Starting /dee2/code/volunteer_pipeline.sh SRR5030990
    current disk space = 160575537152
    free memory = 73933932 
SRR5030990 SRAfilesize
44940c956298837107402d9a47135880  SRR5030990.sra
SRR5030990.sra file validated
SRR5030990 is single end
SRR5030990 is conventional basespace
SRR5030990 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030990_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	32.3485	33.0	31.0	34.0	31.0	34.0
2	32.61725	34.0	31.0	34.0	31.0	34.0
3	32.607	34.0	31.0	34.0	31.0	34.0
4	36.21425	37.0	35.0	37.0	35.0	37.0
5	36.04575	37.0	35.0	37.0	35.0	37.0
6	35.86	37.0	35.0	37.0	35.0	37.0
7	35.87825	37.0	35.0	37.0	35.0	37.0
8	35.94675	37.0	35.0	37.0	35.0	37.0
9	37.62925	39.0	37.0	39.0	35.0	39.0
10	37.497	39.0	37.0	39.0	35.0	39.0
11	37.188	39.0	37.0	39.0	33.0	39.0
12	37.58875	39.0	37.0	39.0	35.0	39.0
13	37.5485	39.0	37.0	39.0	35.0	39.0
14	38.985	40.0	38.0	41.0	35.0	41.0
15	38.8865	40.0	38.0	41.0	35.0	41.0
16	38.99775	40.0	38.0	41.0	35.0	41.0
17	39.08425	40.0	38.0	41.0	35.0	41.0
18	38.886	41.0	38.0	41.0	35.0	41.0
19	38.911	40.0	38.0	41.0	35.0	41.0
20	38.78925	40.0	38.0	41.0	35.0	41.0
21	38.8105	40.0	38.0	41.0	34.0	41.0
22	38.86175	40.0	38.0	41.0	35.0	41.0
23	38.5575	40.0	38.0	41.0	34.0	41.0
24	38.8105	40.0	38.0	41.0	35.0	41.0
25	38.87775	40.0	39.0	41.0	35.0	41.0
26	38.73875	40.0	38.0	41.0	34.0	41.0
27	38.92075	40.0	38.0	41.0	35.0	41.0
28	38.55675	40.0	38.0	41.0	34.0	41.0
29	38.314	40.0	38.0	41.0	33.0	41.0
30	38.453	40.0	38.0	41.0	34.0	41.0
31	38.66125	40.0	38.0	41.0	34.0	41.0
32	38.65525	40.0	38.0	41.0	34.0	41.0
33	38.3095	40.0	38.0	41.0	34.0	41.0
34	38.062	40.0	38.0	41.0	33.0	41.0
35	37.8205	40.0	37.0	41.0	33.0	41.0
36	37.72875	40.0	37.0	41.0	32.0	41.0
37	37.2645	40.0	37.0	41.0	31.0	41.0
38	37.19025	39.0	37.0	41.0	31.0	41.0
39	37.64625	40.0	37.0	41.0	33.0	41.0
40	37.79275	40.0	37.0	41.0	33.0	41.0
41	38.04675	40.0	38.0	41.0	33.0	41.0
42	37.83975	40.0	37.0	41.0	33.0	41.0
43	37.77975	40.0	37.0	41.0	33.0	41.0
44	37.74	40.0	37.0	41.0	33.0	41.0
45	37.75875	40.0	37.0	41.0	33.0	41.0
46	37.482	40.0	37.0	41.0	32.0	41.0
47	37.06725	40.0	36.0	41.0	31.0	41.0
48	36.9175	40.0	36.0	41.0	31.0	41.0
49	37.0615	40.0	36.0	41.0	32.0	41.0
50	36.481	39.0	35.0	41.0	31.0	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
16	2.0
17	3.0
18	0.0
19	5.0
20	7.0
21	6.0
22	4.0
23	5.0
24	7.0
25	8.0
26	19.0
27	19.0
28	30.0
29	25.0
30	42.0
31	47.0
32	85.0
33	128.0
34	174.0
35	209.0
36	259.0
37	403.0
38	687.0
39	1826.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.5	23.974999999999998	51.975	14.549999999999999
2	22.865013774104685	27.89882294014525	19.434009516654143	29.802153769095916
3	24.925	20.974999999999998	22.625	31.474999999999998
4	32.300000000000004	28.000000000000004	13.65	26.05
5	21.375	39.025	26.924999999999997	12.675
6	36.475	16.75	32.324999999999996	14.45
7	16.05	22.725	23.400000000000002	37.824999999999996
8	26.575	27.6	15.25	30.575000000000003
9	21.95	34.875	27.175	16.0
10	22.15	22.825	26.125	28.9
11	28.7	11.175	19.125	41.0
12	16.625	17.25	30.525000000000002	35.6
13	32.1	17.599999999999998	31.974999999999998	18.325
14	32.725	30.65	20.349999999999998	16.275000000000002
15	34.075	23.025000000000002	27.075	15.825
16	18.725	19.075	23.075000000000003	39.125
17	25.224999999999998	21.2	39.900000000000006	13.675
18	27.200000000000003	17.9	28.475	26.424999999999997
19	35.175	14.825	30.675	19.325
20	41.099999999999994	15.275	29.45	14.174999999999999
21	24.325	19.175	30.0	26.5
