Starting /dee2/code/volunteer_pipeline.sh SRR5031069
    current disk space = 160508444672
    free memory = 73951220 
SRR5031069 SRAfilesize
4ff2aae41352b020228b324bc733672c  SRR5031069.sra
SRR5031069.sra file validated
SRR5031069 is single end
SRR5031069 is conventional basespace
SRR5031069 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031069_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	52
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.34	33.0	31.0	34.0	31.0	34.0
2	32.59025	34.0	31.0	34.0	31.0	34.0
3	32.632	34.0	31.0	34.0	31.0	34.0
4	36.2265	37.0	35.0	37.0	35.0	37.0
5	35.935	37.0	35.0	37.0	35.0	37.0
6	35.79725	37.0	35.0	37.0	33.0	37.0
7	35.967	37.0	35.0	37.0	35.0	37.0
8	35.861	37.0	35.0	37.0	35.0	37.0
9	37.578	39.0	37.0	39.0	35.0	39.0
10	37.814	39.0	38.0	39.0	35.0	39.0
11	37.696	39.0	37.0	39.0	35.0	39.0
12	37.67075	39.0	37.0	39.0	35.0	39.0
13	37.61125	39.0	37.0	39.0	35.0	39.0
14	39.02125	40.0	38.0	41.0	36.0	41.0
15	39.03725	40.0	38.0	41.0	36.0	41.0
16	39.00775	40.0	38.0	41.0	35.0	41.0
17	38.933	40.0	38.0	41.0	35.0	41.0
18	39.1	40.0	38.0	41.0	35.0	41.0
19	38.78725	40.0	38.0	41.0	35.0	41.0
20	38.90525	40.0	38.0	41.0	34.0	41.0
21	38.825	40.0	38.0	41.0	34.0	41.0
22	38.95575	40.0	38.0	41.0	35.0	41.0
23	38.763	40.0	38.0	41.0	35.0	41.0
24	38.82575	40.0	38.0	41.0	35.0	41.0
25	39.07825	40.0	39.0	41.0	36.0	41.0
26	38.78525	40.0	38.0	41.0	35.0	41.0
27	38.777	40.0	38.0	41.0	35.0	41.0
28	38.76075	40.0	38.0	41.0	35.0	41.0
29	38.36825	40.0	38.0	41.0	33.0	41.0
30	38.1465	40.0	38.0	41.0	33.0	41.0
31	38.38925	40.0	38.0	41.0	34.0	41.0
32	38.3335	40.0	38.0	41.0	34.0	41.0
33	38.16475	40.0	38.0	41.0	34.0	41.0
34	38.27875	40.0	38.0	41.0	34.0	41.0
35	38.24075	40.0	38.0	41.0	34.0	41.0
36	38.03525	40.0	37.0	41.0	33.0	41.0
37	37.707	40.0	37.0	41.0	32.0	41.0
38	36.98475	39.0	36.0	41.0	31.0	41.0
39	37.39025	39.0	37.0	41.0	31.0	41.0
40	37.53875	40.0	37.0	41.0	32.0	41.0
41	37.73975	40.0	37.0	41.0	33.0	41.0
42	38.001	40.0	37.0	41.0	33.0	41.0
43	38.39225	40.0	38.0	41.0	34.0	41.0
44	38.16975	40.0	38.0	41.0	34.0	41.0
45	38.01525	40.0	38.0	41.0	33.0	41.0
46	37.914	40.0	37.0	41.0	33.0	41.0
47	37.3315	40.0	36.0	41.0	31.0	41.0
48	36.91125	39.0	36.0	41.0	31.0	41.0
49	37.1705	40.0	36.0	41.0	32.0	41.0
50	36.584	39.0	35.0	41.0	31.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
9	1.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	1.0
17	2.0
18	4.0
19	0.0
20	2.0
21	1.0
22	4.0
23	11.0
24	3.0
25	11.0
26	6.0
27	13.0
28	15.0
29	43.0
30	51.0
31	62.0
32	79.0
33	109.0
34	144.0
35	198.0
36	288.0
37	455.0
38	739.0
39	1758.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.55	25.275	48.5	16.675
2	24.793388429752067	26.120711244678184	18.382168795391937	30.703731530177812
3	24.675	18.85	19.975	36.5
4	33.725	26.875	15.1	24.3
5	23.425	37.65	27.075	11.85
6	34.225	14.6	35.25	15.925
7	15.225	23.150000000000002	22.0	39.625
8	25.825	27.975	15.75	30.45
9	22.15	32.7	27.85	17.299999999999997
10	20.625	22.175	28.9	28.299999999999997
11	33.275	10.475	16.825000000000003	39.425
12	16.1	18.7	31.8	33.4
13	29.9	18.175	33.15	18.775
14	29.349999999999998	30.95	20.775	18.925
15	34.975	25.1	26.5	13.425
16	20.525	20.175	23.175	36.125
17	25.75	24.75	35.05	14.45
18	22.5	18.575	30.45	28.475
19	37.425000000000004	14.149999999999999	29.45	18.975
20	45.0	13.375	28.549999999999997	13.075000000000001
21	24.95	20.1	25.650000000000002	29.299999999999997
22	30.025000000000002	12.375	46.150000000000006	11.450000000000001
23	25.05	13.05	45.475	16.425
24	51.449999999999996	14.424999999999999	25.8	8.325000000000001
25	49.975	22.85	16.35	10.825
26	28.675	43.85	14.524999999999999	12.950000000000001
