Starting /dee2/code/volunteer_pipeline.sh SRR5030896
    current disk space = 160665452544
    free memory = 73947732 
SRR5030896 SRAfilesize
ae9df83bd173d282b67e5f1e48a883f0  SRR5030896.sra
SRR5030896.sra file validated
SRR5030896 is single end
SRR5030896 is conventional basespace
SRR5030896 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030896_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	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.3795	33.0	31.0	34.0	31.0	34.0
2	32.736	34.0	31.0	34.0	31.0	34.0
3	32.78475	34.0	31.0	34.0	31.0	34.0
4	36.218	37.0	37.0	37.0	35.0	37.0
5	36.266	37.0	37.0	37.0	35.0	37.0
6	35.98625	37.0	35.0	37.0	35.0	37.0
7	36.14125	37.0	35.0	37.0	35.0	37.0
8	36.167	37.0	36.0	37.0	35.0	37.0
9	37.94725	39.0	38.0	39.0	35.0	39.0
10	37.97725	39.0	38.0	39.0	35.0	39.0
11	37.843	39.0	38.0	39.0	35.0	39.0
12	37.924	39.0	38.0	39.0	35.0	39.0
13	37.83925	39.0	38.0	39.0	35.0	39.0
14	39.29125	41.0	39.0	41.0	36.0	41.0
15	39.2965	41.0	39.0	41.0	36.0	41.0
16	39.24425	40.0	39.0	41.0	36.0	41.0
17	39.36425	41.0	39.0	41.0	36.0	41.0
18	39.3375	41.0	39.0	41.0	36.0	41.0
19	39.1435	40.0	39.0	41.0	36.0	41.0
20	39.173	40.0	39.0	41.0	36.0	41.0
21	39.196	40.0	39.0	41.0	36.0	41.0
22	39.27725	41.0	39.0	41.0	36.0	41.0
23	39.15375	40.0	39.0	41.0	36.0	41.0
24	38.52325	40.0	38.0	41.0	34.0	41.0
25	38.85675	40.0	38.0	41.0	35.0	41.0
26	38.79975	40.0	38.0	41.0	35.0	41.0
27	38.78475	40.0	38.0	41.0	35.0	41.0
28	38.74975	40.0	38.0	41.0	35.0	41.0
29	38.7105	40.0	38.0	41.0	35.0	41.0
30	38.40075	40.0	38.0	41.0	34.0	41.0
31	38.736	40.0	38.0	41.0	35.0	41.0
32	38.89475	40.0	38.0	41.0	35.0	41.0
33	37.34925	40.0	37.0	41.0	31.0	41.0
34	36.675	40.0	37.0	41.0	30.0	41.0
35	32.7215	38.0	31.0	40.0	9.0	41.0
36	29.754	37.0	21.0	40.0	8.0	41.0
37	29.86675	37.0	23.0	39.0	6.0	41.0
38	32.32075	37.0	30.0	40.0	15.0	41.0
39	31.75375	37.0	30.0	40.0	8.0	41.0
40	32.5895	37.0	32.0	40.0	2.0	41.0
41	30.36875	36.0	26.0	40.0	2.0	41.0
42	31.749	37.0	30.0	40.0	2.0	41.0
43	30.475	37.0	26.0	40.0	2.0	41.0
44	31.3485	37.0	30.0	40.0	2.0	41.0
45	29.14125	37.0	24.0	40.0	2.0	41.0
46	27.087	35.0	9.0	39.0	2.0	41.0
47	27.1775	34.0	13.0	39.0	2.0	41.0
48	27.8555	35.0	16.0	39.0	2.0	41.0
49	26.18875	35.0	2.0	40.0	2.0	41.0
50	22.682	30.0	2.0	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
12	2.0
13	0.0
14	2.0
15	0.0
16	0.0
17	1.0
18	2.0
19	2.0
20	12.0
21	8.0
22	22.0
23	37.0
24	39.0
25	61.0
26	94.0
27	158.0
28	72.0
29	103.0
30	153.0
31	145.0
32	188.0
33	175.0
34	231.0
35	245.0
36	313.0
37	476.0
38	641.0
39	818.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.315394242803505	25.33166458072591	44.13016270337922	18.222778473091363
2	24.05	27.900000000000002	20.599999999999998	27.450000000000003
3	24.6	19.650000000000002	21.55	34.2
4	30.225	27.650000000000002	15.725	26.400000000000002
5	21.95	38.625	26.200000000000003	13.225000000000001
6	30.075000000000003	17.224999999999998	37.6	15.1
7	20.525	19.85	24.9	34.725
8	25.575	31.95	16.05	26.424999999999997
9	20.575	34.775	30.2	14.45
10	24.825	19.25	29.9	26.025
11	33.800000000000004	15.475	15.2	35.525
12	17.349999999999998	20.875	30.0	31.775
13	26.825	21.099999999999998	32.5	19.575
14	27.500000000000004	30.625000000000004	23.325000000000003	18.55
15	31.35	24.525	25.85	18.275
16	19.5	21.55	22.425	36.525
17	25.074999999999996	23.0	35.449999999999996	16.475
18	24.325	18.8	31.2	25.674999999999997
19	33.95	15.225	31.825	19.0
20	40.25	16.55	28.449999999999996	14.75
21	25.525	22.1	26.150000000000002	26.224999999999998
22	29.25	13.925	43.5	13.325000000000001
23	24.675	16.375	41.9	17.05
24	47.55	15.575	24.65	12.225
25	46.949999999999996	22.25	17.05	13.750000000000002
