Starting /dee2/code/volunteer_pipeline.sh SRR11699300
    current disk space = 2467021238272
    free memory = 1580936284 
SRR11699300 SRAfilesize
4519f75f74b42155ac73f47fa796add3  SRR11699300.sra
SRR11699300.sra file validated
SRR11699300 is single end
SRR11699300 is conventional basespace
SRR11699300 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699300_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	48
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.31925	32.0	32.0	32.0	32.0	32.0
2	31.507	32.0	32.0	32.0	32.0	32.0
3	31.531	32.0	32.0	32.0	32.0	32.0
4	31.586	32.0	32.0	32.0	32.0	32.0
5	31.60275	32.0	32.0	32.0	32.0	32.0
6	35.23225	36.0	36.0	36.0	36.0	36.0
7	35.15975	36.0	36.0	36.0	36.0	36.0
8	35.19225	36.0	36.0	36.0	36.0	36.0
9	35.06325	36.0	36.0	36.0	36.0	36.0
10-11	35.19625	36.0	36.0	36.0	36.0	36.0
12-13	35.18325	36.0	36.0	36.0	36.0	36.0
14-15	35.197874999999996	36.0	36.0	36.0	36.0	36.0
16-17	35.226124999999996	36.0	36.0	36.0	36.0	36.0
18-19	35.253125	36.0	36.0	36.0	36.0	36.0
20-21	35.092124999999996	36.0	36.0	36.0	36.0	36.0
22-23	35.139125	36.0	36.0	36.0	36.0	36.0
24-25	35.205875000000006	36.0	36.0	36.0	36.0	36.0
26-27	35.092375000000004	36.0	36.0	36.0	36.0	36.0
28-29	35.074875000000006	36.0	36.0	36.0	36.0	36.0
30-31	35.072125	36.0	36.0	36.0	36.0	36.0
32-33	35.0005	36.0	36.0	36.0	36.0	36.0
34-35	35.17	36.0	36.0	36.0	36.0	36.0
36-37	35.022125	36.0	36.0	36.0	36.0	36.0
38-39	35.02825	36.0	36.0	36.0	36.0	36.0
40-41	35.037375	36.0	36.0	36.0	36.0	36.0
42-43	34.979625	36.0	36.0	36.0	36.0	36.0
44-45	35.008624999999995	36.0	36.0	36.0	36.0	36.0
46-47	35.00125	36.0	36.0	36.0	36.0	36.0
48-49	34.688625	36.0	36.0	36.0	34.0	36.0
50-51	34.5745	36.0	36.0	36.0	32.0	36.0
52-53	34.385625000000005	36.0	36.0	36.0	32.0	36.0
54-55	34.173874999999995	36.0	36.0	36.0	32.0	36.0
56-57	33.98650000000001	36.0	36.0	36.0	29.5	36.0
58-59	33.980625	36.0	36.0	36.0	32.0	36.0
60-61	33.908500000000004	36.0	36.0	36.0	32.0	36.0
62-63	33.667	36.0	36.0	36.0	27.0	36.0
64-65	33.713125	36.0	36.0	36.0	29.5	36.0
66-67	33.198125000000005	36.0	32.0	36.0	27.0	36.0
68-69	33.26125	36.0	32.0	36.0	27.0	36.0
70-71	33.236875	36.0	34.0	36.0	27.0	36.0
72-73	32.944125	36.0	34.0	36.0	20.5	36.0
74-75	33.302499999999995	36.0	34.0	36.0	24.0	36.0
76	31.45925	36.0	32.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
22	4.0
23	3.0
24	5.0
25	11.0
26	17.0
27	25.0
28	44.0
29	68.0
30	91.0
31	130.0
32	180.0
33	316.0
34	1060.0
35	2046.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	29.675	30.025000000000002	20.5	19.8
2	29.65	24.7	22.3	23.35
3	27.275	28.525	18.8	25.4
4	33.6	28.7	17.375	20.325
5	23.150000000000002	26.875	22.325	27.650000000000002
6	23.974999999999998	24.5	28.95	22.575
7	34.25	29.775000000000002	19.85	16.125
8	22.05	23.35	34.9	19.7
9	22.400000000000002	35.225	21.325	21.05
10-11	33.5625	25.25	21.475	19.7125
12-13	22.3875	21.0125	26.5125	30.0875
14-15	30.4875	37.5625	17.75	14.2
16-17	23.962500000000002	23.1125	33.074999999999996	19.85
18-19	38.824999999999996	24.224999999999998	20.674999999999997	16.275000000000002
20-21	24.725	33.0625	25.75	16.4625
22-23	32.95	37.125	14.95	14.975
24-25	29.012500000000003	38.475	15.475	17.0375
26-27	28.15	30.862499999999997	19.1375	21.85
28-29	30.325000000000003	28.537499999999998	15.875	25.2625
30-31	35.3375	32.4	10.9125	21.349999999999998
32-33	27.0625	35.949999999999996	15.225	21.762500000000003
34-35	30.475	30.6875	16.525000000000002	22.3125
