Starting /dee2/code/volunteer_pipeline.sh SRR5030986
    current disk space = 160570245120
    free memory = 73944520 
SRR5030986 SRAfilesize
99706c97efe925da68868d0e80aa51ff  SRR5030986.sra
SRR5030986.sra file validated
SRR5030986 is single end
SRR5030986 is conventional basespace
SRR5030986 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030986_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	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.3885	33.0	31.0	34.0	31.0	34.0
2	32.5895	34.0	31.0	34.0	31.0	34.0
3	32.48175	34.0	31.0	34.0	30.0	34.0
4	36.1835	37.0	35.0	37.0	35.0	37.0
5	36.093	37.0	35.0	37.0	35.0	37.0
6	35.74275	37.0	35.0	37.0	33.0	37.0
7	35.7625	37.0	35.0	37.0	35.0	37.0
8	35.988	37.0	35.0	37.0	35.0	37.0
9	37.6615	39.0	37.0	39.0	35.0	39.0
10	37.468	39.0	37.0	39.0	34.0	39.0
11	37.2645	39.0	37.0	39.0	33.0	39.0
12	37.51775	39.0	37.0	39.0	35.0	39.0
13	37.5555	39.0	37.0	39.0	35.0	39.0
14	39.03725	40.0	38.0	41.0	35.0	41.0
15	38.8965	40.0	38.0	41.0	35.0	41.0
16	38.95675	40.0	38.0	41.0	35.0	41.0
17	39.09175	40.0	38.0	41.0	36.0	41.0
18	38.9515	40.0	38.0	41.0	35.0	41.0
19	38.687	40.0	38.0	41.0	34.0	41.0
20	38.8255	40.0	38.0	41.0	35.0	41.0
21	38.85375	40.0	38.0	41.0	35.0	41.0
22	38.94	40.0	39.0	41.0	35.0	41.0
23	38.46225	40.0	38.0	41.0	34.0	41.0
24	38.8405	40.0	38.0	41.0	35.0	41.0
25	39.06875	40.0	39.0	41.0	35.0	41.0
26	38.862	40.0	38.0	41.0	35.0	41.0
27	38.9655	40.0	39.0	41.0	35.0	41.0
28	38.7225	40.0	38.0	41.0	34.0	41.0
29	38.5845	40.0	38.0	41.0	34.0	41.0
30	38.578	40.0	38.0	41.0	34.0	41.0
31	38.76875	40.0	38.0	41.0	34.0	41.0
32	38.72425	40.0	38.0	41.0	35.0	41.0
33	38.5565	40.0	38.0	41.0	34.0	41.0
34	38.58125	40.0	38.0	41.0	34.0	41.0
35	38.4385	40.0	38.0	41.0	34.0	41.0
36	38.20325	40.0	38.0	41.0	34.0	41.0
37	37.67875	40.0	37.0	41.0	32.0	41.0
38	37.4645	40.0	37.0	41.0	32.0	41.0
39	37.8775	40.0	38.0	41.0	33.0	41.0
40	38.04875	40.0	38.0	41.0	33.0	41.0
41	38.2485	40.0	38.0	41.0	33.0	41.0
42	38.24975	40.0	38.0	41.0	34.0	41.0
43	38.21725	40.0	38.0	41.0	34.0	41.0
44	38.291	40.0	38.0	41.0	34.0	41.0
45	38.27075	40.0	38.0	41.0	34.0	41.0
46	37.9575	40.0	38.0	41.0	33.0	41.0
47	37.56325	40.0	37.0	41.0	32.0	41.0
48	37.18	40.0	37.0	41.0	31.0	41.0
49	37.242	40.0	37.0	41.0	32.0	41.0
50	36.79625	40.0	36.0	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
15	1.0
16	1.0
17	3.0
18	1.0
19	4.0
20	0.0
21	4.0
22	2.0
23	2.0
24	5.0
25	9.0
26	10.0
27	17.0
28	25.0
29	34.0
30	56.0
31	59.0
32	78.0
33	92.0
34	151.0
35	199.0
36	264.0
37	395.0
38	680.0
39	1908.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	6.7	24.099999999999998	58.050000000000004	11.15
2	26.34610568494866	25.66992236413724	22.814926120711245	25.169045830202858
3	16.0	19.900000000000002	20.825	43.275000000000006
4	27.0	38.025	13.55	21.425
5	24.275	37.525	28.549999999999997	9.65
6	36.3	15.225	37.075	11.4
7	12.575	25.924999999999997	24.75	36.75
8	25.1	41.5	14.2	19.2
9	15.2	39.725	31.775	13.3
10	17.424999999999997	23.0	27.450000000000003	32.125
11	33.074999999999996	10.299999999999999	13.875000000000002	42.75
12	16.75	16.525000000000002	22.575	44.15
13	18.95	22.525000000000002	40.325	18.2
14	40.025	20.575	27.400000000000002	12.0
15	41.05	19.0	28.050000000000004	11.899999999999999
16	13.100000000000001	25.874999999999996	23.1	37.925
17	25.0	24.0	38.775	12.225
18	29.65	19.400000000000002	27.150000000000002	23.799999999999997
