Starting /dee2/code/volunteer_pipeline.sh SRR11699579
    current disk space = 2458739781632
    free memory = 1171647716 
SRR11699579 SRAfilesize
9b26c45dae33540de7adaab971e1c02f  SRR11699579.sra
SRR11699579.sra file validated
SRR11699579 is single end
SRR11699579 is conventional basespace
SRR11699579 read1 length is 86 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699579_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	49
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.403	32.0	32.0	32.0	32.0	32.0
2	31.4855	32.0	32.0	32.0	32.0	32.0
3	31.63575	32.0	32.0	32.0	32.0	32.0
4	31.623	32.0	32.0	32.0	32.0	32.0
5	31.60325	32.0	32.0	32.0	32.0	32.0
6	35.2455	36.0	36.0	36.0	36.0	36.0
7	35.28475	36.0	36.0	36.0	36.0	36.0
8	35.25175	36.0	36.0	36.0	36.0	36.0
9	35.26025	36.0	36.0	36.0	36.0	36.0
10-11	35.259375	36.0	36.0	36.0	36.0	36.0
12-13	35.3345	36.0	36.0	36.0	36.0	36.0
14-15	35.16225	36.0	36.0	36.0	36.0	36.0
16-17	35.20975	36.0	36.0	36.0	36.0	36.0
18-19	35.350125000000006	36.0	36.0	36.0	36.0	36.0
20-21	35.222875	36.0	36.0	36.0	36.0	36.0
22-23	35.2755	36.0	36.0	36.0	36.0	36.0
24-25	35.202375	36.0	36.0	36.0	36.0	36.0
26-27	35.084875	36.0	36.0	36.0	36.0	36.0
28-29	35.144625	36.0	36.0	36.0	36.0	36.0
30-31	35.1335	36.0	36.0	36.0	36.0	36.0
32-33	35.19475	36.0	36.0	36.0	36.0	36.0
34-35	35.199625	36.0	36.0	36.0	36.0	36.0
36-37	35.1455	36.0	36.0	36.0	36.0	36.0
38-39	35.175125	36.0	36.0	36.0	36.0	36.0
40-41	35.0905	36.0	36.0	36.0	36.0	36.0
42-43	35.08575	36.0	36.0	36.0	36.0	36.0
44-45	34.921375	36.0	36.0	36.0	34.0	36.0
46-47	35.14325	36.0	36.0	36.0	36.0	36.0
48-49	35.0985	36.0	36.0	36.0	36.0	36.0
50-51	34.955875	36.0	36.0	36.0	34.0	36.0
52-53	35.00925	36.0	36.0	36.0	36.0	36.0
54-55	34.751374999999996	36.0	36.0	36.0	36.0	36.0
56-57	34.500625	36.0	36.0	36.0	32.0	36.0
58-59	34.292125	36.0	36.0	36.0	32.0	36.0
60-61	34.28375	36.0	36.0	36.0	32.0	36.0
62-63	34.36525	36.0	36.0	36.0	32.0	36.0
64-65	34.1435	36.0	36.0	36.0	32.0	36.0
66-67	34.254125	36.0	36.0	36.0	32.0	36.0
68-69	34.276624999999996	36.0	36.0	36.0	32.0	36.0
70-71	34.307125	36.0	36.0	36.0	32.0	36.0
72-73	34.356125000000006	36.0	36.0	36.0	32.0	36.0
74-75	34.32925	36.0	36.0	36.0	32.0	36.0
76-77	34.212125	36.0	36.0	36.0	32.0	36.0
78-79	34.239875	36.0	36.0	36.0	32.0	36.0
80-81	34.548874999999995	36.0	36.0	36.0	32.0	36.0
82-83	34.496624999999995	36.0	36.0	36.0	32.0	36.0
84-85	34.61025	36.0	36.0	36.0	32.0	36.0
86	34.0535	36.0	36.0	36.0	32.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	2.0
22	0.0
23	2.0
24	2.0
25	9.0
26	34.0
27	35.0
28	39.0
29	55.0
30	77.0
31	98.0
32	163.0
33	234.0
34	505.0
35	2745.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	36.175000000000004	23.075000000000003	23.7	17.05
2	32.525	19.75	18.775	28.95
3	31.825	24.7	16.525000000000002	26.950000000000003
4	32.5	33.7	16.900000000000002	16.900000000000002
5	22.575	24.175	28.475	24.775
6	21.775	21.75	33.575	22.900000000000002
7	43.475	26.174999999999997	17.275	13.075000000000001
8	20.424999999999997	19.85	43.85	15.875
9	21.75	41.199999999999996	18.35	18.7
10-11	35.25	21.425	26.450000000000003	16.875
12-13	19.2375	17.9875	29.5	33.275
14-15	29.8875	42.75	14.45	12.9125
16-17	23.1625	18.637500000000003	38.625	19.575
18-19	45.800000000000004	18.675	21.925	13.600000000000001
20-21	20.7875	30.599999999999998	28.275	20.3375
22-23	33.5875	39.175	13.825000000000001	13.4125
24-25	30.162499999999998	38.337500000000006	15.174999999999999	16.325
