Starting /dee2/code/volunteer_pipeline.sh SRR11699303
    current disk space = 2467995086848
    free memory = 704692028 
SRR11699303 SRAfilesize
19fc380fa7b1023e42fb3bd84245f454  SRR11699303.sra
SRR11699303.sra file validated
SRR11699303 is single end
SRR11699303 is conventional basespace
SRR11699303 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699303_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	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.1125	32.0	32.0	32.0	32.0	32.0
2	31.3975	32.0	32.0	32.0	32.0	32.0
3	31.3575	32.0	32.0	32.0	32.0	32.0
4	31.55	32.0	32.0	32.0	32.0	32.0
5	31.4355	32.0	32.0	32.0	32.0	32.0
6	34.984	36.0	36.0	36.0	36.0	36.0
7	35.06525	36.0	36.0	36.0	36.0	36.0
8	35.13075	36.0	36.0	36.0	36.0	36.0
9	34.9615	36.0	36.0	36.0	36.0	36.0
10-11	35.14125	36.0	36.0	36.0	36.0	36.0
12-13	34.971500000000006	36.0	36.0	36.0	36.0	36.0
14-15	34.863749999999996	36.0	36.0	36.0	34.0	36.0
16-17	35.1465	36.0	36.0	36.0	36.0	36.0
18-19	35.08225	36.0	36.0	36.0	36.0	36.0
20-21	34.980000000000004	36.0	36.0	36.0	36.0	36.0
22-23	34.971875	36.0	36.0	36.0	36.0	36.0
24-25	35.0405	36.0	36.0	36.0	36.0	36.0
26-27	34.923375	36.0	36.0	36.0	36.0	36.0
28-29	34.903375	36.0	36.0	36.0	34.0	36.0
30-31	34.831374999999994	36.0	36.0	36.0	34.0	36.0
32-33	34.951375	36.0	36.0	36.0	36.0	36.0
34-35	35.02475	36.0	36.0	36.0	36.0	36.0
36-37	34.91575	36.0	36.0	36.0	36.0	36.0
38-39	34.92337499999999	36.0	36.0	36.0	36.0	36.0
40-41	34.848375000000004	36.0	36.0	36.0	36.0	36.0
42-43	34.93425	36.0	36.0	36.0	36.0	36.0
44-45	34.76175	36.0	36.0	36.0	32.0	36.0
46-47	34.928375	36.0	36.0	36.0	36.0	36.0
48-49	34.756375	36.0	36.0	36.0	34.0	36.0
50-51	34.459875	36.0	36.0	36.0	32.0	36.0
52-53	34.461625	36.0	36.0	36.0	32.0	36.0
54-55	34.197625	36.0	36.0	36.0	32.0	36.0
56-57	33.60225	36.0	36.0	36.0	27.0	36.0
58-59	33.191875	36.0	36.0	36.0	24.0	36.0
60-61	33.45075	36.0	36.0	36.0	27.0	36.0
62-63	32.916375	36.0	32.0	36.0	20.5	36.0
64-65	32.757374999999996	36.0	32.0	36.0	24.0	36.0
66-67	32.369	36.0	32.0	36.0	17.5	36.0
68-69	32.584125	36.0	32.0	36.0	21.0	36.0
70-71	32.998	36.0	34.0	36.0	27.0	36.0
72-73	32.54025	36.0	34.0	36.0	14.0	36.0
74-75	32.92375	36.0	34.0	36.0	20.5	36.0
76	30.38075	32.0	27.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
20	1.0
21	2.0
22	6.0
23	6.0
24	4.0
25	12.0
26	30.0
27	42.0
28	58.0
29	94.0
30	108.0
31	152.0
32	220.0
33	366.0
34	1052.0
35	1847.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	35.425000000000004	23.549999999999997	23.3	17.724999999999998
2	21.575	22.0	22.15	34.275
3	32.65	28.95	15.925	22.475
4	29.25	26.224999999999998	25.650000000000002	18.875
5	18.25	24.325	25.825	31.6
6	21.9	23.525	37.25	17.325
7	43.35	26.924999999999997	16.950000000000003	12.775
8	18.35	21.975	44.6	15.075
9	22.55	42.65	15.2	19.6
10-11	35.2875	22.575	27.5625	14.575
12-13	17.7625	19.525000000000002	25.8625	36.85
14-15	29.9375	43.5375	14.887500000000001	11.637500000000001
16-17	26.625	20.2375	31.0375	22.1
18-19	39.175	20.8125	26.2625	13.750000000000002
20-21	22.537499999999998	34.2375	26.9625	16.2625
22-23	37.3625	37.65	11.8125	13.175
24-25	25.4875	40.925	19.2625	14.325
26-27	25.3125	37.6875	18.575	18.425
28-29	27.3	25.2125	24.1125	23.375
30-31	33.887499999999996	32.9375	8.774999999999999	24.4
32-33	29.512500000000003	40.45	10.174999999999999	19.8625
34-35	30.425	32.3125	14.912500000000001	22.35