19	38.45	14.174999999999999	30.475	16.900000000000002
20	50.875	16.725	21.4	11.0
21	20.625	25.6	26.0	27.775
22	30.75	12.2	50.14999999999999	6.9
23	23.7	12.575	51.025	12.7
24	53.2	11.075	29.575000000000003	6.15
25	59.075	20.349999999999998	13.8	6.775
26	31.374999999999996	49.8	10.25	8.575000000000001
27	14.35	56.49999999999999	20.549999999999997	8.6
28	8.175	28.549999999999997	52.025	11.25
29	8.975	10.625	63.24999999999999	17.150000000000002
30	8.95	4.625	40.225	46.2
31	10.925	4.025	48.125	36.925000000000004
32	23.375	4.375	24.474999999999998	47.775
33	56.074999999999996	5.675	12.925	25.324999999999996
34	70.5	6.1	10.125	13.275
35	70.625	5.35	16.45	7.575
36	43.7	6.25	40.2	9.85
37	48.1	8.125	24.075	19.7
38	25.95	11.55	11.65	50.849999999999994
39	13.600000000000001	20.200000000000003	7.7	58.5
40	11.450000000000001	51.15	7.7	29.7
41	20.474999999999998	57.85	6.8500000000000005	14.825
42	51.9	32.25	7.6	8.25
43	60.12499999999999	25.525	6.075	8.275
44	33.525	50.625	5.8500000000000005	10.0
45	15.174999999999999	57.99999999999999	9.700000000000001	17.125
46	8.875	30.25	15.925	44.95
47	7.35	13.350000000000001	41.075	38.224999999999994
48	7.725	9.475	23.724999999999998	59.075
49	10.25	16.925	12.35	60.475
50	16.6	40.475	8.774999999999999	34.150000000000006
>>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	0.5
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	0.5
24	1.0
25	1.5
26	2.0
27	1.5
28	1.0
29	1.0
30	1.0
31	3.5
32	6.0
33	5.5
34	5.0
35	9.0
36	13.0
37	16.0
38	19.0
39	23.5
40	28.0
41	36.0
42	44.0
43	86.0
44	128.0
45	203.5
46	279.0
47	486.5
48	694.0
49	665.5
50	637.0
51	816.0
52	995.0
53	668.5
54	342.0
55	309.0
56	276.0
57	259.5
58	243.0
59	164.5
60	86.0
61	58.0
62	30.0
63	49.0
64	68.0
65	45.5
66	23.0
67	16.0
68	9.0
69	16.0
70	23.0
71	31.5
72	40.0
73	21.5
74	3.0
75	1.5
76	0.0
77	1.0
78	2.0
79	1.0
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	0.0
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	35.15
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.96017069701281	26.700000000000003
2	8.677098150782362	6.1
3	4.694167852062589	4.95
4	2.275960170697013	3.2
5	1.4935988620199145	2.625
6	0.8534850640113799	1.7999999999999998
7	0.7112375533428165	1.7500000000000002
8	0.35561877667140823	1.0
9	0.6401137980085349	2.025
>10	3.769559032716927	26.0
>50	0.2844950213371266	6.2
>100	0.2844950213371266	17.65
>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
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	284	7.1	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	186	4.65	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	122	3.05	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	114	2.85	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	80	2.0	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	66	1.6500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	51	1.275	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	51	1.275	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	50	1.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	46	1.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	43	1.075	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	30	0.75	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	30	0.75	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	29	0.7250000000000001	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGC	22	0.5499999999999999	RNA PCR Primer, Index 5 (97% over 35bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	19	0.475	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	17	0.42500000000000004	No Hit
