Starting /dee2/code/volunteer_pipeline.sh SRR5030833
    current disk space = 160665239552
    free memory = 73934652 
SRR5030833 SRAfilesize
406dedc6ea36f475f55281b635e5abc4  SRR5030833.sra
SRR5030833.sra file validated
SRR5030833 is single end
SRR5030833 is conventional basespace
SRR5030833 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030833_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	32.4155	33.0	31.0	34.0	31.0	34.0
2	32.7235	34.0	31.0	34.0	31.0	34.0
3	32.76625	34.0	31.0	34.0	31.0	34.0
4	36.20675	37.0	37.0	37.0	35.0	37.0
5	36.20375	37.0	37.0	37.0	35.0	37.0
6	35.96375	37.0	35.0	37.0	35.0	37.0
7	36.071	37.0	35.0	37.0	35.0	37.0
8	36.15425	37.0	36.0	37.0	35.0	37.0
9	37.9045	39.0	38.0	39.0	35.0	39.0
10	37.89825	39.0	38.0	39.0	35.0	39.0
11	37.8225	39.0	38.0	39.0	35.0	39.0
12	37.873	39.0	38.0	39.0	35.0	39.0
13	37.817	39.0	38.0	39.0	35.0	39.0
14	39.255	41.0	39.0	41.0	36.0	41.0
15	39.1435	40.0	39.0	41.0	36.0	41.0
16	39.01675	40.0	38.0	41.0	36.0	41.0
17	39.254	40.0	39.0	41.0	36.0	41.0
18	39.2445	41.0	39.0	41.0	36.0	41.0
19	39.076	40.0	39.0	41.0	36.0	41.0
20	39.26475	41.0	39.0	41.0	36.0	41.0
21	39.20775	41.0	39.0	41.0	36.0	41.0
22	39.22	41.0	39.0	41.0	36.0	41.0
23	39.109	40.0	39.0	41.0	36.0	41.0
24	38.5145	40.0	38.0	41.0	34.0	41.0
25	38.731	40.0	38.0	41.0	34.0	41.0
26	38.8075	40.0	38.0	41.0	35.0	41.0
27	38.869	40.0	39.0	41.0	35.0	41.0
28	38.8735	40.0	38.0	41.0	35.0	41.0
29	38.53875	40.0	38.0	41.0	34.0	41.0
30	38.32725	40.0	38.0	41.0	33.0	41.0
31	38.69525	40.0	38.0	41.0	34.0	41.0
32	38.828	40.0	38.0	41.0	35.0	41.0
33	37.5055	40.0	38.0	41.0	32.0	41.0
34	36.632	40.0	37.0	41.0	30.0	41.0
35	32.62125	38.0	30.0	40.0	15.0	41.0
36	28.94425	37.0	16.0	40.0	8.0	41.0
37	29.52025	35.0	22.0	40.0	6.0	41.0
38	32.18775	37.0	30.0	40.0	15.0	41.0
39	31.915	37.0	30.0	40.0	8.0	41.0
40	32.937	38.0	33.0	40.0	8.0	41.0
41	30.55575	36.0	26.0	40.0	2.0	41.0
42	32.1755	37.0	31.0	40.0	2.0	41.0
43	30.42475	37.0	26.0	40.0	2.0	41.0
44	31.5035	38.0	31.0	40.0	2.0	41.0
45	29.0245	36.0	24.0	40.0	2.0	41.0
46	26.8615	34.0	9.0	39.0	2.0	41.0
47	27.144	34.0	13.0	39.0	2.0	41.0
48	27.868	35.0	13.0	40.0	2.0	41.0
49	26.04775	35.0	2.0	40.0	2.0	41.0
50	22.7615	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
14	4.0
15	2.0
16	4.0
17	4.0
18	0.0
19	5.0
20	6.0
21	10.0
22	22.0
23	23.0
24	54.0
25	60.0
26	107.0
27	135.0
28	65.0
29	118.0
30	135.0
31	192.0
32	165.0
33	172.0
34	221.0
35	286.0
36	327.0
37	434.0
38	579.0
39	870.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.561952440550689	25.481852315394242	52.11514392991239	12.841051314142678
2	22.225	27.55	20.075000000000003	30.15
3	24.425	22.275	21.9	31.4
4	30.275000000000002	28.050000000000004	14.45	27.224999999999998
5	21.2	40.9	27.175	10.725
6	34.5	16.675	34.075	14.75
7	16.575	21.075	26.6	35.75
8	27.625	30.7	14.124999999999998	27.55
9	18.4	37.574999999999996	30.4	13.625000000000002
10	23.75	22.425	27.750000000000004	26.075
11	32.2	11.5	17.349999999999998	38.95
12	15.5	20.3	30.075000000000003	34.125
13	31.424999999999997	19.275000000000002	31.474999999999998	17.825
14	32.45	30.825000000000003	21.775	14.95
15	32.675	24.85	27.075	15.4
16	17.825	21.575	21.575	39.025
17	21.95	23.35	39.074999999999996	15.625
18	25.3	18.15	29.299999999999997	27.250000000000004
19	32.800000000000004	14.499999999999998	32.675	20.025000000000002
20	39.75	17.075000000000003	29.325000000000003	13.850000000000001
