Starting /dee2/code/volunteer_pipeline.sh SRR11699478
    current disk space = 2474690523136
    free memory = 708962616 
SRR11699478 SRAfilesize
684761cee4efe208a4349d73cc10abd4  SRR11699478.sra
SRR11699478.sra file validated
SRR11699478 is single end
SRR11699478 is conventional basespace
SRR11699478 read1 length is 86 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699478_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	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.25775	32.0	32.0	32.0	32.0	32.0
2	31.42425	32.0	32.0	32.0	32.0	32.0
3	31.54925	32.0	32.0	32.0	32.0	32.0
4	31.56675	32.0	32.0	32.0	32.0	32.0
5	31.418	32.0	32.0	32.0	32.0	32.0
6	34.948	36.0	36.0	36.0	36.0	36.0
7	35.0335	36.0	36.0	36.0	36.0	36.0
8	34.9495	36.0	36.0	36.0	36.0	36.0
9	34.906	36.0	36.0	36.0	36.0	36.0
10-11	34.948375	36.0	36.0	36.0	34.0	36.0
12-13	34.947625	36.0	36.0	36.0	36.0	36.0
14-15	34.91925	36.0	36.0	36.0	34.0	36.0
16-17	35.034	36.0	36.0	36.0	36.0	36.0
18-19	35.095	36.0	36.0	36.0	36.0	36.0
20-21	35.04	36.0	36.0	36.0	36.0	36.0
22-23	34.989625000000004	36.0	36.0	36.0	36.0	36.0
24-25	34.905625	36.0	36.0	36.0	36.0	36.0
26-27	34.688375	36.0	36.0	36.0	34.0	36.0
28-29	34.878125	36.0	36.0	36.0	34.0	36.0
30-31	34.92125	36.0	36.0	36.0	36.0	36.0
32-33	34.903875	36.0	36.0	36.0	36.0	36.0
34-35	34.83825	36.0	36.0	36.0	34.0	36.0
36-37	34.834	36.0	36.0	36.0	36.0	36.0
38-39	34.860125	36.0	36.0	36.0	36.0	36.0
40-41	34.88725	36.0	36.0	36.0	34.0	36.0
42-43	34.7605	36.0	36.0	36.0	34.0	36.0
44-45	34.692750000000004	36.0	36.0	36.0	32.0	36.0
46-47	34.907875000000004	36.0	36.0	36.0	36.0	36.0
48-49	34.826125	36.0	36.0	36.0	34.0	36.0
50-51	34.634	36.0	36.0	36.0	32.0	36.0
52-53	34.652125	36.0	36.0	36.0	32.0	36.0
54-55	34.229	36.0	36.0	36.0	32.0	36.0
56-57	33.973375000000004	36.0	36.0	36.0	32.0	36.0
58-59	33.691	36.0	36.0	36.0	27.0	36.0
60-61	33.828	36.0	36.0	36.0	29.5	36.0
62-63	33.666375	36.0	36.0	36.0	27.0	36.0
64-65	33.451375	36.0	34.0	36.0	29.5	36.0
66-67	33.169624999999996	36.0	32.0	36.0	27.0	36.0
68-69	33.41225	36.0	32.0	36.0	27.0	36.0
70-71	33.57475	36.0	34.0	36.0	27.0	36.0
72-73	33.39825	36.0	34.0	36.0	29.5	36.0
74-75	33.37425	36.0	36.0	36.0	24.0	36.0
76-77	33.08475	36.0	34.0	36.0	21.0	36.0
78-79	33.464125	36.0	36.0	36.0	29.5	36.0
80-81	33.665499999999994	36.0	36.0	36.0	27.0	36.0
82-83	33.50275	36.0	36.0	36.0	27.0	36.0
84-85	33.80775	36.0	36.0	36.0	27.0	36.0
86	32.57025	36.0	32.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	1.0
22	1.0
23	3.0
24	13.0
25	20.0
26	34.0
27	40.0
28	58.0
29	83.0
30	102.0
31	132.0
32	220.0
33	336.0
34	961.0
35	1996.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	32.299224418313734	25.91943957968476	25.093820365273956	16.687515636727547
2	30.75	21.625	20.3	27.325
3	28.4	27.325	18.0	26.275
4	30.925000000000004	34.875	17.150000000000002	17.05
5	20.375	21.2	33.4	25.025
6	21.705426356589147	21.530382595648913	37.034258564641156	19.72993248312078
7	42.525	25.624999999999996	19.2	12.65
8	20.45	21.5	42.699999999999996	15.35
9	23.05	38.875	18.525	19.55
10-11	34.675	20.75	28.4125	16.162499999999998
12-13	19.2375	19.225	29.125	32.4125
14-15	29.9375	40.2	16.3625	13.5
16-17	20.75	19.975	40.1875	19.0875
18-19	46.5875	18.675	20.525	14.2125
20-21	20.625	27.8125	30.025000000000002	21.5375
22-23	33.125	38.3125	15.037500000000001	13.525
