Starting /dee2/code/volunteer_pipeline.sh SRR5030856
    current disk space = 160669171712
    free memory = 73968616 
SRR5030856 SRAfilesize
72454fa67a4ea5e1b35b6da4b75273b3  SRR5030856.sra
SRR5030856.sra file validated
SRR5030856 is single end
SRR5030856 is conventional basespace
SRR5030856 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030856_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	32.51925	34.0	31.0	34.0	31.0	34.0
2	32.7495	34.0	31.0	34.0	31.0	34.0
3	32.84125	34.0	31.0	34.0	31.0	34.0
4	36.288	37.0	37.0	37.0	35.0	37.0
5	36.3285	37.0	37.0	37.0	35.0	37.0
6	36.08	37.0	36.0	37.0	35.0	37.0
7	36.045	37.0	35.0	37.0	35.0	37.0
8	36.1885	37.0	36.0	37.0	35.0	37.0
9	38.0	39.0	38.0	39.0	35.0	39.0
10	37.99825	39.0	38.0	39.0	35.0	39.0
11	37.85375	39.0	38.0	39.0	35.0	39.0
12	37.8755	39.0	38.0	39.0	35.0	39.0
13	37.84525	39.0	38.0	39.0	35.0	39.0
14	39.30625	41.0	39.0	41.0	36.0	41.0
15	39.24325	41.0	39.0	41.0	36.0	41.0
16	39.24875	40.0	39.0	41.0	36.0	41.0
17	39.43425	41.0	39.0	41.0	36.0	41.0
18	39.36625	41.0	39.0	41.0	36.0	41.0
19	39.13075	41.0	39.0	41.0	36.0	41.0
20	39.131	41.0	39.0	41.0	36.0	41.0
21	39.19275	41.0	39.0	41.0	36.0	41.0
22	39.1655	41.0	39.0	41.0	36.0	41.0
23	38.99725	40.0	39.0	41.0	35.0	41.0
24	38.83075	40.0	39.0	41.0	35.0	41.0
25	39.084	41.0	39.0	41.0	36.0	41.0
26	39.1485	41.0	39.0	41.0	36.0	41.0
27	39.1775	41.0	39.0	41.0	36.0	41.0
28	38.8515	40.0	39.0	41.0	35.0	41.0
29	38.24125	40.0	38.0	41.0	33.0	41.0
30	38.42825	40.0	38.0	41.0	34.0	41.0
31	38.7655	40.0	38.0	41.0	34.0	41.0
32	39.051	41.0	39.0	41.0	35.0	41.0
33	38.029	40.0	38.0	41.0	33.0	41.0
34	37.99675	40.0	38.0	41.0	33.0	41.0
35	37.68525	39.0	37.0	40.0	33.0	41.0
36	33.826	38.0	30.0	40.0	18.0	41.0
37	35.0485	38.0	33.0	40.0	26.0	41.0
38	36.781	39.0	36.0	40.0	31.0	41.0
39	36.7525	39.0	36.0	40.0	30.0	41.0
40	37.0185	39.0	36.0	40.0	31.0	41.0
41	37.013	39.0	36.0	40.0	31.0	41.0
42	37.0445	39.0	37.0	41.0	31.0	41.0
43	36.88175	39.0	36.0	40.0	31.0	41.0
44	36.78975	39.0	36.0	41.0	31.0	41.0
45	36.5635	39.0	36.0	40.0	31.0	41.0
46	34.77875	38.0	34.0	40.0	25.0	41.0
47	35.42075	38.0	35.0	40.0	27.0	41.0
48	35.6705	39.0	35.0	41.0	29.0	41.0
49	34.5185	38.0	34.0	40.0	26.0	41.0
50	30.39425	34.0	28.0	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
13	1.0
14	0.0
15	0.0
16	0.0
17	0.0
18	1.0
19	3.0
20	4.0
21	8.0
22	9.0
23	13.0
24	17.0
25	16.0
26	13.0
27	23.0
28	24.0
29	36.0
30	47.0
31	71.0
32	97.0
33	113.0
34	168.0
35	214.0
36	310.0
37	523.0
38	1044.0
39	1245.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.02750687671918	23.355838959739934	51.11277819454864	15.503875968992247
2	22.775000000000002	26.55	19.900000000000002	30.775000000000002
3	26.35	20.0	22.925	30.725
4	31.45	27.750000000000004	14.499999999999998	26.3
5	20.65	41.525	24.9	12.925
6	32.85	18.7	35.25	13.200000000000001
7	16.275000000000002	21.65	24.775	37.3
8	25.95	29.2	14.174999999999999	30.675
9	22.375	33.975	29.65	14.000000000000002
10	22.0	21.5	29.625	26.875
11	28.249999999999996	13.350000000000001	17.525	40.875
12	15.375	18.55	31.85	34.225
13	31.574999999999996	19.325	30.025000000000002	19.075
14	28.749999999999996	33.175	22.425	15.65
15	34.625	24.375	25.974999999999998	15.024999999999999
16	17.2	22.825	22.175	37.8
17	22.05	22.35	40.400000000000006	15.2
18	22.900000000000002	19.025	31.775	26.3
19	36.55	14.725	30.175	18.55
20	41.699999999999996	16.05	27.500000000000004	14.75
21	22.35	19.1	29.599999999999998	28.95
22	28.625	12.225	47.25	11.899999999999999