36-37	25.2625	35.575	11.75	27.4125
38-39	23.0625	31.5625	16.1375	29.2375
40-41	25.5	27.3375	16.675	30.4875
42-43	28.212500000000002	28.625	19.2375	23.925
44-45	20.925	33.3375	17.299999999999997	28.4375
46-47	21.9	31.0125	16.025	31.0625
48-49	13.600000000000001	27.437499999999996	21.3	37.6625
50-51	13.237499999999999	26.337500000000002	23.3125	37.1125
52-53	15.225	24.675	27.3625	32.737500000000004
54-55	13.4	22.1875	33.2125	31.2
56-57	10.174999999999999	22.825	34.849999999999994	32.15
58-59	10.237499999999999	23.1375	34.599999999999994	32.025
60-61	6.6375	21.975	41.2875	30.099999999999998
62-63	10.7125	23.1625	36.975	29.15
64-65	11.075	24.087500000000002	34.0625	30.775000000000002
66-67	14.3125	15.262500000000001	38.975	31.45
68-69	13.112499999999999	16.5625	39.3375	30.9875
70-71	15.4875	13.8625	43.4	27.250000000000004
72-73	16.287499999999998	13.55	40.5875	29.575000000000003
74-75	17.8	14.399999999999999	38.0625	29.7375
76	12.975	15.65	42.225	29.15
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.5
29	1.0
30	0.5
31	0.0
32	0.0
33	0.0
34	0.5
35	2.5
36	2.5
37	1.0
38	4.5
39	12.5
40	30.5
41	72.0
42	100.0
43	141.0
44	266.5
45	602.0
46	853.0
47	702.0
48	548.0
49	525.5
50	506.0
51	431.0
52	265.5
53	143.5
54	112.0
55	116.5
56	79.0
57	26.5
58	16.0
59	12.5
60	5.5
61	1.5
62	1.0
63	1.0
64	0.5
65	1.0
66	1.5
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	0.5
92	1.0
93	0.5
94	0.5
95	0.5
96	0.0
97	0.0
98	0.0
99	0.5
100	1.0
>>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	65.0
#Duplication Level	Percentage of deduplicated	Percentage of total
1	88.34615384615384	57.425000000000004
2	5.461538461538462	7.1
3	2.076923076923077	4.05
4	0.8846153846153846	2.3
5	0.7692307692307693	2.5
6	0.3076923076923077	1.2
7	0.34615384615384615	1.575
8	0.19230769230769232	1.0
9	0.23076923076923078	1.35
>10	1.2692307692307692	15.25
>50	0.07692307692307693	3.15
>100	0.038461538461538464	3.1
>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	124	3.1	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTC	73	1.825	TruSeq Adapter, Index 1 (97% over 36bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	53	1.325	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	39	0.975	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	33	0.8250000000000001	No Hit
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTC	29	0.7250000000000001	TruSeq Adapter, Index 1 (97% over 36bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	29	0.7250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	27	0.675	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	27	0.675	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	26	0.65	No Hit
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	26	0.65	No Hit
AGCGGAGTAGAGCAGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGGCCTGTAGCTCAGAGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCT	16	0.4	TruSeq Adapter, Index 1 (97% over 36bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	15	0.375	No Hit
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	14	0.35000000000000003	No Hit
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGAGATCGGAAGAGCAC	12	0.3	No Hit
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCTTAAT	12	0.3	TruSeq Adapter, Index 1 (97% over 36bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCTTAA	12	0.3	TruSeq Adapter, Index 1 (97% over 36bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTGAGATCGGAAGAGCACAC	12	0.3	No Hit
