Starting /dee2/code/volunteer_pipeline.sh SRR11699261
    current disk space = 2483437039616
    free memory = 750573116 
SRR11699261 SRAfilesize
e0e894d11bb98c14dd76a1f01d5c2a63  SRR11699261.sra
SRR11699261.sra file validated
SRR11699261 is single end
SRR11699261 is conventional basespace
SRR11699261 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699261_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	30.833	32.0	32.0	32.0	32.0	32.0
2	31.1495	32.0	32.0	32.0	32.0	32.0
3	31.4085	32.0	32.0	32.0	32.0	32.0
4	31.3695	32.0	32.0	32.0	32.0	32.0
5	31.3755	32.0	32.0	32.0	32.0	32.0
6	34.8475	36.0	36.0	36.0	32.0	36.0
7	34.962	36.0	36.0	36.0	32.0	36.0
8	34.98625	36.0	36.0	36.0	36.0	36.0
9	34.74175	36.0	36.0	36.0	32.0	36.0
10-11	34.957125000000005	36.0	36.0	36.0	36.0	36.0
12-13	34.93625	36.0	36.0	36.0	36.0	36.0
14-15	34.812875000000005	36.0	36.0	36.0	32.0	36.0
16-17	34.936625	36.0	36.0	36.0	36.0	36.0
18-19	34.930625	36.0	36.0	36.0	34.0	36.0
20-21	34.7705	36.0	36.0	36.0	34.0	36.0
22-23	34.7775	36.0	36.0	36.0	34.0	36.0
24-25	34.891999999999996	36.0	36.0	36.0	36.0	36.0
26-27	34.725750000000005	36.0	36.0	36.0	32.0	36.0
28-29	34.751374999999996	36.0	36.0	36.0	34.0	36.0
30-31	34.645125	36.0	36.0	36.0	34.0	36.0
32-33	34.693375	36.0	36.0	36.0	32.0	36.0
34-35	34.76075	36.0	36.0	36.0	34.0	36.0
36-37	34.5995	36.0	36.0	36.0	32.0	36.0
38-39	34.75675	36.0	36.0	36.0	34.0	36.0
40-41	34.6875	36.0	36.0	36.0	32.0	36.0
42-43	34.59975	36.0	36.0	36.0	32.0	36.0
44-45	34.713	36.0	36.0	36.0	32.0	36.0
46-47	34.769000000000005	36.0	36.0	36.0	34.0	36.0
48-49	34.569125	36.0	36.0	36.0	32.0	36.0
50-51	34.261375	36.0	36.0	36.0	32.0	36.0
52-53	34.2735	36.0	36.0	36.0	32.0	36.0
54-55	33.809375	36.0	36.0	36.0	29.5	36.0
56-57	33.44262500000001	36.0	36.0	36.0	27.0	36.0
58-59	33.473375000000004	36.0	36.0	36.0	27.0	36.0
60-61	33.549875	36.0	36.0	36.0	27.0	36.0
62-63	33.315625	36.0	34.0	36.0	27.0	36.0
64-65	33.164500000000004	36.0	32.0	36.0	27.0	36.0
66-67	32.65475	36.0	32.0	36.0	27.0	36.0
68-69	32.79	36.0	32.0	36.0	27.0	36.0
70-71	32.95725	36.0	32.0	36.0	27.0	36.0
72-73	32.557500000000005	36.0	32.0	36.0	20.5	36.0
74-75	32.96275	36.0	32.0	36.0	21.0	36.0
76	30.915	36.0	32.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	2.0
22	5.0
23	9.0
24	5.0
25	19.0
26	22.0
27	44.0
28	51.0
29	108.0
30	119.0
31	186.0
32	240.0
33	399.0
34	1034.0
35	1757.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	25.624999999999996	28.625	23.724999999999998	22.025
2	24.375	25.174999999999997	25.35	25.1
3	26.35	32.1	14.549999999999999	27.0
4	32.25	32.6	17.175	17.974999999999998
5	20.8	27.925	25.674999999999997	25.6
6	25.424999999999997	25.174999999999997	30.7	18.7
7	34.25	35.125	17.05	13.575000000000001
8	19.35	26.55	36.375	17.724999999999998
9	23.799999999999997	37.375	16.7	22.125
10-11	32.925	27.5875	21.912499999999998	17.575
12-13	20.5125	22.475	25.900000000000002	31.112499999999997
14-15	31.35	40.1	16.3375	12.2125
16-17	21.725	21.975	36.7375	19.5625
18-19	40.325	22.325	23.2125	14.1375
20-21	22.15	35.112500000000004	26.1	16.6375
22-23	33.1	40.400000000000006	12.4875	14.0125
24-25	30.6875	39.825	13.750000000000002	15.737499999999999
26-27	27.075	31.624999999999996	19.35	21.95
28-29	32.074999999999996	28.712500000000002	15.3625	23.849999999999998
30-31	31.724999999999998	36.875	10.037500000000001	21.3625
32-33	29.362500000000004	36.0	12.587499999999999	22.05
34-35	30.2	28.95	15.1	25.75
36-37	26.787499999999998	35.5125	10.35	27.35
38-39	22.162499999999998	34.725	14.075	29.037499999999998