23	27.474999999999998	14.274999999999999	42.75	15.5
24	50.14999999999999	16.25	24.5	9.1
25	48.325	24.775	16.05	10.85
26	28.449999999999996	44.4	15.075	12.075
27	17.325	46.025	24.55	12.1
28	11.899999999999999	24.4	47.8	15.9
29	10.775	13.825000000000001	56.325	19.075
30	10.825	8.025	36.6	44.55
31	16.6	6.6000000000000005	44.275	32.525
32	28.675	7.124999999999999	21.475	42.725
33	53.300000000000004	9.275	14.825	22.6
34	59.675	8.649999999999999	16.475	15.2
35	61.9	7.95	17.724999999999998	12.425
36	44.175	8.325000000000001	32.725	14.774999999999999
37	43.075	11.0	20.150000000000002	25.775
38	23.799999999999997	15.725	13.4	47.075
39	17.224999999999998	25.275	9.325	48.175000000000004
40	18.0	46.125	10.825	25.05
41	26.575	47.199999999999996	10.0	16.225
42	48.775	30.95	10.525	9.75
43	48.625	31.5	9.625	10.25
44	30.375000000000004	47.025	8.325000000000001	14.274999999999999
45	20.05	48.575	12.775	18.6
46	11.625	28.199999999999996	19.25	40.925
47	10.100000000000001	17.525	37.125	35.25
48	11.475	14.249999999999998	20.95	53.325
49	16.150000000000002	19.7	14.6	49.55
50	21.475	36.425000000000004	13.375	28.725
>>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	0.5
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	0.5
24	1.0
25	0.5
26	0.0
27	1.0
28	2.0
29	1.5
30	1.0
31	7.0
32	13.0
33	21.5
34	30.0
35	34.5
36	39.0
37	51.5
38	64.0
39	59.5
40	55.0
41	57.5
42	60.0
43	87.5
44	115.0
45	168.0
46	221.0
47	326.0
48	431.0
49	525.0
50	619.0
51	704.0
52	789.0
53	629.5
54	470.0
55	487.0
56	504.0
57	381.0
58	258.0
59	173.0
60	88.0
61	66.5
62	45.0
63	66.5
64	88.0
65	57.5
66	27.0
67	20.0
68	13.0
69	15.5
70	18.0
71	27.5
72	37.0
73	20.5
74	4.0
75	3.0
76	2.0
77	1.0
78	0.0
79	2.0
80	4.0
81	2.5
82	1.0
83	0.5
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	0.025
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	0.0
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	42.15
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.63107947805456	32.300000000000004
2	10.320284697508896	8.7
3	3.6773428232502967	4.65
4	2.0759193357058123	3.5000000000000004
5	0.8303677342823249	1.7500000000000002
6	1.0676156583629894	2.7
7	0.7117437722419928	2.1
8	0.6524317912218268	2.1999999999999997
9	0.5931198102016607	2.25
>10	2.965599051008304	23.175
>50	0.41518386714116245	13.475000000000001
>100	0.05931198102016608	3.2
>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	128	3.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	100	2.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	89	2.225	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	85	2.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	82	2.0500000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	71	1.775	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	59	1.4749999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	53	1.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	43	1.075	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	38	0.95	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	36	0.8999999999999999	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGA	29	0.7250000000000001	RNA PCR Primer, Index 7 (97% over 35bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTC	19	0.475	RNA PCR Primer, Index 23 (100% over 44bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	15	0.375	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	14	0.35000000000000003	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	13	0.325	