Starting /dee2/code/volunteer_pipeline.sh SRR5031102
    current disk space = 160475217920
    free memory = 73933704 
SRR5031102 SRAfilesize
efe2341a4a9c46e7df01a53ba82bc208  SRR5031102.sra
SRR5031102.sra file validated
SRR5031102 is single end
SRR5031102 is conventional basespace
SRR5031102 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031102_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	31.8205	31.0	31.0	34.0	30.0	34.0
2	32.374	33.0	31.0	34.0	31.0	34.0
3	32.33875	33.0	31.0	34.0	31.0	34.0
4	36.112	37.0	35.0	37.0	35.0	37.0
5	36.10825	37.0	35.0	37.0	35.0	37.0
6	36.021	37.0	35.0	37.0	35.0	37.0
7	35.7855	37.0	35.0	37.0	35.0	37.0
8	35.588	37.0	35.0	37.0	33.0	37.0
9	36.92875	39.0	37.0	39.0	33.0	39.0
10	36.24475	39.0	35.0	39.0	31.0	39.0
11	37.29075	39.0	37.0	39.0	34.0	39.0
12	37.66525	39.0	37.0	39.0	35.0	39.0
13	37.5105	39.0	37.0	39.0	35.0	39.0
14	38.3595	40.0	38.0	41.0	33.0	41.0
15	36.65475	39.0	36.0	41.0	28.0	41.0
16	36.94225	39.0	36.0	40.0	31.0	41.0
17	36.979	39.0	36.0	40.0	32.0	41.0
18	38.25125	40.0	37.0	41.0	34.0	41.0
19	38.8345	40.0	38.0	41.0	36.0	41.0
20	38.4705	40.0	38.0	41.0	34.0	41.0
21	38.51375	40.0	38.0	41.0	34.0	41.0
22	37.316	39.0	37.0	40.0	32.0	41.0
23	37.83725	39.0	37.0	40.0	33.0	41.0
24	37.194	39.0	37.0	40.0	31.0	41.0
25	38.1005	40.0	37.0	41.0	33.0	41.0
26	37.951	40.0	37.0	41.0	33.0	41.0
27	38.22875	40.0	38.0	41.0	34.0	41.0
28	38.463	40.0	38.0	41.0	34.0	41.0
29	38.27575	40.0	38.0	41.0	34.0	41.0
30	38.728	40.0	38.0	41.0	35.0	41.0
31	38.73525	40.0	38.0	41.0	35.0	41.0
32	38.70875	40.0	38.0	41.0	35.0	41.0
33	38.54725	40.0	38.0	41.0	35.0	41.0
34	37.951	40.0	38.0	41.0	33.0	41.0
35	37.2055	40.0	35.0	41.0	30.0	41.0
36	33.2215	35.0	30.0	39.0	23.0	41.0
37	34.9955	37.0	33.0	39.0	30.0	40.0
38	36.221	38.0	35.0	39.0	30.0	40.0
39	36.52025	38.0	36.0	40.0	30.0	40.0
40	36.888	39.0	37.0	40.0	31.0	41.0
41	37.38875	40.0	37.0	40.0	32.0	41.0
42	37.489	40.0	37.0	41.0	32.0	41.0
43	37.6115	40.0	37.0	41.0	33.0	41.0
44	36.981	39.0	36.0	40.0	31.0	41.0
45	36.888	39.0	36.0	40.0	31.0	41.0
46	36.77475	39.0	36.0	40.0	31.0	41.0
47	35.74075	38.0	34.0	40.0	28.0	41.0
48	36.866	39.0	37.0	40.0	31.0	41.0
49	36.85275	40.0	37.0	41.0	32.0	41.0
50	34.8935	38.0	34.0	40.0	28.0	40.0
>>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
12	1.0
13	0.0
14	1.0
15	1.0
16	1.0
17	3.0
18	2.0
19	4.0
20	4.0
21	9.0
22	11.0
23	10.0
24	7.0
25	7.0
26	12.0
27	13.0
28	22.0
29	39.0
30	42.0
31	65.0
32	93.0
33	134.0
34	191.0
35	268.0
36	471.0
37	763.0
38	1113.0
39	713.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	6.6000000000000005	26.875	54.775	11.75
2	22.40300375469337	28.235294117647058	17.922403003754695	31.439299123904878
3	23.65	21.275	21.6	33.475
4	30.475	31.025000000000002	12.625	25.874999999999996
5	21.0	40.65	28.299999999999997	10.05
6	36.0	16.425	35.699999999999996	11.875
7	12.75	22.075	24.825	40.35
8	26.6	30.775000000000002	13.775	28.849999999999998
9	20.625	37.15	28.925	13.3
10	19.650000000000002	19.925	28.225	32.2
11	31.0	8.7	16.875	43.425000000000004
12	13.375	15.5	32.45	38.675
13	31.874999999999996	16.5	33.7	17.925
14	34.675	30.225	19.925	15.174999999999999
15	35.325	16.825000000000003	29.425	18.425
16	17.549999999999997	17.925	22.125	42.4
17	25.924999999999997	19.025	40.825	14.224999999999998
18	27.650000000000002	17.75	27.025	27.575
19	35.925000000000004	13.900000000000002	33.300000000000004	16.875
20	46.550000000000004	13.775	27.325	12.35
