Starting /dee2/code/volunteer_pipeline.sh SRR5031099
    current disk space = 160477331456
    free memory = 73957276 
SRR5031099 SRAfilesize
12cf6b287629047a78e3e6f05d999a82  SRR5031099.sra
SRR5031099.sra file validated
SRR5031099 is single end
SRR5031099 is conventional basespace
SRR5031099 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031099_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	31.948	31.0	31.0	34.0	30.0	34.0
2	32.48825	33.0	31.0	34.0	31.0	34.0
3	32.498	33.0	31.0	34.0	31.0	34.0
4	36.18625	37.0	35.0	37.0	35.0	37.0
5	36.176	37.0	35.0	37.0	35.0	37.0
6	36.13875	37.0	35.0	37.0	35.0	37.0
7	35.89275	37.0	35.0	37.0	35.0	37.0
8	35.7015	37.0	35.0	37.0	35.0	37.0
9	36.93775	39.0	37.0	39.0	33.0	39.0
10	36.67725	39.0	37.0	39.0	32.0	39.0
11	37.462	39.0	37.0	39.0	34.0	39.0
12	37.715	39.0	37.0	39.0	35.0	39.0
13	37.52075	39.0	37.0	39.0	35.0	39.0
14	38.39575	40.0	38.0	41.0	33.0	41.0
15	37.027	40.0	37.0	41.0	30.0	41.0
16	36.799	39.0	36.0	40.0	31.0	41.0
17	37.125	39.0	37.0	41.0	32.0	41.0
18	38.26775	40.0	37.0	41.0	34.0	41.0
19	38.83525	40.0	38.0	41.0	36.0	41.0
20	38.6315	40.0	38.0	41.0	35.0	41.0
21	38.70725	40.0	38.0	41.0	35.0	41.0
22	37.47175	39.0	37.0	40.0	32.0	41.0
23	37.884	39.0	37.0	40.0	33.0	41.0
24	37.3175	39.0	37.0	40.0	31.0	41.0
25	38.2715	40.0	38.0	41.0	34.0	41.0
26	38.2365	40.0	38.0	41.0	34.0	41.0
27	38.4015	40.0	38.0	41.0	34.0	41.0
28	38.579	40.0	38.0	41.0	34.0	41.0
29	38.6085	40.0	38.0	41.0	34.0	41.0
30	38.8485	40.0	38.0	41.0	35.0	41.0
31	38.929	40.0	38.0	41.0	35.0	41.0
32	38.97425	40.0	38.0	41.0	35.0	41.0
33	39.06275	40.0	39.0	41.0	36.0	41.0
34	38.411	40.0	38.0	41.0	34.0	41.0
35	37.592	40.0	37.0	41.0	30.0	41.0
36	33.08175	35.0	30.0	40.0	23.0	41.0
37	34.98675	37.0	33.0	39.0	30.0	40.0
38	36.38025	38.0	35.0	39.0	31.0	40.0
39	36.80725	38.0	36.0	40.0	32.0	40.0
40	37.12025	39.0	37.0	40.0	32.0	41.0
41	37.53775	39.0	37.0	40.0	33.0	41.0
42	37.43825	40.0	37.0	41.0	32.0	41.0
43	37.47775	40.0	37.0	41.0	32.0	41.0
44	36.4535	39.0	36.0	40.0	30.0	41.0
45	36.7775	39.0	36.0	40.0	31.0	41.0
46	36.65975	39.0	36.0	40.0	31.0	41.0
47	35.77525	38.0	34.0	40.0	28.0	41.0
48	36.74875	39.0	36.0	40.0	31.0	41.0
49	37.07625	40.0	37.0	41.0	32.0	41.0
50	35.348	38.0	34.0	40.0	29.0	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	2.0
14	0.0
15	0.0
16	1.0
17	0.0
18	0.0
19	4.0
20	5.0
21	2.0
22	9.0
23	2.0
24	8.0
25	9.0
26	17.0
27	11.0
28	21.0
29	22.0
30	49.0
31	58.0
32	103.0
33	110.0
34	167.0
35	282.0
36	466.0
37	806.0
38	1196.0
39	650.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.0040020010005	25.512756378189096	51.975987993996995	14.507253626813407
2	21.5	28.499999999999996	16.475	33.525
3	27.175	16.375	19.650000000000002	36.8
4	35.175	29.9	11.799999999999999	23.125
5	20.025000000000002	39.1	27.725	13.15
6	28.599999999999998	13.325000000000001	42.775	15.299999999999999
7	14.725	20.549999999999997	20.925	43.8
8	21.65	29.625	15.725	33.0
9	28.575	32.5	25.900000000000002	13.025
10	22.425	16.150000000000002	31.75	29.675
11	32.625	10.875	14.7	41.8
12	14.124999999999998	17.4	34.449999999999996	34.025
13	30.825000000000003	15.2	33.15	20.825
14	29.675	32.324999999999996	19.25	18.75
15	38.7	17.675	26.174999999999997	17.45
16	16.55	18.6	21.525	43.325
17	27.175	18.5	38.25	16.075
18	25.900000000000002	15.5	34.975	23.625
