Starting /dee2/code/volunteer_pipeline.sh SRR5031027
    current disk space = 160545456128
    free memory = 73932012 
SRR5031027 SRAfilesize
6d96d440f0f4c366b999c7ef7f9d74bb  SRR5031027.sra
SRR5031027.sra file validated
SRR5031027 is single end
SRR5031027 is conventional basespace
SRR5031027 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031027_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	32.30725	33.0	31.0	34.0	30.0	34.0
2	32.54675	34.0	31.0	34.0	31.0	34.0
3	32.52875	34.0	31.0	34.0	31.0	34.0
4	36.12	37.0	35.0	37.0	35.0	37.0
5	36.07975	37.0	35.0	37.0	35.0	37.0
6	35.8245	37.0	35.0	37.0	33.0	37.0
7	35.8695	37.0	35.0	37.0	35.0	37.0
8	35.9585	37.0	35.0	37.0	35.0	37.0
9	37.50925	39.0	37.0	39.0	35.0	39.0
10	37.5015	39.0	37.0	39.0	35.0	39.0
11	37.215	39.0	37.0	39.0	33.0	39.0
12	37.55625	39.0	37.0	39.0	35.0	39.0
13	37.60975	39.0	37.0	39.0	35.0	39.0
14	39.05225	40.0	38.0	41.0	36.0	41.0
15	38.86025	40.0	38.0	41.0	35.0	41.0
16	38.844	40.0	38.0	41.0	35.0	41.0
17	39.00475	40.0	38.0	41.0	35.0	41.0
18	38.9555	40.0	38.0	41.0	35.0	41.0
19	38.76375	40.0	38.0	41.0	34.0	41.0
20	38.76275	40.0	38.0	41.0	34.0	41.0
21	38.80325	40.0	38.0	41.0	35.0	41.0
22	38.85775	40.0	38.0	41.0	35.0	41.0
23	38.54	40.0	38.0	41.0	34.0	41.0
24	38.83875	40.0	38.0	41.0	35.0	41.0
25	39.002	40.0	38.0	41.0	35.0	41.0
26	38.791	40.0	38.0	41.0	35.0	41.0
27	38.91275	40.0	39.0	41.0	35.0	41.0
28	38.61875	40.0	38.0	41.0	34.0	41.0
29	38.27	40.0	38.0	41.0	33.0	41.0
30	38.1615	40.0	38.0	41.0	33.0	41.0
31	38.42425	40.0	38.0	41.0	33.0	41.0
32	38.46375	40.0	38.0	41.0	34.0	41.0
33	38.13625	40.0	38.0	41.0	33.0	41.0
34	38.28725	40.0	38.0	41.0	33.0	41.0
35	37.99775	40.0	38.0	41.0	33.0	41.0
36	37.744	40.0	37.0	41.0	33.0	41.0
37	37.16525	39.0	37.0	41.0	31.0	41.0
38	36.86975	39.0	36.0	40.0	31.0	41.0
39	37.551	40.0	37.0	41.0	32.0	41.0
40	37.61225	40.0	37.0	41.0	33.0	41.0
41	37.7485	40.0	37.0	41.0	32.0	41.0
42	37.691	40.0	37.0	41.0	33.0	41.0
43	37.71375	40.0	37.0	41.0	33.0	41.0
44	37.58275	40.0	37.0	41.0	33.0	41.0
45	37.478	40.0	37.0	41.0	33.0	41.0
46	37.31825	40.0	37.0	41.0	32.0	41.0
47	37.00075	40.0	36.0	41.0	31.0	41.0
48	36.61775	40.0	36.0	41.0	30.0	41.0
49	36.7955	40.0	36.0	41.0	31.0	41.0
50	36.1645	39.0	35.0	41.0	30.0	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
13	1.0
14	0.0
15	1.0
16	1.0
17	0.0
18	4.0
19	2.0
20	4.0
21	2.0
22	2.0
23	10.0
24	6.0
25	9.0
26	14.0
27	33.0
28	33.0
29	39.0
30	52.0
31	60.0
32	75.0
33	109.0
34	150.0
35	206.0
36	280.0
37	436.0
38	746.0
39	1725.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.05	24.6	48.9	16.45
2	25.212819228843266	27.341011517275916	18.552829243865798	28.893340010015024
3	22.475	21.325	22.15	34.050000000000004
4	34.25	27.6	14.2	23.95
5	24.075	36.575	27.375	11.975
6	31.7	16.25	36.85	15.2
7	15.775	23.75	21.25	39.225
8	25.45	27.700000000000003	16.650000000000002	30.2
9	21.6	32.75	27.875	17.775
10	20.974999999999998	22.825	27.6	28.599999999999998
11	34.225	10.225	16.900000000000002	38.65
12	18.05	19.225	29.575000000000003	33.15
13	30.725	16.6	34.675	18.0
14	32.0	29.25	22.45	16.3
15	35.9	22.6	27.750000000000004	13.750000000000002
16	20.424999999999997	16.375	24.349999999999998	38.85
17	27.400000000000002	22.725	35.8	14.075
18	26.424999999999997	16.45	28.999999999999996	28.125
19	34.875	14.649999999999999	33.675	16.8
