Starting /dee2/code/volunteer_pipeline.sh SRR5031084
    current disk space = 160499433472
    free memory = 73932252 
SRR5031084 SRAfilesize
028ff4cb33b964df0192e5d44b053d2d  SRR5031084.sra
SRR5031084.sra file validated
SRR5031084 is single end
SRR5031084 is conventional basespace
SRR5031084 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031084_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	52
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.87525	31.0	31.0	34.0	30.0	34.0
2	32.37125	33.0	31.0	34.0	31.0	34.0
3	32.35625	33.0	31.0	34.0	31.0	34.0
4	36.13075	37.0	35.0	37.0	35.0	37.0
5	36.11525	37.0	35.0	37.0	35.0	37.0
6	36.0085	37.0	35.0	37.0	35.0	37.0
7	35.79025	37.0	35.0	37.0	35.0	37.0
8	35.657	37.0	35.0	37.0	33.0	37.0
9	36.9195	39.0	37.0	39.0	33.0	39.0
10	36.65875	39.0	37.0	39.0	32.0	39.0
11	37.412	39.0	37.0	39.0	34.0	39.0
12	37.6845	39.0	37.0	39.0	35.0	39.0
13	37.469	39.0	37.0	39.0	35.0	39.0
14	38.265	40.0	38.0	41.0	33.0	41.0
15	36.36175	39.0	36.0	41.0	27.0	41.0
16	36.8045	38.0	36.0	40.0	31.0	41.0
17	36.856	39.0	36.0	40.0	31.0	41.0
18	38.176	39.0	37.0	41.0	34.0	41.0
19	38.5945	40.0	38.0	41.0	35.0	41.0
20	38.31775	40.0	38.0	41.0	34.0	41.0
21	38.56025	40.0	38.0	41.0	35.0	41.0
22	37.06425	39.0	36.0	40.0	31.0	41.0
23	37.70075	39.0	37.0	40.0	33.0	41.0
24	36.91125	39.0	36.0	40.0	30.0	41.0
25	37.815	40.0	37.0	41.0	32.0	41.0
26	37.7585	39.0	37.0	41.0	33.0	41.0
27	38.10275	40.0	38.0	41.0	34.0	41.0
28	38.4365	40.0	38.0	41.0	34.0	41.0
29	38.315	40.0	38.0	41.0	34.0	41.0
30	38.8125	40.0	38.0	41.0	35.0	41.0
31	38.75625	40.0	38.0	41.0	35.0	41.0
32	38.7985	40.0	38.0	41.0	35.0	41.0
33	38.7995	40.0	38.0	41.0	35.0	41.0
34	38.16175	40.0	38.0	41.0	33.0	41.0
35	37.321	40.0	36.0	41.0	30.0	41.0
36	32.66225	35.0	30.0	40.0	22.0	41.0
37	34.60575	37.0	33.0	38.0	26.0	40.0
38	35.9325	38.0	35.0	39.0	30.0	40.0
39	36.472	38.0	35.0	40.0	31.0	40.0
40	37.0185	39.0	37.0	40.0	31.0	41.0
41	37.39675	39.0	37.0	40.0	32.0	41.0
42	37.1935	39.0	37.0	40.0	31.0	41.0
43	37.21975	40.0	37.0	41.0	32.0	41.0
44	36.26425	38.0	35.0	40.0	30.0	41.0
45	36.2915	39.0	35.0	40.0	30.0	41.0
46	36.607	39.0	36.0	40.0	30.0	41.0
47	35.55825	38.0	34.0	40.0	28.0	41.0
48	36.68325	39.0	36.0	40.0	31.0	41.0
49	36.7875	40.0	36.0	41.0	31.0	41.0
50	34.92675	38.0	34.0	40.0	28.0	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	0.0
17	0.0
18	3.0
19	3.0
20	6.0
21	7.0
22	8.0
23	10.0
24	9.0
25	10.0
26	10.0
27	14.0
28	27.0
29	25.0
30	41.0
31	77.0
32	104.0
33	152.0
34	204.0
35	286.0
36	538.0
37	757.0
38	1095.0
39	612.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.6499999999999995	26.575	51.449999999999996	14.325
2	21.65206508135169	31.53942428035044	17.04630788485607	29.7622027534418
3	25.3	16.55	21.349999999999998	36.8
4	33.85	30.625000000000004	12.55	22.975
5	18.4	39.300000000000004	29.875	12.425
6	27.05	15.875	41.8	15.275
7	14.45	21.325	18.825	45.4
8	20.3	32.0	16.55	31.15
9	25.15	35.099999999999994	24.625	15.125
10	20.625	16.45	31.25	31.674999999999997
11	33.85	10.6	15.85	39.7
12	13.200000000000001	18.224999999999998	34.2	34.375
13	28.575	15.725	35.075	20.625
14	31.624999999999996	31.6	17.9	18.875
15	36.85	16.475	27.0	19.675
16	18.0	18.7	20.875	42.425000000000004
17	29.225	19.575	36.525	14.674999999999999
18	28.349999999999998	13.775	33.15	24.725
19	37.6	13.025	34.0	15.375
20	49.325	12.825000000000001	24.099999999999998	13.750000000000002