40-41	24.7	27.5875	17.675	30.0375
42-43	26.4625	26.25	19.6375	27.650000000000002
44-45	21.462500000000002	33.4625	15.8875	29.1875
46-47	19.575	31.0125	15.15	34.2625
48-49	17.5625	28.000000000000004	18.7375	35.699999999999996
50-51	15.012500000000001	28.4	19.8	36.7875
52-53	21.4875	27.5875	20.5125	30.412499999999998
54-55	17.2625	28.8375	20.0625	33.8375
56-57	20.575	25.8	21.5	32.125
58-59	17.0875	29.549999999999997	22.6375	30.725
60-61	16.525000000000002	30.0375	24.9	28.537499999999998
62-63	20.1375	28.012500000000003	23.025000000000002	28.825
64-65	19.9625	20.925	26.237500000000004	32.875
66-67	19.4625	17.875	32.1625	30.5
68-69	19.537499999999998	19.0	32.25	29.212500000000002
70-71	21.8125	19.3	33.550000000000004	25.337500000000002
72-73	21.925	13.900000000000002	31.837500000000002	32.337500000000006
74-75	23.125	12.4625	31.85	32.5625
76	20.65	10.299999999999999	42.05	27.0
>>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	0.0
36	1.0
37	2.0
38	2.0
39	5.0
40	6.0
41	10.0
42	16.0
43	28.5
44	64.0
45	122.0
46	157.0
47	293.5
48	788.0
49	887.5
50	629.0
51	570.5
52	477.5
53	360.0
54	277.0
55	197.0
56	83.0
57	48.0
58	47.0
59	32.0
60	11.5
61	4.5
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	0.0
83	0.0
84	0.5
85	0.5
86	0.0
87	0.0
88	0.0
89	0.0
90	1.0
91	1.0
92	0.0
93	0.0
94	0.5
95	0.5
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	57.8
#Duplication Level	Percentage of deduplicated	Percentage of total
1	87.84602076124568	50.775000000000006
2	5.493079584775087	6.35
3	1.8166089965397925	3.15
4	1.2110726643598615	2.8000000000000003
5	0.9948096885813149	2.875
6	0.3027681660899654	1.05
7	0.17301038062283738	0.7000000000000001
8	0.17301038062283738	0.8
9	0.3027681660899654	1.575
>10	1.4705882352941175	17.325
>50	0.17301038062283738	6.625
>100	0.043252595155709346	5.975
>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	239	5.975	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAT	70	1.7500000000000002	TruSeq Adapter, Index 9 (100% over 36bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	70	1.7500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	64	1.6	No Hit
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	61	1.525	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	49	1.225	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	43	1.075	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	42	1.05	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	34	0.8500000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	32	0.8	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	32	0.8	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	31	0.775	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATC	30	0.75	TruSeq Adapter, Index 9 (100% over 37bp)
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	29	0.7250000000000001	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	27	0.675	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	25	0.625	No Hit
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	23	0.575	No Hit
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGA	17	0.42500000000000004	TruSeq Adapter, Index 7 (97% over 35bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATCGGAAGAGCACACGTCTGAACTCCAGTCACGATC	14	0.35000000000000003	TruSeq Adapter, Index 9 (97% over 37bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAT	13	0.325	TruSeq Adapter, Index 9 (100% over 36bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGA	12	0.3	TruSeq Adapter, Index 7 (97% over 35bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	12	0.3	No Hit
