Starting /dee2/code/volunteer_pipeline.sh SRR5030983
    current disk space = 160575324160
    free memory = 73953892 
SRR5030983 SRAfilesize
ca75b20668e55b288d1eef0388778621  SRR5030983.sra
SRR5030983.sra file validated
SRR5030983 is single end
SRR5030983 is conventional basespace
SRR5030983 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030983_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	53
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.31925	33.0	31.0	34.0	31.0	34.0
2	32.505	34.0	31.0	34.0	31.0	34.0
3	32.544	34.0	31.0	34.0	31.0	34.0
4	36.152	37.0	35.0	37.0	35.0	37.0
5	36.0935	37.0	35.0	37.0	35.0	37.0
6	35.88275	37.0	35.0	37.0	35.0	37.0
7	35.82	37.0	35.0	37.0	35.0	37.0
8	35.95575	37.0	35.0	37.0	35.0	37.0
9	37.5655	39.0	37.0	39.0	35.0	39.0
10	37.534	39.0	37.0	39.0	35.0	39.0
11	37.2035	39.0	37.0	39.0	33.0	39.0
12	37.50325	39.0	37.0	39.0	35.0	39.0
13	37.56175	39.0	37.0	39.0	35.0	39.0
14	38.94625	40.0	38.0	41.0	35.0	41.0
15	38.77875	40.0	38.0	41.0	34.0	41.0
16	38.863	40.0	38.0	41.0	35.0	41.0
17	39.00375	40.0	38.0	41.0	35.0	41.0
18	38.94475	41.0	38.0	41.0	35.0	41.0
19	38.7695	40.0	38.0	41.0	35.0	41.0
20	38.671	40.0	38.0	41.0	34.0	41.0
21	38.8485	40.0	38.0	41.0	35.0	41.0
22	38.78875	40.0	38.0	41.0	34.0	41.0
23	38.599	40.0	38.0	41.0	34.0	41.0
24	38.76175	40.0	38.0	41.0	34.0	41.0
25	38.88225	40.0	38.0	41.0	35.0	41.0
26	38.634	40.0	38.0	41.0	34.0	41.0
27	38.76825	40.0	38.0	41.0	35.0	41.0
28	38.507	40.0	38.0	41.0	34.0	41.0
29	38.26725	40.0	38.0	41.0	33.0	41.0
30	38.2165	40.0	38.0	41.0	33.0	41.0
31	38.47425	40.0	38.0	41.0	34.0	41.0
32	38.53075	40.0	38.0	41.0	34.0	41.0
33	38.19675	40.0	38.0	41.0	33.0	41.0
34	38.2275	40.0	38.0	41.0	33.0	41.0
35	37.93425	40.0	38.0	41.0	33.0	41.0
36	37.7325	40.0	37.0	41.0	33.0	41.0
37	37.17225	39.0	37.0	41.0	31.0	41.0
38	37.0915	39.0	36.0	41.0	31.0	41.0
39	37.53425	39.0	37.0	41.0	33.0	41.0
40	37.56	40.0	37.0	41.0	33.0	41.0
41	37.8025	40.0	37.0	41.0	33.0	41.0
42	37.79325	40.0	37.0	41.0	33.0	41.0
43	37.5795	40.0	37.0	41.0	33.0	41.0
44	37.60675	40.0	37.0	41.0	33.0	41.0
45	37.5525	40.0	37.0	41.0	33.0	41.0
46	37.3515	40.0	37.0	41.0	33.0	41.0
47	36.7915	39.0	35.0	41.0	31.0	41.0
48	36.54275	39.0	35.0	41.0	30.0	41.0
49	36.385	39.0	35.0	41.0	30.0	41.0
50	35.68275	38.0	34.0	40.0	29.0	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
13	1.0
14	0.0
15	0.0
16	1.0
17	2.0
18	0.0
19	3.0
20	4.0
21	4.0
22	7.0
23	10.0
24	3.0
25	16.0
26	12.0
27	22.0
28	30.0
29	27.0
30	55.0
31	72.0
32	81.0
33	111.0
34	176.0
35	200.0
36	294.0
37	410.0
38	769.0
39	1690.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.625	25.4	45.550000000000004	19.425
2	24.029065397143572	28.313705838135807	19.09295915810574	28.564269606614882
3	22.75	17.95	23.925	35.375
4	33.074999999999996	27.650000000000002	15.825	23.45
5	23.05	36.625	27.325	13.0
6	33.425	15.1	34.25	17.224999999999998
7	18.375	20.9	21.775	38.95
8	22.45	28.775000000000002	18.325	30.45
9	22.125	31.225	28.025	18.625
10	22.05	22.525000000000002	26.025	29.4
11	33.025	10.85	17.224999999999998	38.9
12	17.224999999999998	18.45	29.225	35.099999999999994
13	29.675	16.975	34.449999999999996	18.9
14	31.225	28.849999999999998	19.675	20.25
15	33.7	23.775	27.400000000000002	15.125
16	20.925	19.325	22.900000000000002	36.85
17	26.85	22.45	37.0	13.700000000000001
18	25.55	17.0	27.525	29.925
19	36.275	13.375	31.45	18.9
20	42.175000000000004	15.925	27.55	14.35