20	44.574999999999996	15.375	26.75	13.3
21	23.150000000000002	20.200000000000003	29.7	26.950000000000003
22	29.95	11.55	47.175	11.325000000000001
23	28.725	12.825000000000001	43.95	14.499999999999998
24	51.65	13.900000000000002	25.6	8.85
25	49.175000000000004	24.75	16.25	9.825000000000001
26	28.775000000000002	44.800000000000004	14.299999999999999	12.125
27	15.85	45.1	25.025	14.025000000000002
28	11.799999999999999	23.225	48.6	16.375
29	13.625000000000002	13.025	54.474999999999994	18.875
30	11.15	6.775	36.25	45.824999999999996
31	15.675	5.75	44.625	33.95
32	29.125	6.1	21.675	43.1
33	53.075	9.675	14.249999999999998	23.0
34	60.375	7.5249999999999995	16.625	15.475
35	64.025	6.550000000000001	19.0	10.424999999999999
36	42.199999999999996	7.3	36.275	14.224999999999998
37	43.675000000000004	12.2	19.5	24.625
38	23.400000000000002	16.900000000000002	12.975	46.725
39	17.5	23.599999999999998	11.1	47.8
40	16.725	46.85	10.925	25.5
41	25.7	47.325	9.125	17.849999999999998
42	47.699999999999996	29.475	11.5	11.325000000000001
43	50.949999999999996	29.675	8.200000000000001	11.175
44	30.525000000000002	46.9	8.875	13.700000000000001
45	19.1	48.05	12.9	19.950000000000003
46	13.225000000000001	26.05	18.425	42.3
47	9.45	15.45	38.25	36.85
48	11.200000000000001	13.025	21.025	54.75
49	13.55	18.525	16.05	51.87500000000001
50	19.8	35.875	13.5	30.825000000000003
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	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	0.5
30	1.0
31	4.0
32	7.0
33	9.0
34	11.0
35	14.5
36	18.0
37	25.5
38	33.0
39	35.0
40	37.0
41	42.0
42	47.0
43	88.0
44	129.0
45	163.0
46	197.0
47	288.5
48	380.0
49	516.5
50	653.0
51	764.5
52	876.0
53	667.5
54	459.0
55	481.5
56	504.0
57	365.0
58	226.0
59	156.0
60	86.0
61	64.0
62	42.0
63	83.0
64	124.0
65	71.5
66	19.0
67	15.0
68	11.0
69	20.0
70	29.0
71	63.5
72	98.0
73	52.0
74	6.0
75	3.5
76	1.0
77	2.0
78	3.0
79	2.5
80	2.0
81	1.5
82	1.0
83	0.5
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	0.0
2	0.15
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	38.074999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.98358502954694	28.549999999999997
2	11.424819435325016	8.7
3	3.545633617859488	4.05
4	2.298095863427446	3.5000000000000004
5	1.510177281680893	2.875
6	0.6565988181221274	1.5
7	0.6565988181221274	1.7500000000000002
8	0.3939592908732764	1.2
9	0.6565988181221274	2.25
>10	3.217334208798424	22.725
>50	0.3939592908732764	11.95
>100	0.2626395272488509	10.95
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	119	2.9749999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	115	2.875	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	103	2.5749999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	101	2.5250000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	80	2.0	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	80	2.0	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	79	1.975	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	77	1.925	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	65	1.625	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	46	1.15	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	43	1.075	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	32	0.8	RNA PCR Primer, Index 5 (97% over 35bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	21	0.525	RNA PCR Primer, Index 1 (100% over 30bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGC	20	0.5	RNA PCR Primer, Index 47 (100% over 50bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	18	0.44999999999999996	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	17	0.42500000000000004	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	16	0.4	No Hit