22	29.15	13.750000000000002	46.300000000000004	10.8
23	27.700000000000003	13.15	44.85	14.299999999999999
24	50.6	14.875	26.375	8.15
25	50.949999999999996	23.95	15.65	9.45
26	28.449999999999996	46.225	15.75	9.575
27	17.224999999999998	46.625	24.725	11.425
28	12.125	24.05	48.875	14.95
29	11.450000000000001	13.625000000000002	55.875	19.05
30	10.575	6.75	36.475	46.2
31	15.875	5.025	45.85	33.25
32	27.425	6.25	21.95	44.375
33	55.300000000000004	7.1499999999999995	13.850000000000001	23.7
34	62.25000000000001	7.225	16.150000000000002	14.374999999999998
35	64.47500000000001	8.05	17.8	9.675
36	41.375	8.05	37.175000000000004	13.4
37	45.275	9.5	19.775000000000002	25.45
38	23.075000000000003	16.425	13.350000000000001	47.15
39	15.85	24.474999999999998	9.2	50.475
40	15.9	47.949999999999996	11.275	24.875
41	25.374999999999996	49.25	8.075000000000001	17.299999999999997
42	49.75	29.925	9.975000000000001	10.35
43	51.65	29.849999999999998	7.6	10.9
44	30.0	47.875	8.325000000000001	13.8
45	17.075000000000003	48.9	14.774999999999999	19.25
46	13.25	26.125	17.825	42.8
47	8.5	15.525	38.125	37.85
48	9.225	13.725000000000001	20.549999999999997	56.49999999999999
49	12.55	20.200000000000003	15.975	51.275000000000006
50	18.05	37.85	14.099999999999998	30.0
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.5
12	1.0
13	1.0
14	1.0
15	0.5
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	1.0
28	2.0
29	2.0
30	2.0
31	6.5
32	11.0
33	12.0
34	13.0
35	15.5
36	18.0
37	23.5
38	29.0
39	30.0
40	31.0
41	42.5
42	54.0
43	73.5
44	93.0
45	155.5
46	218.0
47	332.5
48	447.0
49	589.0
50	731.0
51	812.5
52	894.0
53	651.0
54	408.0
55	426.5
56	445.0
57	332.5
58	220.0
59	147.0
60	74.0
61	59.5
62	45.0
63	74.5
64	104.0
65	71.5
66	39.0
67	26.0
68	13.0
69	20.0
70	27.0
71	47.5
72	68.0
73	36.0
74	4.0
75	2.5
76	1.0
77	2.0
78	3.0
79	3.5
80	4.0
81	2.0
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	0.17500000000000002
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	37.574999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.24750499001996	28.65
2	9.44777112441783	7.1
3	3.992015968063872	4.5
4	2.3286759813705924	3.5000000000000004
5	1.7298735861610113	3.25
6	0.7984031936127743	1.7999999999999998
7	0.665335994677312	1.7500000000000002
8	0.39920159680638717	1.2
9	0.39920159680638717	1.35
>10	3.4597471723220226	26.474999999999998
>50	0.332667997338656	10.100000000000001
>100	0.19960079840319359	10.325
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	166	4.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	130	3.25	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	117	2.9250000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	88	2.1999999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	82	2.0500000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	77	1.925	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	60	1.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	46	1.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	43	1.075	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	39	0.975	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	37	0.9249999999999999	RNA PCR Primer, Index 7 (97% over 35bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	32	0.8	RNA PCR Primer, Index 1 (100% over 33bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	30	0.75	No Hit
