7	0.19138755980861244	0.7000000000000001
8	0.28708133971291866	1.2
9	0.09569377990430622	0.44999999999999996
>10	1.5311004784688995	18.5
>50	0.14354066985645933	5.8999999999999995
>100	0.19138755980861244	13.450000000000001
>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
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAATAT	145	3.6249999999999996	TruSeq Adapter, Index 9 (97% over 36bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATA	145	3.6249999999999996	TruSeq Adapter, Index 9 (97% over 36bp)
CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC	142	3.55	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	106	2.65	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAT	90	2.25	TruSeq Adapter, Index 9 (97% over 36bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAATA	78	1.95	TruSeq Adapter, Index 9 (97% over 36bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAT	68	1.7000000000000002	TruSeq Adapter, Index 9 (97% over 36bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAAT	48	1.2	TruSeq Adapter, Index 9 (97% over 36bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	41	1.0250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAATATCTC	40	1.0	TruSeq Adapter, Index 9 (97% over 36bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	40	1.0	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	37	0.9249999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAA	36	0.8999999999999999	TruSeq Adapter, Index 9 (97% over 36bp)
TTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAATATC	35	0.8750000000000001	TruSeq Adapter, Index 9 (97% over 36bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	35	0.8750000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	34	0.8500000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAA	33	0.8250000000000001	TruSeq Adapter, Index 9 (97% over 36bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	29	0.7250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAATATCT	25	0.625	TruSeq Adapter, Index 9 (97% over 36bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTA	18	0.44999999999999996	TruSeq Adapter, Index 7 (97% over 35bp)
ATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAATATCTCG	17	0.42500000000000004	TruSeq Adapter, Index 9 (97% over 36bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTA	16	0.4	TruSeq Adapter, Index 7 (97% over 35bp)
TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTA	15	0.375	TruSeq Adapter, Index 7 (97% over 35bp)
CAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAATATCTCGTAT	13	0.325	TruSeq Adapter, Index 9 (97% over 36bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAT	13	0.325	TruSeq Adapter, Index 9 (97% over 36bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAATA	12	0.3	TruSeq Adapter, Index 9 (97% over 36bp)
CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GGGCCTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAT	11	0.27499999999999997	TruSeq Adapter, Index 9 (97% over 36bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAT	9	0.22499999999999998	TruSeq Adapter, Index 9 (97% over 36bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
AGCGGAGTAGAGCAGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GCGTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GAAGGATCATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATA	8	0.2	TruSeq Adapter, Index 9 (97% over 36bp)
GCGTTTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AGGGCTATAGCTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAT	7	0.17500000000000002	TruSeq Adapter, Index 9 (97% over 36bp)
GATGAAGAACGTAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAATATCTCGTATG	7	0.17500000000000002	TruSeq Adapter, Index 9 (97% over 36bp)
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CGAGCACCTCTGAGCTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCGTTGTAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAA	6	0.15	TruSeq Adapter, Index 9 (97% over 36bp)
GGTAGTTCGACCGTGGATAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
AAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATA	6	0.15	TruSeq Adapter, Index 9 (97% over 36bp)
GGGATTGTAGTTCAATCGGAAGAGCACACGTCTGAACTCCAGTCACTATA	6	0.15	TruSeq Adapter, Index 10 (97% over 35bp)
TCCGTTGTAGTCTAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTA	6	0.15	TruSeq Adapter, Index 7 (97% over 35bp)
ACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAAT	6	0.15	TruSeq Adapter, Index 9 (97% over 36bp)
GCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGATATGGCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATA	6	0.15	TruSeq Adapter, Index 9 (97% over 36bp)
ACGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAATATCTCG	6	0.15	TruSeq Adapter, Index 9 (97% over 36bp)
AGCGGAGTAGAGCAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CCGTGACCCTTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATA	5	0.125	TruSeq Adapter, Index 9 (97% over 36bp)
AGGATCATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAAT	5	0.125	TruSeq Adapter, Index 9 (97% over 36bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATA	5	0.125	TruSeq Adapter, Index 9 (97% over 36bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGGACGTAGCTCATAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CGACACGACTCTCGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGGGCTATAGCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAT	5	0.125	TruSeq Adapter, Index 9 (97% over 36bp)
CACGACTCTCGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAT	5	0.125	TruSeq Adapter, Index 9 (97% over 36bp)
ATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAATATCTCGTA	5	0.125	TruSeq Adapter, Index 9 (97% over 36bp)
CGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAT	5	0.125	TruSeq Adapter, Index 9 (97% over 36bp)
>>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	0.2	0.0	0.0	0.0	0.0
2	0.725	0.0	0.0	0.0	0.0
3	1.15	0.0	0.0	0.0	0.0
4	1.65	0.0	0.0	0.0	0.0
5	2.55	0.0	0.0	0.0	0.0
6	3.9	0.0	0.0	0.0	0.0
7	4.975	0.0	0.0	0.0	0.0
8	6.775	0.0	0.0	0.0	0.0
9	12.05	0.0	0.0	0.0	0.0
10	16.25	0.0	0.0	0.0	0.0
11	19.8	0.0	0.0	0.0	0.0
12	24.45	0.0	0.0	0.0	0.0
13	32.05	0.0	0.0	0.0	0.0
14	40.65	0.0	0.0	0.0	0.0
15	45.05	0.0	0.0	0.0	0.0
16	49.1	0.0	0.0	0.0	0.0
17	55.875	0.0	0.0	0.0	0.0
18	62.425	0.0	0.0	0.0	0.0
19	65.475	0.0	0.0	0.0	0.0
20	69.375	0.0	0.0	0.0	0.0
21	73.25	0.0	0.0	0.0	0.0
22	77.425	0.0	0.0	0.0	0.0
23	84.125	0.0	0.0	0.0	0.0
24	85.875	0.0	0.0	0.0	0.0
25	89.575	0.0	0.0	0.0	0.0
26	91.35	0.0	0.0	0.0	0.0
27	92.05	0.0	0.0	0.0	0.0
28	92.75	0.0	0.0	0.0	0.0
29	93.45	0.0	0.0	0.0	0.0
30	93.775	0.0	0.0	0.0	0.0
31	94.275	0.0	0.0	0.0	0.0
32	94.475	0.0	0.0	0.0	0.0
33	94.65	0.0	0.0	0.0	0.0
34	94.7	0.0	0.0	0.0	0.0
35	94.8	0.0	0.0	0.0	0.0
36	94.95	0.0	0.0	0.0	0.0
37	94.975	0.0	0.0	0.0	0.0
38	94.975	0.0	0.0	0.0	0.0
39	94.975	0.0	0.0	0.0	0.0
40	94.975	0.0	0.0	0.0	0.0
41	94.975	0.0	0.0	0.0	0.0
42	94.975	0.0	0.0	0.0	0.0
43	94.975	0.0	0.0	0.0	0.0
44	95.0	0.0	0.0	0.0	0.0
45	95.0	0.0	0.0	0.0	0.0
46	95.0	0.0	0.0	0.0	0.0
47	95.0	0.0	0.0	0.0	0.0
48	95.0	0.0	0.0	0.0	0.0
49	95.0	0.0	0.0	0.0	0.0
50	95.0	0.0	0.0	0.0	0.0
51	95.0	0.0	0.0	0.0	0.0
52	95.0	0.0	0.0	0.0	0.0
53	95.0	0.0	0.0	0.0	0.0
54	95.0	0.0	0.0	0.0	0.0
55	95.0	0.0	0.0	0.0	0.0
56	95.0	0.0	0.0	0.0	0.0
57	95.0	0.0	0.0	0.0	0.0
58	95.0	0.0	0.0	0.0	0.0
59	95.0	0.0	0.0	0.0	0.0
60	95.0	0.0	0.0	0.0	0.0
61	95.0	0.0	0.0	0.0	0.0
62	95.0	0.0	0.0	0.0	0.0
63	95.0	0.0	0.0	0.0	0.0
64	95.0	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GGATGTA	15	0.0020658788	70.00001	3
TTGTAGT	15	0.0020658788	70.00001	5
GATGTAG	15	0.0020658788	70.00001	4
GGATTGT	15	0.0020658788	70.00001	2
GTTCAAT	15	0.0020658788	70.00001	10
GATTGTA	15	0.0020658788	70.00001	3
TAGTTCA	15	0.0020658788	70.00001	8
TTGAGAT	15	0.0020658788	70.00001	2
ATTGTAG	15	0.0020658788	70.00001	4
TGTAGTT	15	0.0020658788	70.00001	6
TGTAGCT	15	0.0020658788	70.00001	6
GGGATTG	15	0.0020658788	70.00001	1
GGGATGT	15	0.0020658788	70.00001	2
ATGTAGC	15	0.0020658788	70.00001	5
GGGGATG	15	0.0020658788	70.00001	1
AGTTCAA	15	0.0020658788	70.00001	9
GTAGCTC	15	0.0020658788	70.00001	7
GTAGTTC	15	0.0020658788	70.00001	7
TAGCTCA	20	7.003785E-5	70.0	8
TTAGATC	25	2.1136815E-4	55.999996	16
>>END_MODULE
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453854 READS because READLEN < 1
Read 453854 spots for SRR11699362.sra
Written 453854 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
Rejected 453838 READS because READLEN < 1
Read 453838 spots for SRR11699362.sra
Written 453838 spots for SRR11699362.sra
SRR ids: ['SRR11699362.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_6shzhl3w
SRR11699362.sra spots: 9076776
blocks: [[1, 453838], [453839, 907676], [907677, 1361514], [1361515, 1815352], [1815353, 2269190], [2269191, 2723028], [2723029, 3176866], [3176867, 3630704], [3630705, 4084542], [4084543, 4538380], [4538381, 4992218], [4992219, 5446056], [5446057, 5899894], [5899895, 6353732], [6353733, 6807570], [6807571, 7261408], [7261409, 7715246], [7715247, 8169084], [8169085, 8622922], [8622923, 9076776]]
SRR11699362 file size 1726318
SRR11699362 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 SRR11699362 SRR11699362_1.fastq
Input file:	SRR11699362_1.fastq
trimmed:	SRR11699362-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
Wed Jun 18 21:19:56 2025 >> started