24-25	30.075000000000003	39.637499999999996	15.875	14.4125
26-27	24.712500000000002	33.925	20.7875	20.575
28-29	25.387500000000003	22.9375	20.7125	30.9625
30-31	37.6125	28.9375	11.7125	21.7375
32-33	27.1375	37.15	12.0375	23.674999999999997
34-35	32.925	31.4	16.6	19.075
36-37	31.424999999999997	34.4875	10.35	23.7375
38-39	24.4	37.5625	12.3875	25.650000000000002
40-41	27.6	30.5125	13.125	28.762500000000003
42-43	33.7125	29.075	16.575	20.6375
44-45	23.8875	35.099999999999994	15.0875	25.924999999999997
46-47	26.5	33.725	12.2625	27.5125
48-49	18.0375	30.112499999999997	14.387500000000001	37.4625
50-51	15.725	29.049999999999997	17.9	37.325
52-53	20.6625	25.637500000000003	17.9875	35.712500000000006
54-55	20.5375	21.15	24.0375	34.275
56-57	20.7375	25.587500000000002	18.35	35.325
58-59	22.7375	25.412499999999998	14.725	37.125
60-61	17.9	19.8875	22.3375	39.875
62-63	14.799999999999999	22.325	23.549999999999997	39.324999999999996
64-65	17.724999999999998	30.975	20.0125	31.2875
66-67	17.1375	16.3125	29.862499999999997	36.6875
68-69	16.3	19.5	27.6875	36.512499999999996
70-71	26.1	16.3875	27.750000000000004	29.762499999999996
72-73	21.2875	17.05	28.425	33.2375
74-75	19.975	17.474999999999998	30.5375	32.0125
76-77	20.7875	15.375	33.074999999999996	30.7625
78-79	13.564195524440557	9.388673584198024	41.755219402425304	35.291911488936115
80-81	20.530132533133283	10.140035008752188	41.94798699674919	27.38184546136534
82-83	18.38189320995373	14.517944229085908	38.6644991871952	28.435663373765163
84-85	23.23080770192548	14.116029007251813	35.07126781695424	27.581895473868467
86	20.66033016508254	16.483241620810404	37.49374687343672	25.362681340670335
>>END_MODULE
>>Per sequence GC content	pass
#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	0.5
31	0.5
32	0.0
33	0.0
34	0.0
35	0.5
36	1.0
37	1.5
38	1.0
39	1.0
40	2.0
41	5.5
42	15.0
43	21.0
44	29.5
45	61.0
46	128.5
47	220.0
48	330.5
49	469.0
50	544.0
51	596.0
52	567.5
53	552.5
54	472.5
55	241.0
56	119.5
57	84.0
58	74.0
59	50.0
60	27.0
61	15.0
62	7.5
63	1.5
64	0.0
65	1.0
66	3.5
67	2.5
68	0.5
69	1.0
70	0.5
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	0.5
96	0.5
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.075
2	0.0
3	0.0
4	0.0
5	0.0
6	0.025
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
76-77	0.0
78-79	0.0125
80-81	0.025
82-83	0.0375
84-85	0.025
86	0.05
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
86	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	65.4
#Duplication Level	Percentage of deduplicated	Percentage of total
1	89.6788990825688	58.650000000000006
2	5.084097859327217	6.65
3	1.4143730886850152	2.775
4	0.6498470948012233	1.7000000000000002
5	0.6116207951070336	2.0
6	0.6498470948012233	2.55
7	0.2675840978593272	1.225
8	0.382262996941896	2.0
9	0.11467889908256881	0.675
>10	0.9938837920489296	12.125
>50	0.11467889908256881	5.975
>100	0.0382262996941896	3.675
>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
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	147	3.675	No Hit
CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC	97	2.4250000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	83	2.075	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	59	1.4749999999999999	No Hit