26	28.199999999999996	40.75	15.024999999999999	16.025
27	17.1	44.3	21.6	17.0
28	14.000000000000002	26.775	42.85	16.375
29	12.525	15.8	54.425000000000004	17.25
30	12.25	9.2	34.8	43.75
31	15.75	8.05	45.275	30.925000000000004
32	27.675	7.5	23.875	40.949999999999996
33	47.4	11.4	15.475	25.724999999999998
34	53.849999999999994	7.8	19.975	18.375
35	56.474999999999994	8.625	20.05	14.85
36	59.550000000000004	11.175	15.525	13.750000000000002
37	37.2	14.325	23.200000000000003	25.275
38	26.775	16.25	14.6	42.375
39	19.475	24.825	12.35	43.35
40	18.2	43.125	13.700000000000001	24.975
41	25.924999999999997	42.5	13.900000000000002	17.675
42	45.1	29.925	13.950000000000001	11.025
43	44.025	32.475	11.65	11.85
44	29.5	45.4	9.75	15.35
45	21.275	43.15	12.525	23.05
46	14.575	29.575000000000003	24.6	31.25
47	12.049999999999999	17.65	32.875	37.425000000000004
48	14.000000000000002	13.350000000000001	23.35	49.3
49	15.15	22.95	16.150000000000002	45.75
50	29.925	22.875	12.675	34.525
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	1.0
1	0.5
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	1.5
26	3.0
27	2.0
28	1.0
29	4.0
30	7.0
31	7.5
32	8.0
33	18.5
34	29.0
35	54.0
36	79.0
37	102.0
38	125.0
39	110.5
40	96.0
41	92.5
42	89.0
43	112.5
44	136.0
45	168.0
46	200.0
47	233.0
48	266.0
49	360.0
50	454.0
51	597.5
52	741.0
53	635.5
54	530.0
55	454.5
56	379.0
57	344.0
58	309.0
59	223.5
60	138.0
61	110.0
62	82.0
63	128.0
64	174.0
65	109.5
66	45.0
67	33.5
68	22.0
69	21.0
70	20.0
71	32.5
72	45.0
73	26.0
74	7.0
75	6.5
76	6.0
77	5.5
78	5.0
79	3.0
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	0.125
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	warn
#Total Deduplicated Percentage	51.9
#Duplication Level	Percentage of deduplicated	Percentage of total
1	79.86512524084779	41.449999999999996
2	9.248554913294797	9.6
3	3.1791907514450863	4.95
4	1.6377649325626205	3.4000000000000004
5	1.1560693641618496	3.0
6	0.674373795761079	2.1
7	0.674373795761079	2.45
8	0.4335260115606936	1.7999999999999998
9	0.3371868978805395	1.575
>10	2.697495183044316	24.775
>50	0.04816955684007707	2.125
>100	0.04816955684007707	2.775
>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	111	2.775	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	85	2.125	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	45	1.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	30	0.75	No Hit
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	27	0.675	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (96% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	22	0.5499999999999999	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	22	0.5499999999999999	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGC	20	0.5	RNA PCR Primer, Index 45 (100% over 50bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	20	0.5	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	20	0.5	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	18	0.44999999999999996	No Hit
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	18	0.44999999999999996	No Hit
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	17	0.42500000000000004	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	17	0.42500000000000004	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	16	0.4	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (96% over 28bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	15	0.375	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTC	15	0.375	RNA PCR Primer, Index 45 (100% over 44bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	13	0.325	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	13	0.325	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	13	0.325	RNA PCR Primer, Index 5 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	13	0.325	RNA PCR Primer, Index 1 (96% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	12	0.3	RNA PCR Primer, Index 1 (96% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	12	0.3	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	11	0.27499999999999997	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	11	0.27499999999999997	No Hit