21	24.275	21.875	25.6	28.249999999999996
22	31.874999999999996	13.100000000000001	43.525000000000006	11.5
23	26.450000000000003	12.925	42.699999999999996	17.925
24	50.0	14.924999999999999	26.35	8.725
25	49.55	24.099999999999998	14.725	11.625
26	29.5	42.95	14.274999999999999	13.275
27	16.900000000000002	44.925	23.175	15.0
28	13.675	23.674999999999997	45.675	16.975
29	14.75	12.975	53.5	18.775
30	10.75	7.75	34.65	46.85
31	15.975	5.775	44.9	33.35
32	28.525	6.25	22.875	42.35
33	50.975	9.475	14.05	25.5
34	58.3	7.75	17.5	16.45
35	64.05	7.6	17.275	11.075
36	42.325	9.1	35.175	13.4
37	43.0	12.2	21.45	23.35
38	25.424999999999997	17.8	13.825000000000001	42.95
39	17.150000000000002	22.2	12.65	48.0
40	15.9	44.800000000000004	13.725000000000001	25.575
41	24.675	46.475	9.85	19.0
42	44.925	29.25	13.575000000000001	12.25
43	50.525	27.35	9.8	12.325
44	33.7	44.15	8.85	13.3
45	20.549999999999997	47.5	14.399999999999999	17.549999999999997
46	16.625	25.674999999999997	17.424999999999997	40.275
47	10.625	14.774999999999999	38.2	36.4
48	12.775	12.675	22.0	52.55
49	12.925	18.15	15.375	53.55
50	18.8	34.75	14.224999999999998	32.225
>>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	0.0
14	0.0
15	0.0
16	0.0
17	0.5
18	1.0
19	0.5
20	0.0
21	1.0
22	2.0
23	1.0
24	0.0
25	0.5
26	1.0
27	1.0
28	1.0
29	2.0
30	3.0
31	9.0
32	15.0
33	15.0
34	15.0
35	16.0
36	17.0
37	26.5
38	36.0
39	36.5
40	37.0
41	34.0
42	31.0
43	62.0
44	93.0
45	126.5
46	160.0
47	273.5
48	387.0
49	494.5
50	602.0
51	724.5
52	847.0
53	659.5
54	472.0
55	460.5
56	449.0
57	380.0
58	311.0
59	207.5
60	104.0
61	76.0
62	48.0
63	109.0
64	170.0
65	106.0
66	42.0
67	31.0
68	20.0
69	26.5
70	33.0
71	65.0
72	97.0
73	50.0
74	3.0
75	2.0
76	1.0
77	1.0
78	1.0
79	1.0
80	1.0
81	0.5
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.22499999999999998
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	37.7
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.72944297082228	28.549999999999997
2	9.283819628647215	7.000000000000001
3	3.7135278514588856	4.2
4	3.183023872679045	4.8
5	1.5915119363395225	3.0
6	1.1273209549071617	2.55
7	0.5305039787798408	1.4000000000000001
8	0.6631299734748011	2.0
9	0.5305039787798408	1.7999999999999998
>10	3.116710875331565	24.3
>50	0.1989389920424403	5.975
>100	0.33156498673740054	14.424999999999999
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	128	3.2	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	124	3.1	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	112	2.8000000000000003	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	108	2.7	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	105	2.625	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	100	2.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	84	2.1	RNA PCR Primer, Index 1 (100% over 30bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	55	1.375	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	50	1.