21	23.3	22.650000000000002	24.325	29.725
22	32.574999999999996	9.925	47.675	9.825000000000001
23	25.15	11.75	48.325	14.774999999999999
24	54.05	11.025	26.724999999999998	8.200000000000001
25	52.55	24.925	14.774999999999999	7.75
26	27.650000000000002	48.8	12.75	10.8
27	14.45	49.975	24.7	10.875
28	9.6	24.15	51.300000000000004	14.95
29	11.05	10.424999999999999	58.925000000000004	19.6
30	8.875	5.7	37.475	47.949999999999996
31	12.675	3.85	49.375	34.1
32	28.499999999999996	4.15	21.85	45.5
33	57.62500000000001	7.925	12.425	22.025
34	65.375	6.0249999999999995	15.475	13.125
35	68.825	5.5	17.424999999999997	8.25
36	46.225	5.800000000000001	36.625	11.35
37	47.925000000000004	9.425	19.225	23.425
38	23.25	15.825	10.65	50.275000000000006
39	13.825000000000001	24.925	9.025	52.225
40	13.775	51.0	10.05	25.174999999999997
41	24.025	51.300000000000004	6.9750000000000005	17.7
42	50.824999999999996	30.5	9.9	8.774999999999999
43	53.075	30.75	6.2	9.975000000000001
44	31.2	51.0	5.1499999999999995	12.65
45	17.65	52.800000000000004	11.5	18.05
46	12.125	26.0	17.025000000000002	44.85
47	6.65	13.875000000000002	41.375	38.1
48	9.2	11.875	20.25	58.675
49	11.375	20.4	11.700000000000001	56.525000000000006
50	17.525	38.675	10.9	32.9
>>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	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	0.0
28	0.0
29	0.5
30	1.0
31	2.0
32	3.0
33	4.0
34	5.0
35	7.0
36	9.0
37	17.0
38	25.0
39	23.5
40	22.0
41	26.5
42	31.0
43	62.5
44	94.0
45	120.0
46	146.0
47	282.5
48	419.0
49	488.5
50	558.0
51	757.5
52	957.0
53	708.0
54	459.0
55	519.5
56	580.0
57	451.5
58	323.0
59	210.5
60	98.0
61	71.0
62	44.0
63	75.5
64	107.0
65	77.0
66	47.0
67	34.0
68	21.0
69	17.0
70	13.0
71	21.0
72	29.0
73	17.0
74	5.0
75	3.0
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	0.0
2	0.125
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	41.199999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.88106796116504	31.674999999999997
2	10.072815533980583	8.3
3	3.8834951456310676	4.8
4	2.1237864077669903	3.5000000000000004
5	1.6383495145631068	3.375
6	0.9101941747572815	2.25
7	0.30339805825242716	0.8750000000000001
8	0.6674757281553397	2.1999999999999997
9	0.12135922330097086	0.44999999999999996
>10	2.8519417475728157	18.9
>50	0.3640776699029126	11.725
>100	0.1820388349514563	11.95
>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	167	4.175	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	166	4.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	145	3.6249999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	99	2.475	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	83	2.075	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	83	2.075	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	76	1.9	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	65	1.625	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	63	1.575	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAC	34	0.8500000000000001	RNA PCR Primer, Index 5 (100% over 35bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	31	0.775	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	18	0.44999999999999996	RNA PCR Primer, Index 1 (96% over 30bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 33bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	12	0.3	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	12	0.3	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 31bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACCCTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGC	8	0.2	RNA PCR Primer, Index 8 (100% over 50bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAACAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (96% over 30bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	8	0.2	No Hit