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGAT	12	0.3	TruSeq Adapter, Index 9 (100% over 41bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGCTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	12	0.3	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	12	0.3	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	11	0.27499999999999997	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	10	0.25	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	10	0.25	No Hit
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAGATCGGAAGAGCACA	10	0.25	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	10	0.25	No Hit
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAG	9	0.22499999999999998	TruSeq Adapter, Index 9 (100% over 39bp)
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	9	0.22499999999999998	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	8	0.2	No Hit
ACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	8	0.2	No Hit
GAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAT	8	0.2	TruSeq Adapter, Index 9 (100% over 36bp)
CTAACGAACGAACGATTTGAACAAATCGGAAGAGCACACGTCTGAACTCC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (96% over 28bp)
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AGATCATGTTGCAGCTTCACTAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA	6	0.15	No Hit
CGACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	6	0.15	No Hit
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	6	0.15	No Hit
AACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	6	0.15	No Hit
GGTAGTTCGACCGTGGATTAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGAGATCGGAAGAGCACACG	5	0.125	No Hit
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGTAGATCGGAAGAGCA	5	0.125	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	5	0.125	No Hit
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGA	5	0.125	TruSeq Adapter, Index 9 (100% over 40bp)
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGGCATTTGGTCTAGTGGTATGATTCTCAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
ACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGA	5	0.125	TruSeq Adapter, Index 7 (97% over 35bp)
GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAGATCGGAAGAGCAC	5	0.125	No Hit
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTAGATCGGAAGAGCACA	5	0.125	No Hit
GCACCAGTGGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
AGGGCTATAGCTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAT	5	0.125	TruSeq Adapter, Index 9 (100% over 36bp)
GGGGATGTAGCTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAT	5	0.125	TruSeq Adapter, Index 9 (100% over 36bp)
CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	5	0.125	No Hit
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GGGCCTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAT	5	0.125	TruSeq Adapter, Index 9 (100% 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	0.05	0.0	0.0	0.0	0.0
2	0.075	0.0	0.0	0.0	0.0
3	0.1	0.0	0.0	0.0	0.0
4	0.1	0.0	0.0	0.0	0.0
5	0.15	0.0	0.0	0.0	0.0
6	0.25	0.0	0.0	0.0	0.0
7	0.35	0.0	0.0	0.0	0.0
8	0.45	0.0	0.0	0.0	0.0
9	0.825	0.0	0.0	0.0	0.0
10	1.2	0.0	0.0	0.0	0.0
11	1.7	0.0	0.0	0.0	0.0
12	2.125	0.0	0.0	0.0	0.0
13	3.45	0.0	0.0	0.0	0.0
14	7.175	0.0	0.0	0.0	0.0
15	9.45	0.0	0.0	0.0	0.0
16	10.925	0.0	0.0	0.0	0.0
17	14.45	0.0	0.0	0.0	0.0
18	17.125	0.0	0.0	0.0	0.0
19	19.425	0.0	0.0	0.0	0.0
20	22.8	0.0	0.0	0.0	0.0
21	27.1	0.0	0.0	0.0	0.0
22	32.8	0.0	0.0	0.0	0.0
23	43.55	0.0	0.0	0.0	0.0
