Starting /dee2/code/volunteer_pipeline.sh SRR11699643
    current disk space = 2453636579328
    free memory = 1577777112 
SRR11699643 SRAfilesize
3b7467d09558cc89bae8458d09db962b  SRR11699643.sra
SRR11699643.sra file validated
SRR11699643 is single end
SRR11699643 is conventional basespace
SRR11699643 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699643_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	30.8975	32.0	32.0	32.0	32.0	32.0
2	31.20675	32.0	32.0	32.0	32.0	32.0
3	31.3475	32.0	32.0	32.0	32.0	32.0
4	31.3585	32.0	32.0	32.0	32.0	32.0
5	31.397	32.0	32.0	32.0	32.0	32.0
6	34.7115	36.0	36.0	36.0	32.0	36.0
7	34.92525	36.0	36.0	36.0	36.0	36.0
8	34.9165	36.0	36.0	36.0	32.0	36.0
9	34.653	36.0	36.0	36.0	32.0	36.0
10-11	34.877250000000004	36.0	36.0	36.0	34.0	36.0
12-13	34.86225	36.0	36.0	36.0	32.0	36.0
14-15	34.833749999999995	36.0	36.0	36.0	32.0	36.0
16-17	34.88825	36.0	36.0	36.0	32.0	36.0
18-19	34.910125	36.0	36.0	36.0	34.0	36.0
20-21	34.780375	36.0	36.0	36.0	34.0	36.0
22-23	34.69175	36.0	36.0	36.0	32.0	36.0
24-25	34.7295	36.0	36.0	36.0	34.0	36.0
26-27	34.682249999999996	36.0	36.0	36.0	32.0	36.0
28-29	34.780249999999995	36.0	36.0	36.0	34.0	36.0
30-31	34.7125	36.0	36.0	36.0	34.0	36.0
32-33	34.686125000000004	36.0	36.0	36.0	34.0	36.0
34-35	34.757374999999996	36.0	36.0	36.0	34.0	36.0
36-37	34.755750000000006	36.0	36.0	36.0	32.0	36.0
38-39	34.69725	36.0	36.0	36.0	32.0	36.0
40-41	34.655125	36.0	36.0	36.0	32.0	36.0
42-43	34.60025	36.0	36.0	36.0	32.0	36.0
44-45	34.624375	36.0	36.0	36.0	32.0	36.0
46-47	34.6465	36.0	36.0	36.0	32.0	36.0
48-49	34.376374999999996	36.0	36.0	36.0	32.0	36.0
50-51	34.164125	36.0	36.0	36.0	32.0	36.0
52-53	34.1035	36.0	36.0	36.0	32.0	36.0
54-55	33.940375	36.0	36.0	36.0	29.5	36.0
56-57	33.156125	36.0	36.0	36.0	21.0	36.0
58-59	32.701125000000005	36.0	34.0	36.0	14.0	36.0
60-61	32.2505	36.0	32.0	36.0	14.0	36.0
62-63	31.57875	36.0	32.0	36.0	14.0	36.0
64-65	30.835875	36.0	32.0	36.0	14.0	36.0
66-67	29.1905	32.0	24.0	36.0	14.0	36.0
68-69	28.691125	32.0	20.5	36.0	14.0	36.0
70-71	28.0935	32.0	14.0	36.0	14.0	36.0
72-73	28.424125	34.0	14.0	36.0	14.0	36.0
74-75	28.631875	34.0	14.0	36.0	14.0	36.0
76	25.068	27.0	14.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
18	1.0
19	0.0
20	0.0
21	1.0
22	5.0
23	15.0
24	15.0
25	30.0
26	52.0
27	77.0
28	119.0
29	140.0
30	197.0
31	263.0
32	404.0
33	642.0
34	1207.0
35	832.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	25.724999999999998	31.3	22.025	20.95
2	20.65	27.6	27.525	24.224999999999998
3	24.55	32.2	17.150000000000002	26.1
4	28.375	32.675	18.125	20.825
5	21.8	28.125	23.125	26.950000000000003
6	26.700000000000003	29.425	24.725	19.15
7	32.225	34.225	17.925	15.625
8	20.974999999999998	27.200000000000003	30.325000000000003	21.5
9	24.4	33.625	17.9	24.075
10-11	30.587500000000002	29.6625	22.2	17.549999999999997
12-13	23.7	21.525	24.0625	30.7125
14-15	29.525000000000002	39.4	17.1375	13.9375
16-17	23.7	22.3125	33.1	20.8875
18-19	37.275000000000006	23.6875	23.674999999999997	15.3625
20-21	22.875	35.9375	25.637500000000003	15.55
22-23	32.0125	38.5	14.524999999999999	14.9625
24-25	28.325	38.3125	16.3875	16.975
26-27	29.3375	31.25	19.162499999999998	20.25
28-29	32.975	30.5125	15.825	20.6875
30-31	32.7	36.449999999999996	11.15	19.7
32-33	31.15	37.375	11.625	19.85
34-35	31.3	32.675	12.562499999999998	23.4625
36-37	27.474999999999998	34.875	10.6375	27.0125
38-39	26.325	33.575	12.25	27.85
