Starting /dee2/code/volunteer_pipeline.sh SRR11699632
    current disk space = 2454286487552
    free memory = 1579538812 
SRR11699632 SRAfilesize
297a689343ef7ed71120d7a17baa6cf7  SRR11699632.sra
SRR11699632.sra file validated
SRR11699632 is single end
SRR11699632 is conventional basespace
SRR11699632 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699632_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	52
>>END_MODULE
>>Per base sequence quality	warn
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.1305	32.0	32.0	32.0	32.0	32.0
2	31.27175	32.0	32.0	32.0	32.0	32.0
3	31.49275	32.0	32.0	32.0	32.0	32.0
4	31.4195	32.0	32.0	32.0	32.0	32.0
5	31.37225	32.0	32.0	32.0	32.0	32.0
6	34.92475	36.0	36.0	36.0	32.0	36.0
7	35.00975	36.0	36.0	36.0	36.0	36.0
8	35.01225	36.0	36.0	36.0	36.0	36.0
9	34.9325	36.0	36.0	36.0	32.0	36.0
10-11	35.016625000000005	36.0	36.0	36.0	36.0	36.0
12-13	35.040125	36.0	36.0	36.0	36.0	36.0
14-15	34.93925	36.0	36.0	36.0	36.0	36.0
16-17	35.009375	36.0	36.0	36.0	36.0	36.0
18-19	35.091	36.0	36.0	36.0	36.0	36.0
20-21	34.933875	36.0	36.0	36.0	36.0	36.0
22-23	34.926	36.0	36.0	36.0	36.0	36.0
24-25	34.854	36.0	36.0	36.0	36.0	36.0
26-27	34.707	36.0	36.0	36.0	32.0	36.0
28-29	34.886125	36.0	36.0	36.0	36.0	36.0
30-31	34.83425	36.0	36.0	36.0	36.0	36.0
32-33	34.80375	36.0	36.0	36.0	36.0	36.0
34-35	34.93675	36.0	36.0	36.0	36.0	36.0
36-37	34.907624999999996	36.0	36.0	36.0	36.0	36.0
38-39	34.889875	36.0	36.0	36.0	34.0	36.0
40-41	34.785375	36.0	36.0	36.0	32.0	36.0
42-43	34.722375	36.0	36.0	36.0	32.0	36.0
44-45	34.660375	36.0	36.0	36.0	32.0	36.0
46-47	34.751999999999995	36.0	36.0	36.0	34.0	36.0
48-49	34.541125	36.0	36.0	36.0	32.0	36.0
50-51	34.235875	36.0	36.0	36.0	32.0	36.0
52-53	33.99275	36.0	36.0	36.0	32.0	36.0
54-55	33.803875	36.0	36.0	36.0	29.5	36.0
56-57	32.955625	36.0	34.0	36.0	17.5	36.0
58-59	32.159	36.0	32.0	36.0	14.0	36.0
60-61	31.713625	36.0	32.0	36.0	14.0	36.0
62-63	30.887625	36.0	29.5	36.0	14.0	36.0
64-65	28.8325	34.0	17.5	36.0	14.0	36.0
66-67	27.515749999999997	32.0	14.0	36.0	14.0	36.0
68-69	27.602375000000002	32.0	14.0	36.0	14.0	36.0
70-71	26.825375	32.0	14.0	36.0	14.0	36.0
72-73	26.443375	29.5	14.0	36.0	14.0	36.0
74-75	27.13375	32.0	14.0	36.0	14.0	36.0
76	23.879	21.0	14.0	32.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	1.0
22	1.0
23	13.0
24	22.0
25	38.0
26	63.0
27	72.0
28	93.0
29	169.0
30	239.0
31	340.0
32	461.0
33	737.0
34	1155.0
35	596.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	24.3	28.4	22.575	24.725
2	23.0	26.625	28.425	21.95
3	24.85	35.075	16.425	23.65
4	27.125	37.95	16.650000000000002	18.275
5	20.150000000000002	24.7	24.75	30.4
6	29.95	25.8	26.400000000000002	17.849999999999998
7	31.424999999999997	36.725	17.599999999999998	14.249999999999998
8	20.95	29.375	31.424999999999997	18.25
9	23.575	33.074999999999996	17.775	25.575
10-11	33.35	29.912499999999998	21.3875	15.35
12-13	20.7625	24.675	22.775000000000002	31.7875
14-15	29.5375	39.4875	17.1875	13.7875
16-17	22.15	20.4875	38.1625	19.2
18-19	38.0625	22.7625	24.212500000000002	14.9625
20-21	20.7375	38.5375	24.4	16.325
22-23	30.6875	37.9375	13.7875	17.5875
24-25	29.125	38.125	16.1	16.650000000000002
26-27	25.874999999999996	30.312499999999996	20.8875	22.925
28-29	32.675	27.224999999999998	16.9875	23.1125
30-31	31.162499999999998	37.475	11.325000000000001	20.0375
32-33	30.1375	36.9625	13.0	19.900000000000002
34-35	29.349999999999998	30.162499999999998	14.075	26.4125
36-37	25.75	35.862500000000004	10.4375	27.950000000000003
38-39	24.3875	34.525	12.862499999999999	28.225
40-41	27.725	28.249999999999996	18.475	25.55
42-43	27.762500000000003	26.424999999999997	19.8375	25.974999999999998
44-45	24.837500000000002	36.175000000000004	13.8875	25.1
46-47	22.075	31.624999999999996	14.0875	32.2125
48-49	18.55	26.3	18.0375	37.1125
50-51	19.45	28.1625	17.0125	35.375
52-53	23.8125	22.412499999999998	21.85	31.924999999999997
54-55	21.475	25.0625	19.162499999999998	34.300000000000004
56-57	26.424999999999997	19.1875	21.3125	33.074999999999996
58-59	30.012499999999996	19.5875	21.1375	29.262500000000003
60-61	25.5125	16.075	21.925	36.4875
62-63	20.3875	21.775	21.3875	36.449999999999996