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	11	0.27499999999999997	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	10	0.25	No Hit
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	10	0.25	RNA PCR Primer, Index 3 (100% over 34bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	10	0.25	RNA PCR Primer, Index 1 (96% over 29bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	10	0.25	No Hit
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	10	0.25	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	9	0.22499999999999998	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	9	0.22499999999999998	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	9	0.22499999999999998	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TACCATGATGATAACATAGTTCAGCAGACTTAACTCTGATGAACAATCAT	8	0.2	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	8	0.2	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 32bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	7	0.17500000000000002	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	7	0.17500000000000002	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATTGTCTGCTGGGTTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	7	0.17500000000000002	No Hit
GAGCAATGATGACCCCAACATGCCATCTGAGTGGCTTTGCTGAAATCCAG	7	0.17500000000000002	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	6	0.15	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	6	0.15	RNA PCR Primer, Index 1 (95% over 23bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGC	6	0.15	RNA PCR Primer, Index 1 (96% over 29bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	5	0.125	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	5	0.125	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAATTCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGTGCCAAGGAACTCCAG	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCTA	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CCCCTATGATGAGGACCTTTTCACAGACCTGTACTGATATATCTGTGAGG	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	5	0.125	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
AGACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
>>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	0.6	0.0	0.0	0.0
2	0.0	0.6	0.0	0.0	0.0
3	0.0	0.675	0.0	0.0	0.0
4	0.0	0.725	0.0	0.0	0.0
5	0.0	0.8	0.0	0.0	0.0
6	0.0	0.825	0.0	0.0	0.0
7	0.0	1.25	0.0	0.0	0.0
8	0.0	1.5	0.0	0.0	0.0
9	0.0	1.575	0.0	0.0	0.0
10	0.0	1.65	0.0	0.0	0.0
11	0.0	1.7	0.0	0.0	0.0
12	0.0	1.875	0.0	0.0	0.0
13	0.0	2.0	0.0	0.0	0.0
14	0.0	2.225	0.0	0.0	0.0
15	0.0	2.5	0.0	0.0	0.0
16	0.0	3.075	0.0	0.0	0.0
17	0.0	3.65	0.0	0.0	0.0
18	0.0	4.45	0.0	0.0	0.0
19	0.0	5.15	0.0	0.0	0.0
20	0.0	6.125	0.0	0.0	0.0
21	0.0	10.575	0.0	0.0	0.0
22	0.0	18.55	0.0	0.0	0.0
23	0.0	43.55	0.0	0.0	0.0
24	0.0	55.5	0.0	0.0	0.0
25	0.0	60.95	0.0	0.0	0.0
26	0.0	62.625	0.0	0.0	0.0
27	0.0	63.325	0.0	0.0	0.0
28	0.0	63.775	0.0	0.0	0.0
29	0.0	64.025	0.0	0.0	0.0
30	0.0	64.35	0.0	0.0	0.0
31	0.0	65.05	0.0	0.0	0.0
32	0.0	65.625	0.0	0.0	0.0
33	0.0	66.375	0.0	0.0	0.0
34	0.0	69.675	0.0	0.0	0.0
35	0.0	70.6	0.0	0.0	0.0
36	0.0	71.3	0.0	0.0	0.0
37	0.0	72.3	0.0	0.0	0.0
