Starting /dee2/code/volunteer_pipeline.sh SRR11699273
    current disk space = 2473150234624
    free memory = 1142881604 
SRR11699273 SRAfilesize
b9f663a7abd73767dd0246d0f47088f0  SRR11699273.sra
SRR11699273.sra file validated
SRR11699273 is single end
SRR11699273 is conventional basespace
SRR11699273 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699273_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	49
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.37875	32.0	32.0	32.0	32.0	32.0
2	31.38775	32.0	32.0	32.0	32.0	32.0
3	31.5815	32.0	32.0	32.0	32.0	32.0
4	31.59925	32.0	32.0	32.0	32.0	32.0
5	31.61975	32.0	32.0	32.0	32.0	32.0
6	35.16625	36.0	36.0	36.0	36.0	36.0
7	35.1725	36.0	36.0	36.0	36.0	36.0
8	35.133	36.0	36.0	36.0	36.0	36.0
9	35.06475	36.0	36.0	36.0	36.0	36.0
10-11	35.154875	36.0	36.0	36.0	36.0	36.0
12-13	35.119625	36.0	36.0	36.0	36.0	36.0
14-15	35.12575	36.0	36.0	36.0	36.0	36.0
16-17	35.13125	36.0	36.0	36.0	36.0	36.0
18-19	35.236125	36.0	36.0	36.0	36.0	36.0
20-21	35.01975	36.0	36.0	36.0	36.0	36.0
22-23	35.04875	36.0	36.0	36.0	36.0	36.0
24-25	35.086375000000004	36.0	36.0	36.0	36.0	36.0
26-27	35.013125	36.0	36.0	36.0	36.0	36.0
28-29	35.01325	36.0	36.0	36.0	36.0	36.0
30-31	35.030375	36.0	36.0	36.0	36.0	36.0
32-33	34.935249999999996	36.0	36.0	36.0	36.0	36.0
34-35	34.992000000000004	36.0	36.0	36.0	36.0	36.0
36-37	34.994749999999996	36.0	36.0	36.0	36.0	36.0
38-39	34.985125	36.0	36.0	36.0	36.0	36.0
40-41	34.94825	36.0	36.0	36.0	36.0	36.0
42-43	34.935625	36.0	36.0	36.0	36.0	36.0
44-45	34.879	36.0	36.0	36.0	36.0	36.0
46-47	34.897125	36.0	36.0	36.0	36.0	36.0
48-49	34.722125000000005	36.0	36.0	36.0	34.0	36.0
50-51	34.3845	36.0	36.0	36.0	32.0	36.0
52-53	34.232	36.0	36.0	36.0	32.0	36.0
54-55	33.582125	36.0	36.0	36.0	24.0	36.0
56-57	33.064499999999995	36.0	36.0	36.0	21.0	36.0
58-59	33.125375000000005	36.0	36.0	36.0	24.0	36.0
60-61	33.053125	36.0	36.0	36.0	14.0	36.0
62-63	32.747	36.0	34.0	36.0	14.0	36.0
64-65	32.684875	36.0	32.0	36.0	17.5	36.0
66-67	32.027625	36.0	32.0	36.0	14.0	36.0
68-69	32.044875000000005	36.0	32.0	36.0	14.0	36.0
70-71	32.389625	36.0	32.0	36.0	14.0	36.0
72-73	32.269499999999994	36.0	32.0	36.0	14.0	36.0
74-75	32.3775	36.0	32.0	36.0	14.0	36.0
76	29.63675	32.0	27.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
16	1.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	4.0
23	5.0
24	9.0
25	15.0
26	27.0
27	41.0
28	72.0
29	83.0
30	126.0
31	174.0
32	241.0
33	431.0
34	1004.0
35	1767.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	27.35	26.275	26.125	20.25
2	25.650000000000002	26.150000000000002	21.275	26.924999999999997
3	29.599999999999998	28.125	19.05	23.225
4	32.15	28.175	19.45	20.225
5	21.05	28.975	23.425	26.55
6	23.0	23.125	33.050000000000004	20.825
7	39.5	27.625	17.375	15.5
8	20.775	23.0	37.35	18.875
9	22.2	36.925000000000004	19.675	21.2
10-11	32.9875	23.875	23.150000000000002	19.9875
12-13	20.6125	20.3	25.8125	33.275
14-15	30.475	36.7	17.45	15.375
16-17	24.525	23.875	30.362499999999997	21.2375
18-19	36.8	22.8625	21.375	18.9625
20-21	25.387500000000003	32.75	24.025	17.837500000000002
22-23	33.8125	36.7375	13.850000000000001	15.6
24-25	29.725	36.0625	16.0125	18.2
26-27	26.174999999999997	34.0	18.05	21.775
28-29	26.487500000000004	28.225	19.4375	25.85
30-31	32.1875	30.525000000000002	12.4	24.887500000000003
32-33	27.750000000000004	34.525	14.662500000000001	23.0625
34-35	29.45	31.974999999999998	15.4	23.175
36-37	26.724999999999998	33.675	13.600000000000001	26.0
38-39	26.125	33.125	13.212499999999999	27.537499999999998
40-41	23.5	33.1	14.9375	28.462500000000002
42-43	28.599999999999998	29.799999999999997	16.5	25.1
44-45	21.9625	31.175000000000004	16.975	29.8875