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	13	0.325	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCG	13	0.325	RNA PCR Primer, Index 10 (97% over 36bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGA	12	0.3	RNA PCR Primer, Index 47 (100% over 37bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	12	0.3	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	12	0.3	RNA PCR Primer, Index 1 (100% over 31bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTC	12	0.3	RNA PCR Primer, Index 47 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	11	0.27499999999999997	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	9	0.22499999999999998	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 24bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAG	6	0.15	RNA PCR Primer, Index 47 (100% over 39bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	6	0.15	No Hit
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTAT	5	0.125	RNA PCR Primer, Index 47 (100% over 48bp)
GGAAAGGATGAACGAACTTGGCCTGACCTGGAATTCTCGGGTGCCAAGGA	5	0.125	RNA PCR Primer, Index 1 (100% over 22bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TATTGCACTCGTCCCGGCCTCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	5	0.125	No Hit
TGAGGTAGGAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTGGCCCTCTCTGCCCTTCCGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
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	0.525	0.0	0.0	0.0
2	0.0	0.55	0.0	0.0	0.0
3	0.0	0.7	0.0	0.0	0.0
4	0.0	0.775	0.0	0.0	0.0
5	0.0	0.825	0.0	0.0	0.0
6	0.0	0.85	0.0	0.0	0.0
7	0.0	1.225	0.0	0.0	0.0
8	0.0	1.375	0.0	0.0	0.0
9	0.0	1.425	0.0	0.0	0.0
10	0.0	1.575	0.0	0.0	0.0
11	0.0	1.8	0.0	0.0	0.0
12	0.0	2.175	0.0	0.0	0.0
13	0.0	2.35	0.0	0.0	0.0
14	0.0	2.85	0.0	0.0	0.0
15	0.0	3.575	0.0	0.0	0.0
16	0.0	5.05	0.0	0.0	0.0
17	0.0	5.875	0.0	0.0	0.0
18	0.0	6.8	0.0	0.0	0.0
19	0.0	7.55	0.0	0.0	0.0
20	0.0	8.625	0.0	0.0	0.0
21	0.0	14.15	0.0	0.0	0.0
22	0.0	25.725	0.0	0.0	0.0
23	0.0	54.0	0.0	0.0	0.0
24	0.0	66.625	0.0	0.0	0.0
25	0.0	72.65	0.0	0.0	0.0
26	0.0	73.975	0.0	0.0	0.0
27	0.0	74.875	0.0	0.0	0.0
28	0.0	75.4	0.0	0.0	0.0
29	0.0	76.05	0.0	0.0	0.0
30	0.0	76.625	0.0	0.0	0.0
31	0.0	77.5	0.0	0.0	0.0
32	0.0	78.225	0.0	0.0	0.0
33	0.0	79.45	0.0	0.0	0.0
34	0.0	82.65	0.0	0.0	0.0
35	0.0	83.35	0.0	0.0	0.0
36	0.0	84.15	0.0	0.0	0.0
37	0.0	85.125	0.0	0.0	0.0
38	0.0	85.75	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGAGACC	20	6.952051E-4	44.000004	5
ACAGTGA	20	6.952051E-4	44.000004	3
ACCGGTC	20	6.952051E-4	44.000004	10
AACGCTG	45	2.728484E-10	44.000004	8
ACGCTGT	45	2.728484E-10	44.000004	9
AACCGGT	20	6.952051E-4	44.000004	9
CTGAGAC	20	6.952051E-4	44.000004	4
AGCTTGG	40	5.315087E-9	44.000004	14
TTCAACG	45	2.728484E-10	44.000004	5
GAGCTTG	40	5.315087E-9	44.000004	13
GGATCCG	40	5.315087E-9	44.000004	3
CCGTCTG	40	5.315087E-9	44.000004	7
CCTGAGA	20	6.952051E-4	44.000004	3
TCGGATC	40	5.315087E-9	44.000004	1
CATTCAA	45	2.728484E-10	44.000004	3
