Starting /dee2/code/volunteer_pipeline.sh SRR11699296
    current disk space = 2468718346240
    free memory = 444469812 
SRR11699296 SRAfilesize
d43342dbd0c86736cb4f4e553d05f483  SRR11699296.sra
SRR11699296.sra file validated
SRR11699296 is single end
SRR11699296 is conventional basespace
SRR11699296 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699296_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	76
%GC	50
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.3155	32.0	32.0	32.0	32.0	32.0
2	31.43575	32.0	32.0	32.0	32.0	32.0
3	31.442	32.0	32.0	32.0	32.0	32.0
4	31.498	32.0	32.0	32.0	32.0	32.0
5	31.56875	32.0	32.0	32.0	32.0	32.0
6	35.117	36.0	36.0	36.0	36.0	36.0
7	35.174	36.0	36.0	36.0	36.0	36.0
8	35.2385	36.0	36.0	36.0	36.0	36.0
9	34.89675	36.0	36.0	36.0	32.0	36.0
10-11	35.15275	36.0	36.0	36.0	36.0	36.0
12-13	35.1425	36.0	36.0	36.0	36.0	36.0
14-15	35.08775	36.0	36.0	36.0	36.0	36.0
16-17	35.219125	36.0	36.0	36.0	36.0	36.0
18-19	35.23225	36.0	36.0	36.0	36.0	36.0
20-21	35.058375	36.0	36.0	36.0	36.0	36.0
22-23	35.056375	36.0	36.0	36.0	36.0	36.0
24-25	35.088125	36.0	36.0	36.0	36.0	36.0
26-27	34.975750000000005	36.0	36.0	36.0	36.0	36.0
28-29	35.088875	36.0	36.0	36.0	36.0	36.0
30-31	35.016	36.0	36.0	36.0	36.0	36.0
32-33	35.04475	36.0	36.0	36.0	36.0	36.0
34-35	35.067375	36.0	36.0	36.0	36.0	36.0
36-37	35.068	36.0	36.0	36.0	36.0	36.0
38-39	35.056875	36.0	36.0	36.0	36.0	36.0
40-41	34.973124999999996	36.0	36.0	36.0	36.0	36.0
42-43	34.961625	36.0	36.0	36.0	36.0	36.0
44-45	34.900375	36.0	36.0	36.0	34.0	36.0
46-47	34.98125	36.0	36.0	36.0	36.0	36.0
48-49	34.775875	36.0	36.0	36.0	34.0	36.0
50-51	34.390625	36.0	36.0	36.0	32.0	36.0
52-53	34.201499999999996	36.0	36.0	36.0	32.0	36.0
54-55	33.5515	36.0	36.0	36.0	24.0	36.0
56-57	33.008875	36.0	36.0	36.0	20.5	36.0
58-59	32.813125	36.0	34.0	36.0	14.0	36.0
60-61	32.974125	36.0	36.0	36.0	14.0	36.0
62-63	32.682375	36.0	34.0	36.0	14.0	36.0
64-65	32.886	36.0	32.0	36.0	21.0	36.0
66-67	32.426874999999995	36.0	32.0	36.0	24.0	36.0
68-69	32.817750000000004	36.0	32.0	36.0	27.0	36.0
70-71	33.145875000000004	36.0	34.0	36.0	27.0	36.0
72-73	33.044375	36.0	34.0	36.0	20.5	36.0
74-75	33.237375	36.0	36.0	36.0	20.5	36.0
76	31.197	36.0	32.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	2.0
22	3.0
23	4.0
24	7.0
25	10.0
26	30.0
27	40.0
28	52.0
29	75.0
30	107.0
31	143.0
32	220.0
33	387.0
34	1184.0
35	1736.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	26.825	32.625	20.3	20.25
2	31.55	23.474999999999998	23.5	21.475
3	29.725	29.375	15.8	25.1
4	35.6	27.450000000000003	17.849999999999998	19.1
5	22.775000000000002	27.900000000000002	21.7	27.625
6	23.599999999999998	26.25	29.275000000000002	20.875
7	33.975	33.650000000000006	17.925	14.45
8	21.3	23.674999999999997	37.25	17.775
9	23.375	37.5	18.25	20.875
10-11	33.4875	25.974999999999998	20.9	19.6375
12-13	22.900000000000002	20.849999999999998	25.474999999999998	30.775000000000002
14-15	31.5625	38.85	16.150000000000002	13.4375
16-17	22.5	24.5125	34.0875	18.9
18-19	38.1375	24.0375	21.1875	16.6375
20-21	24.8625	34.975	23.9	16.2625
22-23	35.0125	36.925000000000004	12.875	15.187500000000002
24-25	30.412499999999998	39.275	13.487499999999999	16.825000000000003
26-27	30.425	32.725	15.475	21.375
28-29	28.0875	30.9375	14.2375	26.737499999999997
30-31	34.525	31.5375	9.925	24.0125
32-33	25.7625	34.2	14.2	25.837500000000002
34-35	29.65	29.5375	17.599999999999998	23.2125
36-37	23.2625	35.6	13.462499999999999	27.675
38-39	23.0625	30.312499999999996	17.95	28.675
40-41	21.85	27.962500000000002	16.2375	33.95
42-43	27.500000000000004	27.900000000000002	19.1875	25.412499999999998
44-45	19.8375	33.037499999999994	16.3875	30.7375
46-47	21.349999999999998	32.6125	14.787500000000001	31.25
48-49	16.3875	32.737500000000004	13.6625	37.2125
50-51	13.925	32.3125	15.024999999999999	38.737500000000004
52-53	17.5	31.4375	15.299999999999999	35.7625
54-55	15.4875	29.7375	20.5375	34.2375
56-57	14.649999999999999	33.4875	18.65	33.2125
58-59	15.2125	33.8125	16.075	34.9
60-61	12.8875	31.0125	21.575	34.525
62-63	14.7125	25.362499999999997	23.0625	36.8625
64-65	13.975000000000001	27.175	24.5375	34.3125
66-67	19.675	17.962500000000002	30.099999999999998	32.2625
68-69	15.4875	20.1875	29.1375	35.1875
70-71	20.7	19.2125	30.55	29.5375
72-73	19.525000000000002	17.837500000000002	29.912499999999998	32.725
74-75	17.4125	14.95	31.7375	35.9
76	14.625	16.55	39.15	29.675
>>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	0.5
24	0.5
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.5
33	1.0