27	17.0	46.775	21.6	14.625
28	11.65	25.275	47.475	15.6
29	14.475	13.675	55.300000000000004	16.55
30	10.525	7.025	35.725	46.725
31	13.725000000000001	5.625	48.575	32.074999999999996
32	27.175	6.075	22.625	44.125
33	51.300000000000004	10.95	15.25	22.5
34	60.224999999999994	7.7	16.725	15.35
35	65.3	7.35	17.424999999999997	9.925
36	41.825	7.475	37.25	13.450000000000001
37	46.325	11.700000000000001	20.65	21.325
38	24.675	16.975	12.925	45.425
39	17.424999999999997	21.05	11.975	49.55
40	15.725	45.9	12.45	25.924999999999997
41	23.150000000000002	48.675000000000004	9.275	18.9
42	47.225	29.599999999999998	12.275	10.9
43	52.300000000000004	27.35	8.225	12.125
44	32.925	46.9	7.475	12.7
45	20.775	50.425	11.924999999999999	16.875
46	15.225	27.275	15.7	41.8
47	10.025	16.125	39.775	34.075
48	12.725	13.0	20.45	53.825
49	13.225000000000001	17.775	14.575	54.425000000000004
50	16.6	37.724999999999994	12.225	33.45
>>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	0.5
10	1.0
11	1.0
12	1.0
13	0.5
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.5
20	1.0
21	0.5
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	2.0
28	4.0
29	2.0
30	0.0
31	8.5
32	17.0
33	12.0
34	7.0
35	16.0
36	25.0
37	28.5
38	32.0
39	38.0
40	44.0
41	43.0
42	42.0
43	75.5
44	109.0
45	136.0
46	163.0
47	297.5
48	432.0
49	519.5
50	607.0
51	722.0
52	837.0
53	639.0
54	441.0
55	484.0
56	527.0
57	397.5
58	268.0
59	178.0
60	88.0
61	65.0
62	42.0
63	103.5
64	165.0
65	99.0
66	33.0
67	27.5
68	22.0
69	23.0
70	24.0
71	41.0
72	58.0
73	30.5
74	3.0
75	2.5
76	2.0
77	1.5
78	1.0
79	1.5
80	2.0
81	2.0
82	2.0
83	1.0
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	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.17500000000000002
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	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	36.3
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.10468319559229	26.900000000000002
2	10.81267217630854	7.85
3	4.820936639118457	5.25
4	1.997245179063361	2.9000000000000004
5	1.3774104683195594	2.5
6	0.8953168044077136	1.95
7	0.8264462809917356	2.1
8	0.7575757575757576	2.1999999999999997
9	0.6887052341597797	2.25
>10	3.1680440771349865	23.45
>50	0.2066115702479339	6.525
>100	0.34435261707988984	16.125
>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
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	152	3.8	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	133	3.325	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	128	3.2	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	122	3.05	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	110	2.75	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	92	2.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	86	2.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	83	2.075	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	49	1.225	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	47	1.175	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	45	1.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	43	1.075	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGA	34	0.8500000000000001	RNA PCR Primer, Index 7 (97% over 35bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	28	0.7000000000000001	No Hit
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 33bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGC	16	0.4	RNA PCR Primer, Index 41 (100% over 50bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	13	0.325	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	13	0.325	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	12	0.3	No Hit