21	21.775	22.275	29.525000000000002	26.424999999999997
22	30.375000000000004	9.049999999999999	49.4	11.175
23	27.800000000000004	11.5	47.599999999999994	13.100000000000001
24	53.300000000000004	11.05	27.700000000000003	7.95
25	53.425	24.8	15.1	6.675000000000001
26	29.125	50.449999999999996	12.875	7.55
27	15.925	51.24999999999999	24.5	8.325000000000001
28	9.225	26.825	51.87500000000001	12.075
29	8.799999999999999	11.525	59.675	20.0
30	7.8	4.875	40.925	46.400000000000006
31	12.275	3.5749999999999997	48.725	35.425000000000004
32	27.400000000000002	3.9	21.975	46.725
33	57.325	6.25	13.325000000000001	23.1
34	67.125	5.6000000000000005	13.475000000000001	13.8
35	69.5	4.95	18.7	6.8500000000000005
36	48.075	4.8	35.9	11.225
37	48.9	7.825	19.0	24.275
38	23.974999999999998	14.124999999999998	11.725	50.175000000000004
39	14.924999999999999	25.074999999999996	6.675000000000001	53.325
40	13.3	52.5	7.3999999999999995	26.8
41	24.875	52.55	6.375	16.2
42	51.55	32.675	7.2749999999999995	8.5
43	53.5	32.85	5.45	8.200000000000001
44	31.075000000000003	51.949999999999996	4.3	12.675
45	16.7	53.27499999999999	10.65	19.375
46	9.425	28.050000000000004	18.05	44.474999999999994
47	6.15	15.4	39.074999999999996	39.375
48	7.55	11.899999999999999	20.225	60.324999999999996
49	11.325000000000001	20.424999999999997	12.7	55.55
50	17.825	38.324999999999996	11.899999999999999	31.95
>>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	0.5
14	1.0
15	0.5
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	0.5
26	1.0
27	1.0
28	1.0
29	1.0
30	1.0
31	2.5
32	4.0
33	3.0
34	2.0
35	6.0
36	10.0
37	11.0
38	12.0
39	17.0
40	22.0
41	28.0
42	34.0
43	68.5
44	103.0
45	139.5
46	176.0
47	302.5
48	429.0
49	529.0
50	629.0
51	820.0
52	1011.0
53	794.5
54	578.0
55	518.5
56	459.0
57	350.0
58	241.0
59	165.5
60	90.0
61	65.5
62	41.0
63	48.5
64	56.0
65	44.5
66	33.0
67	25.0
68	17.0
69	16.0
70	15.0
71	22.5
72	30.0
73	16.5
74	3.0
75	1.5
76	0.0
77	0.0
78	0.0
79	0.5
80	1.0
81	0.5
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
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	0.125
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	39.75
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.9182389937107	30.575000000000003
2	8.80503144654088	7.000000000000001
3	4.40251572327044	5.25
4	2.7044025157232707	4.3
5	1.0062893081761006	2.0
6	0.9433962264150944	2.25
7	0.8805031446540881	2.45
8	0.628930817610063	2.0
9	0.5031446540880503	1.7999999999999998
>10	2.6415094339622645	20.525
>50	0.3144654088050315	9.225
>100	0.25157232704402516	12.625
>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
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	148	3.6999999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	133	3.325	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	113	2.825	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	111	2.775	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	93	2.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	91	2.275	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	80	2.0	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	53	1.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	52	1.