36-37	29.349999999999998	29.45	12.3875	28.812500000000004
38-39	28.237499999999997	35.7875	10.15	25.825
40-41	24.099999999999998	35.9	14.3125	25.687500000000004
42-43	29.4125	26.937499999999996	17.4875	26.1625
44-45	21.75	30.7125	15.45	32.087500000000006
46-47	18.95	33.287499999999994	13.825000000000001	33.9375
48-49	18.5375	29.012500000000003	15.9	36.55
50-51	19.525000000000002	22.3875	22.162499999999998	35.925000000000004
52-53	21.349999999999998	24.3875	19.5625	34.699999999999996
54-55	23.225	31.125000000000004	15.037500000000001	30.612499999999997
56-57	19.725	25.2625	17.45	37.5625
58-59	19.8375	22.85	15.6125	41.699999999999996
60-61	24.474999999999998	23.925	16.75	34.849999999999994
62-63	26.0125	21.325	20.8875	31.775
64-65	22.275	22.05	19.375	36.3
66-67	23.3125	17.275	23.375	36.0375
68-69	23.4875	16.3625	25.650000000000002	34.5
70-71	27.8875	15.512500000000001	27.6	28.999999999999996
72-73	22.8875	16.900000000000002	30.0	30.2125
74-75	22.900000000000002	8.9375	31.95	36.2125
76	20.65	8.5	37.05	33.800000000000004
>>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	1.5
37	3.0
38	3.0
39	1.5
40	1.5
41	6.0
42	9.0
43	11.0
44	18.0
45	39.5
46	56.0
47	88.0
48	153.5
49	287.0
50	387.0
51	656.0
52	861.0
53	686.5
54	576.0
55	497.0
56	324.0
57	163.5
58	97.0
59	75.5
60	54.0
61	36.5
62	19.0
63	15.0
64	8.0
65	2.5
66	2.0
67	4.0
68	2.0
69	0.5
70	1.0
71	1.0
72	0.5
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	0.5
95	0.5
96	1.0
97	0.5
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	60.699999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	88.79736408566721	53.900000000000006
2	4.942339373970346	6.0
3	1.9357495881383853	3.5249999999999995
4	0.9060955518945634	2.1999999999999997
5	0.6177924217462932	1.875
6	0.5354200988467875	1.95
7	0.2883031301482702	1.225
8	0.2471169686985173	1.2
9	0.08237232289950577	0.44999999999999996
>10	1.4827018121911038	16.675
>50	0.08237232289950577	3.0
>100	0.08237232289950577	8.0
>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	178	4.45	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	142	3.55	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	66	1.6500000000000001	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	54	1.35	No Hit
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	44	1.0999999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	38	0.95	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCGTTTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	35	0.8750000000000001	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	33	0.8250000000000001	No Hit
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGA	29	0.7250000000000001	TruSeq Adapter, Index 7 (97% over 35bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAC	26	0.65	TruSeq Adapter, Index 6 (97% over 36bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GCACCAGTGGTCTAGTGGTAGAATAGATCGGAAGAGCACACGTCTGAACT	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	19	0.475	No Hit
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCAGATCGGAAGAGCACAC	18	0.44999999999999996	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	17	0.42500000000000004	No Hit
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	15	0.375	No Hit
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGAGATCGGAAGAGCACACGT	14	0.35000000000000003	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACGCGAT	13	0.325	TruSeq Adapter, Index 6 (97% over 36bp)