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	12	0.3	RNA PCR Primer, Index 1 (100% over 33bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	12	0.3	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	12	0.3	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGC	11	0.27499999999999997	RNA PCR Primer, Index 23 (100% over 50bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	11	0.27499999999999997	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	10	0.25	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	10	0.25	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	9	0.22499999999999998	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	9	0.22499999999999998	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	8	0.2	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	8	0.2	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	8	0.2	No Hit
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	8	0.2	RNA PCR Primer, Index 1 (100% over 31bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	7	0.17500000000000002	No Hit
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	7	0.17500000000000002	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 32bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	7	0.17500000000000002	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGTAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTCCATGATGAGCAACACTCACCATCTTTCGTTTGAGTCTCACGACTGTG	6	0.15	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	6	0.15	No Hit
TGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGG	5	0.125	RNA PCR Primer, Index 23 (100% over 39bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	5	0.125	No Hit
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	5	0.125	No Hit
TATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TGCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTG	5	0.125	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCA	5	0.125	No Hit
CGCGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCT	5	0.125	RNA PCR Primer, Index 23 (100% over 43bp)
TTTAGCTGTTAACTAAATTTTCGTAGGTTTAATTCCTGCCAATCTAGCCA	5	0.125	No Hit
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	5	0.125	No Hit
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	5	0.125	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	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	0.275	0.0	0.0	0.0
2	0.0	0.3	0.0	0.0	0.0
3	0.0	0.45	0.0	0.0	0.0
4	0.0	0.45	0.0	0.0	0.0
5	0.0	0.5	0.0	0.0	0.0
6	0.0	0.65	0.0	0.0	0.0
7	0.0	1.225	0.0	0.0	0.0
8	0.0	1.45	0.0	0.0	0.0
9	0.0	1.5	0.0	0.0	0.0
10	0.0	1.675	0.0	0.0	0.0
11	0.0	1.825	0.0	0.0	0.0
12	0.0	2.45	0.0	0.0	0.0
13	0.0	2.925	0.0	0.0	0.0
14	0.0	3.425	0.0	0.0	0.0
15	0.0	3.925	0.0	0.0	0.0
16	0.0	5.225	0.0	0.0	0.0
17	0.0	5.875	0.0	0.0	0.0
18	0.0	6.7	0.0	0.0	0.0
19	0.0	7.475	0.0	0.0	0.0
20	0.0	8.5	0.0	0.0	0.0
21	0.0	14.25	0.0	0.0	0.0
22	0.0	25.375	0.0	0.0	0.0
23	0.0	53.3	0.0	0.0	0.0
24	0.0	65.475	0.0	0.0	0.0
25	0.0	71.575	0.0	0.0	0.0
26	0.0	73.05	0.0	0.0	0.0
27	0.0	73.725	0.0	0.0	0.0
28	0.0	74.475	0.0	0.0	0.0
29	0.0	75.025	0.0	0.0	0.0
30	0.0	75.525	0.0	0.0	0.0
31	0.0	76.25	0.0	0.0	0.0
32	0.0	76.925	0.0	0.0	0.0
33	0.0	77.7	0.0	0.0	0.0
34	0.0	79.7	0.0	0.0	0.0
35	0.0	80.4	0.0	0.0	0.0
36	0.0	80.95	0.0	0.0	0.0
37	0.0	81.45	0.0	0.0	0.0
38	0.0	81.95	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
AACCGGT	20	6.952051E-4	44.000004	9
GGTCTCT	20	6.952051E-4	44.000004	13
GAACCGG	20	6.952051E-4	44.000004	8
GTCTCTT	20	6.952051E-4	44.000004	14