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	49	1.225	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	33	0.8250000000000001	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAT	31	0.775	RNA PCR Primer, Index 1 (100% over 35bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	20	0.5	RNA PCR Primer, Index 1 (100% over 33bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGC	18	0.44999999999999996	RNA PCR Primer, Index 26 (100% over 50bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGACCCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (96% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTC	14	0.35000000000000003	RNA PCR Primer, Index 26 (100% over 44bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	12	0.3	RNA PCR Primer, Index 1 (100% over 31bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	11	0.27499999999999997	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	8	0.2	RNA PCR Primer, Index 1 (100% over 34bp)
TCTACAGTGCACGTGTCTCCAGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGACTCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTCTCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	6	0.15	No Hit
TTTGAACCATCACTCGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	6	0.15	No Hit
AAGCTGCCAGTTGACGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACCCTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATCGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTCGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGCATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (96% over 30bp)
TCGGATCCGTCTGAGCTTGGAATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTACCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	5	0.125	No Hit
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATG	5	0.125	RNA PCR Primer, Index 15 (100% over 36bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGACCCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAACAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (96% over 30bp)
>>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	0.525	0.0	0.0	0.0
2	0.0	0.525	0.0	0.0	0.0
3	0.0	0.65	0.0	0.0	0.0
4	0.0	0.725	0.0	0.0	0.0
5	0.0	0.75	0.0	0.0	0.0
6	0.0	0.8	0.0	0.0	0.0
7	0.0	1.375	0.0	0.0	0.0
8	0.0	1.55	0.0	0.0	0.0
9	0.0	1.625	0.0	0.0	0.0
10	0.0	1.7	0.0	0.0	0.0
11	0.0	1.775	0.0	0.0	0.0
12	0.0	1.85	0.0	0.0	0.0
13	0.0	2.0	0.0	0.0	0.0
14	0.0	2.2	0.0	0.0	0.0
15	0.0	2.675	0.0	0.0	0.0
16	0.0	3.9	0.0	0.0	0.0
17	0.0	4.525	0.0	0.0	0.0
18	0.0	5.525	0.0	0.0	0.0
19	0.0	5.875	0.0	0.0	0.0
20	0.0	6.725	0.0	0.0	0.0
21	0.0	11.5	0.0	0.0	0.0
22	0.0	25.15	0.0	0.0	0.0
23	0.0	57.775	0.0	0.0	0.0
24	0.0	73.05	0.0	0.0	0.0
25	0.0	80.075	0.0	0.0	0.0
26	0.0	81.575	0.0	0.0	0.0
27	0.0	82.35	0.0	0.0	0.0
28	0.0	82.925	0.0	0.0	0.0
29	0.0	83.475	0.0	0.0	0.0
30	0.0	83.9	0.0	0.0	0.0
31	0.0	84.275	0.0	0.0	0.0
32	0.0	84.8	0.0	0.0	0.0
33	0.0	85.375	0.0	0.0	0.0
34	0.0	87.4	0.0	0.0	0.0
35	0.0	88.35	0.0	0.0	0.0
36	0.0	88.775	0.0	0.0	0.0
37	0.0	89.475	0.0	0.0	0.0
38	0.0	89.8	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACAGTGA	20	6.952051E-4	44.000004	3
ACCGGTC	20	6.952051E-4	44.000004	10
AACGCTG	20	6.952051E-4	44.000004	8
ACGCTGT	20	6.952051E-4	44.000004	9
AACCGGT	20	6.952051E-4	44.000004	9
TTCAACG	20	6.952051E-4	44.000004	5
GGTCTCT	20	6.952051E-4	44.000004	13
GAGCTTG	45	2.728484E-10	44.000004	13
GGATCCG	45	2.728484E-10	44.000004	3
CCGTCTG	40	5.315087E-9	44.000004	7
TCGGATC	45	2.728484E-10	44.000004	1
TCAACGC	20	6.952051E-4	44.000004	6
CGGATCC	45	2.728484E-10	44.000004	2
GATTGTA	20	6.952051E-4	44.000004	11
CTTGGCT	20	6.952051E-4	44.000004	16
ATAGTTT	20	6.952051E-4	44.000004	17
GAACCGG	20	6.952051E-4	44.000004	8