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	46	1.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	45	1.125	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	45	1.125	No Hit
TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA	26	0.65	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	25	0.625	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG	24	0.6	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	24	0.6	No Hit
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	21	0.525	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	17	0.42500000000000004	No Hit
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGAGATCGGAAGAGCAC	16	0.4	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	15	0.375	No Hit
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAGATCGGAAGAGCACA	15	0.375	No Hit
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	14	0.35000000000000003	No Hit
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCG	14	0.35000000000000003	TruSeq Adapter, Index 16 (97% over 36bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	14	0.35000000000000003	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	13	0.325	No Hit
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCG	12	0.3	TruSeq Adapter, Index 16 (97% over 36bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	11	0.27499999999999997	No Hit
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGAGATCGGAAGAGCAC	11	0.27499999999999997	No Hit
GGTAGTTCGACCGTGGATTAGATCGGAAGAGCACACGTCTGAACTCCAGT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	10	0.25	No Hit
GCCCCCATCGTCTAGTGGTTCAGGACATCTCTCTTTAGATCGGAAGAGCA	10	0.25	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCACCAGTAGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GCACCAGTAGTCTAGTGGTAGAATAGATCGGAAGAGCACACGTCTGAACT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	9	0.22499999999999998	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTAGATCGGAAGAGCACA	8	0.2	No Hit
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCGTTGTAGTCTAGCTGGTTAGGATAAGATCGGAAGAGCACACGTCTGA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	8	0.2	No Hit
GGGTGTTTGGTCTAGTGGTATGATTCTCAGATCGGAAGAGCACACGTCTG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	8	0.2	No Hit
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAGATCGGAAGAGC	7	0.17500000000000002	No Hit
AGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	6	0.15	No Hit
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CGACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGAGATCGGAAGAGC	6	0.15	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGAGATCGGAAG	6	0.15	No Hit
ATATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCAC	6	0.15	No Hit
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCACCAGTAGTCTAGTGGTAGAATAGTACCCAGATCGGAAGAGCACACGT	6	0.15	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AGATCATGTTGCAGCTTCACTAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	6	0.15	No Hit
GCGACCCCAGGTCAGTCGGGACTACCCGCTAGATCGGAAGAGCACACGTC	6	0.15	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	6	0.15	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	5	0.125	No Hit
CGACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CGACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCA	5	0.125	No Hit
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	5	0.125	No Hit
