Starting /dee2/code/volunteer_pipeline.sh SRR5030919
    current disk space = 160615481344
    free memory = 73933992 
SRR5030919 SRAfilesize
b909e5708bacd4ea366ea72aba5d0774  SRR5030919.sra
SRR5030919.sra file validated
SRR5030919 is single end
SRR5030919 is conventional basespace
SRR5030919 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030919_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	32.4245	33.0	31.0	34.0	31.0	34.0
2	32.65875	34.0	31.0	34.0	31.0	34.0
3	32.79325	34.0	31.0	34.0	31.0	34.0
4	36.21975	37.0	37.0	37.0	35.0	37.0
5	36.328	37.0	37.0	37.0	35.0	37.0
6	36.17075	37.0	36.0	37.0	35.0	37.0
7	36.117	37.0	35.0	37.0	35.0	37.0
8	36.214	37.0	36.0	37.0	35.0	37.0
9	37.96775	39.0	38.0	39.0	35.0	39.0
10	37.987	39.0	38.0	39.0	35.0	39.0
11	37.78775	39.0	38.0	39.0	35.0	39.0
12	37.86975	39.0	38.0	39.0	35.0	39.0
13	37.79975	39.0	38.0	39.0	35.0	39.0
14	39.26475	41.0	39.0	41.0	36.0	41.0
15	39.157	40.0	39.0	41.0	36.0	41.0
16	39.18775	40.0	39.0	41.0	36.0	41.0
17	39.33325	41.0	39.0	41.0	36.0	41.0
18	39.2065	41.0	39.0	41.0	36.0	41.0
19	38.96775	40.0	39.0	41.0	35.0	41.0
20	39.117	41.0	39.0	41.0	36.0	41.0
21	39.151	41.0	39.0	41.0	36.0	41.0
22	39.17925	41.0	39.0	41.0	36.0	41.0
23	38.99325	41.0	39.0	41.0	35.0	41.0
24	38.64775	40.0	38.0	41.0	34.0	41.0
25	38.805	41.0	39.0	41.0	35.0	41.0
26	38.94325	41.0	39.0	41.0	35.0	41.0
27	38.9545	40.0	39.0	41.0	35.0	41.0
28	38.819	40.0	39.0	41.0	35.0	41.0
29	38.27375	40.0	38.0	41.0	34.0	41.0
30	38.5085	40.0	38.0	41.0	34.0	41.0
31	38.55425	40.0	38.0	41.0	34.0	41.0
32	38.71825	40.0	38.0	41.0	35.0	41.0
33	38.07475	40.0	38.0	41.0	33.0	41.0
34	38.0025	40.0	38.0	41.0	33.0	41.0
35	37.80475	40.0	38.0	41.0	33.0	41.0
36	33.7895	38.0	31.0	40.0	21.0	41.0
37	35.65375	38.0	35.0	40.0	30.0	41.0
38	36.95975	39.0	37.0	40.0	31.0	41.0
39	36.86625	39.0	37.0	40.0	31.0	41.0
40	36.96	39.0	37.0	40.0	31.0	41.0
41	37.23525	39.0	37.0	41.0	32.0	41.0
42	37.28275	40.0	37.0	41.0	32.0	41.0
43	37.12125	40.0	37.0	41.0	32.0	41.0
44	36.76175	39.0	37.0	41.0	31.0	41.0
45	36.52675	39.0	36.0	40.0	30.0	41.0
46	34.90325	38.0	34.0	40.0	24.0	41.0
47	35.779	39.0	35.0	40.0	28.0	41.0
48	36.22825	39.0	36.0	41.0	30.0	41.0
49	35.08	39.0	35.0	40.0	28.0	41.0
50	30.18975	34.0	27.0	38.0	2.0	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
16	3.0
17	2.0
18	6.0
19	7.0
20	6.0
21	3.0
22	6.0
23	7.0
24	15.0
25	15.0
26	26.0
27	31.0
28	36.0
29	36.0
30	69.0
31	57.0
32	78.0
33	87.0
34	165.0
35	183.0
36	310.0
37	497.0
38	983.0
39	1372.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.192982456140351	20.776942355889723	58.59649122807018	13.43358395989975
2	21.3	25.825	23.400000000000002	29.475
3	18.775	15.65	20.65	44.925
4	24.375	37.95	10.325	27.35
5	17.4	40.6	29.95	12.049999999999999
6	38.475	16.275000000000002	33.95	11.3
7	12.4	23.65	26.875	37.075
8	26.325	40.875	12.325	20.474999999999998
9	19.025	42.25	27.900000000000002	10.825
10	18.9	18.099999999999998	28.15	34.849999999999994
11	27.925	11.200000000000001	14.05	46.825
12	13.375	16.025	24.45	46.150000000000006
13	22.025	22.925	36.725	18.325
14	38.725	23.425	25.275	12.575
15	35.26763381690846	23.111555777888945	29.114557278639317	12.506253126563283
16	13.375	29.7	17.95	38.975
17	22.2	23.075000000000003	40.8	13.925
18	27.625	21.075	26.775	24.525
19	37.95	13.850000000000001	29.15	19.05
20	46.1	16.175	26.775	10.95
21	23.375	23.125	23.7	29.799999999999997
22	29.75	11.275	51.4	7.575
23	25.3	11.875	50.349999999999994	12.475
24	54.05	13.375	25.825	6.75
25	55.55	22.400000000000002	14.35	7.7
26	27.725	50.449999999999996	12.375	9.45
27	13.525	53.400000000000006	23.125	9.950000000000001
28	9.3	25.074999999999996	53.55	12.075
29	8.9	11.125	61.550000000000004	18.425
30	8.975	5.1	37.525	48.4
31	14.124999999999998	4.25	48.6	33.025
32	25.45	6.0249999999999995	20.849999999999998	47.675
