Starting /dee2/code/volunteer_pipeline.sh SRR5030891
    current disk space = 160628654080
    free memory = 73948420 
SRR5030891 SRAfilesize
b57c080c04bc79c82d864164e9a7141c  SRR5030891.sra
SRR5030891.sra file validated
SRR5030891 is single end
SRR5030891 is conventional basespace
SRR5030891 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030891_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	32.37025	33.0	31.0	34.0	31.0	34.0
2	32.73975	34.0	31.0	34.0	31.0	34.0
3	32.80325	34.0	31.0	34.0	31.0	34.0
4	36.23325	37.0	37.0	37.0	35.0	37.0
5	36.2195	37.0	37.0	37.0	35.0	37.0
6	35.99425	37.0	35.0	37.0	35.0	37.0
7	36.121	37.0	35.0	37.0	35.0	37.0
8	36.1995	37.0	36.0	37.0	35.0	37.0
9	37.9785	39.0	38.0	39.0	35.0	39.0
10	37.95875	39.0	38.0	39.0	35.0	39.0
11	37.92375	39.0	38.0	39.0	35.0	39.0
12	38.005	39.0	38.0	39.0	35.0	39.0
13	37.8635	39.0	38.0	39.0	35.0	39.0
14	39.279	41.0	39.0	41.0	36.0	41.0
15	39.3105	41.0	39.0	41.0	36.0	41.0
16	39.236	40.0	39.0	41.0	36.0	41.0
17	39.33225	41.0	39.0	41.0	36.0	41.0
18	39.37375	41.0	39.0	41.0	36.0	41.0
19	39.1705	40.0	39.0	41.0	36.0	41.0
20	39.1665	40.0	39.0	41.0	36.0	41.0
21	39.26	41.0	39.0	41.0	36.0	41.0
22	39.235	40.0	39.0	41.0	36.0	41.0
23	39.19175	40.0	39.0	41.0	36.0	41.0
24	38.55	40.0	38.0	41.0	34.0	41.0
25	38.70325	40.0	38.0	41.0	34.0	41.0
26	38.85425	40.0	38.0	41.0	35.0	41.0
27	38.853	40.0	38.0	41.0	35.0	41.0
28	38.79375	40.0	38.0	41.0	35.0	41.0
29	38.6245	40.0	38.0	41.0	34.0	41.0
30	38.25225	40.0	38.0	41.0	33.0	41.0
31	38.61025	40.0	38.0	41.0	34.0	41.0
32	38.792	40.0	38.0	41.0	35.0	41.0
33	37.05975	40.0	37.0	41.0	30.0	41.0
34	36.538	40.0	36.0	41.0	30.0	41.0
35	32.95575	38.0	31.0	40.0	15.0	41.0
36	30.00125	37.0	23.0	40.0	8.0	41.0
37	30.16325	36.0	25.0	40.0	7.0	41.0
38	32.69025	37.0	31.0	40.0	20.0	41.0
39	32.268	37.0	30.0	40.0	9.0	41.0
40	32.95475	38.0	32.0	40.0	9.0	41.0
41	30.6865	36.0	26.0	40.0	2.0	41.0
42	32.19975	37.0	31.0	40.0	2.0	41.0
43	30.55875	37.0	27.0	40.0	2.0	41.0
44	31.471	37.0	30.0	40.0	2.0	41.0
45	29.54325	37.0	26.0	40.0	2.0	41.0
46	27.44525	35.0	16.0	39.0	2.0	41.0
47	27.19975	34.0	19.0	39.0	2.0	41.0
48	27.863	35.0	22.0	39.0	2.0	41.0
49	26.13275	34.0	2.0	39.0	2.0	41.0
50	22.4515	30.0	2.0	37.0	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
15	1.0
16	2.0
17	0.0
18	3.0
19	3.0
20	5.0
21	11.0
22	22.0
23	22.0
24	37.0
25	54.0
26	102.0
27	134.0
28	86.0
29	116.0
30	156.0
31	153.0
32	163.0
33	179.0
34	229.0
35	278.0
36	337.0
37	441.0
38	693.0
39	773.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	13.4918648310388	25.406758448060074	43.65456821026283	17.4468085106383
2	26.775	23.65	20.625	28.95
3	22.8	21.0	20.625	35.575
4	31.175000000000004	26.8	16.3	25.724999999999998
5	23.35	38.7	25.724999999999998	12.225
6	29.675	16.225	37.275000000000006	16.825000000000003
7	20.75	20.3	24.975	33.975
8	27.175	30.475	16.950000000000003	25.4
9	19.35	33.35	30.25	17.05
10	25.45	21.025	29.15	24.375
11	37.025000000000006	14.75	15.4	32.824999999999996
12	18.5	23.9	27.150000000000002	30.45
13	26.700000000000003	19.825	33.125	20.349999999999998
14	25.074999999999996	30.975	24.625	19.325
15	32.824999999999996	24.25	25.124999999999996	17.8
16	20.225	21.55	23.375	34.849999999999994
17	23.325000000000003	25.674999999999997	33.525	17.474999999999998
18	21.925	19.275000000000002	32.35	26.450000000000003
19	35.225	16.375	30.45	17.95
20	39.45	16.725	29.5	14.325
21	26.174999999999997	21.025	26.200000000000003	26.6
22	30.125	14.674999999999999	41.6	13.600000000000001
23	25.4	16.275000000000002	40.9	17.424999999999997
24	48.3	15.15	23.575	12.975
25	46.400000000000006	22.425	15.5	15.675
26	26.775	39.5	15.525	18.2
27	17.549999999999997	42.95	21.425	18.075