19	40.5	13.5	29.675	16.325
20	50.3	12.9	23.45	13.350000000000001
21	22.225	22.325	22.45	33.0
22	30.425	11.35	48.125	10.100000000000001
23	26.400000000000002	13.05	47.5	13.05
24	53.0	11.475	26.200000000000003	9.325
25	52.37500000000001	23.45	15.375	8.799999999999999
26	27.35	48.575	13.450000000000001	10.625
27	14.95	50.575	24.025	10.45
28	11.725	25.5	49.125	13.65
29	11.700000000000001	12.0	57.49999999999999	18.8
30	8.55	7.074999999999999	37.974999999999994	46.400000000000006
31	12.3	5.125	48.925000000000004	33.650000000000006
32	26.55	4.75	23.35	45.35
33	55.7	7.3	13.025	23.974999999999998
34	65.9	5.800000000000001	13.8	14.499999999999998
35	66.875	7.75	17.075000000000003	8.3
36	45.85	6.825	35.825	11.5
37	48.275	9.3	20.1	22.325
38	25.674999999999997	14.274999999999999	11.425	48.625
39	14.875	24.175	8.85	52.1
40	13.775	50.875	9.75	25.6
41	24.224999999999998	51.449999999999996	7.6	16.725
42	50.349999999999994	30.225	8.85	10.575
43	53.65	29.925	6.15	10.274999999999999
44	30.975	51.275000000000006	5.2	12.55
45	18.925	53.225	10.75	17.1
46	13.3	25.8	17.9	43.0
47	8.375	14.249999999999998	39.725	37.65
48	9.325	12.35	20.849999999999998	57.475
49	13.075000000000001	18.975	11.625	56.325
50	18.525	38.475	11.325000000000001	31.674999999999997
>>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	0.0
18	0.0
19	0.0
20	0.0
21	0.5
22	1.0
23	0.5
24	0.0
25	1.0
26	2.0
27	1.5
28	1.0
29	1.0
30	1.0
31	1.0
32	1.0
33	5.5
34	10.0
35	13.0
36	16.0
37	17.5
38	19.0
39	24.5
40	30.0
41	31.0
42	32.0
43	57.5
44	83.0
45	103.0
46	123.0
47	223.5
48	324.0
49	423.0
50	522.0
51	710.5
52	899.0
53	699.5
54	500.0
55	594.0
56	688.0
57	534.5
58	381.0
59	250.0
60	119.0
61	81.0
62	43.0
63	65.0
64	87.0
65	70.5
66	54.0
67	37.0
68	20.0
69	17.5
70	15.0
71	17.5
72	20.0
73	13.0
74	6.0
75	4.0
76	2.0
77	1.0
78	0.0
79	0.0
80	0.0
81	0.5
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	0.05
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	40.849999999999994
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.6217870257038	31.3
2	10.159118727050185	8.3
3	3.7943696450428397	4.65
4	2.5091799265605874	4.1000000000000005
5	1.346389228886169	2.75
6	0.8567931456548347	2.1
7	0.8567931456548347	2.45
8	0.4895960832313341	1.6
9	0.42839657282741733	1.575
>10	2.386780905752754	17.95
>50	0.36719706242350064	10.775
>100	0.18359853121175032	12.45
>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
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	214	5.35	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	156	3.9	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	128	3.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	95	2.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	89	2.225	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	75	1.875	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	55	1.375	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	53	1.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGA	35	0.8750000000000001	RNA PCR Primer, Index 7 (97% over 35bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGC	26	0.65	RNA PCR Primer, Index 23 (100% over 50bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	25	0.625	RNA PCR Primer, Index 1 (100% over 33bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (96% over 30bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	12	0.3	No Hit