ATTGTAT	20	6.952051E-4	44.000004	12
GTCTCTT	20	6.952051E-4	44.000004	14
GATCCGT	45	2.728484E-10	44.000004	4
>>END_MODULE
Read 106127 spots for SRR5031102.sra
Written 106127 spots for SRR5031102.sra
Read 106127 spots for SRR5031102.sra
Written 106127 spots for SRR5031102.sra
Read 106127 spots for SRR5031102.sra
Written 106127 spots for SRR5031102.sra
Read 106127 spots for SRR5031102.sra
Written 106127 spots for SRR5031102.sra
Read 106127 spots for SRR5031102.sra
Written 106127 spots for SRR5031102.sra
Read 106127 spots for SRR5031102.sra
Written 106127 spots for SRR5031102.sra
Read 106127 spots for SRR5031102.sra
Written 106127 spots for SRR5031102.sra
Read 106127 spots for SRR5031102.sra
Written 106127 spots for SRR5031102.sra
Read 106127 spots for SRR5031102.sra
Written 106127 spots for SRR5031102.sra
Read 106127 spots for SRR5031102.sra
Written 106127 spots for SRR5031102.sra
Read 106127 spots for SRR5031102.sra
Written 106127 spots for SRR5031102.sra
Read 106127 spots for SRR5031102.sra
Written 106127 spots for SRR5031102.sra
SRR ids: ['SRR5031102.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_0cimfqvr
SRR5031102.sra spots: 1273524
blocks: [[1, 106127], [106128, 212254], [212255, 318381], [318382, 424508], [424509, 530635], [530636, 636762], [636763, 742889], [742890, 849016], [849017, 955143], [955144, 1061270], [1061271, 1167397], [1167398, 1273524]]
SRR5031102 file size 219664
SRR5031102 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031102 SRR5031102_1.fastq
Input file:	SRR5031102_1.fastq
trimmed:	SRR5031102-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 07:24:10 2020 >> started

Wed Mar  4 07:24:11 2020 >> done (0.901s)
1273524 reads processed; of these:
     97 ( 0.01%) short reads filtered out after trimming by size control
      2 ( 0.00%) empty reads filtered out after trimming by size control
1273425 (99.99%) reads available; of these:
 104907 ( 8.24%) trimmed reads available after processing
1168518 (91.76%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     35	  0.00%
 19	     65	  0.01%
 20	     77	  0.01%
 21	    126	  0.01%
 22	    202	  0.02%
 23	    283	  0.02%
 24	    263	  0.02%
 25	    344	  0.03%
 26	    244	  0.02%
 27	    368	  0.03%
 28	    400	  0.03%
 29	    682	  0.05%
 30	    382	  0.03%
 31	    451	  0.04%
 32	    540	  0.04%
 33	   1032	  0.08%
 34	   1389	  0.11%
 35	   3383	  0.27%
 36	   1988	  0.16%
 37	   1859	  0.15%
 38	   1735	  0.14%
 39	   1916	  0.15%
 40	   2329	  0.18%
 41	   2418	  0.19%
 42	   3097	  0.24%
 43	   4845	  0.38%
 44	   5569	  0.44%
 45	   7450	  0.59%
 46	   8324	  0.65%
 47	   7835	  0.62%
 48	  21800	  1.71%
 49	  23476	  1.84%
 50	1168518	 91.76%
1273425 reads passed initial QC


criterion=sequence-density
sequence-density=90.97
sequence-density-rank=1
fanout-score=19.07
fanout-score-rank=2
prefix-density=91.91
prefix-fanout=18.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCC


criterion=fanout-score
sequence-density=3.79
sequence-density-rank=3
fanout-score=68.16
fanout-score-rank=1
prefix-density=91.88
prefix-fanout=2.8
sequence=GAATTCTCGGGGGCCAAGGAACT
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCC -o SRR5031102 -
Input file:	STDIN
trimmed:	SRR5031102-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCC
-- 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 07:24:21 2020 >> started

Wed Mar  4 07:24:23 2020 >> done (1.872s)