28	15.375	25.275	41.699999999999996	17.65
29	16.2	14.649999999999999	51.575	17.575
30	12.325	9.375	33.275	45.025
31	15.725	7.925	45.675	30.675
32	28.225	8.799999999999999	22.400000000000002	40.575
33	46.2	13.350000000000001	14.475	25.974999999999998
34	53.025	8.375	19.6	19.0
35	54.225	9.375	21.025	15.375
36	58.050000000000004	11.3	16.475	14.174999999999999
37	38.7	14.05	21.775	25.474999999999998
38	26.825	17.525	13.65	42.0
39	19.725	25.8	14.000000000000002	40.475
40	18.575	42.9	15.275	23.25
41	26.325	41.475	13.125	19.075
42	45.7	28.15	14.774999999999999	11.375
43	41.075	32.800000000000004	13.075000000000001	13.05
44	29.875	43.8	10.100000000000001	16.225
45	21.875	44.1	12.25	21.775
46	16.975	28.375	23.799999999999997	30.85
47	13.200000000000001	16.625	35.949999999999996	34.225
48	15.1	13.025	23.025000000000002	48.85
49	16.975	22.7	14.875	45.45
50	32.05	21.375	12.825000000000001	33.75
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	1.0
1	0.5
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.5
16	1.0
17	0.5
18	0.0
19	0.0
20	0.0
21	1.0
22	2.0
23	1.0
24	0.0
25	1.5
26	3.0
27	3.0
28	3.0
29	3.0
30	3.0
31	9.0
32	15.0
33	23.0
34	31.0
35	48.5
36	66.0
37	96.0
38	126.0
39	110.0
40	94.0
41	81.0
42	68.0
43	103.5
44	139.0
45	178.0
46	217.0
47	241.0
48	265.0
49	334.5
50	404.0
51	565.0
52	726.0
53	617.5
54	509.0
55	448.0
56	387.0
57	352.0
58	317.0
59	235.5
60	154.0
61	122.0
62	90.0
63	145.0
64	200.0
65	124.5
66	49.0
67	30.5
68	12.0
69	21.0
70	30.0
71	46.0
72	62.0
73	36.0
74	10.0
75	9.0
76	8.0
77	4.5
78	1.0
79	3.5
80	6.0
81	3.5
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	0.125
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	51.7
#Duplication Level	Percentage of deduplicated	Percentage of total
1	81.47969052224371	42.125
2	8.075435203094777	8.35
3	2.998065764023211	4.65
4	1.1121856866537718	2.3
5	1.160541586073501	3.0
6	0.7736943907156674	2.4
7	0.4835589941972921	1.7500000000000002
8	0.24177949709864605	1.0
9	0.3868471953578337	1.7999999999999998
>10	3.1914893617021276	27.175
>50	0.04835589941972921	2.3
>100	0.04835589941972921	3.15
>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
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	126	3.15	No Hit
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	92	2.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	38	0.95	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	26	0.65	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	25	0.625	RNA PCR Primer, Index 1 (100% over 33bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTCGTATGC	21	0.525	RNA PCR Primer, Index 48 (100% over 50bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	21	0.525	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	20	0.5	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (96% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	18	0.44999999999999996	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	18	0.44999999999999996	RNA PCR Primer, Index 5 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	18	0.44999999999999996	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 27bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	17	0.42500000000000004	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	17	0.42500000000000004	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	17	0.42500000000000004	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	16	0.4	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	16	0.4	RNA PCR Primer, Index 1 (96% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	15	0.375	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	15	0.375	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	15	0.375	RNA PCR