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTC	12	0.3	RNA PCR Primer, Index 41 (100% over 44bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAC	11	0.27499999999999997	RNA PCR Primer, Index 6 (97% over 36bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	10	0.25	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	10	0.25	RNA PCR Primer, Index 1 (100% over 25bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 31bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	9	0.22499999999999998	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	8	0.2	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	8	0.2	RNA PCR Primer, Index 6 (100% over 34bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	8	0.2	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	7	0.17500000000000002	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	7	0.17500000000000002	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	7	0.17500000000000002	No Hit
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	7	0.17500000000000002	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	7	0.17500000000000002	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	7	0.17500000000000002	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	6	0.15	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	6	0.15	No Hit
TTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCG	6	0.15	RNA PCR Primer, Index 41 (100% over 45bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ATCCCGGACGAGCCCCCATGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	5	0.125	RNA PCR Primer, Index 1 (100% over 32bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	5	0.125	No Hit
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
GTCGATGATGAGAGCTTTGTTCTGAGCTGGAATTCTCGGGTGCCAAGGAA	5	0.125	RNA PCR Primer, Index 1 (100% over 23bp)
TCCCTGAGACCCTAACTTGTGAAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>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	0.45	0.0	0.0	0.0
2	0.0	0.45	0.0	0.0	0.0
3	0.0	0.475	0.0	0.0	0.0
4	0.0	0.5	0.0	0.0	0.0
5	0.0	0.55	0.0	0.0	0.0
6	0.0	0.75	0.0	0.0	0.0
7	0.0	1.125	0.0	0.0	0.0
8	0.0	1.25	0.0	0.0	0.0
9	0.0	1.325	0.0	0.0	0.0
10	0.0	1.45	0.0	0.0	0.0
11	0.0	1.65	0.0	0.0	0.0
12	0.0	1.975	0.0	0.0	0.0
13	0.0	2.2	0.0	0.0	0.0
14	0.0	2.375	0.0	0.0	0.0
15	0.0	3.0	0.0	0.0	0.0
16	0.0	4.15	0.0	0.0	0.0
17	0.0	4.8	0.0	0.0	0.0
18	0.0	5.775	0.0	0.0	0.0
19	0.0	6.275	0.0	0.0	0.0
20	0.0	7.325	0.0	0.0	0.0
21	0.0	12.2	0.0	0.0	0.0
22	0.0	21.675	0.0	0.0	0.0
23	0.0	51.15	0.0	0.0	0.0
24	0.0	64.25	0.0	0.0	0.0
25	0.0	71.0	0.0	0.0	0.0
26	0.0	72.75	0.0	0.0	0.0
27	0.0	73.825	0.0	0.0	0.0
28	0.0	74.625	0.0	0.0	0.0
29	0.0	75.275	0.0	0.0	0.0
30	0.0	75.9	0.0	0.0	0.0
31	0.0	76.85	0.0	0.0	0.0
32	0.0	77.85	0.0	0.0	0.0
33	0.0	78.925	0.0	0.0	0.0
34	0.0	83.2	0.0	0.0	0.0
35	0.0	84.325	0.0	0.0	0.0
36	0.0	85.25	0.0	0.0	0.0
37	0.0	86.35	0.0	0.0	0.0
38	0.0	86.725	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGAGACC	20	6.952051E-4	44.000004	5
ACTGTTG	20	6.952051E-4	44.000004	18
AACGCTG	20	6.952051E-4	44.000004	8
TGCACTC	20	6.952051E-4	44.000004	4
ACTCGTC	20	6.952051E-4	44.000004	7
GTTGAAG	20	6.952051E-4	44.000004	10
TTGCACT	20	6.952051E-4	44.000004	3
ACGCTGT	20	6.952051E-4	44.000004	9
CAGTTGA	20	6.952051E-4	44.000004	8
CTGAGAC	20	6.952051E-4	44.000004	4
CCAGTTG	20	6.952051E-4	44.000004	7
AACTGTT	20	6.952051E-4	44.000004	17
AGTAGGT	20	6.952051E-4	44.000004	7
TTCAACG	20	6.952051E-4	44.000004	5
CCCGGCC	20	6.952051E-4	44.000004	13
CCTGAGA	20	6.952051E-4	44.000004	3
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
TATTGCA	20	6.952051E-4	44.000004	1
GAAGAAC	20	6.952051E-4	44.000004	13
>>END_MODULE
Read 268892 spots for SRR5031069.sra
