Starting /dee2/code/volunteer_pipeline.sh SRR11699512
    current disk space = 2464401965056
    free memory = 1580258344 
SRR11699512 SRAfilesize
fba09a9b4d9a12ee68e7140005fdb0fb  SRR11699512.sra
SRR11699512.sra file validated
SRR11699512 is single end
SRR11699512 is conventional basespace
SRR11699512 read1 length is 86 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699512_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	86
%GC	48
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.51425	32.0	32.0	32.0	32.0	32.0
2	31.51375	32.0	32.0	32.0	32.0	32.0
3	31.566	32.0	32.0	32.0	32.0	32.0
4	31.4435	32.0	32.0	32.0	32.0	32.0
5	31.53	32.0	32.0	32.0	32.0	32.0
6	35.014	36.0	36.0	36.0	36.0	36.0
7	35.1025	36.0	36.0	36.0	36.0	36.0
8	35.11225	36.0	36.0	36.0	36.0	36.0
9	34.94125	36.0	36.0	36.0	36.0	36.0
10-11	35.15375	36.0	36.0	36.0	36.0	36.0
12-13	35.018875	36.0	36.0	36.0	36.0	36.0
14-15	35.11825	36.0	36.0	36.0	36.0	36.0
16-17	35.104875	36.0	36.0	36.0	36.0	36.0
18-19	35.282	36.0	36.0	36.0	36.0	36.0
20-21	35.09625	36.0	36.0	36.0	36.0	36.0
22-23	35.08125	36.0	36.0	36.0	36.0	36.0
24-25	34.932249999999996	36.0	36.0	36.0	36.0	36.0
26-27	34.804625	36.0	36.0	36.0	34.0	36.0
28-29	34.9095	36.0	36.0	36.0	36.0	36.0
30-31	35.0725	36.0	36.0	36.0	36.0	36.0
32-33	34.927	36.0	36.0	36.0	36.0	36.0
34-35	35.01775000000001	36.0	36.0	36.0	36.0	36.0
36-37	34.950500000000005	36.0	36.0	36.0	36.0	36.0
38-39	35.0075	36.0	36.0	36.0	36.0	36.0
40-41	34.895125	36.0	36.0	36.0	34.0	36.0
42-43	34.782	36.0	36.0	36.0	36.0	36.0
44-45	34.804625	36.0	36.0	36.0	34.0	36.0
46-47	34.957875	36.0	36.0	36.0	36.0	36.0
48-49	34.845	36.0	36.0	36.0	32.0	36.0
50-51	34.7085	36.0	36.0	36.0	32.0	36.0
52-53	34.701375	36.0	36.0	36.0	34.0	36.0
54-55	34.235749999999996	36.0	36.0	36.0	32.0	36.0
56-57	34.058499999999995	36.0	36.0	36.0	32.0	36.0
58-59	33.67	36.0	36.0	36.0	27.0	36.0
60-61	33.407875000000004	36.0	36.0	36.0	24.0	36.0
62-63	33.04325	36.0	34.0	36.0	21.0	36.0
64-65	32.56325	36.0	32.0	36.0	14.0	36.0
66-67	32.022	36.0	32.0	36.0	14.0	36.0
68-69	31.606625	36.0	32.0	36.0	14.0	36.0
70-71	31.506875	36.0	32.0	36.0	14.0	36.0
72-73	31.483	36.0	29.5	36.0	14.0	36.0
74-75	31.435125	36.0	32.0	36.0	14.0	36.0
76-77	31.646	36.0	32.0	36.0	14.0	36.0
78-79	31.41375	36.0	32.0	36.0	14.0	36.0
80-81	31.5965	36.0	32.0	36.0	14.0	36.0
82-83	31.474625000000003	36.0	32.0	36.0	14.0	36.0
84-85	31.70225	36.0	32.0	36.0	14.0	36.0
86	28.34675	36.0	14.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
19	1.0
20	1.0
21	1.0
22	4.0
23	5.0
24	14.0
25	27.0
26	43.0
27	57.0
28	72.0
29	98.0
30	132.0
31	189.0
32	320.0
33	559.0
34	1105.0
35	1372.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	24.356089022255563	27.881970492623154	23.355838959739934	24.406101525381345
2	24.099999999999998	26.3	26.125	23.474999999999998
3	24.875	35.0	17.775	22.35
4	24.875	38.824999999999996	16.375	19.925
5	20.5	26.35	23.025000000000002	30.125
6	27.56378189094547	24.337168584292147	27.088544272136065	21.010505252626313
7	32.0	34.175	16.950000000000003	16.875
8	22.125	28.125	28.499999999999996	21.25
9	23.275000000000002	31.0	19.75	25.974999999999998
10-11	32.725	25.825	23.0375	18.4125
12-13	21.837500000000002	23.3875	23.175	31.6
14-15	29.799999999999997	36.9	16.900000000000002	16.400000000000002
16-17	21.6625	22.825	34.3125	21.2
18-19	38.487500000000004	22.900000000000002	22.1	16.5125
20-21	23.849999999999998	35.3875	23.6375	17.125
22-23	31.55	36.075	16.4375	15.937499999999998
24-25	30.062499999999996	37.7125	16.25	15.975