46-47	19.625	33.475	14.924999999999999	31.974999999999998
48-49	17.25	33.637499999999996	15.687499999999998	33.425
50-51	16.125	28.287499999999998	21.075	34.5125
52-53	15.312500000000002	26.950000000000003	23.125	34.612500000000004
54-55	15.7	31.175000000000004	21.9625	31.162499999999998
56-57	10.525	30.875000000000004	22.662499999999998	35.9375
58-59	11.175	27.0875	23.4875	38.25
60-61	11.0625	27.5875	28.075	33.275
62-63	12.1875	24.5625	31.874999999999996	31.374999999999996
64-65	9.6875	23.8875	27.3875	39.0375
66-67	13.3	22.1	29.512500000000003	35.0875
68-69	11.7125	20.125	34.825	33.3375
70-71	13.925	18.45	36.3	31.324999999999996
72-73	14.424999999999999	18.8	34.1875	32.587500000000006
74-75	16.0875	14.45	35.375	34.0875
76	13.175	13.375	39.975	33.475
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.5
35	0.5
36	0.5
37	1.0
38	3.5
39	7.0
40	14.0
41	38.0
42	56.0
43	79.5
44	144.0
45	272.5
46	360.0
47	551.0
48	690.5
49	604.5
50	570.0
51	537.0
52	404.5
53	247.5
54	190.0
55	165.5
56	113.5
57	62.0
58	38.0
59	25.0
60	11.0
61	8.5
62	7.0
63	8.0
64	6.5
65	2.5
66	0.5
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	0.5
82	0.5
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	0.0
96	0.0
97	0.0
98	0.0
99	0.5
100	1.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10-11	0.0
12-13	0.0
14-15	0.0
16-17	0.0
18-19	0.0
20-21	0.0
22-23	0.0
24-25	0.0
26-27	0.0
28-29	0.0
30-31	0.0
32-33	0.0
34-35	0.0
36-37	0.0
38-39	0.0
40-41	0.0
42-43	0.0
44-45	0.0
46-47	0.0
48-49	0.0
50-51	0.0
52-53	0.0
54-55	0.0
56-57	0.0
58-59	0.0
60-61	0.0
62-63	0.0
64-65	0.0
66-67	0.0
68-69	0.0
70-71	0.0
72-73	0.0
74-75	0.0
76	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
76	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	66.45
#Duplication Level	Percentage of deduplicated	Percentage of total
1	87.32129420617005	58.025000000000006
2	6.583897667419112	8.75
3	1.655379984951091	3.3000000000000003
4	0.9781790820165538	2.6
5	0.9029345372460496	3.0
6	0.5643340857787811	2.25
7	0.41384499623777277	1.925
8	0.33860045146726864	1.7999999999999998
9	0.07524454477050413	0.44999999999999996
>10	1.09104589917231	13.975000000000001
>50	0.07524454477050413	3.925
>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	80	2.0	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAC	77	1.925	TruSeq Adapter, Index 1 (97% over 36bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	49	1.225	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAC	48	1.2	TruSeq Adapter, Index 1 (97% over 36bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	44	1.0999999999999999	No Hit
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA	33	0.8250000000000001	TruSeq Adapter, Index 7 (97% over 35bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCAGATCGGAAGAGCACAC	23	0.575	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	23	0.575	No Hit
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	17	0.42500000000000004	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	17	0.42500000000000004	No Hit
GGGGACGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA	16	0.4	TruSeq Adapter, Index 7 (97% over 35bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	16	0.4	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	16	0.4	No Hit
CAAAATGTCACAGGTTCAAATCCTGTCATCCCTACCAAGATCGGAAGAGC	15	0.375	No Hit
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAG	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	12	0.3	No Hit
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAACTTCAT	12	0.3	TruSeq Adapter, Index 1 (97% over 36bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTAGATCGGAAGAGCACAC	10	0.25	No Hit
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGAGATCGGAAGAGCACACG	8	0.2	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	8	0.2	No Hit