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	9	0.22499999999999998	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 31bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGCCGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	8	0.2	No Hit
CTAGACTGAGGCTCCTTGAGGATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	8	0.2	No Hit
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTC	7	0.17500000000000002	RNA PCR Primer, Index 23 (100% over 44bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AAACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	6	0.15	RNA PCR Primer, Index 6 (100% over 34bp)
TTTGAACCATCACTCGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGACTTCTCGGGTGCCAAGGAACTCCAGTCAC	6	0.15	RNA PCR Primer, Index 1 (96% over 33bp)
TCGGATCCGTCTGAGCTTGGCTATTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGCACTCCAGTCACGAGTGGATCTCGTATGC	6	0.15	RNA PCR Primer, Index 23 (98% over 50bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGACTCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTTGTCCCGGCCTGTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
TGTAAACATCCTACCCTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GCTCGACTCATGGTTTGAACCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTACCTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CTAGACTGAGGCTCCTTGAGGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.85	0.0	0.0	0.0
2	0.0	0.85	0.0	0.0	0.0
3	0.0	1.025	0.0	0.0	0.0
4	0.0	1.075	0.0	0.0	0.0
5	0.0	1.175	0.0	0.0	0.0
6	0.0	1.25	0.0	0.0	0.0
7	0.0	1.625	0.0	0.0	0.0
8	0.0	1.975	0.0	0.0	0.0
9	0.0	2.175	0.0	0.0	0.0
10	0.0	2.425	0.0	0.0	0.0
11	0.0	2.575	0.0	0.0	0.0
12	0.0	2.95	0.0	0.0	0.0
13	0.0	3.2	0.0	0.0	0.0
14	0.0	3.4	0.0	0.0	0.0
15	0.0	3.675	0.0	0.0	0.0
16	0.0	4.825	0.0	0.0	0.0
17	0.0	5.65	0.0	0.0	0.0
18	0.0	6.9	0.0	0.0	0.0
19	0.0	7.325	0.0	0.0	0.0
20	0.0	8.125	0.0	0.0	0.0
21	0.0	12.625	0.0	0.0	0.0
22	0.0	24.45	0.0	0.0	0.0
23	0.0	56.8	0.0	0.0	0.0
24	0.0	71.35	0.0	0.0	0.0
25	0.0	77.3	0.0	0.0	0.0
26	0.0	79.125	0.0	0.0	0.0
27	0.0	80.425	0.0	0.0	0.0
28	0.0	81.05	0.0	0.0	0.0
29	0.0	81.5	0.0	0.0	0.0
30	0.0	81.85	0.0	0.0	0.0
31	0.0	82.45	0.0	0.0	0.0
32	0.0	83.45	0.0	0.0	0.0
33	0.0	84.425	0.0	0.0	0.0
34	0.0	87.4	0.0	0.0	0.0
35	0.0	88.4	0.0	0.0	0.0
36	0.0	89.225	0.0	0.0	0.0
37	0.0	89.95	0.0	0.0	0.0
38	0.0	90.425	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CTTTAAC	20	6.952051E-4	44.000004	12
AGTGGAA	20	6.952051E-4	44.000004	21
AACCTGT	20	6.952051E-4	44.000004	16
GTGAGTG	20	6.952051E-4	44.000004	18
ACCTGTT	20	6.952051E-4	44.000004	17
TAACCTG	20	6.952051E-4	44.000004	15
GGCTTGG	45	2.728484E-10	44.000004	19
CCTTTAA	20	6.952051E-4	44.000004	11
TTGGCTT	45	2.728484E-10	44.000004	17
CCCTTTA	20	6.952051E-4	44.000004	10
TTAACCT	20	6.952051E-4	44.000004	14
TGAGTGG	20	6.952051E-4	44.000004	19
TTTAACC	20	6.952051E-4	44.000004	13
ACAGTGG	25	3.6958358E-5	44.0	4
AACGCTG	35	1.02281774E-7	44.0	8
GGTGAGT	30	1.9515464E-6	44.0	17
TTCACAG	25	3.6958358E-5	44.0	1
ACGCTGT	35	1.02281774E-7	44.0	9
CCTGTTG	25	3.6958358E-5	44.0	18
TAAGTTC	25	3.6958358E-5	44.0	12
>>END_MODULE
Read 145266 spots for SRR5031099.sra
Written 145266 spots for SRR5031099.sra
Read 145266 spots for SRR5031099.sra