64-65	19.950000000000003	16.8	26.887499999999996	36.3625
66-67	21.6125	12.875	30.475	35.0375
68-69	23.8875	15.037500000000001	30.887500000000003	30.1875
70-71	23.4625	16.4375	32.875	27.224999999999998
72-73	24.462500000000002	11.3	28.1375	36.1
74-75	23.125	10.2625	29.2	37.4125
76	16.325	9.700000000000001	40.949999999999996	33.025
>>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	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.5
36	2.5
37	4.0
38	2.0
39	2.0
40	4.5
41	8.5
42	12.0
43	17.0
44	33.5
45	59.0
46	73.0
47	107.0
48	205.0
49	417.0
50	565.0
51	772.0
52	794.0
53	536.5
54	464.0
55	411.0
56	279.0
57	151.5
58	103.0
59	78.5
60	58.5
61	40.0
62	17.0
63	11.5
64	5.0
65	2.0
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	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.5
94	1.0
95	0.5
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	59.575
#Duplication Level	Percentage of deduplicated	Percentage of total
1	87.11707931179185	51.9
2	5.749055812001679	6.8500000000000005
3	2.308015107007973	4.125
4	1.1749895090222409	2.8000000000000003
5	0.7553503986571549	2.25
6	0.5874947545111204	2.1
7	0.20981955518254303	0.8750000000000001
8	0.2937473772555602	1.4000000000000001
9	0.37767519932857746	2.025
>10	1.3008812421317666	13.975000000000001
>50	0.0419639110365086	1.425
>100	0.0839278220730172	10.274999999999999
>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	302	7.55	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	109	2.725	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	57	1.425	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	35	0.8750000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	33	0.8250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	32	0.8	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	32	0.8	No Hit
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGG	25	0.625	TruSeq Adapter, Index 20 (100% over 37bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCAT	23	0.575	TruSeq Adapter, Index 20 (97% over 41bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	22	0.5499999999999999	No Hit
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	20	0.5	No Hit
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	17	0.42500000000000004	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	16	0.4	No Hit
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	15	0.375	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	14	0.35000000000000003	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	14	0.35000000000000003	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	13	0.325	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	13	0.325	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	12	0.3	No Hit
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	10	0.25	No Hit
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CAAAATGTCACAGGTTCAAATCCTGTCATCCCTACCAAGATCGGAAGAGC	10	0.25	No Hit
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	10	0.25	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	10	0.25	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	9	0.22499999999999998	No Hit
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGAGATCGGAAGAGCAC	9	0.22499999999999998	No Hit
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	9	0.22499999999999998	No Hit
GCGTTTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	9	0.22499999999999998	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	8	0.2	No Hit
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCA	8	0.2	No Hit
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTG	8	0.2	TruSeq Adapter, Index 15 (97% over 36bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	8	0.2	No Hit
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTG	8	0.2	TruSeq Adapter, Index 15 (97% over 36bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGT	6	0.15	TruSeq Adapter, Index 1 (97% over 35bp)
CTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	6	0.15	No Hit
CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCC	6	0.15	TruSeq Adapter, Index 20 (100% over 39bp)
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCACCAGTAGTCTAGTGGTAGAATAGTACCCAGATCGGAAGAGCACACGT	6	0.15	No Hit