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GCCCCCATCGTCTAGTGGTTCAGGACATCTCTCTTTAGATCGGAAGAGCA	10	0.25	No Hit
CAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	9	0.22499999999999998	No Hit
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	9	0.22499999999999998	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTT	8	0.2	TruSeq Adapter, Index 1 (97% over 35bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCTTA	7	0.17500000000000002	TruSeq Adapter, Index 1 (97% over 36bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
ACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCT	7	0.17500000000000002	TruSeq Adapter, Index 3 (97% over 35bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTAGATCGGAAGAGC	7	0.17500000000000002	No Hit
GCGACCCCAGGTCAGTCGGGAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	6	0.15	No Hit
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGAGATCGGAAGAGCAC	6	0.15	No Hit
GGGCCTGTAGCTCAGAGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTAGATCGGAAGAGCACA	6	0.15	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	6	0.15	No Hit
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAGATCGGAAGAGCACA	6	0.15	No Hit
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTAGATCGGAAGAGCACACG	6	0.15	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTAGATCGGAAGAGCACAC	5	0.125	No Hit
AGGGATGTAGCGCAGCTTGGTAGCTTTTGTTTTAGATCGGAAGAGCACAC	5	0.125	No Hit
GGGATTGTAGTTCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGGCCTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTC	5	0.125	TruSeq Adapter, Index 1 (97% over 36bp)
CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	5	0.125	No Hit
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CGACACGACTCTCGGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGTCCCATGGTCTAGCGGTTAGGACATTGGACTCTGAGATCGGAAGAGCA	5	0.125	No Hit
GCGACCCCAGGTCAGTCGGGACTACCCGCTGAGTAGATCGGAAGAGCACA	5	0.125	No Hit
GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGAGATCGGAAGAGCA	5	0.125	No Hit
CCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTC	5	0.125	TruSeq Adapter, Index 1 (97% over 36bp)
GCGACCCCAGGTCAGTCGGGACTACCCGCTAGATCGGAAGAGCACACGTC	5	0.125	No Hit
CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGAGC	5	0.125	No Hit
AGCGGAGTAGAGCAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTAGATCGGAAGAGCACA	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	0.0	0.0	0.0	0.0	0.0
2	0.025	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	0.225	0.0	0.0	0.0	0.0
6	0.35	0.0	0.0	0.0	0.0
7	0.4	0.0	0.0	0.0	0.0
8	0.55	0.0	0.0	0.0	0.0
9	0.975	0.0	0.0	0.0	0.0
10	1.525	0.0	0.0	0.0	0.0
11	2.1	0.0	0.0	0.0	0.0
12	2.85	0.0	0.0	0.0	0.0
13	3.9	0.0	0.0	0.0	0.0
14	8.0	0.0	0.0	0.0	0.0
15	9.175	0.0	0.0	0.0	0.0
16	10.625	0.0	0.0	0.0	0.0
17	13.25	0.0	0.0	0.0	0.0
18	16.625	0.0	0.0	0.0	0.0
19	18.8	0.0	0.0	0.0	0.0
20	22.575	0.0	0.0	0.0	0.0
21	26.25	0.0	0.0	0.0	0.0
22	31.9	0.0	0.0	0.0	0.0
23	39.825	0.0	0.0	0.0	0.0
24	43.45	0.0	0.0	0.0	0.0
25	51.3	0.0	0.0	0.0	0.0
26	54.95	0.0	0.0	0.0	0.0
27	57.35	0.0	0.0	0.0	0.0
28	59.975	0.0	0.0	0.0	0.0
29	62.3	0.0	0.0	0.0	0.0
30	65.075	0.0	0.0	0.0	0.0
31	67.4	0.0	0.0	0.0	0.0
32	69.875	0.0	0.0	0.0	0.0
33	72.25	0.0	0.0	0.0	0.0
34	75.175	0.0	0.0	0.0	0.0
35	79.425	0.0	0.0	0.0	0.0
36	84.55	0.0	0.0	0.0	0.0
37	88.5	0.0	0.0	0.0	0.0
38	90.2	0.0	0.0	0.0	0.0
39	91.525	0.0	0.0	0.0	0.0
40	92.3	0.0	0.0	0.0	0.0