Primer, Index 1 (96% over 27bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	15	0.375	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	15	0.375	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 27bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	14	0.35000000000000003	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	14	0.35000000000000003	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	13	0.325	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTC	12	0.3	RNA PCR Primer, Index 48 (100% over 44bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	12	0.3	No Hit
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	12	0.3	No Hit
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	11	0.27499999999999997	No Hit
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	11	0.27499999999999997	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	10	0.25	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	10	0.25	No Hit
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	10	0.25	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	10	0.25	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	10	0.25	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	10	0.25	No Hit
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCC	10	0.25	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	10	0.25	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TACCATGATGATAACATAGTTCAGCAGACTTAACTCTGATGAACAATCAT	9	0.22499999999999998	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	9	0.22499999999999998	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	9	0.22499999999999998	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	8	0.2	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAATTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (95% over 23bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	6	0.15	No Hit
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	6	0.15	RNA PCR Primer, Index 1 (100% over 32bp)
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	6	0.15	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	6	0.15	No Hit
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGGG	6	0.15	No Hit
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	6	0.15	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGTGCCAAGGAACTCCAG	5	0.125	No Hit
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
CTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCTA	5	0.125	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGC	5	0.125	RNA PCR Primer, Index 1 (96% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	5	0.125	No Hit
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CTGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTC	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	0.55	0.0	0.0	0.0
2	0.0	0.575	0.0	0.0	0.0
3	0.0	0.625	0.0	0.0	0.0
4	0.0	0.675	0.0	0.0	0.0
5	0.0	0.7	0.0	0.0	0.0
6	0.0	0.75	0.0	0.0	0.0
7	0.0	1.1	0.0	0.0	0.0
8	0.0	1.25	0.0	0.0	0.0
9	0.0	1.275	0.0	0.0	0.0
10	0.0	1.425	0.0	0.0	0.0
11	0.0	1.6	0.0	0.0	0.0
12	0.0	1.75	0.0	0.0	0.0
13	0.0	1.85	0.0	0.0	0.0
14	0.0	1.975	0.0	0.0	0.0
15	0.0	2.5	0.0	0.0	0.0
16	0.0	3.125	0.0	0.0	0.0
17	0.0	3.75	0.0	0.0	0.0
18	0.0	5.05	0.0	0.0	0.0
19	0.0	5.725	0.0	0.0	0.0
20	0.0	6.45	0.0	0.0	0.0
21	0.0	10.4	0.0	0.0	0.0
22	0.0	18.25	0.0	0.0	0.0
23	0.0	42.55	0.0	0.0	0.0
24	0.0	53.25	0.0	0.0	0.0
25	0.0	57.925	0.0	0.0	0.0
26	0.0	59.4	0.0	0.0	0.0
27	0.0	60.075	0.0	0.0	0.0
28	0.0	60.6	0.0	0.0	0.0
29	0.0	60.85	0.0	0.0	0.0
30	0.0	61.225	0.0	0.0	0.0
31	0.0	61.6	0.0	0.0	0.0
32	0.0	62.375	0.0	0.0	0.0
33	0.0	63.05	0.0	0.0	0.0
34	0.0	67.225	0.0	0.0	0.0
35	0.0	68.5	0.0	0.0	0.0
36	0.0	69.025	0.0	0.0	0.0
37	0.0	70.2	0.0	0.0	0.0