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GACACGACTCTCGGCAACGGATATCTCGGCTCTCAGATCGGAAGAGCACA	5	0.125	No Hit
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTAGATCGGAAGAGCACA	5	0.125	No Hit
ACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGA	5	0.125	No Hit
GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
>>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	0.0	0.0	0.0	0.0	0.0
3	0.0	0.0	0.0	0.0	0.0
4	0.0	0.0	0.0	0.0	0.0
5	0.0	0.0	0.0	0.0	0.0
6	0.0	0.0	0.0	0.0	0.0
7	0.0	0.0	0.0	0.0	0.0
8	0.025	0.0	0.0	0.0	0.0
9	0.125	0.0	0.0	0.0	0.0
10	0.225	0.0	0.0	0.0	0.0
11	0.275	0.0	0.0	0.0	0.0
12	0.325	0.0	0.0	0.0	0.0
13	0.525	0.0	0.0	0.0	0.0
14	1.425	0.0	0.0	0.0	0.0
15	1.775	0.0	0.0	0.0	0.0
16	2.3	0.0	0.0	0.0	0.0
17	3.725	0.0	0.0	0.0	0.0
18	4.725	0.0	0.0	0.0	0.0
19	5.75	0.0	0.0	0.0	0.0
20	7.4	0.0	0.0	0.0	0.0
21	9.825	0.0	0.0	0.0	0.0
22	13.9	0.0	0.0	0.0	0.0
23	20.075	0.0	0.0	0.0	0.0
24	22.975	0.0	0.0	0.0	0.0
25	35.225	0.0	0.0	0.0	0.0
26	38.15	0.0	0.0	0.0	0.0
27	41.075	0.0	0.0	0.0	0.0
28	46.0	0.0	0.0	0.0	0.0
29	48.4	0.0	0.0	0.0	0.0
30	51.15	0.0	0.0	0.0	0.0
31	56.125	0.0	0.0	0.0	0.0
32	58.95	0.0	0.0	0.0	0.0
33	62.2	0.0	0.0	0.0	0.0
34	66.2	0.0	0.0	0.0	0.0
35	70.95	0.0	0.0	0.0	0.0
36	79.525	0.0	0.0	0.0	0.0
37	85.0	0.0	0.0	0.0	0.0
38	87.075	0.0	0.0	0.0	0.0
39	88.225	0.0	0.0	0.0	0.0
40	89.475	0.0	0.0	0.0	0.0
41	90.5	0.0	0.0	0.0	0.0
42	92.4	0.0	0.0	0.0	0.0
43	93.1	0.0	0.0	0.0	0.0
44	93.625	0.0	0.0	0.0	0.0
45	94.15	0.0	0.0	0.0	0.0
46	94.525	0.0	0.0	0.0	0.0
47	94.8	0.0	0.0	0.0	0.0
48	95.0	0.0	0.0	0.0	0.0
49	95.25	0.0	0.0	0.0	0.0
50	95.35	0.0	0.0	0.0	0.0
51	95.475	0.0	0.0	0.0	0.0
52	95.575	0.0	0.0	0.0	0.0
53	95.6	0.0	0.0	0.0	0.0
54	95.675	0.0	0.0	0.0	0.0
55	95.725	0.0	0.0	0.0	0.0
56	95.775	0.0	0.0	0.0	0.0
57	95.8	0.0	0.0	0.0	0.0
58	95.8	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	95.8	0.0	0.0	0.0	0.0
62	95.8	0.0	0.0	0.0	0.0
63	95.8	0.0	0.0	0.0	0.0
64	95.8	0.0	0.0	0.0	0.0
65	95.8	0.0	0.0	0.0	0.0
66	95.8	0.0	0.0	0.0	0.0
67	95.8	0.0	0.0	0.0	0.0
68	95.8	0.0	0.0	0.0	0.0
69	95.8	0.0	0.0	0.0	0.0
70	95.8	0.0	0.0	0.0	0.0
71	95.8	0.0	0.0	0.0	0.0
72	95.8	0.0	0.0	0.0	0.0
73	95.8	0.0	0.0	0.0	0.0
74	95.8	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TTGTAGT	95	0.0	80.0	5
GGATTGT	45	0.0	80.0	2
CCGTTGT	50	0.0	80.0	2
TAGTCTA	55	0.0	80.0	8
GATTGTA	45	0.0	80.0	3
TAGTTCA	45	0.0	80.0	8
ATTGTAG	45	0.0	80.0	4
TGTAGTC	55	0.0	80.0	6
GGGATTG	45	0.0	80.0	1
TCCGTTG	50	0.0	80.0	1
AGTCTAG	55	0.0	80.0	9
AGTTCAA	45	0.0	80.0	9
GTAGTCT	55	0.0	80.0	7
CGTTGTA	55	0.0	72.72727	3
GTTGTAG	55	0.0	72.72727	4
GTAGTTC	50	1.8189894E-12	72.0	7
TGTAGTT	55	5.456968E-12	65.454544	6
GAAAAAA	25	0.009205684	48.0	80
CGCCCTG	20	0.0011825194	40.000004	28-29
GATATTC	20	0.0011825194	40.000004	24-25
>>END_MODULE
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213950 READS because READLEN < 1
Read 213950 spots for SRR11699478.sra
Written 213950 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
Rejected 213940 READS because READLEN < 1
Read 213940 spots for SRR11699478.sra
Written 213940 spots for SRR11699478.sra
SRR ids: ['SRR11699478.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_w6ape9ei
SRR11699478.sra spots: 4278810