GCACCAGTAGTCTAGTGGTAGAATAGTACCAGATCGGAAGAGCACACGTC	12	0.3	No Hit
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GCACCAGTAGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACG	11	0.27499999999999997	TruSeq Adapter, Index 6 (97% over 36bp)
GTCGTTGTAGTATAGTGGTGAGTATTCCCGCCAGATCGGAAGAGCACACG	11	0.27499999999999997	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCTAGATCGGAAGAGCACACG	11	0.27499999999999997	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGTAGATCGGAAGAGCACACGT	10	0.25	No Hit
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACGCGA	10	0.25	TruSeq Adapter, Index 6 (97% over 36bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACGCG	10	0.25	TruSeq Adapter, Index 6 (97% over 36bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAC	9	0.22499999999999998	TruSeq Adapter, Index 6 (97% over 36bp)
GGGCATTTGGTCTAGTGGTATGATTCTCGCTTAGATCGGAAGAGCACACG	8	0.2	No Hit
GGGGACGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGA	8	0.2	TruSeq Adapter, Index 7 (97% over 35bp)
GCGTCTGTAGTCCAACGGTTAGGATAGATCGGAAGAGCACACGTCTGAAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCACCAGTAGTCTAGTGGTAGAATAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	7	0.17500000000000002	No Hit
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCACCAGTAGTCTAGTGGTAGAATAGTACCCAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATC	6	0.15	No Hit
CATGCAAATCTAACGAAGTGCTCCTGGACGAGATCGGAAGAGCACACGTC	6	0.15	No Hit
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GGGCATTTGGTCTAGTGGTATGATTCTCGCAGATCGGAAGAGCACACGTC	6	0.15	No Hit
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGTGTTTGGTCTAGTGGTATGATTCTCGCAGATCGGAAGAGCACACGTC	6	0.15	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	6	0.15	No Hit
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGATCATGTTGCAGCTTCACTAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCGTTTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	6	0.15	No Hit
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	5	0.125	No Hit
GGGGATGTAGCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	5	0.125	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GCACCAGTGGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GCGTCTGTAGTCCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGGTGTTTGGTCTAGTGGTATGATTCTCGCTAGATCGGAAGAGCACACGT	5	0.125	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATACCCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GCACCAGTGGTCTAGTGGTAGAATAGTACCCAGATCGGAAGAGCACACGT	5	0.125	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	5	0.125	No Hit
GGGCATTTGGTCTAGTGGTATGATTCTTGCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTAGATCGGAAGAGCACACGT	5	0.125	No Hit
GCGGGGATAGCTCAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
>>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	0.05	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	0.125	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	0.425	0.0	0.0	0.0	0.0
9	0.9	0.0	0.0	0.0	0.0
10	1.3	0.0	0.0	0.0	0.0
11	1.6	0.0	0.0	0.0	0.0
12	1.925	0.0	0.0	0.0	0.0
13	2.725	0.0	0.0	0.0	0.0
14	4.625	0.0	0.0	0.0	0.0
15	6.7	0.0	0.0	0.0	0.0
16	8.025	0.0	0.0	0.0	0.0
17	11.4	0.0	0.0	0.0	0.0
18	13.325	0.0	0.0	0.0	0.0
19	15.1	0.0	0.0	0.0	0.0
20	18.075	0.0	0.0	0.0	0.0
21	20.8	0.0	0.0	0.0	0.0