26-27	28.091011376422053	32.29153644205526	17.87723465433179	21.7402175271909
28-29	33.366670833854236	29.078634829353668	14.526815851981498	23.0278784848106
30-31	34.325	35.375	10.9625	19.3375
32-33	29.8375	39.4125	10.65	20.1
34-35	31.2625	33.8375	11.637500000000001	23.2625
36-37	26.875	35.325	9.887500000000001	27.9125
38-39	24.474999999999998	32.824999999999996	12.475	30.225
40-41	25.9875	29.212500000000002	16.2125	28.5875
42-43	26.7625	27.3375	20.7	25.2
44-45	22.1875	33.575	16.55	27.6875
46-47	20.7	30.85	16.3375	32.1125
48-49	15.4875	27.987499999999997	18.35	38.175
50-51	15.48943617952244	28.90361295161895	19.17739717464683	36.429553694211776
52-53	17.827228403550443	24.415551943992998	25.028128516064506	32.72909113639205
54-55	15.625	25.8	24.25	34.325
56-57	13.4125	26.2875	28.575	31.724999999999998
58-59	16.3	25.674999999999997	26.1125	31.912499999999998
60-61	13.200000000000001	22.112499999999997	35.0875	29.599999999999998
62-63	11.862499999999999	23.075000000000003	35.525	29.5375
64-65	12.226528316039504	20.55256907113389	36.92961620202525	30.291286410801348
66-67	14.774999999999999	16.650000000000002	36.9375	31.637500000000003
68-69	15.064383047880986	17.039629953744218	38.14226778347293	29.753719214901864
70-71	19.6875	17.599999999999998	38.487500000000004	24.224999999999998
72-73	19.444791796923848	13.680130048768287	34.71301738151807	32.16206077278979
74-75	20.705176294073517	10.640160040010002	36.98424606151538	31.670417604401102
76-77	18.869576091034137	9.115918469426035	39.43978992122046	32.57471551831937
78-79	14.067775415780917	9.878704514192822	45.11691884456671	30.936601225459547
80-81	19.474671669793622	10.8692933083177	43.42714196372733	26.22889305816135
82-83	18.265982734893033	17.052420868259727	36.869761040910795	27.81183535593644
84-85	21.128346259694773	20.778083562672002	35.62672004003002	22.466850137603203
86	19.494494494494493	29.22922922922923	31.556556556556558	19.71971971971972
>>END_MODULE
>>Per sequence GC content	warn
#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	0.5
26	0.5
27	0.0
28	0.0
29	0.0
30	0.5
31	0.5
32	0.5
33	0.5
34	0.0
35	1.5
36	3.0
37	1.5
38	1.0
39	3.0
40	16.0
41	40.0
42	97.5
43	143.0
44	184.0
45	261.0
46	418.5
47	568.0
48	545.0
49	449.5
50	405.0
51	438.5
52	381.5
53	227.0
54	144.5
55	104.0
56	61.0
57	40.0
58	27.0
59	10.0
60	6.0
61	5.0
62	2.5
63	1.5
64	2.0
65	1.0
66	0.5
67	0.5
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	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.025
2	0.0
3	0.0
4	0.0
5	0.0
6	0.05
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	0.0125
28-29	0.0125
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	0.0125
52-53	0.0125
54-55	0.0
56-57	0.0
58-59	0.0
60-61	0.0
62-63	0.0
64-65	0.0125
66-67	0.0
68-69	0.0125
70-71	0.0
72-73	0.0375
74-75	0.025
76-77	0.0375
78-79	0.0375
80-81	0.0625
82-83	0.08750000000000001
84-85	0.075
86	0.1
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
86	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	64.25
#Duplication Level	Percentage of deduplicated	Percentage of total
1	87.8988326848249	56.474999999999994
2	5.680933852140078	7.3
3	1.8287937743190663	3.5249999999999995
4	0.9727626459143969	2.5
5	0.8560311284046693	2.75
6	0.5058365758754864	1.95
7	0.2723735408560311	1.225
8	0.5058365758754864	2.6
9	0.23346303501945526	1.35
>10	1.1673151750972763	12.85
>50	0.0	0.0
>100	0.07782101167315175	7.475
>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	177	4.425	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	122	3.05	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	39	0.975	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	36	0.8999999999999999	No Hit