26-27	23.3875	31.624999999999996	22.6125	22.375
28-29	27.150000000000002	23.5875	19.112499999999997	30.15
30-31	33.025	29.95	12.825000000000001	24.2
32-33	28.3625	32.6875	16.287499999999998	22.662499999999998
34-35	31.087500000000002	29.599999999999998	17.95	21.3625
36-37	28.678584823102888	36.90461307663458	12.189023627953494	22.22777847230904
38-39	27.6875	34.575	12.9	24.837500000000002
40-41	29.6875	31.8125	13.600000000000001	24.9
42-43	31.574999999999996	31.4	15.012500000000001	22.0125
44-45	26.1	35.85	14.05	24.0
46-47	25.0125	32.875	12.2125	29.9
48-49	19.8875	29.975	15.6125	34.525
50-51	19.287499999999998	29.512500000000003	17.5	33.7
52-53	22.112499999999997	23.799999999999997	23.225	30.862499999999997
54-55	19.8625	23.150000000000002	25.3125	31.674999999999997
56-57	20.3375	24.474999999999998	24.9875	30.2
58-59	21.5	23.6875	25.912499999999998	28.9
60-61	16.0	17.875	36.7	29.425
62-63	17.3625	19.625	35.612500000000004	27.400000000000002
64-65	17.775	21.7	33.137499999999996	27.3875
66-67	18.475	14.662500000000001	37.3375	29.525000000000002
68-69	18.5625	15.2125	37.3625	28.8625
70-71	24.0	14.4125	41.15	20.4375
72-73	20.9875	11.662500000000001	43.075	24.275
74-75	18.575	12.3375	42.512499999999996	26.575
76-77	19.0125	10.9125	42.6375	27.437499999999996
78-79	16.650000000000002	9.925	44.675	28.749999999999996
80-81	19.6375	11.774999999999999	42.6125	25.974999999999998
82-83	19.79244811202801	17.14178544636159	37.74693673418354	25.318829707426854
84-85	20.255063765941486	16.441610402600652	37.009252313078264	26.294073518379594
86	21.725	19.025	33.300000000000004	25.95
>>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	0.5
33	0.5
34	0.0
35	0.0
36	0.0
37	0.0
38	2.0
39	4.0
40	8.5
41	20.5
42	57.5
43	87.0
44	124.0
45	190.5
46	291.0
47	458.0
48	599.0
49	635.5
50	627.0
51	587.0
52	426.0
53	241.5
54	158.0
55	101.5
56	45.5
57	26.0
58	20.5
59	10.5
60	4.0
61	3.0
62	3.0
63	2.0
64	2.0
65	2.5
66	1.5
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	0.0
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	0.0
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	0.0125
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	0.0
80-81	0.0
82-83	0.025
84-85	0.025
86	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
86	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	59.599999999999994
#Duplication Level	Percentage of deduplicated	Percentage of total
1	87.16442953020133	51.949999999999996
2	5.369127516778524	6.4
3	1.971476510067114	3.5249999999999995
4	1.6359060402684564	3.9
5	0.587248322147651	1.7500000000000002
6	0.6711409395973155	2.4
7	0.5453020134228188	2.275
8	0.20973154362416108	1.0
9	0.12583892617449663	0.675
>10	1.552013422818792	18.475
>50	0.16778523489932887	7.6499999999999995
>100	0.0	0.0
>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	100	2.5	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	71	1.775	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	69	1.725	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	66	1.6500000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	48	1.2	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	44	1.0999999999999999	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	39	0.975	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	36	0.8999999999999999	No Hit