Written 268892 spots for SRR5031069.sra
Read 268892 spots for SRR5031069.sra
Written 268892 spots for SRR5031069.sra
Read 268892 spots for SRR5031069.sra
Written 268892 spots for SRR5031069.sra
Read 268892 spots for SRR5031069.sra
Written 268892 spots for SRR5031069.sra
Read 268892 spots for SRR5031069.sra
Written 268892 spots for SRR5031069.sra
Read 268892 spots for SRR5031069.sra
Written 268892 spots for SRR5031069.sra
Read 268892 spots for SRR5031069.sra
Written 268892 spots for SRR5031069.sra
Read 268893 spots for SRR5031069.sra
Written 268893 spots for SRR5031069.sra
Read 268892 spots for SRR5031069.sra
Written 268892 spots for SRR5031069.sra
Read 268892 spots for SRR5031069.sra
Written 268892 spots for SRR5031069.sra
Read 268892 spots for SRR5031069.sra
Written 268892 spots for SRR5031069.sra
Read 268892 spots for SRR5031069.sra
Written 268892 spots for SRR5031069.sra
SRR ids: ['SRR5031069.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_wgl1zy21
SRR5031069.sra spots: 3226705
blocks: [[1, 268892], [268893, 537784], [537785, 806676], [806677, 1075568], [1075569, 1344460], [1344461, 1613352], [1613353, 1882244], [1882245, 2151136], [2151137, 2420028], [2420029, 2688920], [2688921, 2957812], [2957813, 3226705]]
SRR5031069 file size 558195
SRR5031069 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031069 SRR5031069_1.fastq
Input file:	SRR5031069_1.fastq
trimmed:	SRR5031069-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 (auto detected)
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	12
Wed Mar  4 07:17:48 2020 >> started

Wed Mar  4 07:17:50 2020 >> done (1.843s)
3226705 reads processed; of these:
    230 ( 0.01%) short reads filtered out after trimming by size control
     12 ( 0.00%) empty reads filtered out after trimming by size control
3226463 (99.99%) reads available; of these:
 162454 ( 5.04%) trimmed reads available after processing
3064009 (94.96%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     78	  0.00%
 19	     90	  0.00%
 20	    185	  0.01%
 21	    209	  0.01%
 22	    388	  0.01%
 23	    530	  0.02%
 24	    507	  0.02%
 25	    670	  0.02%
 26	    551	  0.02%
 27	    711	  0.02%
 28	    845	  0.03%
 29	   1172	  0.04%
 30	    839	  0.03%
 31	    959	  0.03%
 32	   1114	  0.03%
 33	   1215	  0.04%
 34	   1393	  0.04%
 35	   2657	  0.08%
 36	   2526	  0.08%
 37	   2696	  0.08%
 38	   2806	  0.09%
 39	   3102	  0.10%
 40	   3666	  0.11%
 41	   3480	  0.11%
 42	   4640	  0.14%
 43	   6760	  0.21%
 44	   9787	  0.30%
 45	  12168	  0.38%
 46	  16731	  0.52%
 47	  20634	  0.64%
 48	  28649	  0.89%
 49	  30696	  0.95%
 50	3064009	 94.96%
3226463 reads passed initial QC


criterion=sequence-density
sequence-density=85.63
sequence-density-rank=1
fanout-score=20.43
fanout-score-rank=1
prefix-density=87.67
prefix-fanout=20.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGCC


criterion=fanout-score
sequence-density=85.63
sequence-density-rank=1
fanout-score=20.43
fanout-score-rank=1
prefix-density=87.67
prefix-fanout=20.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGCC
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 -l 18 -t 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGCC -o SRR5031069 -
Input file:	STDIN
trimmed:	SRR5031069-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGACGACATCTCGTATGCC
-- 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):		Unknown format (auto detected)
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	12
Wed Mar  4 07:18:05 2020 >> started

Wed Mar  4 07:18:09 2020 >> done (4.141s)
3151429 reads processed; of these:
 181297 ( 5.75%) short reads filtered out after trimming by size control
