Starting /dee2/code/volunteer_pipeline.sh SRR5031047
    current disk space = 160487653376
    free memory = 73946180 
SRR5031047 SRAfilesize
c4060db3b50bd19ad4d8355e3cc5a894  SRR5031047.sra
SRR5031047.sra file validated
SRR5031047 is single end
SRR5031047 is conventional basespace
SRR5031047 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031047_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	32.335	33.0	31.0	34.0	31.0	34.0
2	32.61925	34.0	31.0	34.0	31.0	34.0
3	32.5915	34.0	31.0	34.0	31.0	34.0
4	36.2275	37.0	37.0	37.0	35.0	37.0
5	36.05	37.0	35.0	37.0	35.0	37.0
6	35.80075	37.0	35.0	37.0	35.0	37.0
7	35.97975	37.0	35.0	37.0	35.0	37.0
8	35.82	37.0	35.0	37.0	35.0	37.0
9	37.6015	39.0	37.0	39.0	35.0	39.0
10	37.7535	39.0	38.0	39.0	35.0	39.0
11	37.7175	39.0	37.0	39.0	35.0	39.0
12	37.6965	39.0	37.0	39.0	35.0	39.0
13	37.68725	39.0	37.0	39.0	35.0	39.0
14	39.02525	40.0	38.0	41.0	35.0	41.0
15	39.08275	40.0	38.0	41.0	35.0	41.0
16	39.01075	40.0	38.0	41.0	36.0	41.0
17	38.821	40.0	38.0	41.0	35.0	41.0
18	39.0905	40.0	38.0	41.0	35.0	41.0
19	38.539	40.0	38.0	41.0	34.0	41.0
20	38.87525	40.0	38.0	41.0	35.0	41.0
21	38.80325	40.0	38.0	41.0	34.0	41.0
22	38.94675	40.0	38.0	41.0	35.0	41.0
23	38.67225	40.0	38.0	41.0	34.0	41.0
24	38.798	40.0	38.0	41.0	35.0	41.0
25	38.98925	40.0	38.0	41.0	35.0	41.0
26	38.6385	40.0	38.0	41.0	34.0	41.0
27	38.7845	40.0	38.0	41.0	34.0	41.0
28	38.75075	40.0	38.0	41.0	35.0	41.0
29	38.30825	40.0	38.0	41.0	33.0	41.0
30	38.1665	40.0	38.0	41.0	33.0	41.0
31	38.47875	40.0	38.0	41.0	34.0	41.0
32	38.65875	40.0	38.0	41.0	34.0	41.0
33	38.817	40.0	38.0	41.0	35.0	41.0
34	38.607	40.0	38.0	41.0	34.0	41.0
35	38.36325	40.0	38.0	41.0	34.0	41.0
36	37.91	40.0	37.0	41.0	33.0	41.0
37	37.58675	40.0	37.0	41.0	32.0	41.0
38	36.691	39.0	36.0	41.0	30.0	41.0
39	37.24475	39.0	37.0	41.0	31.0	41.0
40	37.49825	40.0	37.0	41.0	32.0	41.0
41	37.70925	40.0	37.0	41.0	33.0	41.0
42	37.9795	40.0	38.0	41.0	33.0	41.0
43	38.047	40.0	38.0	41.0	33.0	41.0
44	37.7655	40.0	37.0	41.0	33.0	41.0
45	37.70575	40.0	37.0	41.0	33.0	41.0
46	37.67025	40.0	37.0	41.0	33.0	41.0
47	37.0135	40.0	36.0	41.0	31.0	41.0
48	36.81125	40.0	36.0	41.0	31.0	41.0
49	37.1925	40.0	37.0	41.0	32.0	41.0
50	36.53525	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
12	1.0
13	1.0
14	0.0
15	0.0
16	0.0
17	0.0
18	4.0
19	2.0
20	4.0
21	3.0
22	4.0
23	3.0
24	6.0
25	10.0
26	19.0
27	19.0
28	29.0
29	37.0
30	46.0
31	59.0
32	75.0
33	110.0
34	158.0
35	197.0
36	262.0
37	427.0
38	719.0
39	1805.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.575000000000001	25.4	51.525	14.499999999999998
2	23.015276734285	28.174305033809166	17.129977460555974	31.68044077134986
3	24.775	20.25	21.825	33.15
4	32.925	28.975	12.9	25.2
5	22.175	40.550000000000004	26.424999999999997	10.85
6	35.099999999999994	15.45	35.375	14.075
7	14.799999999999999	22.0	23.825	39.375
8	25.324999999999996	29.125	14.924999999999999	30.625000000000004
9	22.975	33.875	28.349999999999998	14.799999999999999
10	20.7	23.275000000000002	28.375	27.650000000000002
11	30.925000000000004	9.975000000000001	17.599999999999998	41.5
12	14.7	16.625	32.85	35.825
13	32.550000000000004	17.625	31.5	18.325
14	31.7	31.8	20.1	16.400000000000002
15	36.075	25.775	26.025	12.125
16	17.75	20.25	22.575	39.425
17	24.275	22.025	39.4	14.299999999999999
18	24.8	18.3	30.5	26.400000000000002
19	37.025000000000006	14.374999999999998	29.45	19.15