33	58.325	6.7	12.15	22.825
34	68.175	6.675000000000001	11.75	13.4
35	68.025	6.225	17.974999999999998	7.775
36	42.6	6.925000000000001	37.925	12.55
37	48.175000000000004	8.825	20.424999999999997	22.575
38	22.825	13.3	10.85	53.025
39	13.925	24.275	6.75	55.05
40	13.15	53.400000000000006	7.3999999999999995	26.05
41	22.625	55.725	7.85	13.8
42	53.5	31.374999999999996	7.449999999999999	7.675
43	55.625	29.425	6.35	8.6
44	27.725	53.325	6.425	12.525
45	14.274999999999999	55.725	11.225	18.775
46	7.5249999999999995	26.924999999999997	18.825	46.725
47	6.25	14.774999999999999	41.275	37.7
48	8.200000000000001	11.725	20.45	59.62499999999999
49	11.55	18.725	12.25	57.475
50	17.95448862215554	40.36009002250563	11.77794448612153	29.9074768692173
>>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	0.5
12	1.0
13	1.0
14	1.0
15	0.5
16	0.0
17	1.0
18	2.0
19	1.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.5
28	1.0
29	1.0
30	1.0
31	6.5
32	12.0
33	15.0
34	18.0
35	24.0
36	30.0
37	32.0
38	34.0
39	35.5
40	37.0
41	39.5
42	42.0
43	72.5
44	103.0
45	155.5
46	208.0
47	399.0
48	590.0
49	613.5
50	637.0
51	829.5
52	1022.0
53	704.0
54	386.0
55	386.0
56	386.0
57	319.0
58	252.0
59	160.5
60	69.0
61	52.5
62	36.0
63	49.0
64	62.0
65	43.5
66	25.0
67	19.5
68	14.0
69	10.5
70	7.0
71	12.5
72	18.0
73	11.0
74	4.0
75	2.5
76	1.0
77	0.5
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	0.25
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.05
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	0.025
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	39.074999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.26359564939219	29.799999999999997
2	9.852847088931542	7.7
3	3.9027511196417146	4.575
4	2.495201535508637	3.9
5	1.599488163787588	3.125
6	1.1516314779270633	2.7
7	0.4478566858605247	1.225
8	0.5118362124120281	1.6
9	0.3198976327575176	1.125
>10	3.071017274472169	24.05
>50	0.19193857965451055	5.65
>100	0.19193857965451055	14.549999999999999
>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	249	6.225	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	187	4.675	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	146	3.65	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	90	2.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	70	1.7500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	66	1.6500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	42	1.05	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	38	0.95	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	32	0.8	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	31	0.775	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTCGTATGC	23	0.575	RNA PCR Primer, Index 40 (100% over 50bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	23	0.575	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	20	0.5	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCT	17	0.42500000000000004	RNA PCR Primer, Index 1 (97% over 35bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	12	0.3	RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	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)
CACCCGTAGAACCGACCTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	7	0.17500000000000002	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	7	0.17500000000000002	No Hit
ACTGGACTTGGAGTCAGAAGGCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTC	7	0.17500000000000002	RNA PCR Primer, Index 40 (100% over 44bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	6	0.15	No Hit
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	6	0.15	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCA	5	0.125	RNA PCR Primer, Index 1 (97% over 37bp)
CTGACCTATGAATTGACAGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CAGGATCACAGAAAAAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	5	0.125	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	5	0.125	No Hit
TTCAAGTAATCCAGGATAGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGATGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
GACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCT	5	0.125	RNA PCR Primer, Index 1 (97% over 35bp)
TTCAAGTAATCCAGGATAGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
AACATTCAACCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
>>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	0.625	0.0	0.0	0.0
2	0.0	0.65	0.0	0.0	0.0
3	0.0	0.725	0.0	0.0	0.0
4	0.0	0.775	0.0	0.0	0.0
5	0.0	0.85	0.0	0.0	0.0
6	0.0	0.925	0.0	0.0	0.0
7	0.0	1.225	0.0	0.0	0.0
8	0.0	1.375	0.0	0.0	0.0
9	0.0	1.425	0.0	0.0	0.0
10	0.0	1.525	0.0	0.0	0.0
11	0.0	1.85	0.0	0.0	0.0
12	0.0	2.2	0.0	0.0	0.0
13	0.0	2.325	0.0	0.0	0.0
14	0.0	2.75	0.0	0.0	0.0
15	0.0	3.35	0.0	0.0	0.0
16	0.0	4.45	0.0	0.0	0.0
17	0.0	5.325	0.0	0.0	0.0
18	0.0	6.175	0.0	0.0	0.0
19	0.0	6.65	0.0	0.0	0.0
20	0.0	7.925	0.0	0.0	0.0
21	0.0	13.225	0.0	0.0	0.0
22	0.0	24.95	0.0	0.0	0.0
23	0.0	59.75	0.0	0.0	0.0
24	0.0	73.85	0.0	0.0	0.0
25	0.0	79.7	0.0	0.0	0.0
26	0.0	80.5	0.0	0.0	0.0
27	0.0	80.95	0.0	0.0	0.0
28	0.0	81.35	0.0	0.0	0.0
29	0.0	81.75	0.0	0.0	0.0
30	0.0	82.125	0.0	0.0	0.0
31	0.0	82.8	0.0	0.0	0.0
32	0.0	83.3	0.0	0.0	0.0
33	0.0	83.925	0.0	0.0	0.0
34	0.0	85.2	0.0	0.0	0.0
35	0.0	85.575	0.0	0.0	0.0
36	0.0	86.2	0.0	0.0	0.0
37	0.0	86.9	0.0	0.0	0.0
38	0.0	87.075	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GGTTGTA	20	6.952051E-4	44.000004	11
CTGAGCT	20	6.952051E-4	44.000004	11
AGTAGGT	20	6.952051E-4	44.000004	7
GGATCCG	20	6.952051E-4	44.000004	3
CCGTCTG	20	6.952051E-4	44.000004	7
TCGGATC	20	6.952051E-4	44.000004	1
CGGATCC	20	6.952051E-4	44.000004	2
GAATGGA	20	6.952051E-4	44.000004	19
ACCTGTT	20	6.952051E-4	44.000004	17
ACATCCT	20	6.952051E-4	44.000004	6
TAGTAGG	20	6.952051E-4	44.000004	6
GATCCGT	20	6.952051E-4	44.000004	4
AGGTTGT	20	6.952051E-4	44.000004	10
GTAGGTT	20	6.952051E-4	44.000004	8
TCCGTCT	20	6.952051E-4	44.000004	6
ATCCGTC	20	6.952051E-4	44.000004	5
CGTCTGA	20	6.952051E-4	44.000004	8
GTTGTAT	20	6.952051E-4	44.000004	12
TAGGTTG	20	6.952051E-4	44.000004	9
AACGCTG	35	1.02281774E-7	44.0	8
>>END_MODULE
Read 283965 spots for SRR5030919.sra
Written 283965 spots for SRR5030919.sra
Read 283965 spots for SRR5030919.sra
Written 283965 spots for SRR5030919.sra
Read 283965 spots for SRR5030919.sra
Written 283965 spots for SRR5030919.sra
Read 283965 spots for SRR5030919.sra
Written 283965 spots for SRR5030919.sra
Read 283965 spots for SRR5030919.sra
Written 283965 spots for SRR5030919.sra
Read 283965 spots for SRR5030919.sra
Written 283965 spots for SRR5030919.sra
Read 283965 spots for SRR5030919.sra
Written 283965 spots for SRR5030919.sra
Read 283965 spots for SRR5030919.sra
Written 283965 spots for SRR5030919.sra
Read 283965 spots for SRR5030919.sra
Written 283965 spots for SRR5030919.sra
Read 283966 spots for SRR5030919.sra
Written 283966 spots for SRR5030919.sra
Read 283965 spots for SRR5030919.sra
Written 283965 spots for SRR5030919.sra
Read 283965 spots for SRR5030919.sra
Written 283965 spots for SRR5030919.sra
SRR ids: ['SRR5030919.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_9iufc46_
SRR5030919.sra spots: 3407581
blocks: [[1, 283965], [283966, 567930], [567931, 851895], [851896, 1135860], [1135861, 1419825], [1419826, 1703790], [1703791, 1987755], [1987756, 2271720], [2271721, 2555685], [2555686, 2839650], [2839651, 3123615], [3123616, 3407581]]
SRR5030919 file size 589533
SRR5030919 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030919 SRR5030919_1.fastq
Input file:	SRR5030919_1.fastq
trimmed:	SRR5030919-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 06:44:57 2020 >> started