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	36	0.8999999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	30	0.75	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAG	24	0.6	TruSeq Adapter, Index 7 (97% over 36bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAG	20	0.5	TruSeq Adapter, Index 7 (97% over 36bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA	17	0.42500000000000004	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	17	0.42500000000000004	No Hit
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	12	0.3	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG	12	0.3	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	12	0.3	No Hit
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	12	0.3	No Hit
TCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	11	0.27499999999999997	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GGGATTGTAGTTCAATTGGTCAGAGCAGATCGGAAGAGCACACGTCTGAA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	10	0.25	No Hit
GCGACCCCAGGTCAGTCGGGAGATCGGAAGAGCACACGTCTGAACTCCAG	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CGACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	9	0.22499999999999998	No Hit
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	9	0.22499999999999998	No Hit
GGTAGTTCGACCGTGGATTAGATCGGAAGAGCACACGTCTGAACTCCAGT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCA	8	0.2	No Hit
GGGATTGTAGTTCAATTGGTCAGAAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTC	8	0.2	No Hit
CCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCTCATGGAGAGTTCGATCCTGGCTAGATCGGAAGAGCACACGTCTGAAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	8	0.2	No Hit
GCGACCCCAGGTCAGTCGGGACTACCCGCTAGATCGGAAGAGCACACGTC	8	0.2	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	8	0.2	No Hit
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
ACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGC	7	0.17500000000000002	TruSeq Adapter, Index 10 (100% over 37bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	6	0.15	No Hit
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAGATCGGAAGAGC	6	0.15	No Hit
AGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACA	6	0.15	No Hit
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	6	0.15	No Hit
TCTCATGGAGAGTTCGATCCTGGCAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
AGCGGAGTAGAGCAGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CGACACGACTCTCGGCAACGGATATCTCGGCTCTCAGATCGGAAGAGCAC	6	0.15	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	6	0.15	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAAAGATCGGAAGAGCA	5	0.125	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAGATCGGAAGA	5	0.125	No Hit
GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCT	5	0.125	TruSeq Adapter, Index 10 (100% over 38bp)
ACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CGACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACA	5	0.125	No Hit
GCCCCCATCGTCTAGTGGTTCAGGACATCTCTCTTTAGATCGGAAGAGCA	5	0.125	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TGGAAGGGGCATGCAGAGGAGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	5	0.125	No Hit
TCAAAAGAGGAAAGGCTTGCGGTGGATAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
ACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCTCATGGAGAGTTCGATCCTGGCTCAGGAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTAGATCGGAAGAGC	5	0.125	No Hit
GAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAG	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	5	0.125	No Hit
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTAT	5	0.125	TruSeq Adapter, Index 10 (100% over 41bp)
CGACACGACTCTCGGCAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GATAAAAGGCTGACGCGGGCTCTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
>>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	0.125	0.0	0.0	0.0	0.0
4	0.125	0.0	0.0	0.0	0.0
5	0.15	0.0	0.0	0.0	0.0
6	0.175	0.0	0.0	0.0	0.0
7	0.2	0.0	0.0	0.0	0.0
8	0.25	0.0	0.0	0.0	0.0
9	0.4	0.0	0.0	0.0	0.0
10	0.525	0.0	0.0	0.0	0.0
11	0.7	0.0	0.0	0.0	0.0
12	1.075	0.0	0.0	0.0	0.0
13	1.625	0.0	0.0	0.0	0.0
14	3.525	0.0	0.0	0.0	0.0
15	4.2	0.0	0.0	0.0	0.0
16	5.2	0.0	0.0	0.0	0.0
17	7.525	0.0	0.0	0.0	0.0
18	10.2	0.0	0.0	0.0	0.0
19	12.375	0.0	0.0	0.0	0.0
20	15.625	0.0	0.0	0.0	0.0
21	19.1	0.0	0.0	0.0	0.0
22	26.625	0.0	0.0	0.0	0.0
23	35.9	0.0	0.0	0.0	0.0
24	40.025	0.0	0.0	0.0	0.0
25	48.875	0.0	0.0	0.0	0.0
26	52.65	0.0	0.0	0.0	0.0
27	56.35	0.0	0.0	0.0	0.0
28	60.6	0.0	0.0	0.0	0.0
29	62.975	0.0	0.0	0.0	0.0
30	65.775	0.0	0.0	0.0	0.0
31	69.075	0.0	0.0	0.0	0.0
32	71.7	0.0	0.0	0.0	0.0
33	74.2	0.0	0.0	0.0	0.0
34	76.925	0.0	0.0	0.0	0.0
35	80.95	0.0	0.0	0.0	0.0
36	84.75	0.0	0.0	0.0	0.0
37	87.125	0.0	0.0	0.0	0.0
38	88.825	0.0	0.0	0.0	0.0
39	89.925	0.0	0.0	0.0	0.0
40	90.8	0.0	0.0	0.0	0.0
41	91.45	0.0	0.0	0.0	0.0
42	92.55	0.0	0.0	0.0	0.0
43	93.025	0.0	0.0	0.0	0.0
44	93.575	0.0	0.0	0.0	0.0
45	93.7	0.0	0.0	0.0	0.0
46	93.85	0.0	0.0	0.0	0.0
47	93.925	0.0	0.0	0.0	0.0
48	94.05	0.0	0.0	0.0	0.0
49	94.25	0.0	0.0	0.0	0.0
50	94.325	0.0	0.0	0.0	0.0
51	94.35	0.0	0.0	0.0	0.0
52	94.35	0.0	0.0	0.0	0.0
53	94.35	0.0	0.0	0.0	0.0
54	94.35	0.0	0.0	0.0	0.0
55	94.35	0.0	0.0	0.0	0.0
56	94.375	0.0	0.0	0.0	0.0
57	94.375	0.0	0.0	0.0	0.0
58	94.375	0.0	0.0	0.0	0.0
59	94.375	0.0	0.0	0.0	0.0
60	94.375	0.0	0.0	0.0	0.0
61	94.375	0.0	0.0	0.0	0.0
62	94.375	0.0	0.0	0.0	0.0
63	94.375	0.0	0.0	0.0	0.0
64	94.375	0.0	0.0	0.0	0.0
65	94.375	0.0	0.0	0.0	0.0
66	94.375	0.0	0.0	0.0	0.0
67	94.375	0.0	0.0	0.0	0.0
68	94.375	0.0	0.0	0.0	0.0
69	94.375	0.0	0.0	0.0	0.0
70	94.375	0.0	0.0	0.0	0.0
71	94.375	0.0	0.0	0.0	0.0
72	94.375	0.0	0.0	0.0	0.0
73	94.375	0.0	0.0	0.0	0.0
74	94.375	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTGTCCT	15	0.0012159165	80.00001	8
TGTCCTA	15	0.0012159165	80.00001	9
TTGTAGT	30	3.1202944E-8	80.00001	5
TCTGGTG	15	0.0012159165	80.00001	4
TTCTGGT	15	0.0012159165	80.00001	3
GGATTGT	15	0.0012159165	80.00001	2
CCGTTGT	15	0.0012159165	80.00001	2
TAGTCTA	15	0.0012159165	80.00001	8
GATTGTA	15	0.0012159165	80.00001	3
TAGTTCA	20	3.6123936E-5	80.00001	8
CTGGTGT	15	0.0012159165	80.00001	5
ATTGTAG	15	0.0012159165	80.00001	4
TATTCTG	15	0.0012159165	80.00001	1
TGTAGTT	15	0.0012159165	80.00001	6
TGTAGTC	15	0.0012159165	80.00001	6
GGGATTG	15	0.0012159165	80.00001	1
TCCGTTG	15	0.0012159165	80.00001	1
CGTTGTA	15	0.0012159165	80.00001	3
ATTCTGG	15	0.0012159165	80.00001	2
TGGTGTC	15	0.0012159165	80.00001	6
>>END_MODULE
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283045 READS because READLEN < 1
Read 283045 spots for SRR11699512.sra
Written 283045 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
Rejected 283026 READS because READLEN < 1
Read 283026 spots for SRR11699512.sra
Written 283026 spots for SRR11699512.sra
SRR ids: ['SRR11699512.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_910ps4d7
SRR11699512.sra spots: 5660539