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTC	13	0.325	RNA PCR Primer, Index 6 (100% over 44bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGC	12	0.3	RNA PCR Primer, Index 5 (97% over 35bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	10	0.25	RNA PCR Primer, Index 1 (100% over 33bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	10	0.25	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	10	0.25	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	9	0.22499999999999998	No Hit
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGC	9	0.22499999999999998	RNA PCR Primer, Index 6 (100% over 50bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	9	0.22499999999999998	No Hit
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	7	0.17500000000000002	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ACTGGACTTGGAGTCAGAAGGCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTATAAAGCAATGAGACTGATTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CGACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	5	0.125	RNA PCR Primer, Index 6 (100% over 34bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
AACATTCATTGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCC	5	0.125	RNA PCR Primer, Index 6 (100% over 36bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	5	0.125	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGAATTCTCGGGTGC	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>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	0.225	0.0	0.0	0.0
2	0.0	0.225	0.0	0.0	0.0
3	0.0	0.275	0.0	0.0	0.0
4	0.0	0.275	0.0	0.0	0.0
5	0.0	0.3	0.0	0.0	0.0
6	0.0	0.325	0.0	0.0	0.0
7	0.0	0.675	0.0	0.0	0.0
8	0.0	0.8	0.0	0.0	0.0
9	0.0	0.925	0.0	0.0	0.0
10	0.0	1.025	0.0	0.0	0.0
11	0.0	1.225	0.0	0.0	0.0
12	0.0	1.3	0.0	0.0	0.0
13	0.0	1.55	0.0	0.0	0.0
14	0.0	1.7	0.0	0.0	0.0
15	0.0	2.125	0.0	0.0	0.0
16	0.0	3.25	0.0	0.0	0.0
17	0.0	3.9	0.0	0.0	0.0
18	0.0	4.775	0.0	0.0	0.0
19	0.0	5.25	0.0	0.0	0.0
20	0.0	6.3	0.0	0.0	0.0
21	0.0	10.15	0.0	0.0	0.0
22	0.0	21.225	0.0	0.0	0.0
23	0.0	56.025	0.0	0.0	0.0
24	0.0	74.15	0.0	0.0	0.0
25	0.0	80.5	0.0	0.0	0.0
26	0.0	81.25	0.0	0.0	0.0
27	0.0	81.8	0.0	0.0	0.0
28	0.0	82.325	0.0	0.0	0.0
29	0.0	82.825	0.0	0.0	0.0
30	0.0	83.225	0.0	0.0	0.0
31	0.0	84.075	0.0	0.0	0.0
32	0.0	84.925	0.0	0.0	0.0
33	0.0	86.05	0.0	0.0	0.0
34	0.0	87.675	0.0	0.0	0.0
35	0.0	88.575	0.0	0.0	0.0
36	0.0	89.325	0.0	0.0	0.0
37	0.0	89.925	0.0	0.0	0.0
38	0.0	90.45	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTAGATT	20	6.952051E-4	44.000004	8
GAGGTAG	40	5.315087E-9	44.000004	2
AAGTAAT	40	5.315087E-9	44.000004	4
TCAAGTA	40	5.315087E-9	44.000004	2
AATCCAG	40	5.315087E-9	44.000004	8
TAAACAT	20	6.952051E-4	44.000004	3
ATCCAGG	40	5.315087E-9	44.000004	9
AAACATC	20	6.952051E-4	44.000004	4
AGTAGGT	20	6.952051E-4	44.000004	7
TTCAAGT	40	5.315087E-9	44.000004	1
AGTAGAT	20	6.952051E-4	44.000004	7
AGGATAG	40	5.315087E-9	44.000004	13
ATAGGCT	40	5.315087E-9	44.000004	16
CATTCAA	40	5.315087E-9	44.000004	3
TAGTTTG	20	6.952051E-4	44.000004	18
GATTGTA	20	6.952051E-4	44.000004	11
ACATCCT	20	6.952051E-4	44.000004	6
ACATTCA	45	2.728484E-10	44.000004	2
GGATAGG	40	5.315087E-9	44.000004	14