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTG	32	0.8	TruSeq Adapter, Index 15 (97% over 36bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	31	0.775	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTGAGATCGGAAGAGCACAC	29	0.7250000000000001	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	26	0.65	No Hit
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	25	0.625	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	24	0.6	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	23	0.575	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	23	0.575	No Hit
TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA	22	0.5499999999999999	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG	21	0.525	No Hit
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGAGATCGGAAGAGCAC	19	0.475	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	17	0.42500000000000004	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTAGATCGGAAGAGCA	17	0.42500000000000004	No Hit
AGCGGAGTAGAGCAGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	16	0.4	No Hit
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGAGATCGGAAGAGCAC	15	0.375	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	15	0.375	No Hit
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	14	0.35000000000000003	No Hit
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	13	0.325	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	13	0.325	No Hit
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	13	0.325	No Hit
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAGATCGGAAGAGC	12	0.3	No Hit
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGT	11	0.27499999999999997	TruSeq Adapter, Index 19 (97% over 36bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTG	11	0.27499999999999997	TruSeq Adapter, Index 15 (97% over 36bp)
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAGATCGGAAGAGCACA	11	0.27499999999999997	No Hit
GCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAG	10	0.25	No Hit
GCCCCCATCGTCTAGTGGTTCAGGACATCTCTCTTTAGATCGGAAGAGCA	10	0.25	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	8	0.2	No Hit
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTAGATCGGAAGAGCACAC	8	0.2	No Hit
GGTAGTTCGACCGTGGATTAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CGACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGAGATCGGAAG	7	0.17500000000000002	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTTCCAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
TCCGTTGTAGTCTAGCTGGTTAGGATAAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	6	0.15	No Hit
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	6	0.15	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	6	0.15	No Hit
GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACAC	6	0.15	No Hit
GCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
ACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGA	6	0.15	No Hit
ATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAG	6	0.15	No Hit
CATATCGGGTAGGTTGTGGTATTTCATTGCTAGATCGGAAGAGCACACGT	6	0.15	No Hit
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAGATCGGAAGAGC	6	0.15	No Hit
GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAGATCGGAAGAG	6	0.15	No Hit
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	6	0.15	No Hit
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	5	0.125	No Hit
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGT	5	0.125	TruSeq Adapter, Index 1 (97% over 35bp)
CGACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTGTAGATCGGAAGAGCACA	5	0.125	No Hit