20	44.925	15.425	26.900000000000002	12.75
21	22.825	20.375	26.6	30.2
22	28.599999999999998	13.825000000000001	47.825	9.75
23	26.0	13.4	44.95	15.65
24	52.2	14.274999999999999	25.575	7.95
25	50.224999999999994	24.6	15.950000000000001	9.225
26	27.450000000000003	48.175000000000004	13.55	10.825
27	16.6	48.15	23.875	11.375
28	11.275	24.875	49.2	14.649999999999999
29	11.325000000000001	13.425	56.45	18.8
30	8.799999999999999	6.6000000000000005	37.525	47.075
31	12.775	4.625	48.55	34.050000000000004
32	27.650000000000002	5.4	21.45	45.5
33	55.675	8.5	13.65	22.175
34	63.14999999999999	7.475	15.1	14.274999999999999
35	65.425	6.2	19.525000000000002	8.85
36	43.725	6.15	37.525	12.6
37	46.75	10.05	19.625	23.575
38	23.150000000000002	16.925	11.675	48.25
39	14.875	24.75	9.575	50.8
40	15.174999999999999	49.65	10.65	24.525
41	24.4	49.275000000000006	9.075	17.25
42	50.824999999999996	28.7	9.975000000000001	10.5
43	51.65	30.95	8.025	9.375
44	30.325000000000003	50.724999999999994	6.1	12.85
45	19.7	50.724999999999994	12.275	17.299999999999997
46	13.125	24.95	18.25	43.675000000000004
47	8.924999999999999	16.225	39.35	35.5
48	9.85	13.275	19.625	57.25
49	14.2	19.125	13.425	53.25
50	18.475	36.9	14.274999999999999	30.349999999999998
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.5
14	1.0
15	0.5
16	0.0
17	0.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	1.0
26	1.0
27	2.0
28	3.0
29	4.0
30	5.0
31	9.5
32	14.0
33	17.0
34	20.0
35	20.0
36	20.0
37	19.0
38	18.0
39	28.5
40	39.0
41	39.5
42	40.0
43	65.0
44	90.0
45	139.0
46	188.0
47	321.0
48	454.0
49	591.5
50	729.0
51	800.5
52	872.0
53	651.0
54	430.0
55	460.5
56	491.0
57	371.0
58	251.0
59	155.0
60	59.0
61	48.0
62	37.0
63	78.5
64	120.0
65	73.5
66	27.0
67	21.0
68	15.0
69	16.5
70	18.0
71	31.0
72	44.0
73	23.5
74	3.0
75	1.5
76	0.0
77	0.5
78	1.0
79	2.0
80	3.0
81	4.0
82	5.0
83	2.5
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	37.225
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.55406312961719	28.125
2	10.342511752854264	7.7
3	3.895231699126931	4.35
4	1.9476158495634655	2.9000000000000004
5	1.6118200134318332	3.0
6	0.8730691739422431	1.95
7	0.9402283411685695	2.45
8	0.47011417058428473	1.4000000000000001
9	0.5372733378106112	1.7999999999999998
>10	3.15648085963734	23.05
>50	0.4029550033579583	10.775
>100	0.2686366689053056	12.5
>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	146	3.65	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	135	3.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	112	2.8000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	107	2.675	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	96	2.4	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	89	2.225	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	80	2.0	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	63	1.575	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	52	1.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	51	1.275	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	49	1.225	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	40	1.0	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	34	0.8500000000000001	RNA PCR Primer, Index 1 (97% over 35bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGC	33	0.8250000000000001	RNA PCR Primer, Index 19 (100% over 50bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	21	0.525	RNA PCR Primer, Index 1 (100% over 33bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	15	0.375	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	14	0.35000000000000003	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTC	13	0.325	RNA PCR Primer, Index 19 (100% over 44bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	11	0.27499999999999997	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	9	0.22499999999999998	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	9	0.22499999999999998	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGGCAATGGTAGAACTCACATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	8	0.2	No Hit
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	8	0.2	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	7	0.17500000000000002	No Hit
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	7	0.17500000000000002	No Hit
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTATTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTTGGAATT	6	0.15	No Hit
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	6	0.15	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTATTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	5	0.125	No Hit
TAAGGCACGCGGTGAATGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
GACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	5	0.125	RNA PCR Primer, Index 1 (97% over 35bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	5	0.125	No Hit
TTTGGCAATGGTAGAACTCACACTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	5	0.125	RNA PCR Primer, Index 6 (100% over 34bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTGAAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	5	0.125	RNA PCR Primer, Index 6 (100% over 34bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	5	0.125	No Hit
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGGCAATGGTAGAACTCACACCGTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
>>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	0.925	0.0	0.0	0.0
2	0.0	0.925	0.0	0.0	0.0
3	0.0	1.05	0.0	0.0	0.0
4	0.0	1.05	0.0	0.0	0.0
5	0.0	1.075	0.0	0.0	0.0
6	0.0	1.15	0.0	0.0	0.0
7	0.0	1.7	0.0	0.0	0.0
8	0.0	1.8	0.0	0.0	0.0
9	0.0	1.9	0.0	0.0	0.0
10	0.0	2.075	0.0	0.0	0.0
11	0.0	2.2	0.0	0.0	0.0
12	0.0	2.425	0.0	0.0	0.0
13	0.0	2.725	0.0	0.0	0.0
14	0.0	2.95	0.0	0.0	0.0
15	0.0	3.225	0.0	0.0	0.0
16	0.0	4.625	0.0	0.0	0.0
17	0.0	5.225	0.0	0.0	0.0
18	0.0	6.05	0.0	0.0	0.0
19	0.0	6.2	0.0	0.0	0.0
20	0.0	6.975	0.0	0.0	0.0
21	0.0	12.525	0.0	0.0	0.0
22	0.0	24.525	0.0	0.0	0.0
23	0.0	55.7	0.0	0.0	0.0
24	0.0	68.625	0.0	0.0	0.0
25	0.0	75.175	0.0	0.0	0.0
26	0.0	77.15	0.0	0.0	0.0
27	0.0	78.0	0.0	0.0	0.0
28	0.0	78.625	0.0	0.0	0.0
29	0.0	79.125	0.0	0.0	0.0
30	0.0	79.7	0.0	0.0	0.0
31	0.0	80.525	0.0	0.0	0.0
32	0.0	81.475	0.0	0.0	0.0
33	0.0	82.5	0.0	0.0	0.0
34	0.0	85.475	0.0	0.0	0.0
35	0.0	86.65	0.0	0.0	0.0
36	0.0	87.35	0.0	0.0	0.0
37	0.0	88.625	0.0	0.0	0.0
38	0.0	89.0	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
TTGCACT	20	6.952051E-4	44.000004	3
AACCGGT	20	6.952051E-4	44.000004	9
CCCGGCC	20	6.952051E-4	44.000004	13
GGTCTCT	20	6.952051E-4	44.000004	13
ACTCTCA	20	6.952051E-4	44.000004	15
TATTGCA	20	6.952051E-4	44.000004	1
ACATCCT	20	6.952051E-4	44.000004	6
GTCCCGG	20	6.952051E-4	44.000004	11
GAACCGG	20	6.952051E-4	44.000004	8
ATTGCAC	20	6.952051E-4	44.000004	2
GTCTCTT	20	6.952051E-4	44.000004	14
AGGCTTG	20	6.952051E-4	44.000004	18