blocks: [[1, 213940], [213941, 427880], [427881, 641820], [641821, 855760], [855761, 1069700], [1069701, 1283640], [1283641, 1497580], [1497581, 1711520], [1711521, 1925460], [1925461, 2139400], [2139401, 2353340], [2353341, 2567280], [2567281, 2781220], [2781221, 2995160], [2995161, 3209100], [3209101, 3423040], [3423041, 3636980], [3636981, 3850920], [3850921, 4064860], [4064861, 4278810]]
SRR11699478 file size 896213
SRR11699478 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 SRR11699478 SRR11699478_1.fastq
Input file:	SRR11699478_1.fastq
trimmed:	SRR11699478-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 06:05:32 2025 >> started

Fri Jun 20 06:05:35 2025 >> done (2.377s)
4278810 reads processed; of these:
 284770 ( 6.66%) short reads filtered out after trimming by size control
    835 ( 0.02%) empty reads filtered out after trimming by size control
3993205 (93.33%) reads available; of these:
3977314 (99.60%) trimmed reads available after processing
  15891 ( 0.40%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  52885	  1.32%
 19	  82572	  2.07%
 20	  95352	  2.39%
 21	 198877	  4.98%
 22	 297068	  7.44%
 23	 144166	  3.61%
 24	 526919	 13.20%
 25	 144329	  3.61%
 26	 123009	  3.08%
 27	 208154	  5.21%
 28	 107078	  2.68%
 29	 130888	  3.28%
 30	 254912	  6.38%
 31	 120813	  3.03%
 32	 138502	  3.47%
 33	 175058	  4.38%
 34	 201511	  5.05%
 35	 316167	  7.92%
 36	 202381	  5.07%
 37	  79885	  2.00%
 38	  58179	  1.46%
 39	  51538	  1.29%
 40	  47454	  1.19%
 41	  77825	  1.95%
 42	  29336	  0.73%
 43	  24491	  0.61%
 44	  19120	  0.48%
 45	  17745	  0.44%
 46	  11856	  0.30%
 47	  10418	  0.26%
 48	  14150	  0.35%
 49	   5727	  0.14%
 50	   3302	  0.08%
 51	   2371	  0.06%
 52	   1401	  0.04%
 53	   1105	  0.03%
 54	    763	  0.02%
 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	      3	  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	      1	  0.00%
 82	      0	  0.00%
 83	      0	  0.00%
 84	      1	  0.00%
 85	      2	  0.00%
 86	  15891	  0.40%
3993205 reads passed initial QC


criterion=sequence-density
sequence-density=8.21
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGGAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGCCA


criterion=fanout-score
sequence-density=0.40
sequence-density-rank=20
fanout-score=23.15
fanout-score-rank=1
prefix-density=9.11
prefix-fanout=1.0
sequence=TTGTAGTCTAGGTGGTTAGGATACTCGG
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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGGAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGCCA -o SRR11699478 -
Input file:	STDIN
trimmed:	SRR11699478-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGGAAGCTGCGGGTTCGAGCCCC
-- 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 06:05:40 2025 >> started

Fri Jun 20 06:05:43 2025 >> done (3.292s)
3105826 reads processed; of these:
   5508 ( 0.18%) short reads filtered out after trimming by size control
 259901 ( 8.37%) empty reads filtered out after trimming by size control
2840417 (91.45%) reads available; of these:
  21823 ( 0.77%) trimmed reads available after processing
2818594 (99.23%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  42152	  1.48%
 19	  65116	  2.29%
 20	  73271	  2.58%
 21	 156498	  5.51%
 22	 230482	  8.11%
 23	 111348	  3.92%
 24	 400529	 14.10%
 25	 111683	  3.93%
 26	  88847	  3.13%
 27	 159627	  5.62%
 28	  82657	  2.91%
 29	  90269	  3.18%
 30	 197653	  6.96%