TCAACGC	45	2.728484E-10	44.000004	6
CGGATCC	40	5.315087E-9	44.000004	2
GAACCGG	20	6.952051E-4	44.000004	8
GATCCGT	40	5.315087E-9	44.000004	4
CCCTGAG	20	6.952051E-4	44.000004	2
>>END_MODULE
Read 140409 spots for SRR5031027.sra
Written 140409 spots for SRR5031027.sra
Read 140409 spots for SRR5031027.sra
Written 140409 spots for SRR5031027.sra
Read 140409 spots for SRR5031027.sra
Written 140409 spots for SRR5031027.sra
Read 140409 spots for SRR5031027.sra
Written 140409 spots for SRR5031027.sra
Read 140409 spots for SRR5031027.sra
Written 140409 spots for SRR5031027.sra
Read 140409 spots for SRR5031027.sra
Written 140409 spots for SRR5031027.sra
Read 140409 spots for SRR5031027.sra
Written 140409 spots for SRR5031027.sra
Read 140409 spots for SRR5031027.sra
Written 140409 spots for SRR5031027.sra
Read 140409 spots for SRR5031027.sra
Written 140409 spots for SRR5031027.sra
Read 140409 spots for SRR5031027.sra
Written 140409 spots for SRR5031027.sra
Read 140409 spots for SRR5031027.sra
Written 140409 spots for SRR5031027.sra
Read 140409 spots for SRR5031027.sra
Written 140409 spots for SRR5031027.sra
SRR ids: ['SRR5031027.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_67hhdhg3
SRR5031027.sra spots: 1684908
blocks: [[1, 140409], [140410, 280818], [280819, 421227], [421228, 561636], [561637, 702045], [702046, 842454], [842455, 982863], [982864, 1123272], [1123273, 1263681], [1263682, 1404090], [1404091, 1544499], [1544500, 1684908]]
SRR5031027 file size 290959
SRR5031027 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031027 SRR5031027_1.fastq
Input file:	SRR5031027_1.fastq
trimmed:	SRR5031027-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 07:09:05 2020 >> started

Wed Mar  4 07:09:07 2020 >> done (1.575s)
1684908 reads processed; of these:
    103 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
1684799 (99.99%) reads available; of these:
  97655 ( 5.80%) trimmed reads available after processing
1587144 (94.20%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     34	  0.00%
 19	     30	  0.00%
 20	     75	  0.00%
 21	    108	  0.01%
 22	    203	  0.01%
 23	    230	  0.01%
 24	    204	  0.01%
 25	    327	  0.02%
 26	    267	  0.02%
 27	    309	  0.02%
 28	    415	  0.02%
 29	    578	  0.03%
 30	    435	  0.03%
 31	    448	  0.03%
 32	    557	  0.03%
 33	    711	  0.04%
 34	    971	  0.06%
 35	   1865	  0.11%
 36	   1581	  0.09%
 37	   1743	  0.10%
 38	   1734	  0.10%
 39	   1811	  0.11%
 40	   1930	  0.11%
 41	   2096	  0.12%
 42	   2772	  0.16%
 43	   3910	  0.23%
 44	   5114	  0.30%
 45	   6585	  0.39%
 46	   9973	  0.59%
 47	  11171	  0.66%
 48	  17636	  1.05%
 49	  21832	  1.30%
 50	1587144	 94.20%
1684799 reads passed initial QC


criterion=sequence-density
sequence-density=85.59
sequence-density-rank=1
fanout-score=21.11
fanout-score-rank=1
prefix-density=87.37
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGCC


criterion=fanout-score
sequence-density=85.59
sequence-density-rank=1
fanout-score=21.11
fanout-score-rank=1
prefix-density=87.37
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGCC -o SRR5031027 -
Input file:	STDIN
trimmed:	SRR5031027-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGCC
-- 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 07:09:19 2020 >> started