CACTCTC	20	6.952051E-4	44.000004	14
AGTGAAC	20	6.952051E-4	44.000004	5
TCTCTTT	20	6.952051E-4	44.000004	15
TCCCGGC	20	6.952051E-4	44.000004	12
GTGAACC	20	6.952051E-4	44.000004	6
CGGTCTC	20	6.952051E-4	44.000004	12
>>END_MODULE
Read 396184 spots for SRR5031047.sra
Written 396184 spots for SRR5031047.sra
Read 396184 spots for SRR5031047.sra
Written 396184 spots for SRR5031047.sra
Read 396184 spots for SRR5031047.sra
Written 396184 spots for SRR5031047.sra
Read 396184 spots for SRR5031047.sra
Written 396184 spots for SRR5031047.sra
Read 396184 spots for SRR5031047.sra
Written 396184 spots for SRR5031047.sra
Read 396184 spots for SRR5031047.sra
Written 396184 spots for SRR5031047.sra
Read 396184 spots for SRR5031047.sra
Written 396184 spots for SRR5031047.sra
Read 396184 spots for SRR5031047.sra
Written 396184 spots for SRR5031047.sra
Read 396190 spots for SRR5031047.sra
Written 396190 spots for SRR5031047.sra
Read 396184 spots for SRR5031047.sra
Written 396184 spots for SRR5031047.sra
Read 396184 spots for SRR5031047.sra
Written 396184 spots for SRR5031047.sra
Read 396184 spots for SRR5031047.sra
Written 396184 spots for SRR5031047.sra
SRR ids: ['SRR5031047.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_5sbjbkkh
SRR5031047.sra spots: 4754214
blocks: [[1, 396184], [396185, 792368], [792369, 1188552], [1188553, 1584736], [1584737, 1980920], [1980921, 2377104], [2377105, 2773288], [2773289, 3169472], [3169473, 3565656], [3565657, 3961840], [3961841, 4358024], [4358025, 4754214]]
SRR5031047 file size 822960
SRR5031047 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031047 SRR5031047_1.fastq
Input file:	SRR5031047_1.fastq
trimmed:	SRR5031047-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 07:13:09 2020 >> started

Wed Mar  4 07:13:13 2020 >> done (4.098s)
4754214 reads processed; of these:
    375 ( 0.01%) short reads filtered out after trimming by size control
      8 ( 0.00%) empty reads filtered out after trimming by size control
4753831 (99.99%) reads available; of these:
 243776 ( 5.13%) trimmed reads available after processing
4510055 (94.87%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    112	  0.00%
 19	    125	  0.00%
 20	    321	  0.01%
 21	    341	  0.01%
 22	    604	  0.01%
 23	    693	  0.01%
 24	    785	  0.02%
 25	    971	  0.02%
 26	    837	  0.02%
 27	   1054	  0.02%
 28	   1199	  0.03%
 29	   1822	  0.04%
 30	   1249	  0.03%
 31	   1396	  0.03%
 32	   1509	  0.03%
 33	   2105	  0.04%
 34	   2600	  0.05%
 35	   5135	  0.11%
 36	   4292	  0.09%
 37	   4925	  0.10%
 38	   4364	  0.09%
 39	   4709	  0.10%
 40	   5475	  0.12%
 41	   5311	  0.11%
 42	   6578	  0.14%
 43	   9706	  0.20%
 44	  13198	  0.28%
 45	  16088	  0.34%
 46	  23560	  0.50%
 47	  30400	  0.64%
 48	  45686	  0.96%
 49	  46626	  0.98%
 50	4510055	 94.87%
4753831 reads passed initial QC


criterion=sequence-density
sequence-density=88.18
sequence-density-rank=1
fanout-score=20.56
fanout-score-rank=1
prefix-density=89.65
prefix-fanout=20.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCC


criterion=fanout-score
sequence-density=88.18
sequence-density-rank=1
fanout-score=20.56
fanout-score-rank=1
prefix-density=89.65
prefix-fanout=20.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCC -o SRR5031047 -
Input file:	STDIN
trimmed:	SRR5031047-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCC
-- 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 07:13:45 2020 >> started

Wed Mar  4 07:13:57 2020 >> done (11.809s)
4647003 reads processed; of these:
 252275 ( 5.43%) short reads filtered out after trimming by size control
  34251 ( 0.74%) empty reads filtered out after trimming by size control
4360477 (93.83%) reads available; of these:
4185898 (96.00%) trimmed reads available after processing
 174579 ( 4.00%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  22444	  0.51%
 19	  46319	  1.06%
 20	 258396	  5.93%
 21	 569870	 13.07%
 22	1408816	 32.31%
 23	 639389	 14.66%
 24	 314279	  7.21%
 25	  85029	  1.95%
 26	  39689	  0.91%
 27	  30301	  0.69%
 28	  32004	  0.73%
 29	  24601	  0.56%
 30	  36763	  0.84%
 31	  45220	  1.04%
 32	  48833	  1.12%
 33	 135532	  3.11%
 34	  48870	  1.12%
 35	  37263	  0.85%
 36	  46803	  1.07%
 37	  22766	  0.52%
 38	  24438	  0.56%
 39	  23185	  0.53%
 40	  34625	  0.79%
 41	  44461	  1.02%
 42	  50336	  1.15%
 43	  34532	  0.79%
 44	  25956	  0.60%
 45	  36700	  0.84%
 46	  26472	  0.61%
 47	  18818	  0.43%
 48	   1831	  0.04%
 49	   2362	  0.05%
 50	 143574	  3.29%


criterion=sequence-density
sequence-density=6.43
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=39
fanout-score=122.82
fanout-score-rank=1
prefix-density=1.58
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:14:27
                             Started mapping on |	Mar 04 07:14:27
                                    Finished on |	Mar 04 07:15:13
       Mapping speed, Million of reads per hour |	349.62

                          Number of input reads |	4467305
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2432822
                        Uniquely mapped reads % |	54.46%
                          Average mapped length |	24.27
                       Number of splices: Total |	2926
            Number of splices: Annotated (sjdb) |	486
                       Number of splices: GT/AG |	2805
                       Number of splices: GC/AG |	19
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	100
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.80
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.06
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1509965
             % of reads mapped to multiple loci |	33.80%
        Number of reads mapped to too many loci |	79449
             % of reads mapped to too many loci |	1.78%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.43%
                     % of reads unmapped: other |	0.53%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	524518	524518	524518
N_multimapping	1509965	1509965	1509965
N_noFeature	103352	129447	1668719
N_ambiguous	1349731	683476	20759
UnstrandedReadsAssigned:979739 PositiveStrandReadsAssigned:1619899 NegativeStrandReadsAssigned:743344
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031047 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: SRR5031047-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,467,305 reads, 1,167,503 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,190 rounds

 109283 SRR5031047.ke.tsv
  52636 SRR5031047.se.tsv
 161919 total
==> SRR5031047.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

==> SRR5031047.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	3
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031047 completed mapping pipeline successfully
