Starting /dee2/code/volunteer_pipeline.sh SRR11699665
    current disk space = 2452389330944
    free memory = 1578533304 
SRR11699665 SRAfilesize
cda643e04d495dcd2544c488329bf62b  SRR11699665.sra
SRR11699665.sra file validated
SRR11699665 is single end
SRR11699665 is conventional basespace
SRR11699665 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699665_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	30.438	32.0	32.0	32.0	27.0	32.0
2	31.08625	32.0	32.0	32.0	32.0	32.0
3	31.20525	32.0	32.0	32.0	32.0	32.0
4	31.19775	32.0	32.0	32.0	32.0	32.0
5	31.27025	32.0	32.0	32.0	32.0	32.0
6	34.6685	36.0	36.0	36.0	32.0	36.0
7	34.776	36.0	36.0	36.0	32.0	36.0
8	34.834	36.0	36.0	36.0	32.0	36.0
9	34.519	36.0	36.0	36.0	32.0	36.0
10-11	34.717375000000004	36.0	36.0	36.0	32.0	36.0
12-13	34.80825	36.0	36.0	36.0	32.0	36.0
14-15	34.74725	36.0	36.0	36.0	32.0	36.0
16-17	34.7735	36.0	36.0	36.0	32.0	36.0
18-19	34.874375	36.0	36.0	36.0	34.0	36.0
20-21	34.742875	36.0	36.0	36.0	32.0	36.0
22-23	34.661375	36.0	36.0	36.0	32.0	36.0
24-25	34.76825	36.0	36.0	36.0	32.0	36.0
26-27	34.545375	36.0	36.0	36.0	32.0	36.0
28-29	34.59075	36.0	36.0	36.0	32.0	36.0
30-31	34.579	36.0	36.0	36.0	32.0	36.0
32-33	34.572	36.0	36.0	36.0	32.0	36.0
34-35	34.599625	36.0	36.0	36.0	32.0	36.0
36-37	34.493125	36.0	36.0	36.0	32.0	36.0
38-39	34.627875	36.0	36.0	36.0	32.0	36.0
40-41	34.468125	36.0	36.0	36.0	32.0	36.0
42-43	34.457375	36.0	36.0	36.0	32.0	36.0
44-45	34.468374999999995	36.0	36.0	36.0	32.0	36.0
46-47	34.462875	36.0	36.0	36.0	32.0	36.0
48-49	34.392625	36.0	36.0	36.0	32.0	36.0
50-51	34.110875	36.0	36.0	36.0	32.0	36.0
52-53	34.230000000000004	36.0	36.0	36.0	32.0	36.0
54-55	33.884625	36.0	36.0	36.0	32.0	36.0
56-57	33.707375	36.0	36.0	36.0	29.5	36.0
58-59	33.218	36.0	36.0	36.0	27.0	36.0
60-61	33.243375	36.0	36.0	36.0	27.0	36.0
62-63	32.850875	36.0	32.0	36.0	17.5	36.0
64-65	32.807625	36.0	32.0	36.0	21.0	36.0
66-67	32.602375	36.0	32.0	36.0	24.0	36.0
68-69	32.132875	36.0	32.0	36.0	17.5	36.0
70-71	32.332625	36.0	32.0	36.0	14.0	36.0
72-73	32.33175	36.0	32.0	36.0	14.0	36.0
74-75	32.77475	36.0	32.0	36.0	14.0	36.0
76	29.53175	32.0	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	1.0
22	3.0
23	5.0
24	12.0
25	25.0
26	38.0
27	65.0
28	80.0
29	115.0
30	143.0
31	189.0
32	245.0
33	406.0
34	1019.0
35	1653.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	32.15	28.475	22.55	16.825000000000003
2	29.25	22.275	21.85	26.625
3	26.75	25.5	16.025	31.724999999999998
4	38.05	27.275	14.85	19.825
5	25.15	25.45	26.674999999999997	22.725
6	21.85	26.700000000000003	30.9	20.549999999999997
7	38.824999999999996	29.375	18.925	12.875
8	22.125	20.825	39.975	17.075000000000003
9	21.4	39.625	18.675	20.3
10-11	35.0625	26.224999999999998	22.5875	16.125
12-13	21.6625	18.275	27.537499999999998	32.525
14-15	30.775000000000002	41.8	15.4875	11.9375
16-17	23.75	19.15	36.3625	20.7375
18-19	43.7	22.537499999999998	21.1625	12.6
20-21	20.7625	31.05	29.6375	18.55
22-23	33.6125	39.2	13.65	13.5375
24-25	29.675	39.537499999999994	14.0125	16.775000000000002
26-27	25.362499999999997	31.25	23.4125	19.975
28-29	29.9	28.8875	17.525	23.6875
30-31	30.25	32.675	14.4375	22.6375
32-33	28.875	31.55	15.3625	24.212500000000002
34-35	30.1375	31.5625	17.025000000000002	21.275
36-37	27.5125	36.55	12.862499999999999	23.075000000000003
38-39	27.0125	32.475	15.475	25.0375
40-41	27.8375	30.837500000000002	14.4875	26.8375
42-43	27.0625	33.0	15.075	24.8625
44-45	25.887500000000003	33.525	13.1375	27.450000000000003
46-47	24.175	29.612500000000004	15.287500000000001	30.925000000000004