40-41	25.074999999999996	31.387500000000003	15.687499999999998	27.85
42-43	26.3	27.462500000000002	18.6125	27.625
44-45	22.237499999999997	32.6	15.287500000000001	29.875
46-47	20.200000000000003	29.825000000000003	16.8	33.175
48-49	17.275	27.537499999999998	19.175	36.012499999999996
50-51	17.849999999999998	28.875	19.5125	33.7625
52-53	20.275000000000002	25.650000000000002	22.675	31.4
54-55	19.1	30.012499999999996	19.3625	31.525
56-57	21.475	27.975	21.1625	29.3875
58-59	21.425	30.85	21.1875	26.5375
60-61	17.4	36.512499999999996	22.900000000000002	23.1875
62-63	16.9875	37.1125	22.9375	22.9625
64-65	15.737499999999999	31.374999999999996	26.1	26.787499999999998
66-67	18.0375	24.637500000000003	29.9375	27.3875
68-69	18.7375	25.087500000000002	31.912499999999998	24.2625
70-71	20.05	24.4375	32.8125	22.7
72-73	19.725	21.3125	30.0875	28.875
74-75	19.45	17.4625	32.9375	30.15
76	13.475000000000001	12.8	43.824999999999996	29.9
>>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	0.5
24	0.5
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.5
31	1.0
32	1.0
33	1.0
34	1.0
35	1.0
36	1.5
37	2.0
38	4.0
39	9.0
40	18.0
41	51.0
42	78.0
43	102.0
44	171.0
45	393.0
46	570.0
47	762.0
48	740.5
49	513.5
50	500.0
51	426.5
52	312.5
53	209.0
54	146.0
55	115.5
56	81.0
57	52.0
58	27.0
59	17.0
60	6.0
61	3.5
62	2.0
63	1.0
64	1.0
65	1.0
66	0.0
67	0.0
68	0.0
69	0.0
70	0.0
71	0.0
72	0.0
73	0.0
74	0.0
75	0.0
76	0.0
77	0.0
78	0.0
79	0.0
80	0.0
81	0.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.5
89	0.5
90	1.0
91	1.0
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	0.0
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	63.349999999999994
#Duplication Level	Percentage of deduplicated	Percentage of total
1	88.67403314917127	56.175
2	4.775059194948698	6.05
3	2.209944751381215	4.2
4	1.0655090765588004	2.7
5	0.7892659826361484	2.5
6	0.5919494869771112	2.25
7	0.31570639305445936	1.4000000000000001
8	0.1973164956590371	1.0
9	0.23677979479084454	1.35
>10	1.0260457774269929	12.950000000000001
>50	0.07892659826361484	4.324999999999999
>100	0.03946329913180742	5.1
>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	204	5.1	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	95	2.375	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	78	1.95	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	46	1.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	41	1.0250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	37	0.9249999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	36	0.8999999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	30	0.75	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTG	29	0.7250000000000001	TruSeq Adapter, Index 15 (97% over 36bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGA	15	0.375	TruSeq Adapter, Index 19 (100% over 37bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	15	0.375	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	15	0.375	No Hit
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	13	0.325	No Hit
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAAT	11	0.27499999999999997	TruSeq Adapter, Index 19 (97% over 41bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGAGATCGGAAGAGCACACGT	10	0.25	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	9	0.22499999999999998	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	8	0.2	No Hit