24	46.475	0.0	0.0	0.0	0.0
25	53.45	0.0	0.0	0.0	0.0
26	57.15	0.0	0.0	0.0	0.0
27	59.825	0.0	0.0	0.0	0.0
28	63.5	0.0	0.0	0.0	0.0
29	65.45	0.0	0.0	0.0	0.0
30	67.95	0.0	0.0	0.0	0.0
31	73.575	0.0	0.0	0.0	0.0
32	75.15	0.0	0.0	0.0	0.0
33	77.275	0.0	0.0	0.0	0.0
34	79.4	0.0	0.0	0.0	0.0
35	82.425	0.0	0.0	0.0	0.0
36	85.95	0.0	0.0	0.0	0.0
37	88.525	0.0	0.0	0.0	0.0
38	89.75	0.0	0.0	0.0	0.0
39	90.675	0.0	0.0	0.0	0.0
40	91.125	0.0	0.0	0.0	0.0
41	91.55	0.0	0.0	0.0	0.0
42	92.225	0.0	0.0	0.0	0.0
43	92.5	0.0	0.0	0.0	0.0
44	92.675	0.0	0.0	0.0	0.0
45	92.8	0.0	0.0	0.0	0.0
46	92.925	0.0	0.0	0.0	0.0
47	93.0	0.0	0.0	0.0	0.0
48	93.075	0.0	0.0	0.0	0.0
49	93.1	0.0	0.0	0.0	0.0
50	93.1	0.0	0.0	0.0	0.0
51	93.1	0.0	0.0	0.0	0.0
52	93.1	0.0	0.0	0.0	0.0
53	93.1	0.0	0.0	0.0	0.0
54	93.125	0.0	0.0	0.0	0.0
55	93.125	0.0	0.0	0.0	0.0
56	93.125	0.0	0.0	0.0	0.0
57	93.125	0.0	0.0	0.0	0.0
58	93.125	0.0	0.0	0.0	0.0
59	93.125	0.0	0.0	0.0	0.0
60	93.125	0.0	0.0	0.0	0.0
61	93.125	0.0	0.0	0.0	0.0
62	93.125	0.0	0.0	0.0	0.0
63	93.125	0.0	0.0	0.0	0.0
64	93.125	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GGATGTA	30	7.878043E-8	70.00001	3
TGGTCAG	35	2.6138878E-9	70.00001	17
AGCTCAG	45	3.6379788E-12	70.00001	9
GCTGGTC	15	0.0020658788	70.00001	15
GATGTAG	30	7.878043E-8	70.00001	4
TAGCTCA	45	3.6379788E-12	70.00001	8
CCGTTGT	30	7.878043E-8	70.00001	2
TAGTCTA	30	7.878043E-8	70.00001	8
CTGGTCA	15	0.0020658788	70.00001	16
TGTAGTC	30	7.878043E-8	70.00001	6
GGGATGT	30	7.878043E-8	70.00001	2
TCCGTTG	30	7.878043E-8	70.00001	1
CGTTGTA	30	7.878043E-8	70.00001	3
ATGTAGC	30	7.878043E-8	70.00001	5
AGTCTAG	30	7.878043E-8	70.00001	9
GGGGATG	30	7.878043E-8	70.00001	1
GTAGTCT	30	7.878043E-8	70.00001	7
GTTGTAG	30	7.878043E-8	70.00001	4
TCTAGCT	20	7.003785E-5	70.0	11
GATACTC	20	7.003785E-5	70.0	24
>>END_MODULE
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Written 216899 spots for SRR11699261.sra
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216905 READS because READLEN < 1
Read 216905 spots for SRR11699261.sra
Written 216905 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
Rejected 216899 READS because READLEN < 1
Read 216899 spots for SRR11699261.sra
Written 216899 spots for SRR11699261.sra
SRR ids: ['SRR11699261.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_jfnqhlpi
SRR11699261.sra spots: 4337986
blocks: [[1, 216899], [216900, 433798], [433799, 650697], [650698, 867596], [867597, 1084495], [1084496, 1301394], [1301395, 1518293], [1518294, 1735192], [1735193, 1952091], [1952092, 2168990], [2168991, 2385889], [2385890, 2602788], [2602789, 2819687], [2819688, 3036586], [3036587, 3253485], [3253486, 3470384], [3470385, 3687283], [3687284, 3904182], [3904183, 4121081], [4121082, 4337986]]
SRR11699261 file size 823912
SRR11699261 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 SRR11699261 SRR11699261_1.fastq
Input file:	SRR11699261_1.fastq
trimmed:	SRR11699261-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 02:25:35 2025 >> started

Wed Jun 18 02:25:37 2025 >> done (1.765s)
4337986 reads processed; of these:
1124878 (25.93%) short reads filtered out after trimming by size control
   2318 ( 0.05%) empty reads filtered out after trimming by size control
3210790 (74.02%) reads available; of these:
3179065 (99.01%) trimmed reads available after processing
  31725 ( 0.99%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 115100	  3.58%
 19	 176973	  5.51%
 20	 193758	  6.03%
 21	 242361	  7.55%
 22	 381247	 11.87%
 23	 137215	  4.27%
 24	 303124	  9.44%