GGCTTGG	20	6.952051E-4	44.000004	19
CCCTGAG	40	5.315087E-9	44.000004	2
AGTGAAC	20	6.952051E-4	44.000004	5
TCTCTTT	20	6.952051E-4	44.000004	15
GTGAACC	20	6.952051E-4	44.000004	6
AGACCCT	40	5.315087E-9	44.000004	7
CGGTCTC	20	6.952051E-4	44.000004	12
TGAACCG	20	6.952051E-4	44.000004	7
CAGTGAA	20	6.952051E-4	44.000004	4
GAGACCC	40	5.315087E-9	44.000004	6
TCCCTGA	40	5.315087E-9	44.000004	1
CCGGTCT	20	6.952051E-4	44.000004	11
ACTGTTG	30	1.9515464E-6	44.0	18
GTTGAAG	30	1.9515464E-6	44.0	10
>>END_MODULE
Read 183721 spots for SRR5030856.sra
Written 183721 spots for SRR5030856.sra
Read 183721 spots for SRR5030856.sra
Written 183721 spots for SRR5030856.sra
Read 183721 spots for SRR5030856.sra
Written 183721 spots for SRR5030856.sra
Read 183721 spots for SRR5030856.sra
Written 183721 spots for SRR5030856.sra
Read 183721 spots for SRR5030856.sra
Written 183721 spots for SRR5030856.sra
Read 183721 spots for SRR5030856.sra
Written 183721 spots for SRR5030856.sra
Read 183721 spots for SRR5030856.sra
Written 183721 spots for SRR5030856.sra
Read 183726 spots for SRR5030856.sra
Written 183726 spots for SRR5030856.sra
Read 183721 spots for SRR5030856.sra
Written 183721 spots for SRR5030856.sra
Read 183721 spots for SRR5030856.sra
Written 183721 spots for SRR5030856.sra
Read 183721 spots for SRR5030856.sra
Written 183721 spots for SRR5030856.sra
Read 183721 spots for SRR5030856.sra
Written 183721 spots for SRR5030856.sra
SRR ids: ['SRR5030856.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_6n0k_2ji
SRR5030856.sra spots: 2204657
blocks: [[1, 183721], [183722, 367442], [367443, 551163], [551164, 734884], [734885, 918605], [918606, 1102326], [1102327, 1286047], [1286048, 1469768], [1469769, 1653489], [1653490, 1837210], [1837211, 2020931], [2020932, 2204657]]
SRR5030856 file size 381035
SRR5030856 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030856 SRR5030856_1.fastq
Input file:	SRR5030856_1.fastq
trimmed:	SRR5030856-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 06:29:16 2020 >> started

Wed Mar  4 06:29:17 2020 >> done (1.127s)
2204657 reads processed; of these:
     96 ( 0.00%) short reads filtered out after trimming by size control
      3 ( 0.00%) empty reads filtered out after trimming by size control
2204558 (100.00%) reads available; of these:
 130977 ( 5.94%) trimmed reads available after processing
2073581 (94.06%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     26	  0.00%
 19	     47	  0.00%
 20	     94	  0.00%
 21	     96	  0.00%
 22	    151	  0.01%
 23	    190	  0.01%
 24	    219	  0.01%
 25	    325	  0.01%
 26	    265	  0.01%
 27	    341	  0.02%
 28	    412	  0.02%
 29	    551	  0.02%
 30	    489	  0.02%
 31	    721	  0.03%
 32	    610	  0.03%
 33	    954	  0.04%
 34	   2262	  0.10%
 35	   2010	  0.09%
 36	   1509	  0.07%
 37	   1685	  0.08%
 38	   1780	  0.08%
 39	   2191	  0.10%
 40	   2233	  0.10%
 41	   2503	  0.11%
 42	   3419	  0.16%
 43	   4435	  0.20%
 44	   7787	  0.35%
 45	   9629	  0.44%
 46	   9148	  0.41%
 47	  13264	  0.60%
 48	  25875	  1.17%
 49	  35756	  1.62%
 50	2073581	 94.06%
2204558 reads passed initial QC


criterion=sequence-density
sequence-density=81.84
sequence-density-rank=1
fanout-score=19.69
fanout-score-rank=1
prefix-density=83.51
prefix-fanout=19.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC


criterion=fanout-score
sequence-density=81.84
sequence-density-rank=1
fanout-score=19.69
fanout-score-rank=1