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	49	1.225	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	48	1.2	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	43	1.075	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCG	32	0.8	RNA PCR Primer, Index 2 (100% over 35bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	25	0.625	RNA PCR Primer, Index 1 (100% over 33bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	21	0.525	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	20	0.5	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	18	0.44999999999999996	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	16	0.4	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	15	0.375	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGC	14	0.35000000000000003	RNA PCR Primer, Index 2 (100% over 50bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTC	13	0.325	RNA PCR Primer, Index 2 (100% over 44bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	13	0.325	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	12	0.3	RNA PCR Primer, Index 1 (100% over 31bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	12	0.3	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	10	0.25	RNA PCR Primer, Index 2 (100% over 34bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	9	0.22499999999999998	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	9	0.22499999999999998	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	8	0.2	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	8	0.2	No Hit
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCCAGGAACTCCAGTCACCG	7	0.17500000000000002	RNA PCR Primer, Index 2 (97% over 35bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AAACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGA	6	0.15	RNA PCR Primer, Index 2 (100% over 36bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
CAACGGAATCCCAAAAGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTAT	5	0.125	RNA PCR Primer, Index 2 (100% over 48bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	5	0.125	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATATGGAATTCTCGGGTGCCA	5	0.125	No Hit
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	5	0.125	RNA PCR Primer, Index 2 (100% over 34bp)
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATTGGAA	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	5	0.125	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
>>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	0.375	0.0	0.0	0.0
2	0.0	0.375	0.0	0.0	0.0
3	0.0	0.525	0.0	0.0	0.0
4	0.0	0.575	0.0	0.0	0.0
5	0.0	0.575	0.0	0.0	0.0
6	0.0	0.625	0.0	0.0	0.0
7	0.0	1.125	0.0	0.0	0.0
8	0.0	1.325	0.0	0.0	0.0
9	0.0	1.475	0.0	0.0	0.0
10	0.0	1.6	0.0	0.0	0.0
11	0.0	1.8	0.0	0.0	0.0
12	0.0	1.975	0.0	0.0	0.0
13	0.0	2.2	0.0	0.0	0.0
14	0.0	2.6	0.0	0.0	0.0
15	0.0	3.025	0.0	0.0	0.0
16	0.0	4.45	0.0	0.0	0.0
17	0.0	5.275	0.0	0.0	0.0
18	0.0	6.425	0.0	0.0	0.0
19	0.0	7.05	0.0	0.0	0.0
20	0.0	8.0	0.0	0.0	0.0
21	0.0	13.275	0.0	0.0	0.0
22	0.0	23.35	0.0	0.0	0.0
23	0.0	50.4	0.0	0.0	0.0
24	0.0	63.525	0.0	0.0	0.0
25	0.0	69.075	0.0	0.0	0.0
26	0.0	70.6	0.0	0.0	0.0
27	0.0	71.425	0.0	0.0	0.0
28	0.0	72.025	0.0	0.0	0.0
29	0.0	72.4	0.0	0.0	0.0
30	0.0	72.8	0.0	0.0	0.0
31	0.0	73.475	0.0	0.0	0.0
32	0.0	74.95	0.0	0.0	0.0
33	0.0	76.375	0.0	0.0	0.0
34	0.0	80.7	0.0	0.0	0.0
35	0.0	81.95	0.0	0.0	0.0
36	0.0	82.775	0.0	0.0	0.0
37	0.0	83.95	0.0	0.0	0.0
38	0.0	84.475	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CGCTGAT	20	6.952051E-4	44.000004	28
TTTGAAC	20	6.952051E-4	44.000004	1
TCCTTGG	20	6.952051E-4	44.000004	19
ACTCGAC	20	6.952051E-4	44.000004	12
TCGACTC	20	6.952051E-4	44.000004	14
TAAACAT	20	6.952051E-4	44.000004	3
AAACATC	20	6.952051E-4	44.000004	4
ACCATCA	20	6.952051E-4	44.000004	6
ACTCCTT	20	6.952051E-4	44.000004	17
CCTTGGA	20	6.952051E-4	44.000004	20
CTGATGG	20	6.952051E-4	44.000004	30