blocks: [[1, 283026], [283027, 566052], [566053, 849078], [849079, 1132104], [1132105, 1415130], [1415131, 1698156], [1698157, 1981182], [1981183, 2264208], [2264209, 2547234], [2547235, 2830260], [2830261, 3113286], [3113287, 3396312], [3396313, 3679338], [3679339, 3962364], [3962365, 4245390], [4245391, 4528416], [4528417, 4811442], [4811443, 5094468], [5094469, 5377494], [5377495, 5660539]]
SRR11699512 file size 1186322
SRR11699512 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 SRR11699512 SRR11699512_1.fastq
Input file:	SRR11699512_1.fastq
trimmed:	SRR11699512-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 14:31:54 2025 >> started

Fri Jun 20 14:31:57 2025 >> done (2.688s)
5660539 reads processed; of these:
 640428 (11.31%) short reads filtered out after trimming by size control
   4867 ( 0.09%) empty reads filtered out after trimming by size control
5015244 (88.60%) reads available; of these:
4993212 (99.56%) trimmed reads available after processing
  22032 ( 0.44%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 121042	  2.41%
 19	 191543	  3.82%
 20	 198579	  3.96%
 21	 459637	  9.16%
 22	 544365	 10.85%
 23	 236146	  4.71%
 24	 544163	 10.85%
 25	 249182	  4.97%
 26	 199532	  3.98%
 27	 231146	  4.61%
 28	 161710	  3.22%
 29	 183942	  3.67%
 30	 187560	  3.74%
 31	 170570	  3.40%
 32	 166043	  3.31%
 33	 168339	  3.36%
 34	 200155	  3.99%
 35	 205735	  4.10%
 36	 145403	  2.90%
 37	  95766	  1.91%
 38	  62994	  1.26%
 39	  57293	  1.14%
 40	  45953	  0.92%
 41	  59904	  1.19%
 42	  27133	  0.54%
 43	  24163	  0.48%
 44	  14558	  0.29%
 45	  11864	  0.24%
 46	   8030	  0.16%
 47	   6217	  0.12%
 48	   6762	  0.13%
 49	   2903	  0.06%
 50	   1782	  0.04%
 51	   1214	  0.02%
 52	    840	  0.02%
 53	    564	  0.01%
 54	    476	  0.01%
 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	      2	  0.00%
 72	      0	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      0	  0.00%
 76	      0	  0.00%
 77	      0	  0.00%
 78	      0	  0.00%
 79	      0	  0.00%
 80	      0	  0.00%
 81	      0	  0.00%
 82	      0	  0.00%
 83	      0	  0.00%
 84	      0	  0.00%
 85	      2	  0.00%
 86	  22032	  0.44%
5015244 reads passed initial QC


criterion=sequence-density
sequence-density=4.70
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCG


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=43
fanout-score=52.52
fanout-score-rank=1
prefix-density=0.29
prefix-fanout=1.0
sequence=GTAGCCAAGTGTGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTCCGACTTCC
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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCG -o SRR11699512 -
Input file:	STDIN
trimmed:	SRR11699512-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCG
-- 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 14:32:04 2025 >> started

Fri Jun 20 14:32:06 2025 >> done (2.067s)
3009147 reads processed; of these:
  14417 ( 0.48%) short reads filtered out after trimming by size control
 142851 ( 4.75%) empty reads filtered out after trimming by size control
2851879 (94.77%) reads available; of these:
  23250 ( 0.82%) trimmed reads available after processing
2828629 (99.18%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  73769	  2.59%
 19	 115965	  4.07%
 20	 113190	  3.97%
 21	 272916	  9.57%
 22	 325261	 11.41%
 23	 140155	  4.91%
 24	 317066	 11.12%
 25	 148644	  5.21%
 26	 109187	  3.83%
 27	 134038	  4.70%
 28	  96185	  3.37%
 29	  97217	  3.41%
 30	 112163	  3.93%
 31	 101373	  3.55%
 32	  85689	  3.00%
 33	  77748	  2.73%
 34	  98490	  3.45%
 35	  93062	  3.26%
 36	  80806	  2.83%