38	0.0	70.625	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGGTAG	20	6.952051E-4	44.000004	2
TAAACAT	20	6.952051E-4	44.000004	3
AAACATC	20	6.952051E-4	44.000004	4
GAGTGGA	20	6.952051E-4	44.000004	20
AGTGGAA	20	6.952051E-4	44.000004	21
GTGAGTG	20	6.952051E-4	44.000004	18
ACATCCT	20	6.952051E-4	44.000004	6
CGGTGAG	20	6.952051E-4	44.000004	16
TGAGGTA	20	6.952051E-4	44.000004	1
AGGTAGT	20	6.952051E-4	44.000004	3
TGTAAAC	20	6.952051E-4	44.000004	1
GTAAACA	20	6.952051E-4	44.000004	2
AACATCC	20	6.952051E-4	44.000004	5
AACGCTG	25	3.6958358E-5	44.0	8
ACGCTGT	25	3.6958358E-5	44.0	9
TTCAACG	25	3.6958358E-5	44.0	5
TCGGTGA	25	3.6958358E-5	44.0	15
CATTCAA	25	3.6958358E-5	44.0	3
TCAACGC	25	3.6958358E-5	44.0	6
ACATTCA	25	3.6958358E-5	44.0	2
>>END_MODULE
Read 248354 spots for SRR5030891.sra
Written 248354 spots for SRR5030891.sra
Read 248354 spots for SRR5030891.sra
Written 248354 spots for SRR5030891.sra
Read 248354 spots for SRR5030891.sra
Written 248354 spots for SRR5030891.sra
Read 248354 spots for SRR5030891.sra
Written 248354 spots for SRR5030891.sra
Read 248354 spots for SRR5030891.sra
Written 248354 spots for SRR5030891.sra
Read 248354 spots for SRR5030891.sra
Written 248354 spots for SRR5030891.sra
Read 248354 spots for SRR5030891.sra
Written 248354 spots for SRR5030891.sra
Read 248354 spots for SRR5030891.sra
Written 248354 spots for SRR5030891.sra
Read 248354 spots for SRR5030891.sra
Written 248354 spots for SRR5030891.sra
Read 248354 spots for SRR5030891.sra
Written 248354 spots for SRR5030891.sra
Read 248354 spots for SRR5030891.sra
Written 248354 spots for SRR5030891.sra
Read 248359 spots for SRR5030891.sra
Written 248359 spots for SRR5030891.sra
SRR ids: ['SRR5030891.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_rwbgumoe
SRR5030891.sra spots: 2980253
blocks: [[1, 248354], [248355, 496708], [496709, 745062], [745063, 993416], [993417, 1241770], [1241771, 1490124], [1490125, 1738478], [1738479, 1986832], [1986833, 2235186], [2235187, 2483540], [2483541, 2731894], [2731895, 2980253]]
SRR5030891 file size 515466
SRR5030891 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030891 SRR5030891_1.fastq
Input file:	SRR5030891_1.fastq
trimmed:	SRR5030891-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 06:38:01 2020 >> started

Wed Mar  4 06:38:02 2020 >> done (1.622s)
2980253 reads processed; of these:
    164 ( 0.01%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
2980084 (99.99%) reads available; of these:
 362595 (12.17%) trimmed reads available after processing
2617489 (87.83%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     46	  0.00%
 19	     71	  0.00%
 20	    129	  0.00%
 21	    167	  0.01%
 22	    266	  0.01%
 23	    378	  0.01%
 24	    403	  0.01%
 25	    644	  0.02%
 26	    519	  0.02%
 27	    662	  0.02%
 28	    922	  0.03%
 29	   1265	  0.04%
 30	    969	  0.03%
 31	   1435	  0.05%
 32	   3480	  0.12%
 33	  10352	  0.35%
 34	  21636	  0.73%
 35	   5309	  0.18%
 36	   5956	  0.20%
 37	   3576	  0.12%
 38	   6695	  0.22%
 39	   6968	  0.23%
 40	  12990	  0.44%
 41	   6843	  0.23%
 42	  18856	  0.63%
 43	   8263	  0.28%
 44	  30934	  1.04%
 45	  22973	  0.77%
 46	  22848	  0.77%
 47	  24277	  0.81%
 48	  61984	  2.08%
 49	  80779	  2.71%
 50	2617489	 87.83%
2980084 reads passed initial QC


criterion=sequence-density
sequence-density=70.45
sequence-density-rank=1
fanout-score=21.65
fanout-score-rank=2
prefix-density=73.32
prefix-fanout=20.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTCGTATGCC


criterion=fanout-score
sequence-density=3.03
sequence-density-rank=3
fanout-score=75.49
fanout-score-rank=1
prefix-density=72.44
prefix-fanout=3.2