Wed Mar  4 06:45:01 2020 >> done (3.822s)
3407581 reads processed; of these:
    116 ( 0.00%) short reads filtered out after trimming by size control
      7 ( 0.00%) empty reads filtered out after trimming by size control
3407458 (100.00%) reads available; of these:
 176927 ( 5.19%) trimmed reads available after processing
3230531 (94.81%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     44	  0.00%
 19	     58	  0.00%
 20	    132	  0.00%
 21	    176	  0.01%
 22	    370	  0.01%
 23	    357	  0.01%
 24	    340	  0.01%
 25	    447	  0.01%
 26	    373	  0.01%
 27	    497	  0.01%
 28	    734	  0.02%
 29	   1350	  0.04%
 30	    830	  0.02%
 31	    999	  0.03%
 32	    928	  0.03%
 33	   1207	  0.04%
 34	   2981	  0.09%
 35	   2685	  0.08%
 36	   1983	  0.06%
 37	   2105	  0.06%
 38	   2369	  0.07%
 39	   2556	  0.08%
 40	   2956	  0.09%
 41	   3471	  0.10%
 42	   4398	  0.13%
 43	   5896	  0.17%
 44	  11227	  0.33%
 45	  11658	  0.34%
 46	  10454	  0.31%
 47	  15786	  0.46%
 48	  36594	  1.07%
 49	  50966	  1.50%
 50	3230531	 94.81%
3407458 reads passed initial QC