48-49	19.25	30.012499999999996	16.8625	33.875
50-51	17.1125	32.8625	15.4	34.625
52-53	21.4	23.674999999999997	22.7	32.225
54-55	21.475	24.625	21.587500000000002	32.3125
56-57	25.224999999999998	28.8875	20.0125	25.874999999999996
58-59	19.525000000000002	31.5375	21.3875	27.55
60-61	18.8125	28.712500000000002	23.1	29.375
62-63	24.275	25.424999999999997	22.875	27.425
64-65	23.375	26.35	24.212500000000002	26.0625
66-67	22.7375	22.9875	27.487499999999997	26.787499999999998
68-69	22.3	21.912499999999998	28.125	27.6625
70-71	24.15	20.25	30.7375	24.8625
72-73	27.6875	21.212500000000002	27.025	24.075
74-75	25.087500000000002	20.3625	29.5	25.05
76	19.025	14.05	42.425000000000004	24.5
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.5
36	0.5
37	0.0
38	1.0
39	3.0
40	5.0
41	12.0
42	18.0
43	30.5
44	66.0
45	133.5
46	178.0
47	296.0
48	741.5
49	829.0
50	589.0
51	539.5
52	477.0
53	396.0
54	328.0
55	227.5
56	106.5
57	70.0
58	54.0
59	39.5
60	15.0
61	4.0
62	3.0
63	2.5
64	1.5
65	0.5
66	0.0
67	0.0
68	0.0
69	0.0
70	0.0
71	0.0
72	0.0
73	0.0
74	0.0
75	0.0
76	0.0
77	0.0
78	0.0
79	0.0
80	0.0
81	0.0
82	0.5
83	1.0
84	0.5
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.5
91	0.5
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	57.825
#Duplication Level	Percentage of deduplicated	Percentage of total
1	87.33246865542586	50.5
2	5.706874189364462	6.6000000000000005
3	2.03199308257674	3.5249999999999995
4	1.0808473843493298	2.5
5	0.8214440121054908	2.375
6	0.6917423259835711	2.4
7	0.43233895373973197	1.7500000000000002
8	0.25940337224383914	1.2
9	0.17293558149589278	0.8999999999999999
>10	1.297016861219196	17.150000000000002
>50	0.08646779074794639	3.95
>100	0.08646779074794639	7.1499999999999995
>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	152	3.8	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	134	3.35	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	89	2.225	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	69	1.725	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	48	1.2	No Hit
AGCGGAGTAGAGCAGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	47	1.175	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	44	1.0999999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	40	1.0	No Hit
GGGCCTGTAGCTCAGAGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	37	0.9249999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTA	34	0.8500000000000001	TruSeq Adapter, Index 3 (97% over 36bp)
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	29	0.7250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	29	0.7250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	29	0.7250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGCGGATGTAGCCAAGTGGAAGATCGGAAGAGCACACGTCTGAACTCCAG	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	25	0.625	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AGCGGAGTAGAGCAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCCCCCATCGTCTAGTGGTTCAGGACATCTCTCTTTAGATCGGAAGAGCA	18	0.44999999999999996	No Hit
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTAGATCGGAAGAGCACACG	17	0.42500000000000004	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTAGATCGGAAGAGCACA	17	0.42500000000000004	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTAGATCGGAAGAGCACA	16	0.4	No Hit
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	16	0.4	No Hit
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTAGATCGGAAGAGCACA	16	0.4	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	14	0.35000000000000003	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	13	0.325	No Hit