Written 145266 spots for SRR5031099.sra
Read 145266 spots for SRR5031099.sra
Written 145266 spots for SRR5031099.sra
Read 145266 spots for SRR5031099.sra
Written 145266 spots for SRR5031099.sra
Read 145266 spots for SRR5031099.sra
Written 145266 spots for SRR5031099.sra
Read 145266 spots for SRR5031099.sra
Written 145266 spots for SRR5031099.sra
Read 145266 spots for SRR5031099.sra
Written 145266 spots for SRR5031099.sra
Read 145266 spots for SRR5031099.sra
Written 145266 spots for SRR5031099.sra
Read 145266 spots for SRR5031099.sra
Written 145266 spots for SRR5031099.sra
Read 145266 spots for SRR5031099.sra
Written 145266 spots for SRR5031099.sra
Read 145273 spots for SRR5031099.sra
Written 145273 spots for SRR5031099.sra
Read 145266 spots for SRR5031099.sra
Written 145266 spots for SRR5031099.sra
SRR ids: ['SRR5031099.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_9ccvfjr7
SRR5031099.sra spots: 1743199
blocks: [[1, 145266], [145267, 290532], [290533, 435798], [435799, 581064], [581065, 726330], [726331, 871596], [871597, 1016862], [1016863, 1162128], [1162129, 1307394], [1307395, 1452660], [1452661, 1597926], [1597927, 1743199]]
SRR5031099 file size 301064
SRR5031099 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031099 SRR5031099_1.fastq
Input file:	SRR5031099_1.fastq
trimmed:	SRR5031099-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- end quality threshold (-q):		10
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ (auto detected)
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	12
Wed Mar  4 07:23:57 2020 >> started

Wed Mar  4 07:23:59 2020 >> done (1.449s)
1743199 reads processed; of these:
    134 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
1743059 (99.99%) reads available; of these:
 145550 ( 8.35%) trimmed reads available after processing
1597509 (91.65%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     47	  0.00%
 19	     60	  0.00%
 20	    128	  0.01%
 21	    147	  0.01%
 22	    243	  0.01%
 23	    240	  0.01%
 24	    304	  0.02%
 25	    410	  0.02%
 26	    330	  0.02%
 27	    394	  0.02%
 28	    481	  0.03%
 29	    665	  0.04%
 30	    407	  0.02%
 31	    552	  0.03%
 32	    789	  0.05%
 33	   1441	  0.08%
 34	   2035	  0.12%
 35	   5480	  0.31%
 36	   2966	  0.17%
 37	   2808	  0.16%
 38	   2729	  0.16%
 39	   2950	  0.17%
 40	   3465	  0.20%
 41	   3637	  0.21%
 42	   4565	  0.26%
 43	   7051	  0.40%
 44	   7569	  0.43%
 45	  10891	  0.62%
 46	  14397	  0.83%
 47	  11184	  0.64%
 48	  28108	  1.61%
 49	  29077	  1.67%
 50	1597509	 91.65%
1743059 reads passed initial QC


criterion=sequence-density
sequence-density=89.74
sequence-density-rank=1
fanout-score=19.17
fanout-score-rank=2
prefix-density=90.90
prefix-fanout=18.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC


criterion=fanout-score
sequence-density=3.75
sequence-density-rank=3
fanout-score=77.41
fanout-score-rank=1
prefix-density=91.23
prefix-fanout=3.2
sequence=GAATTCTCGGGGGCCAAGGAACT
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 SRR5031099 -
Input file:	STDIN
trimmed:	SRR5031099-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 07:24:10 2020 >> started

Wed Mar  4 07:24:12 2020 >> done (2.218s)
1704324 reads processed; of these:
 104524 ( 6.13%) short reads filtered out after trimming by size control
  15873 ( 0.93%) empty reads filtered out after trimming by size control
1583927 (92.94%) reads available; of these:
1534534 (96.88%) trimmed reads available after processing
  49393 ( 3.12%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   9536	  0.60%
 19	  16814	  1.06%
 20	 103775	  6.55%
 21	 191973	 12.12%
 22	 544963	 34.41%
 23	 241668	 15.26%
 24	 112971	  7.13%
 25	  33249	  2.10%
 26	  15716	  0.99%
 27	  11490	  0.73%
 28	  12521	  0.79%
 29	   9440	  0.60%
 30	  13324	  0.84%
 31	  17438	  1.10%
 32	  16833	  1.06%
 33	  55979	  3.53%
 34	  19357	  1.22%
 35	  15448	  0.98%
 36	  17645	  1.11%
 37	   7382	  0.47%
 38	   8184	  0.52%
 39	   6925	  0.44%
 40	   9438	  0.60%
 41	  10639	  0.67%
 42	  11270	  0.71%
 43	   7436	  0.47%
 44	   5464	  0.34%
 45	   7178	  0.45%
 46	   4975	  0.31%
 47	   3634	  0.23%
 48	    560	  0.04%
 49	   1090	  0.07%
 50	  39612	  2.50%


criterion=sequence-density
sequence-density=9.52
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=12
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=0.49
sequence-density-rank=36
fanout-score=32.76
fanout-score-rank=1
prefix-density=15.80
prefix-fanout=1.0
sequence=CTGAGCTTGGCA
                                 Started job on |	Mar 04 07:24:44
                             Started mapping on |	Mar 04 07:24:45
                                    Finished on |	Mar 04 07:25:09
       Mapping speed, Million of reads per hour |	243.40

                          Number of input reads |	1622662
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	901381
                        Uniquely mapped reads % |	55.55%
                          Average mapped length |	23.77
                       Number of splices: Total |	3338
            Number of splices: Annotated (sjdb) |	1097
                       Number of splices: GT/AG |	3275
                       Number of splices: GC/AG |	36
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	27
                      Mismatch rate per base, % |	0.32%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.66
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	546504
             % of reads mapped to multiple loci |	33.68%
        Number of reads mapped to too many loci |	27753
             % of reads mapped to too many loci |	1.71%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.37%
                     % of reads unmapped: other |	0.69%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	174777	174777	174777
N_multimapping	546504	546504	546504
N_noFeature	44809	53896	548265
N_ambiguous	530901	211862	5592
UnstrandedReadsAssigned:325671 PositiveStrandReadsAssigned:635623 NegativeStrandReadsAssigned:347524
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031099 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: SRR5031099-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,622,662 reads, 453,834 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,113 rounds

 109283 SRR5031099.ke.tsv
  52636 SRR5031099.se.tsv
 161919 total
==> SRR5031099.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

==> SRR5031099.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031099 completed mapping pipeline successfully