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCA	6	0.15	TruSeq Adapter, Index 20 (97% over 39bp)
GGGATTGTAGTTCAATTGGTCAGAGCAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGC	6	0.15	TruSeq Adapter, Index 20 (100% over 38bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	6	0.15	No Hit
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGTAGATCGGAAGAGCA	5	0.125	No Hit
GCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAG	5	0.125	No Hit
TCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
ATACTGTAGGGGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATC	5	0.125	No Hit
CGACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACA	5	0.125	No Hit
AAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGA	5	0.125	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	5	0.125	No Hit
ACAAAATGTCACAGGTTCAAATCCTGTCATCCCTACCAAGATCGGAAGAG	5	0.125	No Hit
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTAGATCGGAAGAGC	5	0.125	No Hit
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAGATC	5	0.125	No Hit
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTG	5	0.125	TruSeq Adapter, Index 15 (97% over 36bp)
>>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	0.175	0.0	0.0	0.0	0.0
3	0.225	0.0	0.0	0.0	0.0
4	0.275	0.0	0.0	0.0	0.0
5	0.35	0.0	0.0	0.0	0.0
6	0.4	0.0	0.0	0.0	0.0
7	0.45	0.0	0.0	0.0	0.0
8	0.6	0.0	0.0	0.0	0.0
9	1.4	0.0	0.0	0.0	0.0
10	1.65	0.0	0.0	0.0	0.0
11	2.125	0.0	0.0	0.0	0.0
12	2.6	0.0	0.0	0.0	0.0
13	3.775	0.0	0.0	0.0	0.0
14	4.875	0.0	0.0	0.0	0.0
15	5.95	0.0	0.0	0.0	0.0
16	7.125	0.0	0.0	0.0	0.0
17	8.85	0.0	0.0	0.0	0.0
18	11.125	0.0	0.0	0.0	0.0
19	12.55	0.0	0.0	0.0	0.0
20	15.125	0.0	0.0	0.0	0.0
21	18.45	0.0	0.0	0.0	0.0
22	24.875	0.0	0.0	0.0	0.0
23	36.75	0.0	0.0	0.0	0.0
24	39.875	0.0	0.0	0.0	0.0
25	45.875	0.0	0.0	0.0	0.0
26	49.275	0.0	0.0	0.0	0.0
27	52.175	0.0	0.0	0.0	0.0
28	54.825	0.0	0.0	0.0	0.0
29	57.15	0.0	0.0	0.0	0.0
30	59.85	0.0	0.0	0.0	0.0
31	64.35	0.0	0.0	0.0	0.0
32	66.975	0.0	0.0	0.0	0.0
33	69.875	0.0	0.0	0.0	0.0
34	72.6	0.0	0.0	0.0	0.0
35	76.25	0.0	0.0	0.0	0.0
36	80.475	0.0	0.0	0.0	0.0
37	83.825	0.0	0.0	0.0	0.0
38	86.0	0.0	0.0	0.0	0.0
39	87.425	0.0	0.0	0.0	0.0
40	88.95	0.0	0.0	0.0	0.0
41	89.9	0.0	0.0	0.0	0.0
42	91.225	0.0	0.0	0.0	0.0
43	91.875	0.0	0.0	0.0	0.0
44	92.5	0.0	0.0	0.0	0.0
45	92.85	0.0	0.0	0.0	0.0
46	93.45	0.0	0.0	0.0	0.0
47	93.95	0.0	0.0	0.0	0.0
48	94.2	0.0	0.0	0.0	0.0
49	94.775	0.0	0.0	0.0	0.0
50	94.925	0.0	0.0	0.0	0.0
51	95.025	0.0	0.0	0.0	0.0
52	95.075	0.0	0.0	0.0	0.0
53	95.125	0.0	0.0	0.0	0.0
54	95.15	0.0	0.0	0.0	0.0
55	95.175	0.0	0.0	0.0	0.0
56	95.175	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	95.25	0.0	0.0	0.0	0.0
61	95.275	0.0	0.0	0.0	0.0
62	95.275	0.0	0.0	0.0	0.0
63	95.275	0.0	0.0	0.0	0.0
64	95.275	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TCTTCTG	15	0.0020658788	70.00001	70
TTGAAAG	20	7.003785E-5	70.0	17
TGAAAGA	20	7.003785E-5	70.0	18
GAAAGAT	20	7.003785E-5	70.0	19
TTTGAAA	25	2.1136815E-4	55.999996	16
TGCCGTC	45	1.300772E-6	46.666668	70
AAAGATC	35	0.00111172	40.000004	20
CTAACGA	90	2.588422E-9	35.000004	1
ATGCCGT	75	1.0602234E-6	32.666668	70
TAACGAA	100	7.2541297E-9	31.499998	2
GAACGAA	105	1.1683369E-8	30.000002	6
TATGCCG	85	2.820525E-6	28.823528	69
AACGATT	120	4.2920874E-8	26.250002	11
GAACGAT	120	4.2920874E-8	26.250002	10
GATTTGA	120	4.2920874E-8	26.250002	14
ATTTGAA	120	4.2920874E-8	26.250002	15
ACGATTT	120	4.2920874E-8	26.250002	12
CGATTTG	120	4.2920874E-8	26.250002	13
GTATGCC	95	6.71178E-6	25.789474	68
AAGATCG	90	1.5026014E-4	23.333334	21
>>END_MODULE
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327930 READS because READLEN < 1
Read 327930 spots for SRR11699632.sra
Written 327930 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
Rejected 327918 READS because READLEN < 1
Read 327918 spots for SRR11699632.sra
Written 327918 spots for SRR11699632.sra
SRR ids: ['SRR11699632.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ur6ccvog
SRR11699632.sra spots: 6558372