41	93.125	0.0	0.0	0.0	0.0
42	93.95	0.0	0.0	0.0	0.0
43	94.25	0.0	0.0	0.0	0.0
44	94.6	0.0	0.0	0.0	0.0
45	94.85	0.0	0.0	0.0	0.0
46	95.1	0.0	0.0	0.0	0.0
47	95.25	0.0	0.0	0.0	0.0
48	95.325	0.0	0.0	0.0	0.0
49	95.4	0.0	0.0	0.0	0.0
50	95.55	0.0	0.0	0.0	0.0
51	95.575	0.0	0.0	0.0	0.0
52	95.725	0.0	0.0	0.0	0.0
53	95.725	0.0	0.0	0.0	0.0
54	95.725	0.0	0.0	0.0	0.0
55	95.75	0.0	0.0	0.0	0.0
56	95.75	0.0	0.0	0.0	0.0
57	95.75	0.0	0.0	0.0	0.0
58	95.775	0.0	0.0	0.0	0.0
59	95.8	0.0	0.0	0.0	0.0
60	95.8	0.0	0.0	0.0	0.0
61	95.825	0.0	0.0	0.0	0.0
62	95.825	0.0	0.0	0.0	0.0
63	95.825	0.0	0.0	0.0	0.0
64	95.825	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGGTCAG	15	0.0020658788	70.00001	17
TCTAGCT	15	0.0020658788	70.00001	11
TCAGGAT	15	0.0020658788	70.00001	20
GCTGGTC	15	0.0020658788	70.00001	15
AGTGGTA	15	0.0020658788	70.00001	14
TAGCTGG	15	0.0020658788	70.00001	13
CCGTTGT	15	0.0020658788	70.00001	2
GGTCAGG	15	0.0020658788	70.00001	18
CTGGTCA	15	0.0020658788	70.00001	16
TGTAGCT	15	0.0020658788	70.00001	6
CTAGCTG	15	0.0020658788	70.00001	12
GTCTAGC	15	0.0020658788	70.00001	10
TCCGTTG	15	0.0020658788	70.00001	1
CAGGATA	15	0.0020658788	70.00001	21
GTCAGGA	15	0.0020658788	70.00001	19
AGCTGGT	15	0.0020658788	70.00001	14
GCTCAGA	15	0.0020658788	70.00001	10
AGCTCAG	25	2.3570374E-6	70.0	9
TAGCTCA	25	2.3570374E-6	70.0	8
GTAGCTC	25	2.3570374E-6	70.0	7
>>END_MODULE
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288776 READS because READLEN < 1
Read 288776 spots for SRR11699300.sra
Written 288776 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
Rejected 288768 READS because READLEN < 1
Read 288768 spots for SRR11699300.sra
Written 288768 spots for SRR11699300.sra
SRR ids: ['SRR11699300.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_tnyjk34k
SRR11699300.sra spots: 5775368
blocks: [[1, 288768], [288769, 577536], [577537, 866304], [866305, 1155072], [1155073, 1443840], [1443841, 1732608], [1732609, 2021376], [2021377, 2310144], [2310145, 2598912], [2598913, 2887680], [2887681, 3176448], [3176449, 3465216], [3465217, 3753984], [3753985, 4042752], [4042753, 4331520], [4331521, 4620288], [4620289, 4909056], [4909057, 5197824], [5197825, 5486592], [5486593, 5775368]]
SRR11699300 file size 1097632
SRR11699300 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 SRR11699300 SRR11699300_1.fastq
Input file:	SRR11699300_1.fastq
trimmed:	SRR11699300-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 11:10:26 2025 >> started

Wed Jun 18 11:10:29 2025 >> done (2.383s)
5775368 reads processed; of these:
1094859 (18.96%) short reads filtered out after trimming by size control
   2183 ( 0.04%) empty reads filtered out after trimming by size control
4678326 (81.00%) reads available; of these:
4593775 (98.19%) trimmed reads available after processing
  84551 ( 1.81%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 142325	  3.04%
 19	 223801	  4.78%
 20	 210268	  4.49%
 21	 318482	  6.81%
 22	 456636	  9.76%
 23	 204870	  4.38%
 24	 450940	  9.64%
 25	 214158	  4.58%
 26	 150609	  3.22%
 27	 169362	  3.62%
 28	 133377	  2.85%
 29	 139021	  2.97%
 30	 188216	  4.02%
 31	 134597	  2.88%
 32	 139763	  2.99%
 33	 180584	  3.86%
 34	 242947	  5.19%
 35	 289878	  6.20%
 36	 247000	  5.28%
 37	 103002	  2.20%
 38	  65541	  1.40%
 39	  48321	  1.03%
 40	  39786	  0.85%
 41	  38655	  0.83%
 42	  27249	  0.58%
 43	  20403	  0.44%
 44	  13980	  0.30%
 45	      0	  0.00%