ATAGTTT	20	6.952051E-4	44.000004	17
>>END_MODULE
Read 282036 spots for SRR5030986.sra
Written 282036 spots for SRR5030986.sra
Read 282036 spots for SRR5030986.sra
Written 282036 spots for SRR5030986.sra
Read 282036 spots for SRR5030986.sra
Written 282036 spots for SRR5030986.sra
Read 282036 spots for SRR5030986.sra
Written 282036 spots for SRR5030986.sra
Read 282036 spots for SRR5030986.sra
Written 282036 spots for SRR5030986.sra
Read 282036 spots for SRR5030986.sra
Written 282036 spots for SRR5030986.sra
Read 282036 spots for SRR5030986.sra
Written 282036 spots for SRR5030986.sra
Read 282036 spots for SRR5030986.sra
Written 282036 spots for SRR5030986.sra
Read 282036 spots for SRR5030986.sra
Written 282036 spots for SRR5030986.sra
Read 282036 spots for SRR5030986.sra
Written 282036 spots for SRR5030986.sra
Read 282036 spots for SRR5030986.sra
Written 282036 spots for SRR5030986.sra
Read 282047 spots for SRR5030986.sra
Written 282047 spots for SRR5030986.sra
SRR ids: ['SRR5030986.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_8vpi8b2u
SRR5030986.sra spots: 3384443
blocks: [[1, 282036], [282037, 564072], [564073, 846108], [846109, 1128144], [1128145, 1410180], [1410181, 1692216], [1692217, 1974252], [1974253, 2256288], [2256289, 2538324], [2538325, 2820360], [2820361, 3102396], [3102397, 3384443]]
SRR5030986 file size 585534
SRR5030986 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030986 SRR5030986_1.fastq
Input file:	SRR5030986_1.fastq
trimmed:	SRR5030986-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 07:00:17 2020 >> started

Wed Mar  4 07:00:19 2020 >> done (1.997s)
3384443 reads processed; of these:
    234 ( 0.01%) short reads filtered out after trimming by size control
      7 ( 0.00%) empty reads filtered out after trimming by size control
3384202 (99.99%) reads available; of these:
 182766 ( 5.40%) trimmed reads available after processing
3201436 (94.60%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     71	  0.00%
 19	     83	  0.00%
 20	    149	  0.00%
 21	    242	  0.01%
 22	    424	  0.01%
 23	    450	  0.01%
 24	    425	  0.01%
 25	    561	  0.02%
 26	    455	  0.01%
 27	    619	  0.02%
 28	    741	  0.02%
 29	   1557	  0.05%
 30	    787	  0.02%
 31	    786	  0.02%
 32	    774	  0.02%
 33	   1143	  0.03%
 34	   1553	  0.05%
 35	   2962	  0.09%
 36	   2502	  0.07%
 37	   2906	  0.09%
 38	   2701	  0.08%
 39	   2925	  0.09%
 40	   3267	  0.10%
 41	   3596	  0.11%
 42	   4772	  0.14%
 43	   6890	  0.20%
 44	  10073	  0.30%
 45	  13653	  0.40%
 46	  17294	  0.51%
 47	  22177	  0.66%
 48	  35996	  1.06%
 49	  40232	  1.19%
 50	3201436	 94.60%
3384202 reads passed initial QC


criterion=sequence-density
sequence-density=89.47
sequence-density-rank=1
fanout-score=18.25
fanout-score-rank=1
prefix-density=91.17
prefix-fanout=17.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC


criterion=fanout-score
sequence-density=89.47
sequence-density-rank=1
fanout-score=18.25
fanout-score-rank=1
prefix-density=91.17
prefix-fanout=17.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC -o SRR5030986 -
Input file:	STDIN
trimmed:	SRR5030986-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC
-- 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 07:00:35 2020 >> started

Wed Mar  4 07:00:41 2020 >> done (5.223s)
3308998 reads processed; of these:
 145113 ( 4.39%) short reads filtered out after trimming by size control
   8399 ( 0.25%) empty reads filtered out after trimming by size control
3155486 (95.36%) reads available; of these:
3045911 (96.53%) trimmed reads available after processing
 109575 ( 3.47%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  15596	  0.49%
 19	  35268	  1.12%
 20	 139853	  4.43%
 21	 383993	 12.17%
 22	1129880	 35.81%
 23	 609717	 19.32%
 24	 204343	  6.48%
 25	  34154	  1.08%
 26	  17577	  0.56%
 27	  17235	  0.55%
 28	  19195	  0.61%
 29	  15201	  0.48%
 30	  25492	  0.81%
 31	  36184	  1.15%
 32	  33889	  1.07%
 33	  59535	  1.89%
 34	  28475	  0.90%
 35	  21058	  0.67%
 36	  23658	  0.75%
 37	  13811	  0.44%
 38	  15255	  0.48%
 39	  14289	  0.45%
 40	  18607	  0.59%
 41	  27149	  0.86%
 42	  30740	  0.97%
 43	  23925	  0.76%
 44	  18870	  0.60%
 45	  20218	  0.64%
 46	  15466	  0.49%
 47	  11584	  0.37%
 48	   1234	  0.04%
 49	   2228	  0.07%
 50	  91807	  2.91%


criterion=sequence-density
sequence-density=4.72
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=21
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.42
sequence-density-rank=30
fanout-score=8.87
fanout-score-rank=1
prefix-density=3.75
prefix-fanout=1.0
sequence=TAGTAGGTTGTGTGGTTTT
                                 Started job on |	Mar 04 07:01:17
                             Started mapping on |	Mar 04 07:01:18
                                    Finished on |	Mar 04 07:01:43
       Mapping speed, Million of reads per hour |	465.22

                          Number of input reads |	3230690
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1467567
                        Uniquely mapped reads % |	45.43%
                          Average mapped length |	24.26
                       Number of splices: Total |	1455
            Number of splices: Annotated (sjdb) |	175
                       Number of splices: GT/AG |	1295
                       Number of splices: GC/AG |	16
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	144
                      Mismatch rate per base, % |	0.17%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.65
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.13
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1452222
             % of reads mapped to multiple loci |	44.95%
        Number of reads mapped to too many loci |	64450
             % of reads mapped to too many loci |	1.99%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	6.91%
                     % of reads unmapped: other |	0.72%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	310901	310901	310901
N_multimapping	1452222	1452222	1452222
N_noFeature	79327	93759	1125225
N_ambiguous	768862	477508	10508
UnstrandedReadsAssigned:619378 PositiveStrandReadsAssigned:896300 NegativeStrandReadsAssigned:331834
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5030986 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: SRR5030986-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,230,690 reads, 589,746 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,106 rounds

 109283 SRR5030986.ke.tsv
  52636 SRR5030986.se.tsv
 161919 total
==> SRR5030986.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

==> SRR5030986.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030986 completed mapping pipeline successfully
