Starting /dee2/code/volunteer_pipeline.sh SRR5031060
    current disk space = 160507150336
    free memory = 73934636 
SRR5031060 SRAfilesize
c7d64409c50ffd341bee4d1c99fe022f  SRR5031060.sra
SRR5031060.sra file validated
SRR5031060 is single end
SRR5031060 is conventional basespace
SRR5031060 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031060_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	32.27575	33.0	31.0	34.0	31.0	34.0
2	32.62975	34.0	31.0	34.0	31.0	34.0
3	32.635	34.0	31.0	34.0	31.0	34.0
4	36.2125	37.0	35.0	37.0	35.0	37.0
5	35.89325	37.0	35.0	37.0	35.0	37.0
6	35.7665	37.0	35.0	37.0	33.0	37.0
7	35.84525	37.0	35.0	37.0	35.0	37.0
8	35.728	37.0	35.0	37.0	33.0	37.0
9	37.4195	39.0	37.0	39.0	35.0	39.0
10	37.66975	39.0	37.0	39.0	35.0	39.0
11	37.5615	39.0	37.0	39.0	35.0	39.0
12	37.558	39.0	37.0	39.0	35.0	39.0
13	37.574	39.0	37.0	39.0	35.0	39.0
14	38.974	40.0	38.0	41.0	35.0	41.0
15	38.69625	40.0	38.0	41.0	34.0	41.0
16	38.82975	40.0	38.0	41.0	35.0	41.0
17	38.65525	40.0	38.0	41.0	34.0	41.0
18	38.83325	40.0	38.0	41.0	35.0	41.0
19	38.47575	40.0	38.0	41.0	34.0	41.0
20	38.6635	40.0	38.0	41.0	34.0	41.0
21	38.70225	40.0	38.0	41.0	34.0	41.0
22	38.845	40.0	38.0	41.0	35.0	41.0
23	38.6595	40.0	38.0	41.0	34.0	41.0
24	38.52225	40.0	38.0	41.0	34.0	41.0
25	38.74825	40.0	38.0	41.0	35.0	41.0
26	38.43	40.0	38.0	41.0	34.0	41.0
27	38.499	40.0	38.0	41.0	34.0	41.0
28	38.4155	40.0	38.0	41.0	34.0	41.0
29	37.96875	40.0	38.0	41.0	33.0	41.0
30	38.00975	40.0	38.0	41.0	33.0	41.0
31	38.23125	40.0	38.0	41.0	33.0	41.0
32	38.04975	40.0	38.0	41.0	33.0	41.0
33	38.169	40.0	38.0	41.0	33.0	41.0
34	38.334	40.0	38.0	41.0	34.0	41.0
35	38.078	40.0	38.0	41.0	33.0	41.0
36	37.8435	40.0	37.0	41.0	33.0	41.0
37	37.44725	40.0	37.0	41.0	31.0	41.0
38	36.658	39.0	36.0	41.0	30.0	41.0
39	37.22625	39.0	37.0	41.0	31.0	41.0
40	37.5195	40.0	37.0	41.0	33.0	41.0
41	37.665	40.0	37.0	41.0	33.0	41.0
42	37.86575	40.0	37.0	41.0	33.0	41.0
43	38.03475	40.0	38.0	41.0	33.0	41.0
44	37.73925	40.0	37.0	41.0	33.0	41.0
45	37.719	40.0	37.0	41.0	33.0	41.0
46	37.70575	40.0	37.0	41.0	33.0	41.0
47	37.285	40.0	37.0	41.0	32.0	41.0
48	36.9285	40.0	36.0	41.0	31.0	41.0
49	37.109	40.0	36.0	41.0	32.0	41.0
50	36.5065	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
14	1.0
15	0.0
16	0.0
17	2.0
18	6.0
19	2.0
20	3.0
21	4.0
22	10.0
23	7.0
24	7.0
25	12.0
26	15.0
27	18.0
28	24.0
29	40.0
30	58.0
31	62.0
32	77.0
33	112.0
34	197.0
35	202.0
36	274.0
37	416.0
38	683.0
39	1768.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.425	24.95	52.849999999999994	12.775
2	25.737868934467233	25.812906453226613	19.909954977488745	28.53926963481741
3	22.725	23.474999999999998	21.6	32.2
4	33.475	28.199999999999996	14.424999999999999	23.9
5	25.75	37.75	25.900000000000002	10.6
6	35.949999999999996	16.8	32.324999999999996	14.924999999999999
7	16.375	23.45	24.2	35.975
8	27.825	29.625	14.95	27.6
9	19.275000000000002	35.525	29.075	16.125
10	20.549999999999997	24.75	26.525	28.175
11	33.4	9.825000000000001	16.0	40.775
12	15.625	19.7	29.925	34.75
13	29.599999999999998	20.150000000000002	33.725	16.525000000000002
14	34.475	27.325	23.35	14.85
15	35.3	23.825	26.724999999999998	14.149999999999999
16	18.375	19.525000000000002	23.35	38.75
17	23.625	23.65	38.35	14.374999999999998
18	25.75	17.175	28.825	28.249999999999996
19	33.225	14.625	34.150000000000006	18.0
20	43.2	14.899999999999999	27.975	13.925
21	22.875	19.325	29.825000000000003	27.975
22	28.175	12.45	49.5	9.875
23	27.675	12.4	45.775	14.149999999999999
24	52.449999999999996	13.25	26.224999999999998	8.075000000000001
25	52.15	24.15	14.825	8.875
26	27.775	49.375	13.325000000000001	9.525
27	15.7	48.75	25.05	10.5
28	11.025	24.65	50.849999999999994	13.475000000000001
29	11.450000000000001	12.325	55.625	20.599999999999998
30	9.725	6.375	38.425	45.475
31	13.425	5.025	45.975	35.575
32	28.4	5.3	22.875	43.425000000000004
33	56.15	7.249999999999999	13.950000000000001	22.650000000000002
34	65.17500000000001	6.925000000000001	14.35	13.55
35	63.675000000000004	6.800000000000001	19.85	9.675
36	43.15	6.9750000000000005	37.2	12.675