22	25.85	0.0	0.0	0.0	0.0
23	33.9	0.0	0.0	0.0	0.0
24	36.925	0.0	0.0	0.0	0.0
25	45.125	0.0	0.0	0.0	0.0
26	49.575	0.0	0.0	0.0	0.0
27	52.825	0.0	0.0	0.0	0.0
28	55.35	0.0	0.0	0.0	0.0
29	57.625	0.0	0.0	0.0	0.0
30	60.475	0.0	0.0	0.0	0.0
31	67.45	0.0	0.0	0.0	0.0
32	72.5	0.0	0.0	0.0	0.0
33	80.3	0.0	0.0	0.0	0.0
34	82.95	0.0	0.0	0.0	0.0
35	84.4	0.0	0.0	0.0	0.0
36	87.025	0.0	0.0	0.0	0.0
37	88.45	0.0	0.0	0.0	0.0
38	89.8	0.0	0.0	0.0	0.0
39	90.75	0.0	0.0	0.0	0.0
40	91.65	0.0	0.0	0.0	0.0
41	92.125	0.0	0.0	0.0	0.0
42	92.875	0.0	0.0	0.0	0.0
43	93.325	0.0	0.0	0.0	0.0
44	93.65	0.0	0.0	0.0	0.0
45	93.875	0.0	0.0	0.0	0.0
46	94.5	0.0	0.0	0.0	0.0
47	94.7	0.0	0.0	0.0	0.0
48	94.85	0.0	0.0	0.0	0.0
49	95.15	0.0	0.0	0.0	0.0
50	95.25	0.0	0.0	0.0	0.0
51	95.375	0.0	0.0	0.0	0.0
52	95.475	0.0	0.0	0.0	0.0
53	95.575	0.0	0.0	0.0	0.0
54	95.6	0.0	0.0	0.0	0.0
55	95.6	0.0	0.0	0.0	0.0
56	95.65	0.0	0.0	0.0	0.0
57	95.675	0.0	0.0	0.0	0.0
58	95.7	0.0	0.0	0.0	0.0
59	95.725	0.0	0.0	0.0	0.0
60	95.725	0.0	0.0	0.0	0.0
61	95.725	0.0	0.0	0.0	0.0
62	95.725	0.0	0.0	0.0	0.0
63	95.725	0.0	0.0	0.0	0.0
64	95.725	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GGATGTA	15	0.0020658788	70.00001	3
ATTGGTC	15	0.0020658788	70.00001	15
AGTGGTA	15	0.0020658788	70.00001	14
GATGTAG	15	0.0020658788	70.00001	4
CCCATCG	15	0.0020658788	70.00001	4
TAGTTCA	15	0.0020658788	70.00001	8
ACTCAGA	15	0.0020658788	70.00001	27
TGTAGCT	15	0.0020658788	70.00001	6
GGGATGT	15	0.0020658788	70.00001	2
GTCTAGC	45	3.6379788E-12	70.00001	10
CCCCCAT	15	0.0020658788	70.00001	2
ATGTAGC	15	0.0020658788	70.00001	5
ATACTCA	15	0.0020658788	70.00001	25
AGTCTAG	45	3.6379788E-12	70.00001	9
CCCCATC	15	0.0020658788	70.00001	3
GGGGATG	15	0.0020658788	70.00001	1
TACTCAG	15	0.0020658788	70.00001	26
GTAGTTC	15	0.0020658788	70.00001	7
GTAGTCT	45	3.6379788E-12	70.00001	7
AATTGGT	15	0.0020658788	70.00001	14
>>END_MODULE
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312883 READS because READLEN < 1
Read 312883 spots for SRR11699303.sra
Written 312883 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
Rejected 312872 READS because READLEN < 1
Read 312872 spots for SRR11699303.sra
Written 312872 spots for SRR11699303.sra
SRR ids: ['SRR11699303.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_j3fg0wgz
SRR11699303.sra spots: 6257451
blocks: [[1, 312872], [312873, 625744], [625745, 938616], [938617, 1251488], [1251489, 1564360], [1564361, 1877232], [1877233, 2190104], [2190105, 2502976], [2502977, 2815848], [2815849, 3128720], [3128721, 3441592], [3441593, 3754464], [3754465, 4067336], [4067337, 4380208], [4380209, 4693080], [4693081, 5005952], [5005953, 5318824], [5318825, 5631696], [5631697, 5944568], [5944569, 6257451]]
SRR11699303 file size 1189435
SRR11699303 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 SRR11699303 SRR11699303_1.fastq
Input file:	SRR11699303_1.fastq
trimmed:	SRR11699303-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 09:46:37 2025 >> started

Wed Jun 18 09:46:40 2025 >> done (2.669s)
6257451 reads processed; of these:
 996146 (15.92%) short reads filtered out after trimming by size control
   3148 ( 0.05%) empty reads filtered out after trimming by size control
5258157 (84.03%) reads available; of these:
5138740 (97.73%) trimmed reads available after processing
 119417 ( 2.27%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 139033	  2.64%