  19608 ( 0.62%) empty reads filtered out after trimming by size control
2950524 (93.62%) reads available; of these:
2798445 (94.85%) trimmed reads available after processing
 152079 ( 5.15%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  16754	  0.57%
 19	  29366	  1.00%
 20	 151018	  5.12%
 21	 337891	 11.45%
 22	 920308	 31.19%
 23	 419953	 14.23%
 24	 191854	  6.50%
 25	  52198	  1.77%
 26	  25810	  0.87%
 27	  21932	  0.74%
 28	  23880	  0.81%
 29	  18660	  0.63%
 30	  26580	  0.90%
 31	  32385	  1.10%
 32	  37372	  1.27%
 33	 138724	  4.70%
 34	  37563	  1.27%
 35	  28016	  0.95%
 36	  33657	  1.14%
 37	  17983	  0.61%
 38	  18207	  0.62%
 39	  18292	  0.62%
 40	  26679	  0.90%
 41	  35227	  1.19%
 42	  40355	  1.37%
 43	  28231	  0.96%
 44	  21731	  0.74%
 45	  28087	  0.95%
 46	  20801	  0.70%
 47	  16463	  0.56%
 48	   1390	  0.05%
 49	   1801	  0.06%
 50	 131356	  4.45%


criterion=sequence-density
sequence-density=6.92
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.64
sequence-density-rank=21
fanout-score=12.51
fanout-score-rank=1
prefix-density=8.03
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:18:29
                             Started mapping on |	Mar 04 07:18:29
                                    Finished on |	Mar 04 07:18:54
       Mapping speed, Million of reads per hour |	435.68

                          Number of input reads |	3025558
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1557244
                        Uniquely mapped reads % |	51.47%
                          Average mapped length |	24.93
                       Number of splices: Total |	1909
            Number of splices: Annotated (sjdb) |	313
                       Number of splices: GT/AG |	1797
                       Number of splices: GC/AG |	22
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	90
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.75
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.23
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1019185
             % of reads mapped to multiple loci |	33.69%
        Number of reads mapped to too many loci |	68491
             % of reads mapped to too many loci |	2.26%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.95%
                     % of reads unmapped: other |	0.63%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	449129	449129	449129
N_multimapping	1019185	1019185	1019185
N_noFeature	73782	93926	1069900
N_ambiguous	881323	464014	14642
UnstrandedReadsAssigned:602139 PositiveStrandReadsAssigned:999304 NegativeStrandReadsAssigned:472702
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031069 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: 109,282
[index] number of k-mers: 92,755,666
[index] number of equivalence classes: 769,752
[quant] running in single-end mode
[quant] will process file 1: SRR5031069-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,025,558 reads, 769,191 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,147 rounds

 109283 SRR5031069.ke.tsv
  52636 SRR5031069.se.tsv
 161919 total
==> SRR5031069.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSMUST00000177564.1	16	4.59059	0	0
ENSMUST00000196221.1	9	3.70903	0	0
ENSMUST00000179664.1	11	4.02702	0	0
ENSMUST00000178537.1	12	4.16231	0	0
ENSMUST00000178862.1	14	4.39563	0	0
ENSMUST00000179520.1	11	4.02702	0	0
ENSMUST00000179883.1	16	4.59059	0	0
ENSMUST00000195858.1	10	3.87667	0	0
ENSMUST00000179932.1	12	4.16231	0	0

==> SRR5031069.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031069 completed mapping pipeline successfully