37	44.975	9.1	21.725	24.2
38	24.5	13.875000000000002	12.375	49.25
39	15.275	23.95	9.45	51.324999999999996
40	14.75	49.45	10.025	25.775
41	25.650000000000002	50.6	7.825	15.925
42	51.1	28.725	9.5	10.674999999999999
43	52.87500000000001	29.125	7.7	10.299999999999999
44	30.275000000000002	49.675000000000004	6.4	13.65
45	17.025000000000002	50.475	12.15	20.349999999999998
46	12.65	25.85	19.075	42.425000000000004
47	8.95	14.000000000000002	38.1	38.95
48	10.299999999999999	12.425	20.1	57.175
49	11.799999999999999	21.025	12.25	54.925000000000004
50	18.925	39.0	11.35	30.725
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.5
4	1.0
5	0.5
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.5
22	1.0
23	1.0
24	1.0
25	1.0
26	1.0
27	1.0
28	1.0
29	1.0
30	1.0
31	5.0
32	9.0
33	8.0
34	7.0
35	12.0
36	17.0
37	22.0
38	27.0
39	30.0
40	33.0
41	34.0
42	35.0
43	91.0
44	147.0
45	181.5
46	216.0
47	357.5
48	499.0
49	596.5
50	694.0
51	789.0
52	884.0
53	648.5
54	413.0
55	410.5
56	408.0
57	311.5
58	215.0
59	150.0
60	85.0
61	65.0
62	45.0
63	89.5
64	134.0
65	74.5
66	15.0
67	15.5
68	16.0
69	15.0
70	14.0
71	39.0
72	64.0
73	36.0
74	8.0
75	5.5
76	3.0
77	2.5
78	2.0
79	2.0
80	2.0
81	2.0
82	2.0
83	1.0
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	0.05
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	37.1
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.28032345013477	28.299999999999997
2	8.62533692722372	6.4
3	4.31266846361186	4.8
4	2.4932614555256065	3.6999999999999997
5	1.5498652291105122	2.875
6	1.1455525606469004	2.55
7	0.8086253369272237	2.1
8	0.40431266846361186	1.2
9	0.20215633423180593	0.675
>10	3.436657681940701	22.7
>50	0.4716981132075472	12.4
>100	0.2695417789757413	12.3
>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
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	152	3.8	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	125	3.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	112	2.8000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	103	2.5749999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	86	2.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	78	1.95	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	78	1.95	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	76	1.9	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	63	1.575	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	60	1.5	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	55	1.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	39	0.975	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	33	0.8250000000000001	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	21	0.525	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	20	0.5	RNA PCR Primer, Index 1 (100% over 30bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	19	0.475	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	16	0.4	RNA PCR Primer, Index 7 (100% over 35bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTC	13	0.325	RNA PCR Primer, Index 32 (100% over 44bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	12	0.3	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGC	11	0.27499999999999997	RNA PCR Primer, Index 32 (100% over 50bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	10	0.25	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	10	0.25	No Hit
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	10	0.25	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	10	0.25	No Hit
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 25bp)
TTTGGCAATGGTAGAACTCACACCGTGGAATTCTCGGGTGCCAAGGAACT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 25bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCAAG	8	0.2	No Hit
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGGCAATGGTAGAACTCACTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	8	0.2	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	6	0.15	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	6	0.15	No Hit
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTGGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGGCAATGGTAGAACTCACATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	5	0.125	RNA PCR Primer, Index 7 (100% over 35bp)
CAACGGAATCCCAAAAGCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	5	0.125	No Hit
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	5	0.125	RNA PCR Primer, Index 2 (100% over 34bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TAGCACCATCTGAAATCGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
ACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTTGGAAT	5	0.125	No Hit
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	5	0.125	RNA PCR Primer, Index 2 (100% over 34bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGGCAATGGTAGAACTCACACCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
GAATACCGGGTGCTGTAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	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	0.275	0.0	0.0	0.0
2	0.0	0.325	0.0	0.0	0.0
3	0.0	0.325	0.0	0.0	0.0
4	0.0	0.325	0.0	0.0	0.0
5	0.0	0.325	0.0	0.0	0.0
6	0.0	0.4	0.0	0.0	0.0
7	0.0	0.8	0.0	0.0	0.0
8	0.0	0.875	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	1.2	0.0	0.0	0.0
12	0.0	1.475	0.0	0.0	0.0
13	0.0	1.7	0.0	0.0	0.0
14	0.0	1.925	0.0	0.0	0.0
15	0.0	2.2	0.0	0.0	0.0
16	0.0	3.125	0.0	0.0	0.0
17	0.0	3.875	0.0	0.0	0.0
18	0.0	4.825	0.0	0.0	0.0
19	0.0	5.525	0.0	0.0	0.0
20	0.0	6.55	0.0	0.0	0.0
21	0.0	11.475	0.0	0.0	0.0
22	0.0	24.375	0.0	0.0	0.0
23	0.0	54.425	0.0	0.0	0.0
24	0.0	68.425	0.0	0.0	0.0
25	0.0	74.175	0.0	0.0	0.0
26	0.0	75.875	0.0	0.0	0.0
27	0.0	76.85	0.0	0.0	0.0
28	0.0	77.65	0.0	0.0	0.0
29	0.0	78.525	0.0	0.0	0.0
30	0.0	79.15	0.0	0.0	0.0
31	0.0	80.05	0.0	0.0	0.0
32	0.0	81.6	0.0	0.0	0.0
33	0.0	82.725	0.0	0.0	0.0
34	0.0	85.3	0.0	0.0	0.0
35	0.0	86.2	0.0	0.0	0.0
36	0.0	86.825	0.0	0.0	0.0
37	0.0	87.95	0.0	0.0	0.0
38	0.0	88.45	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGGTAG	50	1.2732926E-11	44.531647	2
TCGGATC	25	3.4343255E-5	44.531647	1
CGGATCC	25	3.4343255E-5	44.531647	2
TGAGGTA	45	2.419256E-10	44.531647	1
TCACAGT	45	2.419256E-10	44.531647	1
CACAGTG	45	2.419256E-10	44.531647	2
TGTAAAC	30	1.7904422E-6	44.531647	1
GTAAACA	30	1.7904422E-6	44.531647	2
ACATTCA	20	6.54202E-4	44.531643	2
CCCTGAG	20	6.54202E-4	44.531643	2
AACATTC	20	6.54202E-4	44.531643	1
TCCCTGA	20	6.54202E-4	44.531643	1
GTAGATT	25	3.7082697E-5	43.975002	8
ACAGTGA	45	2.746674E-10	43.975002	3
ACCGGTC	45	2.746674E-10	43.975002	10
AACCGGT	45	2.746674E-10	43.975002	9
CTGAGCT	25	3.7082697E-5	43.975002	11
TAAACAT	30	1.9592044E-6	43.975002	3
TTGTATA	25	3.7082697E-5	43.975002	13
AAACATC	30	1.9592044E-6	43.975002	4
>>END_MODULE
Read 214680 spots for SRR5031060.sra
Written 214680 spots for SRR5031060.sra
Read 214680 spots for SRR5031060.sra
Written 214680 spots for SRR5031060.sra
Read 214680 spots for SRR5031060.sra
Written 214680 spots for SRR5031060.sra
Read 214680 spots for SRR5031060.sra
Written 214680 spots for SRR5031060.sra
Read 214680 spots for SRR5031060.sra
Written 214680 spots for SRR5031060.sra
Read 214680 spots for SRR5031060.sra
Written 214680 spots for SRR5031060.sra
Read 214680 spots for SRR5031060.sra
Written 214680 spots for SRR5031060.sra
Read 214680 spots for SRR5031060.sra
Written 214680 spots for SRR5031060.sra
Read 214680 spots for SRR5031060.sra
Written 214680 spots for SRR5031060.sra
Read 214680 spots for SRR5031060.sra
Written 214680 spots for SRR5031060.sra
Read 214680 spots for SRR5031060.sra
Written 214680 spots for SRR5031060.sra
Read 214683 spots for SRR5031060.sra
Written 214683 spots for SRR5031060.sra
SRR ids: ['SRR5031060.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_z_ze1jbj
SRR5031060.sra spots: 2576163
blocks: [[1, 214680], [214681, 429360], [429361, 644040], [644041, 858720], [858721, 1073400], [1073401, 1288080], [1288081, 1502760], [1502761, 1717440], [1717441, 1932120], [1932121, 2146800], [2146801, 2361480], [2361481, 2576163]]
SRR5031060 file size 445438
SRR5031060 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031060 SRR5031060_1.fastq
Input file:	SRR5031060_1.fastq
trimmed:	SRR5031060-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 07:15:48 2020 >> started