blocks: [[1, 327918], [327919, 655836], [655837, 983754], [983755, 1311672], [1311673, 1639590], [1639591, 1967508], [1967509, 2295426], [2295427, 2623344], [2623345, 2951262], [2951263, 3279180], [3279181, 3607098], [3607099, 3935016], [3935017, 4262934], [4262935, 4590852], [4590853, 4918770], [4918771, 5246688], [5246689, 5574606], [5574607, 5902524], [5902525, 6230442], [6230443, 6558372]]
SRR11699632 file size 1246739
SRR11699632 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 SRR11699632 SRR11699632_1.fastq
Input file:	SRR11699632_1.fastq
trimmed:	SRR11699632-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 14:45:03 2025 >> started

Sat Jun 21 14:45:07 2025 >> done (4.011s)
6558372 reads processed; of these:
1082489 (16.51%) short reads filtered out after trimming by size control
   4447 ( 0.07%) empty reads filtered out after trimming by size control
5471436 (83.43%) reads available; of these:
5327619 (97.37%) trimmed reads available after processing
 143817 ( 2.63%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 111874	  2.04%
 19	 185340	  3.39%
 20	 221318	  4.04%
 21	 391065	  7.15%
 22	 719091	 13.14%
 23	 176386	  3.22%
 24	 411411	  7.52%
 25	 231286	  4.23%
 26	 172889	  3.16%
 27	 192924	  3.53%
 28	 148629	  2.72%
 29	 171441	  3.13%
 30	 290420	  5.31%
 31	 185580	  3.39%
 32	 209222	  3.82%
 33	 199102	  3.64%
 34	 252851	  4.62%
 35	 267240	  4.88%
 36	 210789	  3.85%
 37	 137146	  2.51%
 38	  95646	  1.75%
 39	  87023	  1.59%
 40	  63603	  1.16%
 41	  81616	  1.49%
 42	  47336	  0.87%
 43	  37883	  0.69%
 44	  28503	  0.52%
 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	      2	  0.00%
 75	      3	  0.00%
 76	 143817	  2.63%
5471436 reads passed initial QC


criterion=sequence-density
sequence-density=4.13
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=13
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATA


criterion=fanout-score
sequence-density=0.28
sequence-density-rank=24
fanout-score=14.67
fanout-score-rank=1
prefix-density=2.73
prefix-fanout=1.5
sequence=GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTG
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 14:45:17
                             Started mapping on |	Jun 21 14:45:18
                                    Finished on |	Jun 21 14:45:29
       Mapping speed, Million of reads per hour |	1790.65

                          Number of input reads |	5471436
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	449144
                        Uniquely mapped reads % |	8.21%
                          Average mapped length |	25.68
                       Number of splices: Total |	8694
            Number of splices: Annotated (sjdb) |	3716
                       Number of splices: GT/AG |	7760
                       Number of splices: GC/AG |	455
                       Number of splices: AT/AC |	7
               Number of splices: Non-canonical |	472
                      Mismatch rate per base, % |	1.02%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.52
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	605102
             % of reads mapped to multiple loci |	11.06%
        Number of reads mapped to too many loci |	1263222
             % of reads mapped to too many loci |	23.09%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.51%
                     % of reads unmapped: other |	50.13%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	4417190	4417190	4417190
N_multimapping	605102	605102	605102
N_noFeature	381734	393486	435426
N_ambiguous	2028	33	33
UnstrandedReadsAssigned:65382 PositiveStrandReadsAssigned:55625 NegativeStrandReadsAssigned:13685
Dataset is classified unstranded
MeadianReadLen=27 20thPercentileLength=22 echo kmer=19
SRR11699632 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: SRR11699632-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 5,471,436 reads, 1,051,708 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 874 rounds

  72540 SRR11699632.ke.tsv
  44303 SRR11699632.se.tsv
 116843 total
==> SRR11699632.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	2	0.6299
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

==> SRR11699632.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699632 completed mapping pipeline successfully