 46	      0	  0.00%
 47	      0	  0.00%
 48	      0	  0.00%
 49	      0	  0.00%
 50	      0	  0.00%
 51	      0	  0.00%
 52	      0	  0.00%
 53	      0	  0.00%
 54	      0	  0.00%
 55	      0	  0.00%
 56	      0	  0.00%
 57	      0	  0.00%
 58	      0	  0.00%
 59	      0	  0.00%
 60	      0	  0.00%
 61	      0	  0.00%
 62	      0	  0.00%
 63	      0	  0.00%
 64	      0	  0.00%
 65	      0	  0.00%
 66	      0	  0.00%
 67	      0	  0.00%
 68	      0	  0.00%
 69	      0	  0.00%
 70	      0	  0.00%
 71	      0	  0.00%
 72	      0	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      4	  0.00%
 76	  84551	  1.81%
4678326 reads passed initial QC


criterion=sequence-density
sequence-density=3.24
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=16
prefix-density=0.03
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAAGACCCGGGTT


criterion=fanout-score
sequence-density=1.20
sequence-density-rank=5
fanout-score=21.65
fanout-score-rank=1
prefix-density=1.21
prefix-fanout=21.4
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCTTAATCTCGTATGCCGTCTTCTGCTTGA
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 11:10:52
                             Started mapping on |	Jun 18 11:10:52
                                    Finished on |	Jun 18 11:11:04
       Mapping speed, Million of reads per hour |	1403.50

                          Number of input reads |	4678326
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	458996
                        Uniquely mapped reads % |	9.81%
                          Average mapped length |	25.44
                       Number of splices: Total |	9188
            Number of splices: Annotated (sjdb) |	4461
                       Number of splices: GT/AG |	8413
                       Number of splices: GC/AG |	515
                       Number of splices: AT/AC |	6
               Number of splices: Non-canonical |	254
                      Mismatch rate per base, % |	1.03%
                         Deletion rate per base |	0.02%
                        Deletion average length |	1.38
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.33
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	614446
             % of reads mapped to multiple loci |	13.13%
        Number of reads mapped to too many loci |	1168010
             % of reads mapped to too many loci |	24.97%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.63%
                     % of reads unmapped: other |	46.46%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3604884	3604884	3604884
N_multimapping	614446	614446	614446
N_noFeature	372071	386296	442189
N_ambiguous	2643	44	25
UnstrandedReadsAssigned:84282 PositiveStrandReadsAssigned:72656 NegativeStrandReadsAssigned:16782
Dataset is classified unstranded
MeadianReadLen=26 20thPercentileLength=22 echo kmer=19
SRR11699300 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: SRR11699300-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,678,326 reads, 1,149,157 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 852 rounds

  72540 SRR11699300.ke.tsv
  44303 SRR11699300.se.tsv
 116843 total
==> SRR11699300.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	5	1.45919
Zm00001eb323640_T001	3273	3174	1	0.305079
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

==> SRR11699300.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699300 completed mapping pipeline successfully