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGT	5	0.125	TruSeq Adapter, Index 1 (97% over 35bp)
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGAGATCGGAAGAGC	5	0.125	No Hit
CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGGATTGTAGTTCAATTGGTCAGAGCAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
CACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GCCCTTTTAACTCAGTGGTAGAGTAATGCCATGAGATCGGAAGAGCACAC	5	0.125	No Hit
GGTTCCATGGTCTAGCGGTTAGGACATTGGACTCTGAGATCGGAAGAGCA	5	0.125	No Hit
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	0.0	0.0	0.0	0.0	0.0
9	0.05	0.0	0.0	0.0	0.0
10	0.1	0.0	0.0	0.0	0.0
11	0.125	0.0	0.0	0.0	0.0
12	0.275	0.0	0.0	0.0	0.0
13	0.525	0.0	0.0	0.0	0.0
14	2.075	0.0	0.0	0.0	0.0
15	2.8	0.0	0.0	0.0	0.0
16	3.675	0.0	0.0	0.0	0.0
17	5.125	0.0	0.0	0.0	0.0
18	6.9	0.0	0.0	0.0	0.0
19	7.875	0.0	0.0	0.0	0.0
20	9.75	0.0	0.0	0.0	0.0
21	11.85	0.0	0.0	0.0	0.0
22	15.55	0.0	0.0	0.0	0.0
23	21.8	0.0	0.0	0.0	0.0
24	24.475	0.0	0.0	0.0	0.0
25	30.85	0.0	0.0	0.0	0.0
26	34.0	0.0	0.0	0.0	0.0
27	36.675	0.0	0.0	0.0	0.0
28	40.725	0.0	0.0	0.0	0.0
29	42.95	0.0	0.0	0.0	0.0
30	46.0	0.0	0.0	0.0	0.0
31	50.575	0.0	0.0	0.0	0.0
32	53.275	0.0	0.0	0.0	0.0
33	57.35	0.0	0.0	0.0	0.0
34	62.3	0.0	0.0	0.0	0.0
35	67.525	0.0	0.0	0.0	0.0
36	74.425	0.0	0.0	0.0	0.0
37	79.025	0.0	0.0	0.0	0.0
38	81.85	0.0	0.0	0.0	0.0
39	83.6	0.0	0.0	0.0	0.0
40	84.95	0.0	0.0	0.0	0.0
41	86.3	0.0	0.0	0.0	0.0
42	89.8	0.0	0.0	0.0	0.0
43	90.85	0.0	0.0	0.0	0.0
44	91.85	0.0	0.0	0.0	0.0
45	92.525	0.0	0.0	0.0	0.0
46	93.05	0.0	0.0	0.0	0.0
47	93.475	0.0	0.0	0.0	0.0
48	93.75	0.0	0.0	0.0	0.0
49	94.325	0.0	0.0	0.0	0.0
50	94.625	0.0	0.0	0.0	0.0
51	94.775	0.0	0.0	0.0	0.0
52	94.925	0.0	0.0	0.0	0.0
53	95.05	0.0	0.0	0.0	0.0
54	95.125	0.0	0.0	0.0	0.0
55	95.15	0.0	0.0	0.0	0.0
56	95.15	0.0	0.0	0.0	0.0
57	95.175	0.0	0.0	0.0	0.0
58	95.175	0.0	0.0	0.0	0.0
59	95.225	0.0	0.0	0.0	0.0
60	95.225	0.0	0.0	0.0	0.0
61	95.225	0.0	0.0	0.0	0.0
62	95.225	0.0	0.0	0.0	0.0
63	95.25	0.0	0.0	0.0	0.0
64	95.25	0.0	0.0	0.0	0.0
65	95.25	0.0	0.0	0.0	0.0
66	95.25	0.0	0.0	0.0	0.0
67	95.25	0.0	0.0	0.0	0.0
68	95.25	0.0	0.0	0.0	0.0
69	95.25	0.0	0.0	0.0	0.0
70	95.25	0.0	0.0	0.0	0.0
71	95.25	0.0	0.0	0.0	0.0
72	95.25	0.0	0.0	0.0	0.0
73	95.25	0.0	0.0	0.0	0.0
74	95.25	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GGCTGTA	15	0.0012159165	80.00001	4
CCATGGT	15	0.0012159165	80.00001	5
CCGTTGT	20	3.6123936E-5	80.00001	2
TAGTCTA	20	3.6123936E-5	80.00001	8
CCCATCG	15	0.0012159165	80.00001	4
CCATCGT	15	0.0012159165	80.00001	5
TGTAGTC	30	3.1202944E-8	80.00001	6
TCGTCTA	15	0.0012159165	80.00001	8
TCCGTTG	20	3.6123936E-5	80.00001	1
CCCCCAT	15	0.0012159165	80.00001	2
ATCGTCT	15	0.0012159165	80.00001	7
AGTCTAG	20	3.6123936E-5	80.00001	9
CCCCATC	15	0.0012159165	80.00001	3
GTAGTCT	20	3.6123936E-5	80.00001	7
CGTCTAG	15	0.0012159165	80.00001	9
CATCGTC	15	0.0012159165	80.00001	6
GCCCCCA	15	0.0012159165	80.00001	1
TTGTAGT	55	0.0	80.0	5
GGATTGT	35	9.076757E-10	80.0	2
GATTGTA	35	9.076757E-10	80.0	3
>>END_MODULE
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237461 READS because READLEN < 1
Read 237461 spots for SRR11699579.sra
Written 237461 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
Rejected 237452 READS because READLEN < 1
Read 237452 spots for SRR11699579.sra
Written 237452 spots for SRR11699579.sra
SRR ids: ['SRR11699579.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_do2ql8je
SRR11699579.sra spots: 4749049