21	22.575	21.0	29.625	26.8
22	27.325	13.525	48.075	11.075
23	25.874999999999996	13.4	45.824999999999996	14.899999999999999
24	50.949999999999996	13.475000000000001	25.75	9.825000000000001
25	50.6	23.625	15.5	10.274999999999999
26	28.325	46.949999999999996	12.975	11.75
27	16.2	48.025	24.224999999999998	11.55
28	12.125	25.974999999999998	48.825	13.075000000000001
29	10.35	14.149999999999999	56.15	19.35
30	9.0	7.199999999999999	38.3	45.5
31	14.524999999999999	5.675	46.325	33.475
32	27.025	5.75	22.325	44.9
33	54.025	8.075000000000001	14.575	23.325000000000003
34	62.875	6.6000000000000005	13.55	16.975
35	60.650000000000006	7.55	20.45	11.35
36	61.45	8.450000000000001	18.0	12.1
37	41.925000000000004	10.025	20.525	27.525
38	24.2	14.549999999999999	13.975000000000001	47.275
39	18.0	25.95	8.525	47.525
40	14.075	48.9	10.9	26.125
41	27.975	46.150000000000006	9.575	16.3
42	50.2	31.025000000000002	9.175	9.6
43	47.85	34.475	8.475000000000001	9.2
44	30.0	50.075	7.5249999999999995	12.4
45	18.35	47.025	10.424999999999999	24.2
46	12.075	28.275	24.95	34.699999999999996
47	8.975	16.150000000000002	34.075	40.8
48	9.3	12.825000000000001	21.425	56.45
49	12.625	25.624999999999996	13.175	48.575
50	30.925000000000004	27.05	9.525	32.5
>>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	0.5
14	1.0
15	0.5
16	0.0
17	0.0
18	0.0
19	0.5
20	1.0
21	1.0
22	1.0
23	1.0
24	1.0
25	1.0
26	1.0
27	1.0
28	1.0
29	1.5
30	2.0
31	5.5
32	9.0
33	11.5
34	14.0
35	28.0
36	42.0
37	54.0
38	66.0
39	68.0
40	70.0
41	64.0
42	58.0
43	80.0
44	102.0
45	168.5
46	235.0
47	300.5
48	366.0
49	475.0
50	584.0
51	732.5
52	881.0
53	689.5
54	498.0
55	438.0
56	378.0
57	328.0
58	278.0
59	205.0
60	132.0
61	98.0
62	64.0
63	84.5
64	105.0
65	68.5
66	32.0
67	24.5
68	17.0
69	15.5
70	14.0
71	24.5
72	35.0
73	20.5
74	6.0
75	3.0
76	0.0
77	0.5
78	1.0
79	1.5
80	2.0
81	2.5
82	3.0
83	1.5
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.125
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	50.925
#Duplication Level	Percentage of deduplicated	Percentage of total
1	81.00147275405007	41.25
2	7.7074128620520375	7.85
3	3.5346097201767304	5.4
4	1.9636720667648502	4.0
5	0.7854688267059401	2.0
6	0.5400098183603338	1.6500000000000001
7	0.6872852233676976	2.45
8	0.6872852233676976	2.8000000000000003
9	0.29455081001472755	1.35
>10	2.7000490918016693	26.174999999999997
>50	0.0	0.0
>100	0.09818360333824251	5.075
>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
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	102	2.55	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	101	2.5250000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	50	1.25	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	43	1.075	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	40	1.0	RNA PCR Primer, Index 1 (96% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	31	0.775	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	30	0.75	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	21	0.525	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (96% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	18	0.44999999999999996	RNA PCR Primer, Index 7 (100% over 35bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	16	0.4	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	15	0.375	RNA PCR Primer, Index 1 (96% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGC	15	0.375	RNA PCR Primer, Index 28 (100% over 50bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	14	0.35000000000000003	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	13	0.325	RNA PCR Primer, Index 1 (96% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	12	0.3	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTC	12	0.3	RNA PCR Primer, Index 28 (100% over 44bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	11	0.27499999999999997	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	11	0.27499999999999997	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	10	0.25	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	10	0.25	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	10	0.25	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	9	0.22499999999999998	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	8	0.2	No Hit
TTTGGCAATGGTAGAACTCACTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	8	0.2	No Hit
TTTGGCAATGGTAGAACTCACACCTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	8	0.2	No Hit
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	8	0.2	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	7	0.17500000000000002	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	7	0.17500000000000002	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAATTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (95% over 23bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	7	0.17500000000000002	No Hit
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	7	0.17500000000000002	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGGCAATGGTAGAACTCACACTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	6	0.15	No Hit
TTTGGCAATGGTAGAACTCACATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	5	0.125	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	5	0.125	No Hit
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTGTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGGG	5	0.125	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAATTCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	5	0.125	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.4	0.0	0.0	0.0
2	0.0	0.45	0.0	0.0	0.0
3	0.0	0.55	0.0	0.0	0.0
4	0.0	0.6	0.0	0.0	0.0
5	0.0	0.65	0.0	0.0	0.0
6	0.0	0.7	0.0	0.0	0.0
7	0.0	1.175	0.0	0.0	0.0
8	0.0	1.3	0.0	0.0	0.0
9	0.0	1.325	0.0	0.0	0.0
10	0.0	1.375	0.0	0.0	0.0
11	0.0	1.575	0.0	0.0	0.0
12	0.0	1.775	0.0	0.0	0.0
13	0.0	1.925	0.0	0.0	0.0
14	0.0	2.175	0.0	0.0	0.0
15	0.0	2.425	0.0	0.0	0.0
16	0.0	3.425	0.0	0.0	0.0
17	0.0	3.975	0.0	0.0	0.0
18	0.0	4.85	0.0	0.0	0.0
19	0.0	5.4	0.0	0.0	0.0
20	0.0	6.125	0.0	0.0	0.0
21	0.0	10.7	0.0	0.0	0.0
22	0.0	22.5	0.0	0.0	0.0
23	0.0	51.85	0.0	0.0	0.0
24	0.0	65.025	0.0	0.0	0.0
25	0.0	71.675	0.0	0.0	0.0
26	0.0	73.05	0.0	0.0	0.0
27	0.0	73.825	0.0	0.0	0.0
28	0.0	74.3	0.0	0.0	0.0
29	0.0	74.375	0.0	0.0	0.0
30	0.0	74.8	0.0	0.0	0.0
31	0.0	75.45	0.0	0.0	0.0
32	0.0	76.4	0.0	0.0	0.0
33	0.0	77.175	0.0	0.0	0.0
34	0.0	79.025	0.0	0.0	0.0
35	0.0	79.875	0.0	0.0	0.0
36	0.0	80.35	0.0	0.0	0.0
37	0.0	80.85	0.0	0.0	0.0
38	0.0	81.375	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CTCTTTT	20	6.952051E-4	44.000004	16
GCTGGAA	20	6.952051E-4	44.000004	20
GCTTGGC	20	6.952051E-4	44.000004	15
TCTCTTT	20	6.952051E-4	44.000004	15
CTGTTGG	20	6.952051E-4	44.000004	19
ACAGTGA	30	1.9515464E-6	44.0	3
ACCGGTC	30	1.9515464E-6	44.0	10
AACGCTG	25	3.6958358E-5	44.0	8
GAGGTAG	30	1.9515464E-6	44.0	2
ACGCTGT	25	3.6958358E-5	44.0	9