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	10	0.25	No Hit
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	10	0.25	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGAGATCGGAAGAGCACAC	10	0.25	No Hit
GCCCCCATCGTCTAGTGGTTCAGGACATCTCTCTTAGATCGGAAGAGCAC	9	0.22499999999999998	No Hit
GTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTAGATCGGAAGAGCACAC	9	0.22499999999999998	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	9	0.22499999999999998	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	8	0.2	No Hit
GGTGGCTGTAGTTTAGTGGTTAGAATTCCACGTTAGATCGGAAGAGCACA	8	0.2	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	8	0.2	No Hit
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	8	0.2	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTAGATCGGAAGAGCACAC	7	0.17500000000000002	No Hit
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
GGGATTGTAGTTCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
ACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTAGATCGGAAGAGC	7	0.17500000000000002	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTAGATCGGAAGAGCACAC	7	0.17500000000000002	No Hit
AGGGATGTAGCGCAGCTTGGTAGCTTTTGTTTTAGATCGGAAGAGCACAC	6	0.15	No Hit
GGGCATTTGGTCTAGTGGTATGATTCTCGCTTAGATCGGAAGAGCACACG	6	0.15	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	6	0.15	No Hit
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTAGATCGGAAGAGCACA	6	0.15	No Hit
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGA	6	0.15	No Hit
TGATGGTACGTGCTACTCGGATAACCGTAGTAGATCGGAAGAGCACACGT	6	0.15	No Hit
CGACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGT	6	0.15	No Hit
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAG	6	0.15	TruSeq Adapter, Index 3 (97% over 37bp)
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTAGATCGGAAGAGCACAC	6	0.15	No Hit
GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGAGATCGGAAGAGCA	6	0.15	No Hit
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	6	0.15	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCAGATCGGAAGAGCAC	6	0.15	No Hit
GCCCCCATCGTCTAGTGTTCAGGACATCTCTCTTTAGATCGGAAGAGCAC	6	0.15	No Hit
GATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGG	6	0.15	No Hit
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATCCTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAGAGAT	5	0.125	TruSeq Adapter, Index 3 (97% over 37bp)
TCCGTTGTAGTCTAGTTGGTCAGGATACTTGGCTCTAGATCGGAAGAGCA	5	0.125	No Hit
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	5	0.125	No Hit
CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGTGGCTGTAGTTTAGTGGTAAGAATTCTACGTTAGATCGGAAGAGCACA	5	0.125	No Hit
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGAGATCGGAAGAGCAC	5	0.125	No Hit
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTA	5	0.125	TruSeq Adapter, Index 3 (97% over 36bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGCCTGTAGCTCAGAGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAG	5	0.125	No Hit
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	5	0.125	No Hit
GAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
ATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAG	5	0.125	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTAGATCGGAAGAGCA	5	0.125	No Hit
CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGAGC	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	0.05	0.0	0.0	0.0	0.0
2	0.05	0.0	0.0	0.0	0.0
3	0.05	0.0	0.0	0.0	0.0
4	0.05	0.0	0.0	0.0	0.0
5	0.075	0.0	0.0	0.0	0.0
6	0.1	0.0	0.0	0.0	0.0