38	0.0	72.65	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	20	6.952051E-4	44.000004	8
ACGCTGT	20	6.952051E-4	44.000004	9
TTCAACG	20	6.952051E-4	44.000004	5
TCGGTGA	20	6.952051E-4	44.000004	15
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
ACATTCA	20	6.952051E-4	44.000004	2
AACTCCG	20	6.952051E-4	44.000004	44
GCTGTCG	20	6.952051E-4	44.000004	11
GGCCAGG	20	6.952051E-4	44.000004	36
CTGTCGG	20	6.952051E-4	44.000004	12
ATTCAAC	20	6.952051E-4	44.000004	4
GTCGGTG	20	6.952051E-4	44.000004	14
AACATTC	20	6.952051E-4	44.000004	1
TGTCGGT	20	6.952051E-4	44.000004	13
CAACGCT	20	6.952051E-4	44.000004	7
CGCTGTC	20	6.952051E-4	44.000004	10
AAGTAAT	30	1.9515464E-6	44.0	4
TCAAGTA	30	1.9515464E-6	44.0	2
ATCCAGG	30	1.9515464E-6	44.0	9
>>END_MODULE
Read 341042 spots for SRR5030896.sra
Written 341042 spots for SRR5030896.sra
Read 341042 spots for SRR5030896.sra
Written 341042 spots for SRR5030896.sra
Read 341042 spots for SRR5030896.sra
Written 341042 spots for SRR5030896.sra
Read 341042 spots for SRR5030896.sra
Written 341042 spots for SRR5030896.sra
Read 341042 spots for SRR5030896.sra
Written 341042 spots for SRR5030896.sra
Read 341042 spots for SRR5030896.sra
Written 341042 spots for SRR5030896.sra
Read 341042 spots for SRR5030896.sra
Written 341042 spots for SRR5030896.sra
Read 341042 spots for SRR5030896.sra
Written 341042 spots for SRR5030896.sra
Read 341042 spots for SRR5030896.sra
Written 341042 spots for SRR5030896.sra
Read 341042 spots for SRR5030896.sra
Written 341042 spots for SRR5030896.sra
Read 341042 spots for SRR5030896.sra
Written 341042 spots for SRR5030896.sra
Read 341046 spots for SRR5030896.sra
Written 341046 spots for SRR5030896.sra
SRR ids: ['SRR5030896.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_iqtuprpz
SRR5030896.sra spots: 4092508
blocks: [[1, 341042], [341043, 682084], [682085, 1023126], [1023127, 1364168], [1364169, 1705210], [1705211, 2046252], [2046253, 2387294], [2387295, 2728336], [2728337, 3069378], [3069379, 3410420], [3410421, 3751462], [3751463, 4092508]]
SRR5030896 file size 708249
SRR5030896 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030896 SRR5030896_1.fastq
Input file:	SRR5030896_1.fastq
trimmed:	SRR5030896-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 06:39:33 2020 >> started

Wed Mar  4 06:39:37 2020 >> done (3.946s)
4092508 reads processed; of these:
    187 ( 0.00%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
4092312 (100.00%) reads available; of these:
 467980 (11.44%) trimmed reads available after processing
3624332 (88.56%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     69	  0.00%
 19	     81	  0.00%
 20	    138	  0.00%
 21	    199	  0.00%
 22	    368	  0.01%
 23	    477	  0.01%
 24	    577	  0.01%
 25	    752	  0.02%
 26	    616	  0.02%
 27	    834	  0.02%
 28	   1106	  0.03%
 29	   1598	  0.04%
 30	   1193	  0.03%
 31	   1669	  0.04%
 32	   4176	  0.10%
 33	  14120	  0.35%
 34	  32106	  0.78%
 35	   7688	  0.19%
 36	   8416	  0.21%
 37	   4669	  0.11%
 38	   9198	  0.22%
 39	   8606	  0.21%
 40	  16393	  0.40%
 41	   9195	  0.22%
 42	  22162	  0.54%
 43	  10486	  0.26%
 44	  45693	  1.12%
 45	  26672	  0.65%
 46	  26635	  0.65%
 47	  28091	  0.69%
 48	  83359	  2.04%
 49	 100638	  2.46%
 50	3624332	 88.56%
4092312 reads passed initial QC


criterion=sequence-density
sequence-density=72.43
sequence-density-rank=1
fanout-score=21.38
fanout-score-rank=2
prefix-density=75.02
prefix-fanout=20.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC


criterion=fanout-score
sequence-density=3.27
sequence-density-rank=3
fanout-score=69.98
fanout-score-rank=1
prefix-density=74.57