 31	  93146	  3.28%
 32	  90355	  3.18%
 33	  92036	  3.24%
 34	 122313	  4.31%
 35	 136202	  4.80%
 36	 144156	  5.08%
 37	  57389	  2.02%
 38	  43089	  1.52%
 39	  38369	  1.35%
 40	  32473	  1.14%
 41	  60051	  2.11%
 42	  22245	  0.78%
 43	  18480	  0.65%
 44	  14755	  0.52%
 45	  13705	  0.48%
 46	   9073	  0.32%
 47	   7920	  0.28%
 48	  11042	  0.39%
 49	   4352	  0.15%
 50	   2500	  0.09%
 51	   1804	  0.06%
 52	   1041	  0.04%
 53	    853	  0.03%
 54	    602	  0.02%
 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	      3	  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	      1	  0.00%
 82	      2	  0.00%
 83	    768	  0.03%
 84	      0	  0.00%
 85	      2	  0.00%
 86	  11558	  0.41%


criterion=sequence-density
sequence-density=9.78
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=12
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATA


criterion=fanout-score
sequence-density=0.44
sequence-density-rank=19
fanout-score=23.07
fanout-score-rank=1
prefix-density=9.95
prefix-fanout=1.0
sequence=TTGTAGTCTAGGTGGTTAGGATACTCGG
                                 Started job on |	Jun 20 06:06:08
                             Started mapping on |	Jun 20 06:06:09
                                    Finished on |	Jun 20 06:06:26
       Mapping speed, Million of reads per hour |	789.42

                          Number of input reads |	3727796
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	459626
                        Uniquely mapped reads % |	12.33%
                          Average mapped length |	25.43
                       Number of splices: Total |	10686
            Number of splices: Annotated (sjdb) |	5137
                       Number of splices: GT/AG |	10140
                       Number of splices: GC/AG |	366
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	179
                      Mismatch rate per base, % |	1.09%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.45
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.29
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	641090
             % of reads mapped to multiple loci |	17.20%
        Number of reads mapped to too many loci |	1085524
             % of reads mapped to too many loci |	29.12%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.46%
                     % of reads unmapped: other |	35.89%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2627080	2627080	2627080
N_multimapping	641090	641090	641090
N_noFeature	368103	381692	442606
N_ambiguous	3487	45	25
UnstrandedReadsAssigned:88036 PositiveStrandReadsAssigned:77889 NegativeStrandReadsAssigned:16995
Dataset is classified unstranded
MeadianReadLen=27 20thPercentileLength=22 echo kmer=19
SRR11699478 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: SRR11699478-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,727,796 reads, 1,079,037 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 945 rounds

  72540 SRR11699478.ke.tsv
  44303 SRR11699478.se.tsv
 116843 total
==> SRR11699478.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	4	1.33298
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	3	1.43412

==> SRR11699478.se.tsv <==
Zm00001eb015280	1
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699478 completed mapping pipeline successfully