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	30	0.75	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTC	27	0.675	RNA PCR Primer, Index 10 (100% over 44bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	20	0.5	RNA PCR Primer, Index 1 (100% over 30bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGC	18	0.44999999999999996	RNA PCR Primer, Index 10 (100% over 50bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	16	0.4	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	16	0.4	No Hit
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	15	0.375	RNA PCR Primer, Index 1 (100% over 31bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 25bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	11	0.27499999999999997	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	10	0.25	No Hit
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	9	0.22499999999999998	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TATGCAAGGGCAAGCTCTCTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	8	0.2	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	7	0.17500000000000002	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTATTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	7	0.17500000000000002	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAG	7	0.17500000000000002	RNA PCR Primer, Index 7 (97% over 36bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	6	0.15	No Hit
CTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTATTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	6	0.15	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	6	0.15	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	5	0.125	RNA PCR Primer, Index 7 (97% over 35bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	5	0.125	No Hit
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGC	5	0.125	RNA PCR Primer, Index 10 (100% over 37bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TATTGCACTTGTCCCGGCCTGTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTGGAATTC	5	0.125	No Hit
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	5	0.125	No Hit
ACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
>>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	0.475	0.0	0.0	0.0
2	0.0	0.5	0.0	0.0	0.0
3	0.0	0.6	0.0	0.0	0.0
4	0.0	0.65	0.0	0.0	0.0
5	0.0	0.65	0.0	0.0	0.0
6	0.0	0.75	0.0	0.0	0.0
7	0.0	1.7	0.0	0.0	0.0
8	0.0	1.8	0.0	0.0	0.0
9	0.0	1.825	0.0	0.0	0.0
10	0.0	1.9	0.0	0.0	0.0
11	0.0	2.175	0.0	0.0	0.0
12	0.0	2.425	0.0	0.0	0.0
13	0.0	2.675	0.0	0.0	0.0
14	0.0	3.0	0.0	0.0	0.0
15	0.0	3.65	0.0	0.0	0.0
16	0.0	5.05	0.0	0.0	0.0
17	0.0	5.775	0.0	0.0	0.0
18	0.0	7.075	0.0	0.0	0.0
19	0.0	7.725	0.0	0.0	0.0
20	0.0	9.0	0.0	0.0	0.0
21	0.0	15.2	0.0	0.0	0.0
22	0.0	26.85	0.0	0.0	0.0
23	0.0	56.225	0.0	0.0	0.0
24	0.0	69.125	0.0	0.0	0.0
25	0.0	75.275	0.0	0.0	0.0
26	0.0	77.2	0.0	0.0	0.0
27	0.0	78.0	0.0	0.0	0.0
28	0.0	78.7	0.0	0.0	0.0
29	0.0	79.3	0.0	0.0	0.0
30	0.0	79.825	0.0	0.0	0.0
31	0.0	80.6	0.0	0.0	0.0
32	0.0	82.325	0.0	0.0	0.0
33	0.0	83.2	0.0	0.0	0.0
34	0.0	85.125	0.0	0.0	0.0
35	0.0	86.0	0.0	0.0	0.0
36	0.0	86.7	0.0	0.0	0.0
37	0.0	87.425	0.0	0.0	0.0
38	0.0	87.8	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AAGTAAT	45	2.728484E-10	44.000004	4
TCAAGTA	45	2.728484E-10	44.000004	2
AATCCAG	45	2.728484E-10	44.000004	8
ATCCAGG	45	2.728484E-10	44.000004	9
TTCAAGT	45	2.728484E-10	44.000004	1
AGGATAG	45	2.728484E-10	44.000004	13
ATAGGCT	40	5.315087E-9	44.000004	16
TCCAGGA	45	2.728484E-10	44.000004	10
ACATCCT	20	6.952051E-4	44.000004	6
GGATAGG	40	5.315087E-9	44.000004	14
CTTGGCT	20	6.952051E-4	44.000004	16