AACCGGT	30	1.9515464E-6	44.0	9
TTCAACG	25	3.6958358E-5	44.0	5
GAGCTTG	25	3.6958358E-5	44.0	13
GGATCCG	25	3.6958358E-5	44.0	3
CCGTCTG	25	3.6958358E-5	44.0	7
TCGGATC	25	3.6958358E-5	44.0	1
CATTCAA	30	1.9515464E-6	44.0	3
TCAACGC	25	3.6958358E-5	44.0	6
CGGATCC	25	3.6958358E-5	44.0	2
ACATTCA	30	1.9515464E-6	44.0	2
>>END_MODULE
Read 234916 spots for SRR5030833.sra
Written 234916 spots for SRR5030833.sra
Read 234916 spots for SRR5030833.sra
Written 234916 spots for SRR5030833.sra
Read 234916 spots for SRR5030833.sra
Written 234916 spots for SRR5030833.sra
Read 234916 spots for SRR5030833.sra
Written 234916 spots for SRR5030833.sra
Read 234916 spots for SRR5030833.sra
Written 234916 spots for SRR5030833.sra
Read 234916 spots for SRR5030833.sra
Written 234916 spots for SRR5030833.sra
Read 234916 spots for SRR5030833.sra
Written 234916 spots for SRR5030833.sra
Read 234916 spots for SRR5030833.sra
Written 234916 spots for SRR5030833.sra
Read 234916 spots for SRR5030833.sra
Written 234916 spots for SRR5030833.sra
Read 234916 spots for SRR5030833.sra
Written 234916 spots for SRR5030833.sra
Read 234916 spots for SRR5030833.sra
Written 234916 spots for SRR5030833.sra
Read 234916 spots for SRR5030833.sra
Written 234916 spots for SRR5030833.sra
SRR ids: ['SRR5030833.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_0uevkgfv
SRR5030833.sra spots: 2818992
blocks: [[1, 234916], [234917, 469832], [469833, 704748], [704749, 939664], [939665, 1174580], [1174581, 1409496], [1409497, 1644412], [1644413, 1879328], [1879329, 2114244], [2114245, 2349160], [2349161, 2584076], [2584077, 2818992]]
SRR5030833 file size 487516
SRR5030833 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030833 SRR5030833_1.fastq
Input file:	SRR5030833_1.fastq
trimmed:	SRR5030833-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 06:22:33 2020 >> started

Wed Mar  4 06:22:35 2020 >> done (1.541s)
2818992 reads processed; of these:
    163 ( 0.01%) short reads filtered out after trimming by size control
      8 ( 0.00%) empty reads filtered out after trimming by size control
2818821 (99.99%) reads available; of these:
 320198 (11.36%) trimmed reads available after processing
2498623 (88.64%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     45	  0.00%
 19	     56	  0.00%
 20	    126	  0.00%
 21	    159	  0.01%
 22	    312	  0.01%
 23	    365	  0.01%
 24	    339	  0.01%
 25	    526	  0.02%
 26	    443	  0.02%
 27	    609	  0.02%
 28	    715	  0.03%
 29	   1254	  0.04%
 30	    886	  0.03%
 31	   1213	  0.04%
 32	   3084	  0.11%
 33	   8967	  0.32%
 34	  24000	  0.85%
 35	   5232	  0.19%
 36	   5397	  0.19%
 37	   3222	  0.11%
 38	   6317	  0.22%
 39	   5495	  0.19%
 40	  11373	  0.40%
 41	   6494	  0.23%
 42	  16494	  0.59%
 43	   7050	  0.25%
 44	  35880	  1.27%
 45	  18282	  0.65%
 46	  15971	  0.57%
 47	  18033	  0.64%
 48	  57370	  2.04%
 49	  64489	  2.29%
 50	2498623	 88.64%
2818821 reads passed initial QC


criterion=sequence-density
sequence-density=80.20
sequence-density-rank=1
fanout-score=21.37
fanout-score-rank=3
prefix-density=82.74
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCC


criterion=fanout-score
sequence-density=1.71
sequence-density-rank=5
fanout-score=449.23
fanout-score-rank=1
prefix-density=81.98
prefix-fanout=9.4
sequence=GGAATTCTCGGTGCCAAGGA
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCC -o SRR5030833 -