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTTGTCCCGGCCTGTATTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	6	0.15	RNA PCR Primer, Index 1 (100% over 34bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGCCGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	6	0.15	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTC	6	0.15	RNA PCR Primer, Index 8 (100% over 44bp)
TCCAGCATCAGTGATTTTGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ATCATGATGGGCTCCTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTATAAAGCAATGAGACTGATTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGACCCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCCGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	5	0.125	No Hit
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATGTAGTATGGTCCACATCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	5	0.125	No Hit
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCCTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGCCTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGAACTGAATTCCATAGGCTGTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGACTCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>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	0.3	0.0	0.0	0.0
2	0.0	0.3	0.0	0.0	0.0
3	0.0	0.4	0.0	0.0	0.0
4	0.0	0.425	0.0	0.0	0.0
5	0.0	0.5	0.0	0.0	0.0
6	0.0	0.5	0.0	0.0	0.0
7	0.0	0.8	0.0	0.0	0.0
8	0.0	0.95	0.0	0.0	0.0
9	0.0	0.975	0.0	0.0	0.0
10	0.0	1.1	0.0	0.0	0.0
11	0.0	1.225	0.0	0.0	0.0
12	0.0	1.45	0.0	0.0	0.0
13	0.0	1.575	0.0	0.0	0.0
14	0.0	1.725	0.0	0.0	0.0
15	0.0	2.05	0.0	0.0	0.0
16	0.0	3.375	0.0	0.0	0.0
17	0.0	3.875	0.0	0.0	0.0
18	0.0	4.9	0.0	0.0	0.0
19	0.0	5.275	0.0	0.0	0.0
20	0.0	6.125	0.0	0.0	0.0
21	0.0	10.675	0.0	0.0	0.0
22	0.0	23.075	0.0	0.0	0.0
23	0.0	55.725	0.0	0.0	0.0
24	0.0	69.95	0.0	0.0	0.0
25	0.0	75.8	0.0	0.0	0.0
26	0.0	77.275	0.0	0.0	0.0
27	0.0	77.975	0.0	0.0	0.0
28	0.0	78.575	0.0	0.0	0.0
29	0.0	79.075	0.0	0.0	0.0
30	0.0	79.425	0.0	0.0	0.0
31	0.0	80.275	0.0	0.0	0.0
32	0.0	81.275	0.0	0.0	0.0
33	0.0	81.8	0.0	0.0	0.0
34	0.0	85.425	0.0	0.0	0.0
35	0.0	86.625	0.0	0.0	0.0
36	0.0	87.525	0.0	0.0	0.0
37	0.0	88.15	0.0	0.0	0.0
38	0.0	88.425	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGGTAG	20	6.952051E-4	44.000004	2
GTTTGGA	20	6.952051E-4	44.000004	20
AATTTGT	20	6.952051E-4	44.000004	16
CCTGTAG	20	6.952051E-4	44.000004	4
GTGAGTT	20	6.952051E-4	44.000004	18
ACATTCA	40	5.315087E-9	44.000004	2
GAGTTGG	20	6.952051E-4	44.000004	20
GTCCCGG	20	6.952051E-4	44.000004	11
GCTGTCG	40	5.315087E-9	44.000004	11
CGAATTT	20	6.952051E-4	44.000004	14
CCCTGTA	20	6.952051E-4	44.000004	3
ACCCTGT	20	6.952051E-4	44.000004	2
GAATTTG	20	6.952051E-4	44.000004	15
GCTTGGC	20	6.952051E-4	44.000004	15
TGAGGTA	20	6.952051E-4	44.000004	1
TACCCTG	20	6.952051E-4	44.000004	1
AGGTAGT	20	6.952051E-4	44.000004	3
CTGTCGG	40	5.315087E-9	44.000004	12
TGAGTTG	20	6.952051E-4	44.000004	19