1245438 reads processed; of these:
  74172 ( 5.96%) short reads filtered out after trimming by size control
   8619 ( 0.69%) empty reads filtered out after trimming by size control
1162647 (93.35%) reads available; of these:
1130978 (97.28%) trimmed reads available after processing
  31669 ( 2.72%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   6253	  0.54%
 19	  14370	  1.24%
 20	  76963	  6.62%
 21	 168861	 14.52%
 22	 420065	 36.13%
 23	 191103	 16.44%
 24	  88290	  7.59%
 25	  20505	  1.76%
 26	   9899	  0.85%
 27	   7317	  0.63%
 28	   7628	  0.66%
 29	   5603	  0.48%
 30	   7311	  0.63%
 31	   8649	  0.74%
 32	   9695	  0.83%
 33	  26452	  2.28%
 34	   8812	  0.76%
 35	   6449	  0.55%
 36	   7579	  0.65%
 37	   3518	  0.30%
 38	   3715	  0.32%
 39	   3275	  0.28%
 40	   4913	  0.42%
 41	   6328	  0.54%
 42	   6709	  0.58%
 43	   4282	  0.37%
 44	   2949	  0.25%
 45	   4480	  0.39%
 46	   3047	  0.26%
 47	   2205	  0.19%
 48	    361	  0.03%
 49	    543	  0.05%
 50	  24518	  2.11%


criterion=sequence-density
sequence-density=9.39
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=11
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=2.25
sequence-density-rank=6
fanout-score=17.85
fanout-score-rank=1
prefix-density=2.26
prefix-fanout=17.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGC
                                 Started job on |	Mar 04 07:24:42
                             Started mapping on |	Mar 04 07:24:42
                                    Finished on |	Mar 04 07:25:08
       Mapping speed, Million of reads per hour |	164.86

                          Number of input reads |	1190634
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	627905
                        Uniquely mapped reads % |	52.74%
                          Average mapped length |	23.22
                       Number of splices: Total |	2255
            Number of splices: Annotated (sjdb) |	522
                       Number of splices: GT/AG |	2209
                       Number of splices: GC/AG |	18
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	27
                      Mismatch rate per base, % |	0.35%
                         Deletion rate per base |	0.00%
                        Deletion average length |	2.00
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	455814
             % of reads mapped to multiple loci |	38.28%
        Number of reads mapped to too many loci |	15511
             % of reads mapped to too many loci |	1.30%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.23%
                     % of reads unmapped: other |	0.44%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	106915	106915	106915
N_multimapping	455814	455814	455814
N_noFeature	32030	36583	423960
N_ambiguous	362759	181771	3746
UnstrandedReadsAssigned:233116 PositiveStrandReadsAssigned:409551 NegativeStrandReadsAssigned:200199
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031102 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: SRR5031102-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,190,634 reads, 307,303 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,027 rounds

 109283 SRR5031102.ke.tsv
  52636 SRR5031102.se.tsv
 161919 total
==> SRR5031102.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

==> SRR5031102.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031102 completed mapping pipeline successfully