 37	  53095	  1.86%
 38	  36021	  1.26%
 39	  32993	  1.16%
 40	  24839	  0.87%
 41	  35474	  1.24%
 42	  16069	  0.56%
 43	  14445	  0.51%
 44	   8610	  0.30%
 45	   7128	  0.25%
 46	   4770	  0.17%
 47	   3713	  0.13%
 48	   4039	  0.14%
 49	   1710	  0.06%
 50	   1057	  0.04%
 51	    743	  0.03%
 52	    498	  0.02%
 53	    314	  0.01%
 54	    268	  0.01%
 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	      1	  0.00%
 72	      0	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      0	  0.00%
 76	      0	  0.00%
 77	      0	  0.00%
 78	      2	  0.00%
 79	      0	  0.00%
 80	      1	  0.00%
 81	      1	  0.00%
 82	      2	  0.00%
 83	   1318	  0.05%
 84	      0	  0.00%
 85	      1	  0.00%
 86	  11843	  0.42%


criterion=sequence-density
sequence-density=2.34
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=14
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAAGACCCGGGT


criterion=fanout-score
sequence-density=0.17
sequence-density-rank=20
fanout-score=23.79
fanout-score-rank=1
prefix-density=0.88
prefix-fanout=4.6
sequence=GTCTAGTGGTATGATTCTCGCTT
                                 Started job on |	Jun 20 14:33:03
                             Started mapping on |	Jun 20 14:33:03
                                    Finished on |	Jun 20 14:33:20
       Mapping speed, Million of reads per hour |	1028.75

                          Number of input reads |	4857976
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	450428
                        Uniquely mapped reads % |	9.27%
                          Average mapped length |	24.21
                       Number of splices: Total |	12425
            Number of splices: Annotated (sjdb) |	5554
                       Number of splices: GT/AG |	11311
                       Number of splices: GC/AG |	926
                       Number of splices: AT/AC |	9
               Number of splices: Non-canonical |	179
                      Mismatch rate per base, % |	1.14%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.53
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.34
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	478829
             % of reads mapped to multiple loci |	9.86%
        Number of reads mapped to too many loci |	1036379
             % of reads mapped to too many loci |	21.33%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	6.05%
                     % of reads unmapped: other |	53.49%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3928719	3928719	3928719
N_multimapping	478829	478829	478829
N_noFeature	352252	367595	431802
N_ambiguous	3351	61	15
UnstrandedReadsAssigned:94825 PositiveStrandReadsAssigned:82772 NegativeStrandReadsAssigned:18611
Dataset is classified unstranded
MeadianReadLen=25 20thPercentileLength=21 echo kmer=19
SRR11699512 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: SRR11699512-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,857,976 reads, 963,990 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 883 rounds

  72540 SRR11699512.ke.tsv
  44303 SRR11699512.se.tsv
 116843 total
==> SRR11699512.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	6	1.91434
Zm00001eb323640_T001	3273	3174	0	0
Zm00001eb314140_T001	893	794	0	0
Zm00001eb080260_T001	3529	3430	0	0
Zm00001eb026490_T001	2433	2334	1	0.453569
Zm00001eb026490_T002	2229	2130	0	0
Zm00001eb026490_T003	2220	2121	0	0
Zm00001eb281360_T001	2412	2313	0	0

==> SRR11699512.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699512 completed mapping pipeline successfully