7	0.15	0.0	0.0	0.0	0.0
8	0.25	0.0	0.0	0.0	0.0
9	0.475	0.0	0.0	0.0	0.0
10	0.625	0.0	0.0	0.0	0.0
11	0.8	0.0	0.0	0.0	0.0
12	1.025	0.0	0.0	0.0	0.0
13	1.625	0.0	0.0	0.0	0.0
14	3.475	0.0	0.0	0.0	0.0
15	4.0	0.0	0.0	0.0	0.0
16	5.1	0.0	0.0	0.0	0.0
17	7.925	0.0	0.0	0.0	0.0
18	11.25	0.0	0.0	0.0	0.0
19	12.9	0.0	0.0	0.0	0.0
20	16.325	0.0	0.0	0.0	0.0
21	19.875	0.0	0.0	0.0	0.0
22	23.425	0.0	0.0	0.0	0.0
23	30.25	0.0	0.0	0.0	0.0
24	33.05	0.0	0.0	0.0	0.0
25	37.45	0.0	0.0	0.0	0.0
26	41.875	0.0	0.0	0.0	0.0
27	44.45	0.0	0.0	0.0	0.0
28	51.6	0.0	0.0	0.0	0.0
29	53.6	0.0	0.0	0.0	0.0
30	56.3	0.0	0.0	0.0	0.0
31	58.8	0.0	0.0	0.0	0.0
32	61.6	0.0	0.0	0.0	0.0
33	64.675	0.0	0.0	0.0	0.0
34	68.625	0.0	0.0	0.0	0.0
35	75.3	0.0	0.0	0.0	0.0
36	80.875	0.0	0.0	0.0	0.0
37	85.8	0.0	0.0	0.0	0.0
38	88.125	0.0	0.0	0.0	0.0
39	89.825	0.0	0.0	0.0	0.0
40	90.975	0.0	0.0	0.0	0.0
41	92.175	0.0	0.0	0.0	0.0
42	93.1	0.0	0.0	0.0	0.0
43	93.8	0.0	0.0	0.0	0.0
44	94.375	0.0	0.0	0.0	0.0
45	94.775	0.0	0.0	0.0	0.0
46	95.15	0.0	0.0	0.0	0.0
47	95.5	0.0	0.0	0.0	0.0
48	95.775	0.0	0.0	0.0	0.0
49	95.975	0.0	0.0	0.0	0.0
50	96.15	0.0	0.0	0.0	0.0
51	96.275	0.0	0.0	0.0	0.0
52	96.325	0.0	0.0	0.0	0.0
53	96.375	0.0	0.0	0.0	0.0
54	96.375	0.0	0.0	0.0	0.0
55	96.375	0.0	0.0	0.0	0.0
56	96.425	0.0	0.0	0.0	0.0
57	96.425	0.0	0.0	0.0	0.0
58	96.425	0.0	0.0	0.0	0.0
59	96.425	0.0	0.0	0.0	0.0
60	96.425	0.0	0.0	0.0	0.0
61	96.425	0.0	0.0	0.0	0.0
62	96.425	0.0	0.0	0.0	0.0
63	96.425	0.0	0.0	0.0	0.0
64	96.425	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
CTATAGC	15	0.0020658788	70.00001	5
TTGTAGT	35	2.6138878E-9	70.00001	5
GGCAACG	15	0.0020658788	70.00001	11
AGGGCTA	15	0.0020658788	70.00001	1
GATGTAG	15	0.0020658788	70.00001	4
GCTATAG	15	0.0020658788	70.00001	4
ATAGCTC	15	0.0020658788	70.00001	7
TGTAGTC	30	7.878043E-8	70.00001	6
GGGATGT	15	0.0020658788	70.00001	2
GGCTATA	15	0.0020658788	70.00001	3
ATGTAGC	15	0.0020658788	70.00001	5
CGGCAAC	15	0.0020658788	70.00001	10
TATAGCT	15	0.0020658788	70.00001	6
GGGCTAT	15	0.0020658788	70.00001	2
TCTAGCT	25	2.3570374E-6	70.0	11
GCTGGTC	25	2.3570374E-6	70.0	15
TCGGCAA	20	7.003785E-5	70.0	9
CTCTCGG	20	7.003785E-5	70.0	6
TAGCTGG	25	2.3570374E-6	70.0	13
>>END_MODULE
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268307 READS because READLEN < 1
Read 268307 spots for SRR11699665.sra
Written 268307 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
Rejected 268294 READS because READLEN < 1
Read 268294 spots for SRR11699665.sra
Written 268294 spots for SRR11699665.sra
SRR ids: ['SRR11699665.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ji310zvk
SRR11699665.sra spots: 5365893
blocks: [[1, 268294], [268295, 536588], [536589, 804882], [804883, 1073176], [1073177, 1341470], [1341471, 1609764], [1609765, 1878058], [1878059, 2146352], [2146353, 2414646], [2414647, 2682940], [2682941, 2951234], [2951235, 3219528], [3219529, 3487822], [3487823, 3756116], [3756117, 4024410], [4024411, 4292704], [4292705, 4560998], [4560999, 4829292], [4829293, 5097586], [5097587, 5365893]]
SRR11699665 file size 1019656
SRR11699665 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 SRR11699665 SRR11699665_1.fastq
Input file:	SRR11699665_1.fastq
trimmed:	SRR11699665-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
Sat Jun 21 20:45:54 2025 >> started

Sat Jun 21 20:45:57 2025 >> done (2.933s)
5365893 reads processed; of these:
1166881 (21.75%) short reads filtered out after trimming by size control
   9723 ( 0.18%) empty reads filtered out after trimming by size control
4189289 (78.07%) reads available; of these:
4102525 (97.93%) trimmed reads available after processing
  86764 ( 2.07%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 123721	  2.95%
 19	 227184	  5.42%
 20	 202076	  4.82%
 21	 211861	  5.06%
 22	 312897	  7.47%
 23	 147585	  3.52%
 24	 255322	  6.09%
 25	 197416	  4.71%
 26	 140569	  3.36%
 27	 339177	  8.10%
 28	 115607	  2.76%
 29	 125439	  2.99%
 30	 135944	  3.25%
 31	 123140	  2.94%
 32	 153074	  3.65%
 33	 192720	  4.60%
 34	 322059	  7.69%
 35	 230116	  5.49%
 36	 183474	  4.38%
 37	  91124	  2.18%
 38	  61318	  1.46%
 39	  49967	  1.19%
 40	  42630	  1.02%
 41	  47222	  1.13%
 42	  29788	  0.71%
 43	  23686	  0.57%
 44	  17404	  0.42%
 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	      1	  0.00%
 69	      0	  0.00%
 70	      0	  0.00%
 71	      0	  0.00%
 72	      0	  0.00%
 73	      0	  0.00%
 74	      1	  0.00%
 75	      3	  0.00%
 76	  86764	  2.07%
4189289 reads passed initial QC


criterion=sequence-density
sequence-density=8.08
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=14
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAA


criterion=fanout-score
sequence-density=0.30
sequence-density-rank=23
fanout-score=23.56
fanout-score-rank=1
prefix-density=7.11
prefix-fanout=1.0
sequence=GTCTAGCTGGTTAGGATATTCGG
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 21 20:46:19
                             Started mapping on |	Jun 21 20:46:20
                                    Finished on |	Jun 21 20:46:31
       Mapping speed, Million of reads per hour |	1371.04

                          Number of input reads |	4189289
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	266518
                        Uniquely mapped reads % |	6.36%
                          Average mapped length |	26.14
                       Number of splices: Total |	6240
            Number of splices: Annotated (sjdb) |	3086
                       Number of splices: GT/AG |	5540
                       Number of splices: GC/AG |	375
                       Number of splices: AT/AC |	5
               Number of splices: Non-canonical |	320
                      Mismatch rate per base, % |	1.06%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.57
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.09
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	427639
             % of reads mapped to multiple loci |	10.21%
        Number of reads mapped to too many loci |	1314786
             % of reads mapped to too many loci |	31.38%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.75%
                     % of reads unmapped: other |	46.29%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3495132	3495132	3495132
N_multimapping	427639	427639	427639
N_noFeature	214428	222275	257100
N_ambiguous	1609	26	19
UnstrandedReadsAssigned:50481 PositiveStrandReadsAssigned:44217 NegativeStrandReadsAssigned:9399
Dataset is classified unstranded
MeadianReadLen=27 20thPercentileLength=22 echo kmer=19
SRR11699665 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: SRR11699665-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,189,289 reads, 1,179,844 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 835 rounds

  72540 SRR11699665.ke.tsv
  44303 SRR11699665.se.tsv
 116843 total
==> SRR11699665.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	0	0
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

==> SRR11699665.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699665 completed mapping pipeline successfully