34	0.5
35	0.0
36	0.0
37	0.0
38	0.5
39	2.0
40	6.0
41	12.5
42	16.0
43	31.5
44	69.0
45	127.5
46	164.0
47	259.0
48	609.0
49	720.0
50	576.0
51	602.5
52	567.0
53	429.5
54	354.0
55	259.0
56	126.5
57	85.0
58	81.0
59	56.5
60	19.0
61	4.5
62	3.0
63	3.0
64	2.5
65	1.0
66	0.5
67	1.0
68	0.5
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	0.5
98	1.0
99	1.5
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	62.724999999999994
#Duplication Level	Percentage of deduplicated	Percentage of total
1	88.9198884017537	55.775
2	4.463929852530889	5.6000000000000005
3	1.8732562774013553	3.5249999999999995
4	1.3949780789159028	3.5000000000000004
5	0.6377042646472698	2.0
6	0.3985651654045437	1.5
7	0.11956954962136308	0.525
8	0.3188521323236349	1.6
9	0.07971303308090873	0.44999999999999996
>10	1.5544041450777202	14.524999999999999
>50	0.19928258270227184	8.375
>100	0.03985651654045436	2.625
>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	105	2.625	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGA	95	2.375	TruSeq Adapter, Index 2 (97% over 36bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGA	67	1.675	TruSeq Adapter, Index 2 (97% over 36bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	60	1.5	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	59	1.4749999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AGCGGAGTAGAGCAGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	54	1.35	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	43	1.075	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	34	0.8500000000000001	No Hit
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	25	0.625	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGAC	22	0.5499999999999999	TruSeq Adapter, Index 4 (97% over 37bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	20	0.5	No Hit
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	18	0.44999999999999996	No Hit
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGACCAAT	17	0.42500000000000004	TruSeq Adapter, Index 4 (97% over 41bp)
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	17	0.42500000000000004	No Hit
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGAGATCGGAAGAGCAC	15	0.375	No Hit
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	14	0.35000000000000003	No Hit
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AGCGGAGTAGAGCAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCCCCCATCGTCTAGTGGTTCAGGACATCTCTCTTTAGATCGGAAGAGCA	12	0.3	No Hit
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGACC	12	0.3	TruSeq Adapter, Index 4 (97% over 38bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGGATTGTAGTTCAATCGGAAGAGCACACGTCTGAACTCCAGTCACAGAC	11	0.27499999999999997	TruSeq Adapter, Index 13 (97% over 35bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAG	11	0.27499999999999997	TruSeq Adapter, Index 2 (97% over 35bp)
GGCGGATGTAGCCAAGTGGAAGATCGGAAGAGCACACGTCTGAACTCCAG	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	11	0.27499999999999997	No Hit
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGTAGATCGGAAGAGCA	10	0.25	No Hit
GTCTACGCTGGTTCAAATCCAGCTCGGCCCACCAAGATCGGAAGAGCACA	10	0.25	No Hit
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTAGATCGGAAGAGC	10	0.25	No Hit
AACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	10	0.25	No Hit
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGCCTGTAGCTCAGAGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	10	0.25	No Hit
AAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAG	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)
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
AAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AAAGGCTGACGCGGGCTCTAGATCGGAAGAGCACACGTCTGAACTCCAGT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	8	0.2	No Hit
TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTGAGATCGGAAGAGCACAC	8	0.2	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTAGATCGGAAGAGCACA	8	0.2	No Hit
GAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAG	7	0.17500000000000002	TruSeq Adapter, Index 2 (97% over 35bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGACCAA	7	0.17500000000000002	TruSeq Adapter, Index 4 (97% over 40bp)
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGCAGATCGGAAGAGCA	6	0.15	No Hit
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	6	0.15	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	6	0.15	No Hit
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGAGATCGGAAGAGCAC	6	0.15	No Hit
CGACACGACTCTCGGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CGACACGACTCTCGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	6	0.15	No Hit
GCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGAGATCGGAAGAGCACACG	5	0.125	No Hit
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TAAAAGGCTGACGCGGGCTCTAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	5	0.125	No Hit
TGACTGGTCGTAGGTTCGAATCCTACTTGGGGAGCCAAGATCGGAAGAGC	5	0.125	No Hit
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	5	0.125	No Hit
GAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGA	5	0.125	TruSeq Adapter, Index 2 (97% over 36bp)
GGGGACGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAG	5	0.125	TruSeq Adapter, Index 2 (97% over 35bp)
ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGACC	5	0.125	TruSeq Adapter, Index 4 (97% over 38bp)
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTAGATCGGAAGAGCACA	5	0.125	No Hit
ACAAAATGTCACAGGTTCAAATCCTGTCATCCCTACCAAGATCGGAAGAG	5	0.125	No Hit
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	5	0.125	No Hit
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAGATCGGAAGAGC	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	0.15	0.0	0.0	0.0	0.0
3	0.25	0.0	0.0	0.0	0.0
4	0.3	0.0	0.0	0.0	0.0
5	0.45	0.0	0.0	0.0	0.0
6	0.55	0.0	0.0	0.0	0.0
7	0.675	0.0	0.0	0.0	0.0
8	0.95	0.0	0.0	0.0	0.0
9	1.775	0.0	0.0	0.0	0.0
10	2.35	0.0	0.0	0.0	0.0
11	2.85	0.0	0.0	0.0	0.0
12	4.125	0.0	0.0	0.0	0.0
13	5.7	0.0	0.0	0.0	0.0
14	11.95	0.0	0.0	0.0	0.0
15	14.075	0.0	0.0	0.0	0.0
16	16.45	0.0	0.0	0.0	0.0
17	20.8	0.0	0.0	0.0	0.0
18	25.65	0.0	0.0	0.0	0.0
19	28.3	0.0	0.0	0.0	0.0
20	31.575	0.0	0.0	0.0	0.0
21	36.55	0.0	0.0	0.0	0.0
22	42.0	0.0	0.0	0.0	0.0
23	48.075	0.0	0.0	0.0	0.0
24	51.6	0.0	0.0	0.0	0.0
25	58.2	0.0	0.0	0.0	0.0
26	61.875	0.0	0.0	0.0	0.0
27	63.775	0.0	0.0	0.0	0.0
28	66.25	0.0	0.0	0.0	0.0
29	67.875	0.0	0.0	0.0	0.0
30	69.75	0.0	0.0	0.0	0.0
31	71.8	0.0	0.0	0.0	0.0
32	73.6	0.0	0.0	0.0	0.0
33	75.55	0.0	0.0	0.0	0.0
34	78.025	0.0	0.0	0.0	0.0
35	81.525	0.0	0.0	0.0	0.0
36	86.275	0.0	0.0	0.0	0.0
37	89.925	0.0	0.0	0.0	0.0
38	91.55	0.0	0.0	0.0	0.0
39	92.5	0.0	0.0	0.0	0.0
40	93.125	0.0	0.0	0.0	0.0
41	93.425	0.0	0.0	0.0	0.0
42	93.825	0.0	0.0	0.0	0.0
43	94.4	0.0	0.0	0.0	0.0
44	94.625	0.0	0.0	0.0	0.0
45	94.825	0.0	0.0	0.0	0.0
46	94.925	0.0	0.0	0.0	0.0
47	95.05	0.0	0.0	0.0	0.0
48	95.125	0.0	0.0	0.0	0.0
49	95.275	0.0	0.0	0.0	0.0
50	95.325	0.0	0.0	0.0	0.0
51	95.325	0.0	0.0	0.0	0.0
52	95.325	0.0	0.0	0.0	0.0
53	95.325	0.0	0.0	0.0	0.0
54	95.35	0.0	0.0	0.0	0.0
55	95.375	0.0	0.0	0.0	0.0
56	95.4	0.0	0.0	0.0	0.0
57	95.4	0.0	0.0	0.0	0.0
58	95.4	0.0	0.0	0.0	0.0
59	95.425	0.0	0.0	0.0	0.0
60	95.425	0.0	0.0	0.0	0.0
61	95.425	0.0	0.0	0.0	0.0
62	95.425	0.0	0.0	0.0	0.0
63	95.425	0.0	0.0	0.0	0.0
64	95.425	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTAGAGC	15	0.0020658788	70.00001	7
CGGAGTA	15	0.0020658788	70.00001	3
CAGTTAG	15	0.0020658788	70.00001	13
AGTAGAG	15	0.0020658788	70.00001	6
GGTCAGA	15	0.0020658788	70.00001	18
GCGGAGT	15	0.0020658788	70.00001	2
AGCAGTT	15	0.0020658788	70.00001	11
GAGCAGT	15	0.0020658788	70.00001	10
GCAGTTA	15	0.0020658788	70.00001	12
AGAGCAG	15	0.0020658788	70.00001	9
AGCGGAG	15	0.0020658788	70.00001	1
GGGATGT	15	0.0020658788	70.00001	2
GTCTAGC	15	0.0020658788	70.00001	10
TAGAGCA	15	0.0020658788	70.00001	8
GGAGTAG	15	0.0020658788	70.00001	4
AGTTAGA	15	0.0020658788	70.00001	14
TGGTCAG	20	7.003785E-5	70.0	17
GGATGTA	20	0.0064587677	52.5	3
GATGTAG	20	0.0064587677	52.5	4
GAGTAGA	20	0.0064587677	52.5	5
>>END_MODULE
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
Rejected 340150 READS because READLEN < 1
Read 340150 spots for SRR11699296.sra
Written 340150 spots for SRR11699296.sra
Rejected 340140 READS because READLEN < 1
Read 340140 spots for SRR11699296.sra
Written 340140 spots for SRR11699296.sra
SRR ids: ['SRR11699296.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_z5kiwfi8
SRR11699296.sra spots: 6802810
blocks: [[1, 340140], [340141, 680280], [680281, 1020420], [1020421, 1360560], [1360561, 1700700], [1700701, 2040840], [2040841, 2380980], [2380981, 2721120], [2721121, 3061260], [3061261, 3401400], [3401401, 3741540], [3741541, 4081680], [4081681, 4421820], [4421821, 4761960], [4761961, 5102100], [5102101, 5442240], [5442241, 5782380], [5782381, 6122520], [6122521, 6462660], [6462661, 6802810]]
SRR11699296 file size 1293287
SRR11699296 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 SRR11699296 SRR11699296_1.fastq
Input file:	SRR11699296_1.fastq
trimmed:	SRR11699296-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 09:05:45 2025 >> started