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTAGATCGGAAGAGCACACG	8	0.2	No Hit
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
CGACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
ACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTCT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCGTTTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
CAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGTAGTTCGACCGTGGATAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GCGACGTTGCTTTTTGATCAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	6	0.15	No Hit
AAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCA	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)
ACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CGACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGT	6	0.15	No Hit
AACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAGATCGGAAGAGCACA	6	0.15	No Hit
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	6	0.15	No Hit
AGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCCCCCATCGTCTAGTGGTTCAGGACAAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	6	0.15	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	6	0.15	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GGTAGTTCGACCGTGGATTAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCAAAAGAGGAAAGGCTTGCGGTGGATAAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	5	0.125	No Hit
CGACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
ACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGT	5	0.125	TruSeq Adapter, Index 1 (97% over 35bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCAGATCGGAAGAGCACAC	5	0.125	No Hit
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGT	5	0.125	TruSeq Adapter, Index 1 (97% over 35bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTG	5	0.125	TruSeq Adapter, Index 15 (97% over 36bp)
AGCGGAGTAGAGCAGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGAGATCGGAAGAGCAC	5	0.125	No Hit
TATTCTGGTGTCCTAGGCGTAGAGAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GCGACCCCAGGTCAGTCGGGACTACCCGCTGAGTAGATCGGAAGAGCACA	5	0.125	No Hit
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAA	5	0.125	TruSeq Adapter, Index 19 (97% over 39bp)
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTAGATCGGAAGAGCACA	5	0.125	No Hit
TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTGAGATCGGAAGAGCACAC	5	0.125	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	5	0.125	No Hit
GAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCTAGATCGGAAGAGCACACG	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	0.025	0.0	0.0	0.0	0.0
2	0.075	0.0	0.0	0.0	0.0
3	0.075	0.0	0.0	0.0	0.0
4	0.075	0.0	0.0	0.0	0.0
5	0.1	0.0	0.0	0.0	0.0
6	0.175	0.0	0.0	0.0	0.0
7	0.225	0.0	0.0	0.0	0.0
8	0.275	0.0	0.0	0.0	0.0
9	0.675	0.0	0.0	0.0	0.0
10	0.975	0.0	0.0	0.0	0.0
11	1.1	0.0	0.0	0.0	0.0
12	1.575	0.0	0.0	0.0	0.0
13	2.675	0.0	0.0	0.0	0.0
14	4.475	0.0	0.0	0.0	0.0
15	5.525	0.0	0.0	0.0	0.0
16	6.6	0.0	0.0	0.0	0.0
17	9.425	0.0	0.0	0.0	0.0
18	12.325	0.0	0.0	0.0	0.0
19	14.425	0.0	0.0	0.0	0.0
20	17.35	0.0	0.0	0.0	0.0
21	21.75	0.0	0.0	0.0	0.0
22	27.95	0.0	0.0	0.0	0.0
23	37.425	0.0	0.0	0.0	0.0
24	40.9	0.0	0.0	0.0	0.0
25	47.675	0.0	0.0	0.0	0.0
26	52.85	0.0	0.0	0.0	0.0
27	56.55	0.0	0.0	0.0	0.0
28	61.275	0.0	0.0	0.0	0.0
29	63.725	0.0	0.0	0.0	0.0
30	67.475	0.0	0.0	0.0	0.0
31	71.775	0.0	0.0	0.0	0.0
32	74.85	0.0	0.0	0.0	0.0
33	78.25	0.0	0.0	0.0	0.0
34	81.275	0.0	0.0	0.0	0.0