criterion=sequence-density
sequence-density=88.04
sequence-density-rank=1
fanout-score=17.16
fanout-score-rank=1
prefix-density=89.12
prefix-fanout=16.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTCGTATGCC


criterion=fanout-score
sequence-density=88.04
sequence-density-rank=1
fanout-score=17.16
fanout-score-rank=1
prefix-density=89.12
prefix-fanout=16.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTCGTATGCC -o SRR5030919 -
Input file:	STDIN
trimmed:	SRR5030919-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTCGTATGCC
-- 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 06:45:23 2020 >> started

Wed Mar  4 06:45:31 2020 >> done (7.886s)
3330886 reads processed; of these:
 175526 ( 5.27%) short reads filtered out after trimming by size control
  24758 ( 0.74%) empty reads filtered out after trimming by size control
3130602 (93.99%) reads available; of these:
2926013 (93.46%) trimmed reads available after processing
 204589 ( 6.54%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  21865	  0.70%
 19	  41471	  1.32%
 20	 174840	  5.58%
 21	 409844	 13.09%
 22	1164788	 37.21%
 23	 512379	 16.37%
 24	 183976	  5.88%
 25	  29361	  0.94%
 26	  15019	  0.48%
 27	  13960	  0.45%
 28	  15142	  0.48%
 29	  12313	  0.39%
 30	  21734	  0.69%
 31	  25111	  0.80%
 32	  28696	  0.92%
 33	  46292	  1.48%
 34	  25625	  0.82%
 35	  17834	  0.57%
 36	  19909	  0.64%
 37	  11270	  0.36%
 38	  11849	  0.38%
 39	  12569	  0.40%
 40	  16496	  0.53%
 41	  20104	  0.64%
 42	  20515	  0.66%
 43	  16192	  0.52%
 44	  13990	  0.45%
 45	  15330	  0.49%
 46	  12279	  0.39%
 47	  10896	  0.35%
 48	   2074	  0.07%
 49	   7231	  0.23%
 50	 179648	  5.74%


criterion=sequence-density
sequence-density=4.35
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=17
prefix-density=0.01
prefix-fanout=1.0
sequence=TGTAAACATCCT


criterion=fanout-score
sequence-density=0.42
sequence-density-rank=30
fanout-score=15.91
fanout-score-rank=1
prefix-density=6.66
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 06:46:00
                             Started mapping on |	Mar 04 06:46:01
                                    Finished on |	Mar 04 06:46:26
       Mapping speed, Million of reads per hour |	461.83

                          Number of input reads |	3207174
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1686910
                        Uniquely mapped reads % |	52.60%
                          Average mapped length |	25.16
                       Number of splices: Total |	1302
            Number of splices: Annotated (sjdb) |	203
                       Number of splices: GT/AG |	1202
                       Number of splices: GC/AG |	16
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	83
                      Mismatch rate per base, % |	0.15%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.58
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.13
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1261014
             % of reads mapped to multiple loci |	39.32%
        Number of reads mapped to too many loci |	53352
             % of reads mapped to too many loci |	1.66%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.84%
                     % of reads unmapped: other |	0.58%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	259250	259250	259250
N_multimapping	1261014	1261014	1261014
N_noFeature	62707	75820	1295235
N_ambiguous	955290	617357	13134
UnstrandedReadsAssigned:668913 PositiveStrandReadsAssigned:993733 NegativeStrandReadsAssigned:378541
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030919 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: SRR5030919-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,207,174 reads, 758,153 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,142 rounds

 109283 SRR5030919.ke.tsv
  52636 SRR5030919.se.tsv
 161919 total
==> SRR5030919.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

==> SRR5030919.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030919 completed mapping pipeline successfully