Wed Jun 18 09:05:48 2025 >> done (3.536s)
6802810 reads processed; of these:
1871627 (27.51%) short reads filtered out after trimming by size control
   2441 ( 0.04%) empty reads filtered out after trimming by size control
4928742 (72.45%) reads available; of these:
4868894 (98.79%) trimmed reads available after processing
  59848 ( 1.21%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 194327	  3.94%
 19	 261360	  5.30%
 20	 354862	  7.20%
 21	 377678	  7.66%
 22	 466902	  9.47%
 23	 232817	  4.72%
 24	 459384	  9.32%
 25	 209677	  4.25%
 26	 162934	  3.31%
 27	 173207	  3.51%
 28	 133149	  2.70%
 29	 139023	  2.82%
 30	 157808	  3.20%
 31	 124908	  2.53%
 32	 137098	  2.78%
 33	 185667	  3.77%
 34	 243916	  4.95%
 35	 297438	  6.03%
 36	 242787	  4.93%
 37	 102610	  2.08%
 38	  60263	  1.22%
 39	  40629	  0.82%
 40	  34703	  0.70%
 41	  32404	  0.66%
 42	  19908	  0.40%
 43	  13812	  0.28%
 44	   9620	  0.20%
 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	      0	  0.00%
 75	      2	  0.00%
 76	  59848	  1.21%
4928742 reads passed initial QC