35	84.325	0.0	0.0	0.0	0.0
36	87.5	0.0	0.0	0.0	0.0
37	89.375	0.0	0.0	0.0	0.0
38	90.775	0.0	0.0	0.0	0.0
39	91.875	0.0	0.0	0.0	0.0
40	92.65	0.0	0.0	0.0	0.0
41	93.075	0.0	0.0	0.0	0.0
42	93.725	0.0	0.0	0.0	0.0
43	94.175	0.0	0.0	0.0	0.0
44	94.525	0.0	0.0	0.0	0.0
45	94.575	0.0	0.0	0.0	0.0
46	94.7	0.0	0.0	0.0	0.0
47	94.85	0.0	0.0	0.0	0.0
48	94.95	0.0	0.0	0.0	0.0
49	95.075	0.0	0.0	0.0	0.0
50	95.075	0.0	0.0	0.0	0.0
51	95.1	0.0	0.0	0.0	0.0
52	95.125	0.0	0.0	0.0	0.0
53	95.125	0.0	0.0	0.0	0.0
54	95.125	0.0	0.0	0.0	0.0
55	95.125	0.0	0.0	0.0	0.0
56	95.125	0.0	0.0	0.0	0.0
57	95.125	0.0	0.0	0.0	0.0
58	95.125	0.0	0.0	0.0	0.0
59	95.125	0.0	0.0	0.0	0.0
60	95.125	0.0	0.0	0.0	0.0
61	95.125	0.0	0.0	0.0	0.0
62	95.125	0.0	0.0	0.0	0.0
63	95.125	0.0	0.0	0.0	0.0
64	95.125	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TTCTGCT	15	0.0020658788	70.00001	68
TCTTCTG	15	0.0020658788	70.00001	66
CTTCTGC	15	0.0020658788	70.00001	67
TTGAAAG	25	2.1136815E-4	55.999996	17
AAAGATC	25	2.1136815E-4	55.999996	20
TGAAAGA	25	2.1136815E-4	55.999996	18
GAAAGAT	25	2.1136815E-4	55.999996	19
TTGTAGT	20	0.0064587677	52.5	5
TCTGCTT	20	0.0064587677	52.5	69
ATCCTAA	35	1.7350067E-5	50.000004	1
TTTGAAA	30	5.201195E-4	46.666668	16
TCCTAAC	45	7.661899E-5	38.88889	2
CCTAACG	45	7.661899E-5	38.88889	3
TAACGAA	90	2.588422E-9	35.000004	2
CTAACGA	90	2.588422E-9	35.000004	1
GAACGAT	95	4.3928594E-9	33.157898	10
GAACGAA	95	4.3928594E-9	33.157898	6
CCGTCTT	45	0.003819767	31.111113	70
GCCGTCT	45	0.003819767	31.111113	69
ATTTGAA	105	1.1683369E-8	30.000002	15
>>END_MODULE
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 223001 READS because READLEN < 1
Read 223001 spots for SRR11699643.sra
Written 223001 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
Rejected 222990 READS because READLEN < 1
Read 222990 spots for SRR11699643.sra
Written 222990 spots for SRR11699643.sra
SRR ids: ['SRR11699643.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_s68xmscx
SRR11699643.sra spots: 4459811
blocks: [[1, 222990], [222991, 445980], [445981, 668970], [668971, 891960], [891961, 1114950], [1114951, 1337940], [1337941, 1560930], [1560931, 1783920], [1783921, 2006910], [2006911, 2229900], [2229901, 2452890], [2452891, 2675880], [2675881, 2898870], [2898871, 3121860], [3121861, 3344850], [3344851, 3567840], [3567841, 3790830], [3790831, 4013820], [4013821, 4236810], [4236811, 4459811]]
SRR11699643 file size 847111
SRR11699643 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 SRR11699643 SRR11699643_1.fastq
Input file:	SRR11699643_1.fastq
trimmed:	SRR11699643-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
Sat Jun 21 16:31:06 2025 >> started

Sat Jun 21 16:31:09 2025 >> done (3.656s)
4459811 reads processed; of these:
 805289 (18.06%) short reads filtered out after trimming by size control
   3356 ( 0.08%) empty reads filtered out after trimming by size control
3651166 (81.87%) reads available; of these:
3613365 (98.96%) trimmed reads available after processing
  37801 ( 1.04%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 119508	  3.27%
 19	 178021	  4.88%
 20	 207551	  5.68%
 21	 271210	  7.43%
 22	 390924	 10.71%
 23	 176908	  4.85%
 24	 294712	  8.07%
 25	 225554	  6.18%
 26	 154787	  4.24%
 27	 188961	  5.18%
 28	 126894	  3.48%
 29	 136640	  3.74%
 30	 165383	  4.53%
 31	 137944	  3.78%
 32	 144217	  3.95%
 33	 137720	  3.77%
 34	 128494	  3.52%
 35	 122707	  3.36%
 36	  89672	  2.46%