blocks: [[1, 237452], [237453, 474904], [474905, 712356], [712357, 949808], [949809, 1187260], [1187261, 1424712], [1424713, 1662164], [1662165, 1899616], [1899617, 2137068], [2137069, 2374520], [2374521, 2611972], [2611973, 2849424], [2849425, 3086876], [3086877, 3324328], [3324329, 3561780], [3561781, 3799232], [3799233, 4036684], [4036685, 4274136], [4274137, 4511588], [4511589, 4749049]]
SRR11699579 file size 994945
SRR11699579 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 SRR11699579 SRR11699579_1.fastq
Input file:	SRR11699579_1.fastq
trimmed:	SRR11699579-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 03:46:08 2025 >> started

Sat Jun 21 03:46:12 2025 >> done (3.612s)
4749049 reads processed; of these:
 434798 ( 9.16%) short reads filtered out after trimming by size control
    599 ( 0.01%) empty reads filtered out after trimming by size control
4313652 (90.83%) reads available; of these:
4294384 (99.55%) trimmed reads available after processing
  19268 ( 0.45%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  61188	  1.42%
 19	  93372	  2.16%
 20	 115346	  2.67%
 21	 180240	  4.18%
 22	 313529	  7.27%
 23	 142941	  3.31%
 24	 356127	  8.26%
 25	 154838	  3.59%
 26	 121481	  2.82%
 27	 225480	  5.23%
 28	 108712	  2.52%
 29	 131582	  3.05%
 30	 220552	  5.11%
 31	 137656	  3.19%
 32	 169907	  3.94%
 33	 259249	  6.01%
 34	 249401	  5.78%
 35	 319185	  7.40%
 36	 212776	  4.93%
 37	 115754	  2.68%
 38	  76776	  1.78%
 39	  64012	  1.48%
 40	  62639	  1.45%
 41	 167300	  3.88%
 42	  45396	  1.05%
 43	  40572	  0.94%
 44	  33236	  0.77%
 45	  27241	  0.63%
 46	  20146	  0.47%
 47	  16607	  0.38%
 48	  23526	  0.55%
 49	   9303	  0.22%
 50	   6172	  0.14%
 51	   5222	  0.12%
 52	   2888	  0.07%
 53	   2387	  0.06%
 54	   1637	  0.04%
 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	      0	  0.00%
 76	      0	  0.00%
 77	      1	  0.00%
 78	      0	  0.00%
 79	      0	  0.00%
 80	      0	  0.00%
 81	      0	  0.00%
 82	      0	  0.00%
 83	      0	  0.00%
 84	      0	  0.00%
 85	      7	  0.00%
 86	  19268	  0.45%
4313652 reads passed initial QC


criterion=sequence-density
sequence-density=7.01
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGGAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGCCA


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=41
fanout-score=191.68
fanout-score-rank=1
prefix-density=1.00
prefix-fanout=1.0
sequence=AGCCAAGTGTGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCT
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 SRR11699579 -
Input file:	STDIN
trimmed:	SRR11699579-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
Sat Jun 21 03:46:25 2025 >> started

Sat Jun 21 03:46:29 2025 >> done (3.653s)
3235239 reads processed; of these:
   4726 ( 0.15%) short reads filtered out after trimming by size control
 231045 ( 7.14%) empty reads filtered out after trimming by size control
2999468 (92.71%) reads available; of these:
  21839 ( 0.73%) trimmed reads available after processing
2977629 (99.27%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  46685	  1.56%
 19	  71077	  2.37%
 20	  85791	  2.86%
 21	 135627	  4.52%
 22	 233871	  7.80%
 23	 106245	  3.54%
 24	 261026	  8.70%
 25	 115721	  3.86%
 26	  83034	  2.77%
 27	 166324	  5.55%
 28	  80692	  2.69%
 29	  87932	  2.93%
 30	 164860	  5.50%
 31	 102339	  3.41%
 32	 113568	  3.79%
 33	 144732	  4.83%
 34	 145659	  4.86%
 35	 171846	  5.73%
 36	 147637	  4.92%
 37	  79443	  2.65%
 38	  55011	  1.83%
 39	  46359	  1.55%