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAGATCGGAAGA	8	0.2	No Hit
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	8	0.2	No Hit
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	8	0.2	No Hit
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GCGTTTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	8	0.2	No Hit
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAACTTCA	8	0.2	TruSeq Adapter, Index 1 (97% over 36bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAAAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
AGGGCTATAGCTCAGTTCGGTAGAGCAAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAACT	7	0.17500000000000002	TruSeq Adapter, Index 1 (97% over 36bp)
GCACCAGTGGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GCCCCCATCGTCTAGTGGTTCAGGACAAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGAGC	7	0.17500000000000002	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCTAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
GGTAGTTCGACCGTGGATTAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAATCAGATCGGAAGAG	6	0.15	No Hit
GCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAG	6	0.15	No Hit
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCA	6	0.15	No Hit
CTAACGAACGAACGATTTGAACAGATCGGAAGGGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (96% over 28bp)
ACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGAG	6	0.15	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	6	0.15	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGAGATCGGAAGAGCACACGT	6	0.15	No Hit
CCGACCTTAGCTCAGTTGGTAGAGCAGATCGGAAGAGCACACGTCTGAAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAGATC	6	0.15	No Hit
TTTGGAACCCTGAACAGACCGCCGGTGTTAAGCCGGAGGAAGGAGATCGG	6	0.15	No Hit
TGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
AGGGATGTAGCGCAGCTTGGTAGCAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TTAAATTCAAGTCTCTTGGCTCTTTAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGTAGTTCGACCGTGGATAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GCACCAGTAGTCTAGTGGTAGAATAGTACCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	5	0.125	No Hit
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA	5	0.125	TruSeq Adapter, Index 7 (97% over 35bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCA	5	0.125	No Hit
ACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA	5	0.125	TruSeq Adapter, Index 7 (97% over 35bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	5	0.125	No Hit
TGGAACCCTGAACAGACCGCCGGTGTTAAGCCGGAGGAAGGAGATCGGAA	5	0.125	No Hit
GAGAATTTCTGGAAGGGCTCCCTCTCTTCGGAGAGGGTAAAGCCCTACAG	5	0.125	No Hit
GGGTGTTTGGTCTAGTGGTATGATTCTCAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GTAAGCCCACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ACAAAATGTCACAGGTTCAAATCCTGTCATCCCTACCAAGATCGGAAGAG	5	0.125	No Hit
TGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAA	5	0.125	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAACTTCATCTC	5	0.125	TruSeq Adapter, Index 1 (97% over 36bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGTCCATAGCTCAGTGGTAGAGCAAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	5	0.125	No Hit
TACCTGGTTGATCCTGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
>>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	0.075	0.0	0.0	0.0	0.0
2	0.175	0.0	0.0	0.0	0.0
3	0.325	0.0	0.0	0.0	0.0
4	0.35	0.0	0.0	0.0	0.0
5	0.375	0.0	0.0	0.0	0.0
6	0.65	0.0	0.0	0.0	0.0
7	0.75	0.0	0.0	0.0	0.0
8	1.1	0.0	0.0	0.0	0.0
9	1.625	0.0	0.0	0.0	0.0
10	2.125	0.0	0.0	0.0	0.0
11	2.775	0.0	0.0	0.0	0.0
12	3.675	0.0	0.0	0.0	0.0
13	4.575	0.0	0.0	0.0	0.0
14	8.925	0.0	0.0	0.0	0.0
15	11.275	0.0	0.0	0.0	0.0
16	12.725	0.0	0.0	0.0	0.0