sequence=GAATTCTCGGGGGCCAAGGAACT
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -t 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTCGTATGCC -o SRR5030891 -
Input file:	STDIN
trimmed:	SRR5030891-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTCGTATGCC
-- 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 06:38:17 2020 >> started

Wed Mar  4 06:38:20 2020 >> done (3.196s)
2896138 reads processed; of these:
 122557 ( 4.23%) short reads filtered out after trimming by size control
  15508 ( 0.54%) empty reads filtered out after trimming by size control
2758073 (95.23%) reads available; of these:
2191260 (79.45%) trimmed reads available after processing
 566813 (20.55%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  17536	  0.64%
 19	  23228	  0.84%
 20	 115198	  4.18%
 21	 248090	  9.00%
 22	 669381	 24.27%
 23	 328286	 11.90%
 24	 147673	  5.35%
 25	  43021	  1.56%
 26	  23346	  0.85%
 27	  18790	  0.68%
 28	  20538	  0.74%
 29	  16749	  0.61%
 30	  21852	  0.79%
 31	  24867	  0.90%
 32	  26822	  0.97%
 33	 129961	  4.71%
 34	  31582	  1.15%
 35	  22673	  0.82%
 36	  30566	  1.11%
 37	  15808	  0.57%
 38	  18481	  0.67%
 39	  18885	  0.68%
 40	  31990	  1.16%
 41	  34342	  1.25%
 42	  41687	  1.51%
 43	  28586	  1.04%
 44	  26970	  0.98%
 45	  29938	  1.09%
 46	  25674	  0.93%
 47	  21374	  0.77%
 48	   8747	  0.32%
 49	  16874	  0.61%
 50	 478558	 17.35%


criterion=sequence-density
sequence-density=5.35
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.59
sequence-density-rank=25
fanout-score=11.24
fanout-score-rank=1
prefix-density=6.62
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 06:38:41
                             Started mapping on |	Mar 04 06:38:41
                                    Finished on |	Mar 04 06:39:03
       Mapping speed, Million of reads per hour |	465.06

                          Number of input reads |	2842019
                      Average input read length |	31
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1533986
                        Uniquely mapped reads % |	53.98%
                          Average mapped length |	30.24
                       Number of splices: Total |	1777
            Number of splices: Annotated (sjdb) |	255
                       Number of splices: GT/AG |	1659
                       Number of splices: GC/AG |	26
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	92
                      Mismatch rate per base, % |	0.22%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.32
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	807229
             % of reads mapped to multiple loci |	28.40%
        Number of reads mapped to too many loci |	68011
             % of reads mapped to too many loci |	2.39%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	14.68%
                     % of reads unmapped: other |	0.55%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	500804	500804	500804
N_multimapping	807229	807229	807229
N_noFeature	74792	94047	1136519
N_ambiguous	844131	507258	18553
UnstrandedReadsAssigned:615063 PositiveStrandReadsAssigned:932681 NegativeStrandReadsAssigned:378914
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030891 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: SRR5030891-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,842,019 reads, 669,124 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,103 rounds

 109283 SRR5030891.ke.tsv
  52636 SRR5030891.se.tsv
 161919 total
==> SRR5030891.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

==> SRR5030891.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030891 completed mapping pipeline successfully