CTGTAGA	20	6.952051E-4	44.000004	5
>>END_MODULE
Read 132439 spots for SRR5031084.sra
Written 132439 spots for SRR5031084.sra
Read 132439 spots for SRR5031084.sra
Written 132439 spots for SRR5031084.sra
Read 132439 spots for SRR5031084.sra
Written 132439 spots for SRR5031084.sra
Read 132439 spots for SRR5031084.sra
Written 132439 spots for SRR5031084.sra
Read 132439 spots for SRR5031084.sra
Written 132439 spots for SRR5031084.sra
Read 132439 spots for SRR5031084.sra
Written 132439 spots for SRR5031084.sra
Read 132439 spots for SRR5031084.sra
Written 132439 spots for SRR5031084.sra
Read 132439 spots for SRR5031084.sra
Written 132439 spots for SRR5031084.sra
Read 132439 spots for SRR5031084.sra
Written 132439 spots for SRR5031084.sra
Read 132439 spots for SRR5031084.sra
Written 132439 spots for SRR5031084.sra
Read 132450 spots for SRR5031084.sra
Written 132450 spots for SRR5031084.sra
Read 132439 spots for SRR5031084.sra
Written 132439 spots for SRR5031084.sra
SRR ids: ['SRR5031084.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_op8rv32y
SRR5031084.sra spots: 1589279
blocks: [[1, 132439], [132440, 264878], [264879, 397317], [397318, 529756], [529757, 662195], [662196, 794634], [794635, 927073], [927074, 1059512], [1059513, 1191951], [1191952, 1324390], [1324391, 1456829], [1456830, 1589279]]
SRR5031084 file size 274396
SRR5031084 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031084 SRR5031084_1.fastq
Input file:	SRR5031084_1.fastq
trimmed:	SRR5031084-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 07:20:20 2020 >> started

Wed Mar  4 07:20:21 2020 >> done (1.100s)
1589279 reads processed; of these:
    119 ( 0.01%) short reads filtered out after trimming by size control
      4 ( 0.00%) empty reads filtered out after trimming by size control
1589156 (99.99%) reads available; of these:
 134789 ( 8.48%) trimmed reads available after processing
1454367 (91.52%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     41	  0.00%
 19	     77	  0.00%
 20	    125	  0.01%
 21	    141	  0.01%
 22	    288	  0.02%
 23	    300	  0.02%
 24	    306	  0.02%
 25	    440	  0.03%
 26	    290	  0.02%
 27	    373	  0.02%
 28	    452	  0.03%
 29	    725	  0.05%
 30	    464	  0.03%
 31	    539	  0.03%
 32	    741	  0.05%
 33	   1405	  0.09%
 34	   1780	  0.11%
 35	   5046	  0.32%
 36	   2751	  0.17%
 37	   2504	  0.16%
 38	   2313	  0.15%
 39	   2501	  0.16%
 40	   2817	  0.18%
 41	   3215	  0.20%
 42	   3784	  0.24%
 43	   6142	  0.39%
 44	   6288	  0.40%
 45	   9266	  0.58%
 46	  13026	  0.82%
 47	   9822	  0.62%
 48	  28600	  1.80%
 49	  28227	  1.78%
 50	1454367	 91.52%
1589156 reads passed initial QC


criterion=sequence-density
sequence-density=89.75
sequence-density-rank=1
fanout-score=19.40
fanout-score-rank=3
prefix-density=91.31
prefix-fanout=19.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC


criterion=fanout-score
sequence-density=3.96
sequence-density-rank=3
fanout-score=72.30
fanout-score-rank=1
prefix-density=91.66
prefix-fanout=3.1
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC -o SRR5031084 -
Input file:	STDIN
trimmed:	SRR5031084-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC
-- 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 07:20:32 2020 >> started

Wed Mar  4 07:20:35 2020 >> done (2.333s)
1553842 reads processed; of these:
  83198 ( 5.35%) short reads filtered out after trimming by size control
   6447 ( 0.41%) empty reads filtered out after trimming by size control
1464197 (94.23%) reads available; of these:
1417146 (96.79%) trimmed reads available after processing
  47051 ( 3.21%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   8158	  0.56%
 19	  16313	  1.11%
 20	 101821	  6.95%
 21	 188016	 12.84%
 22	 517830	 35.37%
 23	 225322	 15.39%
 24	  96882	  6.62%
 25	  26228	  1.79%
 26	  12983	  0.89%
 27	  10357	  0.71%
 28	  10986	  0.75%
 29	   8443	  0.58%
 30	  12389	  0.85%
 31	  14882	  1.02%
 32	  15384	  1.05%
 33	  51300	  3.50%
 34	  15264	  1.04%
 35	  11703	  0.80%
 36	  12769	  0.87%
 37	   5998	  0.41%
 38	   7077	  0.48%
 39	   5689	  0.39%
 40	   8434	  0.58%
 41	   8987	  0.61%
 42	   9195	  0.63%
 43	   6001	  0.41%
 44	   4398	  0.30%
 45	   5978	  0.41%
 46	   4290	  0.29%
 47	   3028	  0.21%
 48	    529	  0.04%
 49	    883	  0.06%
 50	  36680	  2.51%


criterion=sequence-density
sequence-density=11.04
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=10
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=2.20
sequence-density-rank=5
fanout-score=18.77
fanout-score-rank=1
prefix-density=2.24
prefix-fanout=18.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGC
                                 Started job on |	Mar 04 07:21:09
                             Started mapping on |	Mar 04 07:21:10
                                    Finished on |	Mar 04 07:21:35
       Mapping speed, Million of reads per hour |	215.93

                          Number of input reads |	1499511
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	817413
                        Uniquely mapped reads % |	54.51%
                          Average mapped length |	23.50
                       Number of splices: Total |	2646
            Number of splices: Annotated (sjdb) |	782
                       Number of splices: GT/AG |	2601
                       Number of splices: GC/AG |	29
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	16
                      Mismatch rate per base, % |	0.30%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.68
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	519169
             % of reads mapped to multiple loci |	34.62%
        Number of reads mapped to too many loci |	24281
             % of reads mapped to too many loci |	1.62%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.56%
                     % of reads unmapped: other |	0.69%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	162929	162929	162929
N_multimapping	519169	519169	519169
N_noFeature	38163	45707	504289
N_ambiguous	480672	196480	5154
UnstrandedReadsAssigned:298578 PositiveStrandReadsAssigned:575226 NegativeStrandReadsAssigned:307970
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031084 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: SRR5031084-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,499,511 reads, 411,695 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,077 rounds

 109283 SRR5031084.ke.tsv
  52636 SRR5031084.se.tsv
 161919 total
==> SRR5031084.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

==> SRR5031084.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031084 completed mapping pipeline successfully