CATCACT	20	6.952051E-4	44.000004	8
ACATTCA	20	6.952051E-4	44.000004	2
AACCATC	20	6.952051E-4	44.000004	5
GCTGTCG	20	6.952051E-4	44.000004	11
GAACCAT	20	6.952051E-4	44.000004	4
CCATCAC	20	6.952051E-4	44.000004	7
CACTCGA	20	6.952051E-4	44.000004	11
GCTGATG	20	6.952051E-4	44.000004	29
GCTTGGC	20	6.952051E-4	44.000004	15
>>END_MODULE
Read 239122 spots for SRR5030983.sra
Written 239122 spots for SRR5030983.sra
Read 239122 spots for SRR5030983.sra
Written 239122 spots for SRR5030983.sra
Read 239122 spots for SRR5030983.sra
Written 239122 spots for SRR5030983.sra
Read 239122 spots for SRR5030983.sra
Written 239122 spots for SRR5030983.sra
Read 239122 spots for SRR5030983.sra
Written 239122 spots for SRR5030983.sra
Read 239122 spots for SRR5030983.sra
Written 239122 spots for SRR5030983.sra
Read 239122 spots for SRR5030983.sra
Written 239122 spots for SRR5030983.sra
Read 239122 spots for SRR5030983.sra
Written 239122 spots for SRR5030983.sra
Read 239122 spots for SRR5030983.sra
Written 239122 spots for SRR5030983.sra
Read 239122 spots for SRR5030983.sra
Written 239122 spots for SRR5030983.sra
Read 239122 spots for SRR5030983.sra
Written 239122 spots for SRR5030983.sra
Read 239125 spots for SRR5030983.sra
Written 239125 spots for SRR5030983.sra
SRR ids: ['SRR5030983.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_yo6g4c0n
SRR5030983.sra spots: 2869467
blocks: [[1, 239122], [239123, 478244], [478245, 717366], [717367, 956488], [956489, 1195610], [1195611, 1434732], [1434733, 1673854], [1673855, 1912976], [1912977, 2152098], [2152099, 2391220], [2391221, 2630342], [2630343, 2869467]]
SRR5030983 file size 496275
SRR5030983 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030983 SRR5030983_1.fastq
Input file:	SRR5030983_1.fastq
trimmed:	SRR5030983-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 06:59:36 2020 >> started

Wed Mar  4 06:59:38 2020 >> done (1.815s)
2869467 reads processed; of these:
    283 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
2869178 (99.99%) reads available; of these:
 176224 ( 6.14%) trimmed reads available after processing
2692954 (93.86%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     84	  0.00%
 19	     92	  0.00%
 20	    129	  0.00%
 21	    195	  0.01%
 22	    295	  0.01%
 23	    386	  0.01%
 24	    439	  0.02%
 25	    607	  0.02%
 26	    452	  0.02%
 27	    587	  0.02%
 28	    607	  0.02%
 29	    948	  0.03%
 30	    723	  0.03%
 31	    781	  0.03%
 32	    920	  0.03%
 33	   1188	  0.04%
 34	   1394	  0.05%
 35	   2796	  0.10%
 36	   2540	  0.09%
 37	   2981	  0.10%
 38	   3044	  0.11%
 39	   3192	  0.11%
 40	   3412	  0.12%
 41	   3485	  0.12%
 42	   4727	  0.16%
 43	   6600	  0.23%
 44	   8835	  0.31%
 45	  11815	  0.41%
 46	  18467	  0.64%
 47	  20218	  0.70%
 48	  33037	  1.15%
 49	  41248	  1.44%
 50	2692954	 93.86%
2869178 reads passed initial QC


criterion=sequence-density
sequence-density=83.92
sequence-density-rank=1
fanout-score=21.62
fanout-score-rank=1
prefix-density=86.20
prefix-fanout=21.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCC


criterion=fanout-score
sequence-density=83.92
sequence-density-rank=1
fanout-score=21.62
fanout-score-rank=1
prefix-density=86.20
prefix-fanout=21.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCC -o SRR5030983 -
Input file:	STDIN
trimmed:	SRR5030983-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCC
-- 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 06:59:56 2020 >> started

Wed Mar  4 07:00:00 2020 >> done (3.715s)
2800864 reads processed; of these:
 158646 ( 5.66%) short reads filtered out after trimming by size control
  14324 ( 0.51%) empty reads filtered out after trimming by size control
2627894 (93.82%) reads available; of these:
2470999 (94.03%) trimmed reads available after processing
 156895 ( 5.97%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  14446	  0.55%
 19	  28539	  1.09%
 20	 133373	  5.08%
 21	 288961	 11.00%
 22	 780339	 29.69%
 23	 362064	 13.78%
 24	 156626	  5.96%
 25	  43445	  1.65%
 26	  23220	  0.88%
 27	  18062	  0.69%
 28	  20073	  0.76%
 29	  16310	  0.62%
 30	  25049	  0.95%
 31	  41115	  1.56%
 32	  33807	  1.29%
 33	 132263	  5.03%
 34	  36418	  1.39%
 35	  28679	  1.09%
 36	  34428	  1.31%
 37	  16947	  0.64%
 38	  18815	  0.72%
 39	  17467	  0.66%
 40	  27759	  1.06%
 41	  34161	  1.30%
 42	  41041	  1.56%
 43	  29218	  1.11%
 44	  20527	  0.78%
 45	  28089	  1.07%
 46	  21372	  0.81%
 47	  16217	  0.62%
 48	   1613	  0.06%
 49	   2833	  0.11%
 50	 134618	  5.12%


criterion=sequence-density
sequence-density=7.57
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=0.59
sequence-density-rank=22
fanout-score=12.60
fanout-score-rank=1
prefix-density=7.38
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTTT
                                 Started job on |	Mar 04 07:00:44
                             Started mapping on |	Mar 04 07:00:45
                                    Finished on |	Mar 04 07:01:14
       Mapping speed, Million of reads per hour |	334.70

                          Number of input reads |	2696208
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1359589
                        Uniquely mapped reads % |	50.43%
                          Average mapped length |	25.09
                       Number of splices: Total |	1914
            Number of splices: Annotated (sjdb) |	352
                       Number of splices: GT/AG |	1810
                       Number of splices: GC/AG |	19
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	84
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.80
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	885161
             % of reads mapped to multiple loci |	32.83%
        Number of reads mapped to too many loci |	70630
             % of reads mapped to too many loci |	2.62%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	13.50%
                     % of reads unmapped: other |	0.63%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	451458	451458	451458
N_multimapping	885161	885161	885161
N_noFeature	84613	103475	934948
N_ambiguous	751196	389344	15915
UnstrandedReadsAssigned:523780 PositiveStrandReadsAssigned:866770 NegativeStrandReadsAssigned:408726
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030983 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: SRR5030983-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,696,208 reads, 655,599 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 860 rounds

 109283 SRR5030983.ke.tsv
  52636 SRR5030983.se.tsv
 161919 total
==> SRR5030983.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

==> SRR5030983.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030983 completed mapping pipeline successfully