Wed Mar  4 07:15:50 2020 >> done (1.534s)
2576163 reads processed; of these:
    289 ( 0.01%) short reads filtered out after trimming by size control
      7 ( 0.00%) empty reads filtered out after trimming by size control
2575867 (99.99%) reads available; of these:
 126801 ( 4.92%) trimmed reads available after processing
2449066 (95.08%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     75	  0.00%
 19	     80	  0.00%
 20	    145	  0.01%
 21	    213	  0.01%
 22	    340	  0.01%
 23	    385	  0.01%
 24	    391	  0.02%
 25	    521	  0.02%
 26	    427	  0.02%
 27	    552	  0.02%
 28	    662	  0.03%
 29	   1037	  0.04%
 30	    648	  0.03%
 31	    714	  0.03%
 32	    780	  0.03%
 33	    954	  0.04%
 34	   1246	  0.05%
 35	   2189	  0.08%
 36	   2020	  0.08%
 37	   2396	  0.09%
 38	   2223	  0.09%
 39	   2479	  0.10%
 40	   2677	  0.10%
 41	   2826	  0.11%
 42	   3788	  0.15%
 43	   5316	  0.21%
 44	   6914	  0.27%
 45	   8166	  0.32%
 46	  11775	  0.46%
 47	  15584	  0.61%
 48	  24551	  0.95%
 49	  24727	  0.96%
 50	2449066	 95.08%
2575867 reads passed initial QC