 25	 185521	  5.78%
 26	 109707	  3.42%
 27	 144860	  4.51%
 28	  84946	  2.65%
 29	  92777	  2.89%
 30	 228048	  7.10%
 31	  82967	  2.58%
 32	  86692	  2.70%
 33	 104581	  3.26%
 34	 114200	  3.56%
 35	 131606	  4.10%
 36	  94913	  2.96%
 37	  44466	  1.38%
 38	  29151	  0.91%
 39	  23358	  0.73%
 40	  17970	  0.56%
 41	  27924	  0.87%
 42	  11637	  0.36%
 43	   8598	  0.27%
 44	   5362	  0.17%
 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	      1	  0.00%
 66	      0	  0.00%
 67	      0	  0.00%
 68	      0	  0.00%
 69	      0	  0.00%
 70	      0	  0.00%
 71	      0	  0.00%
 72	      1	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      1	  0.00%
 76	  31725	  0.99%
3210790 reads passed initial QC


criterion=sequence-density
sequence-density=7.52
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=15
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATA


criterion=fanout-score
sequence-density=0.47
sequence-density-rank=20
fanout-score=22.13
fanout-score-rank=1
prefix-density=1.86
prefix-fanout=5.6
sequence=TAGCTCAGTGGTAGAGCGGTCGGCTGTT
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 18 02:26:06
                             Started mapping on |	Jun 18 02:26:06
                                    Finished on |	Jun 18 02:26:20
       Mapping speed, Million of reads per hour |	825.63

                          Number of input reads |	3210790
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	283551
                        Uniquely mapped reads % |	8.83%
                          Average mapped length |	23.88
                       Number of splices: Total |	6017
            Number of splices: Annotated (sjdb) |	2703
                       Number of splices: GT/AG |	5576
                       Number of splices: GC/AG |	321
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	118
                      Mismatch rate per base, % |	1.07%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.46
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.17
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	467880
             % of reads mapped to multiple loci |	14.57%
        Number of reads mapped to too many loci |	814842
             % of reads mapped to too many loci |	25.38%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	4.70%
                     % of reads unmapped: other |	46.52%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2459359	2459359	2459359
N_multimapping	467880	467880	467880
N_noFeature	227248	237664	271748
N_ambiguous	1411	15	12
UnstrandedReadsAssigned:54892 PositiveStrandReadsAssigned:45872 NegativeStrandReadsAssigned:11791
Dataset is classified unstranded
MeadianReadLen=25 20thPercentileLength=21 echo kmer=19
SRR11699261 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: SRR11699261-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,210,790 reads, 729,690 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 892 rounds

  72540 SRR11699261.ke.tsv
  44303 SRR11699261.se.tsv
 116843 total
==> SRR11699261.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	1	0.486146
Zm00001eb323640_T001	3273	3174	0	0
Zm00001eb314140_T001	893	794	0	0
Zm00001eb080260_T001	3529	3430	1	0.470272
Zm00001eb026490_T001	2433	2334	0	0
Zm00001eb026490_T002	2229	2130	0	0
Zm00001eb026490_T003	2220	2121	0	0
Zm00001eb281360_T001	2412	2313	0	0

==> SRR11699261.se.tsv <==
Zm00001eb015280	2
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699261 completed mapping pipeline successfully