 37	  59710	  1.64%
 38	  41892	  1.15%
 39	  34139	  0.94%
 40	  23828	  0.65%
 41	  24326	  0.67%
 42	  14694	  0.40%
 43	  10603	  0.29%
 44	   6363	  0.17%
 45	      0	  0.00%
 46	      0	  0.00%
 47	      0	  0.00%
 48	      0	  0.00%
 49	      0	  0.00%
 50	      0	  0.00%
 51	      0	  0.00%
 52	      0	  0.00%
 53	      0	  0.00%
 54	      0	  0.00%
 55	      0	  0.00%
 56	      0	  0.00%
 57	      0	  0.00%
 58	      0	  0.00%
 59	      0	  0.00%
 60	      0	  0.00%
 61	      0	  0.00%
 62	      0	  0.00%
 63	      0	  0.00%
 64	      0	  0.00%
 65	      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	      1	  0.00%
 75	      2	  0.00%
 76	  37801	  1.04%
3651166 reads passed initial QC


criterion=sequence-density
sequence-density=3.41
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=13
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAAGACCCGGGTT


criterion=fanout-score
sequence-density=0.58
sequence-density-rank=10
fanout-score=17.52
fanout-score-rank=1
prefix-density=0.54
prefix-fanout=17.5
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAATCTCGTAT
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 21 16:31:32
                             Started mapping on |	Jun 21 16:31:33
                                    Finished on |	Jun 21 16:31:45
       Mapping speed, Million of reads per hour |	1095.35

                          Number of input reads |	3651166
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	257862
                        Uniquely mapped reads % |	7.06%
                          Average mapped length |	24.23
                       Number of splices: Total |	6331
            Number of splices: Annotated (sjdb) |	2659
                       Number of splices: GT/AG |	5747
                       Number of splices: GC/AG |	396
                       Number of splices: AT/AC |	6
               Number of splices: Non-canonical |	182
                      Mismatch rate per base, % |	1.23%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.36
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.29
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	357866
             % of reads mapped to multiple loci |	9.80%
        Number of reads mapped to too many loci |	787953
             % of reads mapped to too many loci |	21.58%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.59%
                     % of reads unmapped: other |	55.97%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3035438	3035438	3035438
N_multimapping	357866	357866	357866
N_noFeature	210515	217754	249228
N_ambiguous	1418	18	11
UnstrandedReadsAssigned:45929 PositiveStrandReadsAssigned:40090 NegativeStrandReadsAssigned:8623
Dataset is classified unstranded
MeadianReadLen=25 20thPercentileLength=21 echo kmer=19
SRR11699643 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: SRR11699643-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,651,166 reads, 747,853 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 882 rounds

  72540 SRR11699643.ke.tsv
  44303 SRR11699643.se.tsv
 116843 total
==> SRR11699643.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	2	0.833155
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

==> SRR11699643.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	1
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699643 completed mapping pipeline successfully