Wed Jun 18 21:36:35 2025 >> done (999.584s)
9076776 reads processed; of these:
5902092 (65.02%) short reads filtered out after trimming by size control
  23354 ( 0.26%) empty reads filtered out after trimming by size control
3151330 (34.72%) reads available; of these:
3119807 (99.00%) trimmed reads available after processing
  31523 ( 1.00%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 295662	  9.38%
 19	 392164	 12.44%
 20	 351530	 11.15%
 21	 423584	 13.44%
 22	 655743	 20.81%
 23	 180596	  5.73%
 24	 343718	 10.91%
 25	 153461	  4.87%
 26	  76095	  2.41%
 27	  59545	  1.89%
 28	  41890	  1.33%
 29	  36512	  1.16%
 30	  32113	  1.02%
 31	  23123	  0.73%
 32	  15510	  0.49%
 33	  12932	  0.41%
 34	   9108	  0.29%
 35	   7448	  0.24%
 36	   4080	  0.13%
 37	   1838	  0.06%
 38	    985	  0.03%
 39	    721	  0.02%
 40	    448	  0.01%
 41	    481	  0.02%
 42	    246	  0.01%
 43	    166	  0.01%
 44	    104	  0.00%
 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	      1	  0.00%
 76	  31523	  1.00%
3151330 reads passed initial QC