 19	 182239	  3.47%
 20	 195149	  3.71%
 21	 334080	  6.35%
 22	 561063	 10.67%
 23	 191953	  3.65%
 24	 525322	  9.99%
 25	 262886	  5.00%
 26	 187987	  3.58%
 27	 170282	  3.24%
 28	 139452	  2.65%
 29	 164284	  3.12%
 30	 408536	  7.77%
 31	 322517	  6.13%
 32	 446578	  8.49%
 33	 178742	  3.40%
 34	 114951	  2.19%
 35	 170225	  3.24%
 36	  98477	  1.87%
 37	  71716	  1.36%
 38	  53618	  1.02%
 39	  50441	  0.96%
 40	  38048	  0.72%
 41	  57839	  1.10%
 42	  31019	  0.59%
 43	  25281	  0.48%
 44	  17018	  0.32%
 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	      3	  0.00%
 76	 119417	  2.27%
5258157 reads passed initial QC


criterion=sequence-density
sequence-density=6.71
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=17
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATA


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=36
fanout-score=38.97
fanout-score-rank=1
prefix-density=0.20
prefix-fanout=1.0
sequence=TAGCCAAGTGTGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTC
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 09:47:15
                             Started mapping on |	Jun 18 09:47:15
                                    Finished on |	Jun 18 09:47:30
       Mapping speed, Million of reads per hour |	1261.96

                          Number of input reads |	5258157
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	456932
                        Uniquely mapped reads % |	8.69%
                          Average mapped length |	24.31
                       Number of splices: Total |	9219
            Number of splices: Annotated (sjdb) |	3123
                       Number of splices: GT/AG |	8377
                       Number of splices: GC/AG |	562
                       Number of splices: AT/AC |	7
               Number of splices: Non-canonical |	273
                      Mismatch rate per base, % |	1.37%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.44
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.37
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1264819
             % of reads mapped to multiple loci |	24.05%
        Number of reads mapped to too many loci |	1197010
             % of reads mapped to too many loci |	22.76%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	6.45%
                     % of reads unmapped: other |	38.04%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3536406	3536406	3536406
N_multimapping	1264819	1264819	1264819
N_noFeature	387804	406204	436736
N_ambiguous	1864	27	44
UnstrandedReadsAssigned:67264 PositiveStrandReadsAssigned:50701 NegativeStrandReadsAssigned:20152
Dataset is classified unstranded
MeadianReadLen=27 20thPercentileLength=22 echo kmer=19
SRR11699303 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: SRR11699303-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 5,258,157 reads, 1,184,601 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 879 rounds

  72540 SRR11699303.ke.tsv
  44303 SRR11699303.se.tsv
 116843 total
==> SRR11699303.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	3	0.896038
Zm00001eb323640_T001	3273	3174	1	0.31223
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

==> SRR11699303.se.tsv <==
Zm00001eb015280	1
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699303 completed mapping pipeline successfully