AGTAATC	45	2.728484E-10	44.000004	5
TAATCCA	45	2.728484E-10	44.000004	7
GCTTGGC	20	6.952051E-4	44.000004	15
GACTGGA	20	6.952051E-4	44.000004	14
CAGGATA	45	2.728484E-10	44.000004	12
GTAATCC	45	2.728484E-10	44.000004	6
GATAGGC	40	5.315087E-9	44.000004	15
CCAGGAT	45	2.728484E-10	44.000004	11
CAAGTAA	45	2.728484E-10	44.000004	3
>>END_MODULE
Read 293266 spots for SRR5030990.sra
Written 293266 spots for SRR5030990.sra
Read 293266 spots for SRR5030990.sra
Written 293266 spots for SRR5030990.sra
Read 293266 spots for SRR5030990.sra
Written 293266 spots for SRR5030990.sra
Read 293266 spots for SRR5030990.sra
Written 293266 spots for SRR5030990.sra
Read 293266 spots for SRR5030990.sra
Written 293266 spots for SRR5030990.sra
Read 293266 spots for SRR5030990.sra
Written 293266 spots for SRR5030990.sra
Read 293266 spots for SRR5030990.sra
Written 293266 spots for SRR5030990.sra
Read 293266 spots for SRR5030990.sra
Written 293266 spots for SRR5030990.sra
Read 293266 spots for SRR5030990.sra
Written 293266 spots for SRR5030990.sra
Read 293266 spots for SRR5030990.sra
Written 293266 spots for SRR5030990.sra
Read 293266 spots for SRR5030990.sra
Written 293266 spots for SRR5030990.sra
Read 293274 spots for SRR5030990.sra
Written 293274 spots for SRR5030990.sra
SRR ids: ['SRR5030990.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_aah2tptv
SRR5030990.sra spots: 3519200
blocks: [[1, 293266], [293267, 586532], [586533, 879798], [879799, 1173064], [1173065, 1466330], [1466331, 1759596], [1759597, 2052862], [2052863, 2346128], [2346129, 2639394], [2639395, 2932660], [2932661, 3225926], [3225927, 3519200]]
SRR5030990 file size 608892
SRR5030990 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030990 SRR5030990_1.fastq
Input file:	SRR5030990_1.fastq
trimmed:	SRR5030990-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 07:00:55 2020 >> started

Wed Mar  4 07:00:57 2020 >> done (2.187s)
3519200 reads processed; of these:
    333 ( 0.01%) short reads filtered out after trimming by size control
     12 ( 0.00%) empty reads filtered out after trimming by size control
3518855 (99.99%) reads available; of these:
 190990 ( 5.43%) trimmed reads available after processing
3327865 (94.57%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     86	  0.00%
 19	     95	  0.00%
 20	    214	  0.01%
 21	    262	  0.01%
 22	    475	  0.01%
 23	    521	  0.01%
 24	    492	  0.01%
 25	    725	  0.02%
 26	    598	  0.02%
 27	    780	  0.02%
 28	    823	  0.02%
 29	   1347	  0.04%
 30	    905	  0.03%
 31	    966	  0.03%
 32	   1114	  0.03%
 33	   1507	  0.04%
 34	   1822	  0.05%
 35	   3274	  0.09%
 36	   2851	  0.08%
 37	   3471	  0.10%
 38	   3273	  0.09%
 39	   3351	  0.10%
 40	   3750	  0.11%
 41	   4157	  0.12%
 42	   5291	  0.15%
 43	   7841	  0.22%
 44	  10755	  0.31%
 45	  13009	  0.37%
 46	  17814	  0.51%
 47	  22258	  0.63%
 48	  35328	  1.00%
 49	  41835	  1.19%
 50	3327865	 94.57%
3518855 reads passed initial QC


criterion=sequence-density
sequence-density=87.91
sequence-density-rank=1
fanout-score=20.00
fanout-score-rank=1
prefix-density=89.38
prefix-fanout=19.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCC


criterion=fanout-score
sequence-density=87.91
sequence-density-rank=1
fanout-score=20.00
fanout-score-rank=1
prefix-density=89.38
prefix-fanout=19.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCC -o SRR5030990 -
Input file:	STDIN
trimmed:	SRR5030990-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCC
-- 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 07:01:16 2020 >> started

Wed Mar  4 07:01:21 2020 >> done (5.336s)
3438881 reads processed; of these:
 250547 ( 7.29%) short reads filtered out after trimming by size control
  18464 ( 0.54%) empty reads filtered out after trimming by size control
3169870 (92.18%) reads available; of these:
3037192 (95.81%) trimmed reads available after processing
 132678 ( 4.19%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  18099	  0.57%
 19	  39416	  1.24%
 20	 195881	  6.18%
 21	 429872	 13.56%
 22	1028262	 32.44%
 23	 449753	 14.19%
 24	 216535	  6.83%
 25	  52806	  1.67%
 26	  27741	  0.88%
 27	  22044	  0.70%
 28	  22951	  0.72%
 29	  16554	  0.52%
 30	  28482	  0.90%
 31	  47727	  1.51%
 32	  38551	  1.22%
 33	  79367	  2.50%
 34	  30252	  0.95%
 35	  24169	  0.76%
 36	  27427	  0.87%
 37	  15998	  0.50%
 38	  16222	  0.51%
 39	  16065	  0.51%
 40	  24003	  0.76%
 41	  32915	  1.04%
 42	  39716	  1.25%
 43	  28140	  0.89%
 44	  20573	  0.65%
 45	  28546	  0.90%
 46	  21540	  0.68%
 47	  15152	  0.48%
 48	   1356	  0.04%
 49	   2417	  0.08%
 50	 111338	  3.51%


criterion=sequence-density
sequence-density=6.36
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=41
fanout-score=100.36
fanout-score-rank=1
prefix-density=1.94
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:01:42
                             Started mapping on |	Mar 04 07:01:43
                                    Finished on |	Mar 04 07:02:09
       Mapping speed, Million of reads per hour |	449.98

                          Number of input reads |	3249844
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1757159
                        Uniquely mapped reads % |	54.07%
                          Average mapped length |	24.29
                       Number of splices: Total |	2006
            Number of splices: Annotated (sjdb) |	660
                       Number of splices: GT/AG |	1894
                       Number of splices: GC/AG |	23
                       Number of splices: AT/AC |	6
               Number of splices: Non-canonical |	83
                      Mismatch rate per base, % |	0.18%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.71
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.07
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1106207
             % of reads mapped to multiple loci |	34.04%
        Number of reads mapped to too many loci |	67398
             % of reads mapped to too many loci |	2.07%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.13%
                     % of reads unmapped: other |	0.69%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	386478	386478	386478
N_multimapping	1106207	1106207	1106207
N_noFeature	97618	116371	1218332
N_ambiguous	967360	496961	15646
UnstrandedReadsAssigned:692181 PositiveStrandReadsAssigned:1143827 NegativeStrandReadsAssigned:523181
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030990 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: SRR5030990-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,249,844 reads, 823,907 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,111 rounds

 109283 SRR5030990.ke.tsv
  52636 SRR5030990.se.tsv
 161919 total
==> SRR5030990.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

==> SRR5030990.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030990 completed mapping pipeline successfully