criterion=sequence-density
sequence-density=0.63
sequence-density-rank=1
fanout-score=5.64
fanout-score-rank=2
prefix-density=0.92
prefix-fanout=3.9
sequence=GTCTAGTGGTAGAATAGTACCCTGCCACGG


criterion=fanout-score
sequence-density=0.15
sequence-density-rank=18
fanout-score=23.62
fanout-score-rank=1
prefix-density=0.92
prefix-fanout=3.9
sequence=GTCTAGTGGTATGATTCTCGCTT
                                 Started job on |	Jun 18 21:40:34
                             Started mapping on |	Jun 18 21:41:10
                                    Finished on |	Jun 18 21:44:32
       Mapping speed, Million of reads per hour |	56.16

                          Number of input reads |	3151330
                      Average input read length |	22
                                    UNIQUE READS:
                   Uniquely mapped reads number |	336432
                        Uniquely mapped reads % |	10.68%
                          Average mapped length |	21.14
                       Number of splices: Total |	5578
            Number of splices: Annotated (sjdb) |	2017
                       Number of splices: GT/AG |	5231
                       Number of splices: GC/AG |	314
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	32
                      Mismatch rate per base, % |	1.02%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.28
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.12
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	376151
             % of reads mapped to multiple loci |	11.94%
        Number of reads mapped to too many loci |	440462
             % of reads mapped to too many loci |	13.98%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	2.64%
                     % of reads unmapped: other |	60.77%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2438747	2438747	2438747
N_multimapping	376151	376151	376151
N_noFeature	282557	294009	322433
N_ambiguous	2570	16	21
UnstrandedReadsAssigned:51305 PositiveStrandReadsAssigned:42407 NegativeStrandReadsAssigned:13978
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=19 echo kmer=19
SRR11699362 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: SRR11699362-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,151,330 reads, 420,729 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 823 rounds

  72540 SRR11699362.ke.tsv
  44303 SRR11699362.se.tsv
 116843 total
==> SRR11699362.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	5	3.59495
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	0.0296249	0.0331801
Zm00001eb026490_T003	2220	2121	0.970375	1.09144
Zm00001eb281360_T001	2412	2313	0	0

==> SRR11699362.se.tsv <==
Zm00001eb015280	1
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699362 completed mapping pipeline successfully