17	15.25	0.0	0.0	0.0	0.0
18	17.1	0.0	0.0	0.0	0.0
19	18.975	0.0	0.0	0.0	0.0
20	21.6	0.0	0.0	0.0	0.0
21	24.3	0.0	0.0	0.0	0.0
22	28.675	0.0	0.0	0.0	0.0
23	33.85	0.0	0.0	0.0	0.0
24	36.35	0.0	0.0	0.0	0.0
25	42.675	0.0	0.0	0.0	0.0
26	46.125	0.0	0.0	0.0	0.0
27	48.75	0.0	0.0	0.0	0.0
28	51.925	0.0	0.0	0.0	0.0
29	54.1	0.0	0.0	0.0	0.0
30	56.375	0.0	0.0	0.0	0.0
31	60.75	0.0	0.0	0.0	0.0
32	63.875	0.0	0.0	0.0	0.0
33	68.525	0.0	0.0	0.0	0.0
34	71.95	0.0	0.0	0.0	0.0
35	74.5	0.0	0.0	0.0	0.0
36	77.0	0.0	0.0	0.0	0.0
37	79.625	0.0	0.0	0.0	0.0
38	81.625	0.0	0.0	0.0	0.0
39	83.375	0.0	0.0	0.0	0.0
40	84.85	0.0	0.0	0.0	0.0
41	86.25	0.0	0.0	0.0	0.0
42	87.75	0.0	0.0	0.0	0.0
43	88.875	0.0	0.0	0.0	0.0
44	89.85	0.0	0.0	0.0	0.0
45	90.525	0.0	0.0	0.0	0.0
46	91.175	0.0	0.0	0.0	0.0
47	91.725	0.0	0.0	0.0	0.0
48	92.2	0.0	0.0	0.0	0.0
49	92.7	0.0	0.0	0.0	0.0
50	93.1	0.0	0.0	0.0	0.0
51	93.25	0.0	0.0	0.0	0.0
52	93.4	0.0	0.0	0.0	0.0
53	93.5	0.0	0.0	0.0	0.0
54	93.55	0.0	0.0	0.0	0.0
55	93.55	0.0	0.0	0.0	0.0
56	93.575	0.0	0.0	0.0	0.0
57	93.6	0.0	0.0	0.0	0.0
58	93.6	0.0	0.0	0.0	0.0
59	93.6	0.0	0.0	0.0	0.0
60	93.625	0.0	0.0	0.0	0.0
61	93.625	0.0	0.0	0.0	0.0
62	93.675	0.0	0.0	0.0	0.0
63	93.675	0.0	0.0	0.0	0.0
64	93.675	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TTCAATT	15	0.0020658788	70.00001	11
ATTGGTC	15	0.0020658788	70.00001	15
CACCGCC	15	0.0020658788	70.00001	26
GGATTGT	15	0.0020658788	70.00001	2
ACCGCCC	15	0.0020658788	70.00001	27
CAATTGG	15	0.0020658788	70.00001	13
TCAATTG	15	0.0020658788	70.00001	12
GGTCAGA	15	0.0020658788	70.00001	18
GTTCAAT	15	0.0020658788	70.00001	10
GATTGTA	15	0.0020658788	70.00001	3
CAGAGCA	15	0.0020658788	70.00001	21
GAGCACC	15	0.0020658788	70.00001	23
ATTGTAG	15	0.0020658788	70.00001	4
TCAGAGC	15	0.0020658788	70.00001	20
AGCACCG	15	0.0020658788	70.00001	24
TTGGTCA	15	0.0020658788	70.00001	16
GCACCGC	15	0.0020658788	70.00001	25
GTCAGAG	15	0.0020658788	70.00001	19
AGTTCAA	15	0.0020658788	70.00001	9
GCTCAGA	30	7.878043E-8	70.00001	10
>>END_MODULE
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
Rejected 231756 READS because READLEN < 1
Read 231756 spots for SRR11699273.sra
Written 231756 spots for SRR11699273.sra
Rejected 231752 READS because READLEN < 1
Read 231752 spots for SRR11699273.sra
Written 231752 spots for SRR11699273.sra
SRR ids: ['SRR11699273.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_v0bn3yg4
SRR11699273.sra spots: 4635044
blocks: [[1, 231752], [231753, 463504], [463505, 695256], [695257, 927008], [927009, 1158760], [1158761, 1390512], [1390513, 1622264], [1622265, 1854016], [1854017, 2085768], [2085769, 2317520], [2317521, 2549272], [2549273, 2781024], [2781025, 3012776], [3012777, 3244528], [3244529, 3476280], [3476281, 3708032], [3708033, 3939784], [3939785, 4171536], [4171537, 4403288], [4403289, 4635044]]
SRR11699273 file size 880480
SRR11699273 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 SRR11699273 SRR11699273_1.fastq
Input file:	SRR11699273_1.fastq
trimmed:	SRR11699273-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- end quality threshold (-q):		10
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ 
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	20
Wed Jun 18 05:04:33 2025 >> started

Wed Jun 18 05:04:35 2025 >> done (1.971s)
4635044 reads processed; of these:
 830593 (17.92%) short reads filtered out after trimming by size control
   6927 ( 0.15%) empty reads filtered out after trimming by size control
3797524 (81.93%) reads available; of these:
3608284 (95.02%) trimmed reads available after processing
 189240 ( 4.98%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  92260	  2.43%
 19	 120723	  3.18%
 20	 141077	  3.71%
 21	 222200	  5.85%
 22	 258514	  6.81%