prefix-density=83.51
prefix-fanout=19.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC -o SRR5030856 -
Input file:	STDIN
trimmed:	SRR5030856-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC
-- 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 06:29:29 2020 >> started

Wed Mar  4 06:29:32 2020 >> done (2.386s)
2150788 reads processed; of these:
 145588 ( 6.77%) short reads filtered out after trimming by size control
   8491 ( 0.39%) empty reads filtered out after trimming by size control
1996709 (92.84%) reads available; of these:
1785947 (89.44%) trimmed reads available after processing
 210762 (10.56%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  17176	  0.86%
 19	  23948	  1.20%
 20	 125940	  6.31%
 21	 254640	 12.75%
 22	 601983	 30.15%
 23	 257390	 12.89%
 24	 130144	  6.52%
 25	  32697	  1.64%
 26	  17446	  0.87%
 27	  13443	  0.67%
 28	  14393	  0.72%
 29	  10833	  0.54%
 30	  14421	  0.72%
 31	  17048	  0.85%
 32	  17496	  0.88%
 33	  45149	  2.26%
 34	  15148	  0.76%
 35	  11615	  0.58%
 36	  12239	  0.61%
 37	   9079	  0.45%
 38	   9351	  0.47%
 39	  10614	  0.53%
 40	  15767	  0.79%
 41	  21932	  1.10%
 42	  25296	  1.27%
 43	  17811	  0.89%
 44	  14178	  0.71%
 45	  18295	  0.92%
 46	  13740	  0.69%
 47	  10902	  0.55%
 48	   2085	  0.10%
 49	   6750	  0.34%
 50	 187760	  9.40%


criterion=sequence-density
sequence-density=5.17
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=38
fanout-score=59.04
fanout-score-rank=1
prefix-density=1.27
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:29:52
                             Started mapping on |	Mar 04 06:29:52
                                    Finished on |	Mar 04 06:30:15
       Mapping speed, Million of reads per hour |	320.94

                          Number of input reads |	2050479
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1174344
                        Uniquely mapped reads % |	57.27%
                          Average mapped length |	26.60
                       Number of splices: Total |	1334
            Number of splices: Annotated (sjdb) |	188
                       Number of splices: GT/AG |	1254
                       Number of splices: GC/AG |	18
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	62
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.52
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	628165
             % of reads mapped to multiple loci |	30.64%
        Number of reads mapped to too many loci |	34613
             % of reads mapped to too many loci |	1.69%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.89%
                     % of reads unmapped: other |	0.52%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	247970	247970	247970
N_multimapping	628165	628165	628165
N_noFeature	52196	64629	814262
N_ambiguous	666942	354295	12669
UnstrandedReadsAssigned:455206 PositiveStrandReadsAssigned:755420 NegativeStrandReadsAssigned:347413
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030856 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: SRR5030856-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,050,479 reads, 547,305 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,056 rounds

 109283 SRR5030856.ke.tsv
  52636 SRR5030856.se.tsv
 161919 total
==> SRR5030856.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

==> SRR5030856.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030856 completed mapping pipeline successfully