Input file:	STDIN
trimmed:	SRR5030833-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCC
-- 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 06:22:48 2020 >> started

Wed Mar  4 06:22:52 2020 >> done (3.190s)
2749221 reads processed; of these:
 114388 ( 4.16%) short reads filtered out after trimming by size control
  15514 ( 0.56%) empty reads filtered out after trimming by size control
2619319 (95.27%) reads available; of these:
2293904 (87.58%) trimmed reads available after processing
 325415 (12.42%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  14178	  0.54%
 19	  24197	  0.92%
 20	 124293	  4.75%
 21	 327488	 12.50%
 22	 790543	 30.18%
 23	 372767	 14.23%
 24	 177112	  6.76%
 25	  46437	  1.77%
 26	  21523	  0.82%
 27	  16105	  0.61%
 28	  16175	  0.62%
 29	  13283	  0.51%
 30	  18413	  0.70%
 31	  27574	  1.05%
 32	  22574	  0.86%
 33	  59221	  2.26%
 34	  23869	  0.91%
 35	  18668	  0.71%
 36	  26918	  1.03%
 37	  11319	  0.43%
 38	  12745	  0.49%
 39	  12117	  0.46%
 40	  19560	  0.75%
 41	  23112	  0.88%
 42	  31523	  1.20%
 43	  19515	  0.75%
 44	  19255	  0.74%
 45	  19727	  0.75%
 46	  15960	  0.61%
 47	  13068	  0.50%
 48	   5860	  0.22%
 49	   9926	  0.38%
 50	 264294	 10.09%


criterion=sequence-density
sequence-density=6.15
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=39
fanout-score=263.26
fanout-score-rank=1
prefix-density=2.43
prefix-fanout=1.7
sequence=TTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:23:13
                             Started mapping on |	Mar 04 06:23:14
                                    Finished on |	Mar 04 06:23:37
       Mapping speed, Million of reads per hour |	420.87

                          Number of input reads |	2688919
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1468852
                        Uniquely mapped reads % |	54.63%
                          Average mapped length |	26.81
                       Number of splices: Total |	1382
            Number of splices: Annotated (sjdb) |	197
                       Number of splices: GT/AG |	1273
                       Number of splices: GC/AG |	13
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	96
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.21
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	887313
             % of reads mapped to multiple loci |	33.00%
        Number of reads mapped to too many loci |	50675
             % of reads mapped to too many loci |	1.88%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.98%
                     % of reads unmapped: other |	0.51%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	332754	332754	332754
N_multimapping	887313	887313	887313
N_noFeature	66805	80622	1098521
N_ambiguous	775485	455336	13818
UnstrandedReadsAssigned:626562 PositiveStrandReadsAssigned:932894 NegativeStrandReadsAssigned:356513
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030833 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: SRR5030833-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,688,919 reads, 640,617 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,123 rounds

 109283 SRR5030833.ke.tsv
  52636 SRR5030833.se.tsv
 161919 total
==> SRR5030833.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

==> SRR5030833.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030833 completed mapping pipeline successfully