Wed Mar  4 07:09:22 2020 >> done (2.933s)
1645618 reads processed; of these:
 107696 ( 6.54%) short reads filtered out after trimming by size control
   8762 ( 0.53%) empty reads filtered out after trimming by size control
1529160 (92.92%) reads available; of these:
1437727 (94.02%) trimmed reads available after processing
  91433 ( 5.98%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   9316	  0.61%
 19	  18353	  1.20%
 20	  83545	  5.46%
 21	 193439	 12.65%
 22	 478632	 31.30%
 23	 219815	 14.37%
 24	  92081	  6.02%
 25	  23616	  1.54%
 26	  12482	  0.82%
 27	  10871	  0.71%
 28	  11039	  0.72%
 29	   9152	  0.60%
 30	  14193	  0.93%
 31	  16129	  1.05%
 32	  18693	  1.22%
 33	  58055	  3.80%
 34	  17399	  1.14%
 35	  13849	  0.91%
 36	  16409	  1.07%
 37	   8130	  0.53%
 38	   8757	  0.57%
 39	   8546	  0.56%
 40	  12320	  0.81%
 41	  15959	  1.04%
 42	  18930	  1.24%
 43	  13897	  0.91%
 44	  10202	  0.67%
 45	  13471	  0.88%
 46	  10701	  0.70%
 47	   8816	  0.58%
 48	    870	  0.06%
 49	   1486	  0.10%
 50	  80007	  5.23%


criterion=sequence-density
sequence-density=7.59
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=2.21
sequence-density-rank=8
fanout-score=20.62
fanout-score-rank=1
prefix-density=2.27
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGC
                                 Started job on |	Mar 04 07:09:45
                             Started mapping on |	Mar 04 07:09:46
                                    Finished on |	Mar 04 07:10:11
       Mapping speed, Million of reads per hour |	225.84

                          Number of input reads |	1568341
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	785850
                        Uniquely mapped reads % |	50.11%
                          Average mapped length |	24.57
                       Number of splices: Total |	856
            Number of splices: Annotated (sjdb) |	198
                       Number of splices: GT/AG |	799
                       Number of splices: GC/AG |	17
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	39
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.69
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.23
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	548175
             % of reads mapped to multiple loci |	34.95%
        Number of reads mapped to too many loci |	39720
             % of reads mapped to too many loci |	2.53%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.74%
                     % of reads unmapped: other |	0.67%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	234316	234316	234316
N_multimapping	548175	548175	548175
N_noFeature	38651	48468	538580
N_ambiguous	444308	229046	7517
UnstrandedReadsAssigned:302891 PositiveStrandReadsAssigned:508336 NegativeStrandReadsAssigned:239753
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031027 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: SRR5031027-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,568,341 reads, 398,405 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,054 rounds

 109283 SRR5031027.ke.tsv
  52636 SRR5031027.se.tsv
 161919 total
==> SRR5031027.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

==> SRR5031027.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031027 completed mapping pipeline successfully