 40	  42407	  1.41%
 41	 124335	  4.15%
 42	  33408	  1.11%
 43	  29075	  0.97%
 44	  24870	  0.83%
 45	  20254	  0.68%
 46	  14995	  0.50%
 47	  12332	  0.41%
 48	  17471	  0.58%
 49	   6895	  0.23%
 50	   4555	  0.15%
 51	   3849	  0.13%
 52	   2154	  0.07%
 53	   1721	  0.06%
 54	   1202	  0.04%
 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	      0	  0.00%
 76	      0	  0.00%
 77	      1	  0.00%
 78	      0	  0.00%
 79	      0	  0.00%
 80	      0	  0.00%
 81	      2	  0.00%
 82	      2	  0.00%
 83	   1652	  0.06%
 84	      0	  0.00%
 85	      3	  0.00%
 86	  12806	  0.43%


criterion=sequence-density
sequence-density=7.36
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=15
prefix-density=0.03
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAAGACCCGGGTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=45
fanout-score=211.27
fanout-score-rank=1
prefix-density=1.08
prefix-fanout=1.0
sequence=TAGCCAAGTGTGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCT
                                 Started job on |	Jun 21 03:47:29
                             Started mapping on |	Jun 21 03:47:29
                                    Finished on |	Jun 21 03:47:53
       Mapping speed, Million of reads per hour |	611.68

                          Number of input reads |	4077881
                      Average input read length |	30
                                    UNIQUE READS:
                   Uniquely mapped reads number |	363733
                        Uniquely mapped reads % |	8.92%
                          Average mapped length |	26.72
                       Number of splices: Total |	8026
            Number of splices: Annotated (sjdb) |	4092
                       Number of splices: GT/AG |	7403
                       Number of splices: GC/AG |	385
                       Number of splices: AT/AC |	10
               Number of splices: Non-canonical |	228
                      Mismatch rate per base, % |	1.04%
                         Deletion rate per base |	0.02%
                        Deletion average length |	1.34
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.57
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	574071
             % of reads mapped to multiple loci |	14.08%
        Number of reads mapped to too many loci |	1231618
             % of reads mapped to too many loci |	30.20%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.85%
                     % of reads unmapped: other |	40.95%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3140077	3140077	3140077
N_multimapping	574071	574071	574071
N_noFeature	293369	305960	348993
N_ambiguous	2194	35	14
UnstrandedReadsAssigned:68170 PositiveStrandReadsAssigned:57738 NegativeStrandReadsAssigned:14726
Dataset is classified unstranded
MeadianReadLen=30 20thPercentileLength=23 echo kmer=19
SRR11699579 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: SRR11699579-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,077,881 reads, 1,037,708 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 943 rounds

  72540 SRR11699579.ke.tsv
  44303 SRR11699579.se.tsv
 116843 total
==> SRR11699579.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	4	1.334
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

==> SRR11699579.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	1
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699579 completed mapping pipeline successfully