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC -o SRR5030896 -
Input file:	STDIN
trimmed:	SRR5030896-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC
-- 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 06:39:57 2020 >> started

Wed Mar  4 06:40:06 2020 >> done (8.663s)
3980194 reads processed; of these:
 181953 ( 4.57%) short reads filtered out after trimming by size control
  24542 ( 0.62%) empty reads filtered out after trimming by size control
3773699 (94.81%) reads available; of these:
3053657 (80.92%) trimmed reads available after processing
 720042 (19.08%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  23159	  0.61%
 19	  34342	  0.91%
 20	 168167	  4.46%
 21	 364447	  9.66%
 22	 980442	 25.98%
 23	 462769	 12.26%
 24	 212285	  5.63%
 25	  57770	  1.53%
 26	  30782	  0.82%
 27	  25848	  0.68%
 28	  28193	  0.75%
 29	  22105	  0.59%
 30	  30171	  0.80%
 31	  34567	  0.92%
 32	  38237	  1.01%
 33	 131389	  3.48%
 34	  42306	  1.12%
 35	  31890	  0.85%
 36	  42298	  1.12%
 37	  20419	  0.54%
 38	  23078	  0.61%
 39	  23612	  0.63%
 40	  37842	  1.00%
 41	  43362	  1.15%
 42	  54314	  1.44%
 43	  35996	  0.95%
 44	  32730	  0.87%
 45	  38903	  1.03%
 46	  33398	  0.89%
 47	  26129	  0.69%
 48	  11059	  0.29%
 49	  21350	  0.57%
 50	 610340	 16.17%


criterion=sequence-density
sequence-density=5.97
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=0.59
sequence-density-rank=21
fanout-score=11.23
fanout-score-rank=1
prefix-density=6.64
prefix-fanout=1.0
sequence=TGAGCTTGGCTATTT
                                 Started job on |	Mar 04 06:40:38
                             Started mapping on |	Mar 04 06:40:39
                                    Finished on |	Mar 04 06:41:07
       Mapping speed, Million of reads per hour |	499.61

                          Number of input reads |	3885817
                      Average input read length |	30
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2139087
                        Uniquely mapped reads % |	55.05%
                          Average mapped length |	29.69
                       Number of splices: Total |	2364
            Number of splices: Annotated (sjdb) |	321
                       Number of splices: GT/AG |	2204
                       Number of splices: GC/AG |	32
                       Number of splices: AT/AC |	4
               Number of splices: Non-canonical |	124
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.31
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1151056
             % of reads mapped to multiple loci |	29.62%
        Number of reads mapped to too many loci |	84000
             % of reads mapped to too many loci |	2.16%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.61%
                     % of reads unmapped: other |	0.56%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	595674	595674	595674
N_multimapping	1151056	1151056	1151056
N_noFeature	98645	122218	1591328
N_ambiguous	1180414	712722	20646
UnstrandedReadsAssigned:860028 PositiveStrandReadsAssigned:1304147 NegativeStrandReadsAssigned:527113
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030896 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: SRR5030896-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,885,817 reads, 924,503 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,142 rounds

 109283 SRR5030896.ke.tsv
  52636 SRR5030896.se.tsv
 161919 total
==> SRR5030896.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

==> SRR5030896.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	1
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030896 completed mapping pipeline successfully