criterion=sequence-density
sequence-density=87.66
sequence-density-rank=1
fanout-score=21.17
fanout-score-rank=1
prefix-density=89.52
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCC


criterion=fanout-score
sequence-density=87.66
sequence-density-rank=1
fanout-score=21.17
fanout-score-rank=1
prefix-density=89.52
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCC -o SRR5031060 -
Input file:	STDIN
trimmed:	SRR5031060-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCC
-- 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 07:16:05 2020 >> started

Wed Mar  4 07:16:09 2020 >> done (3.966s)
2517325 reads processed; of these:
 124559 ( 4.95%) short reads filtered out after trimming by size control
  11325 ( 0.45%) empty reads filtered out after trimming by size control
2381441 (94.60%) reads available; of these:
2276459 (95.59%) trimmed reads available after processing
 104982 ( 4.41%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  15314	  0.64%
 19	  27309	  1.15%
 20	 118378	  4.97%
 21	 309175	 12.98%
 22	 769325	 32.31%
 23	 368549	 15.48%
 24	 169992	  7.14%
 25	  44864	  1.88%
 26	  21449	  0.90%
 27	  17614	  0.74%
 28	  18140	  0.76%
 29	  15278	  0.64%
 30	  21044	  0.88%
 31	  38546	  1.62%
 32	  24275	  1.02%
 33	  65585	  2.75%
 34	  23192	  0.97%
 35	  18261	  0.77%
 36	  23758	  1.00%
 37	  11322	  0.48%
 38	  13583	  0.57%
 39	  12076	  0.51%
 40	  18933	  0.80%
 41	  21763	  0.91%
 42	  25193	  1.06%
 43	  18108	  0.76%
 44	  14526	  0.61%
 45	  18959	  0.80%
 46	  14237	  0.60%
 47	  12754	  0.54%
 48	   1145	  0.05%
 49	   1356	  0.06%
 50	  87438	  3.67%


criterion=sequence-density
sequence-density=4.17
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AAGCTGCCAGTTGAAGAACTGTA


criterion=fanout-score
sequence-density=0.03
sequence-density-rank=38
fanout-score=108.90
fanout-score-rank=1
prefix-density=3.02
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:16:31
                             Started mapping on |	Mar 04 07:16:32
                                    Finished on |	Mar 04 07:16:58
       Mapping speed, Million of reads per hour |	337.84

                          Number of input reads |	2439983
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1239998
                        Uniquely mapped reads % |	50.82%
                          Average mapped length |	24.27
                       Number of splices: Total |	1417
            Number of splices: Annotated (sjdb) |	225
                       Number of splices: GT/AG |	1333
                       Number of splices: GC/AG |	13
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	71
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.64
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	879629
             % of reads mapped to multiple loci |	36.05%
        Number of reads mapped to too many loci |	62691
             % of reads mapped to too many loci |	2.57%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.28%
                     % of reads unmapped: other |	1.28%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	320356	320356	320356
N_multimapping	879629	879629	879629
N_noFeature	78066	90106	891372
N_ambiguous	659786	355289	13134
UnstrandedReadsAssigned:502146 PositiveStrandReadsAssigned:794603 NegativeStrandReadsAssigned:335492
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031060 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: SRR5031060-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,439,983 reads, 605,747 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,093 rounds

 109283 SRR5031060.ke.tsv
  52636 SRR5031060.se.tsv
 161919 total
==> SRR5031060.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

==> SRR5031060.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031060 completed mapping pipeline successfully