 23	 130605	  3.44%
 24	 307241	  8.09%
 25	 167858	  4.42%
 26	 135014	  3.56%
 27	 153659	  4.05%
 28	 110769	  2.92%
 29	 120492	  3.17%
 30	 222065	  5.85%
 31	 161253	  4.25%
 32	 196738	  5.18%
 33	 153066	  4.03%
 34	 135111	  3.56%
 35	 132664	  3.49%
 36	 120054	  3.16%
 37	 105016	  2.77%
 38	  83946	  2.21%
 39	  77753	  2.05%
 40	  59718	  1.57%
 41	  74189	  1.95%
 42	  47834	  1.26%
 43	  43829	  1.15%
 44	  34630	  0.91%
 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	      2	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      4	  0.00%
 76	 189240	  4.98%
3797524 reads passed initial QC


criterion=sequence-density
sequence-density=5.57
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=15
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAAGACCCGGGTT


criterion=fanout-score
sequence-density=4.21
sequence-density-rank=2
fanout-score=24.73
fanout-score-rank=1
prefix-density=4.38
prefix-fanout=23.8
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAACTTCATCTCGTATGCCGTCTTCTGCTTG
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    1 (100.00%) aligned >1 times
100.00% overall alignment rate
Potential adapter found in reference sequence. Continuing without clipping.
                                 Started job on |	Jun 18 05:05:50
                             Started mapping on |	Jun 18 05:05:50
                                    Finished on |	Jun 18 05:06:02
       Mapping speed, Million of reads per hour |	1139.26

                          Number of input reads |	3797524
                      Average input read length |	31
                                    UNIQUE READS:
                   Uniquely mapped reads number |	311469
                        Uniquely mapped reads % |	8.20%
                          Average mapped length |	25.99
                       Number of splices: Total |	8316
            Number of splices: Annotated (sjdb) |	2617
                       Number of splices: GT/AG |	7493
                       Number of splices: GC/AG |	536
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	284
                      Mismatch rate per base, % |	1.43%
                         Deletion rate per base |	0.02%
                        Deletion average length |	1.39
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.22
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	545290
             % of reads mapped to multiple loci |	14.36%
        Number of reads mapped to too many loci |	910480
             % of reads mapped to too many loci |	23.98%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.62%
                     % of reads unmapped: other |	41.84%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2940765	2940765	2940765
N_multimapping	545290	545290	545290
N_noFeature	263779	273041	300496
N_ambiguous	1761	35	25
UnstrandedReadsAssigned:45929 PositiveStrandReadsAssigned:38393 NegativeStrandReadsAssigned:10948
Dataset is classified unstranded
MeadianReadLen=29 20thPercentileLength=22 echo kmer=19
SRR11699273 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: SRR11699273-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,797,524 reads, 843,170 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 791 rounds

  72540 SRR11699273.ke.tsv
  44303 SRR11699273.se.tsv
 116843 total
==> SRR11699273.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	4	1.53037
Zm00001eb323640_T001	3273	3174	2	0.799901
Zm00001eb314140_T001	893	794	1	1.59879
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

==> SRR11699273.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	1
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699273 completed mapping pipeline successfully