criterion=sequence-density
sequence-density=2.69
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGG


criterion=fanout-score
sequence-density=0.73
sequence-density-rank=8
fanout-score=20.43
fanout-score-rank=1
prefix-density=0.71
prefix-fanout=20.4
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGACCAATCTCGTATGCCGTCTTCTGCTTGA
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -f sanger -l 18 -t 20 -x GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGG -o SRR11699296 -
Input file:	STDIN
trimmed:	SRR11699296-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGG
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ 
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	20
Wed Jun 18 09:05:55 2025 >> started

Wed Jun 18 09:05:56 2025 >> done (1.119s)
1642914 reads processed; of these:
   4905 ( 0.30%) short reads filtered out after trimming by size control
  44726 ( 2.72%) empty reads filtered out after trimming by size control
1593283 (96.98%) reads available; of these:
  10377 ( 0.65%) trimmed reads available after processing
1582906 (99.35%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  64849	  4.07%
 19	  87162	  5.47%
 20	 117045	  7.35%
 21	 125336	  7.87%
 22	 155146	  9.74%
 23	  77696	  4.88%
 24	 151513	  9.51%
 25	  69621	  4.37%
 26	  53676	  3.37%
 27	  57438	  3.61%
 28	  44331	  2.78%
 29	  45506	  2.86%
 30	  52777	  3.31%
 31	  41437	  2.60%
 32	  44601	  2.80%
 33	  55070	  3.46%
 34	  77253	  4.85%
 35	  79607	  5.00%
 36	  70022	  4.39%
 37	  33752	  2.12%
 38	  20037	  1.26%
 39	  13370	  0.84%
 40	  11410	  0.72%
 41	  10752	  0.67%
 42	   6526	  0.41%
 43	   4472	  0.28%
 44	   3172	  0.20%
 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	   1144	  0.07%
 74	      0	  0.00%
 75	      0	  0.00%
 76	  18561	  1.16%


criterion=sequence-density
sequence-density=2.60
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=16
prefix-density=0.04
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAA


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=43
fanout-score=273.05
fanout-score-rank=1
prefix-density=1.42
prefix-fanout=1.0
sequence=GTAGCCAAGTGTGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTC
                                 Started job on |	Jun 18 09:06:27
                             Started mapping on |	Jun 18 09:06:27
                                    Finished on |	Jun 18 09:06:39
       Mapping speed, Million of reads per hour |	1463.73

                          Number of input reads |	4879111
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	500924
                        Uniquely mapped reads % |	10.27%
                          Average mapped length |	24.60
                       Number of splices: Total |	8405
            Number of splices: Annotated (sjdb) |	3982
                       Number of splices: GT/AG |	7722
                       Number of splices: GC/AG |	442
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	238
                      Mismatch rate per base, % |	0.81%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.39
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.11
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	551614
             % of reads mapped to multiple loci |	11.31%
        Number of reads mapped to too many loci |	1284032
             % of reads mapped to too many loci |	26.32%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	4.94%
                     % of reads unmapped: other |	47.17%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3826573	3826573	3826573
N_multimapping	551614	551614	551614
N_noFeature	417597	435370	480826
N_ambiguous	2372	32	17
UnstrandedReadsAssigned:80955 PositiveStrandReadsAssigned:65522 NegativeStrandReadsAssigned:20081
Dataset is classified unstranded
MeadianReadLen=25 20thPercentileLength=21 echo kmer=19
SRR11699296 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: SRR11699296-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,879,111 reads, 1,087,771 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 907 rounds

  72540 SRR11699296.ke.tsv
  44303 SRR11699296.se.tsv
 116843 total
==> SRR11699296.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	2	0.591107
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

==> SRR11699296.se.tsv <==
Zm00001eb015280	2
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699296 completed mapping pipeline successfully
