Starting /dee2/code/volunteer_pipeline.sh SRR5030927
    current disk space = 160626294784
    free memory = 73942076 
SRR5030927 SRAfilesize
4410078794f0e9f7092cae2d9b4a168d  SRR5030927.sra
SRR5030927.sra file validated
SRR5030927 is single end
SRR5030927 is conventional basespace
SRR5030927 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030927_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	51
>>END_MODULE
>>Per base sequence quality	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.43	33.0	31.0	34.0	31.0	34.0
2	32.756	34.0	31.0	34.0	31.0	34.0
3	32.77125	34.0	31.0	34.0	31.0	34.0
4	36.2495	37.0	37.0	37.0	35.0	37.0
5	36.27	37.0	37.0	37.0	35.0	37.0
6	35.98875	37.0	35.0	37.0	35.0	37.0
7	36.08625	37.0	35.0	37.0	35.0	37.0
8	36.1785	37.0	36.0	37.0	35.0	37.0
9	37.93375	39.0	38.0	39.0	35.0	39.0
10	37.94375	39.0	38.0	39.0	35.0	39.0
11	37.861	39.0	38.0	39.0	35.0	39.0
12	37.902	39.0	38.0	39.0	35.0	39.0
13	37.85275	39.0	38.0	39.0	35.0	39.0
14	39.38175	41.0	39.0	41.0	36.0	41.0
15	39.41625	41.0	39.0	41.0	36.0	41.0
16	39.14925	40.0	39.0	41.0	36.0	41.0
17	39.16575	40.0	39.0	41.0	36.0	41.0
18	39.252	41.0	39.0	41.0	36.0	41.0
19	39.003	40.0	39.0	41.0	36.0	41.0
20	39.14425	40.0	39.0	41.0	36.0	41.0
21	39.138	40.0	39.0	41.0	36.0	41.0
22	39.237	41.0	39.0	41.0	36.0	41.0
23	39.0795	40.0	39.0	41.0	36.0	41.0
24	38.251	40.0	38.0	41.0	34.0	41.0
25	38.56225	40.0	38.0	41.0	34.0	41.0
26	38.51175	40.0	38.0	41.0	34.0	41.0
27	38.54125	40.0	38.0	41.0	34.0	41.0
28	38.77325	40.0	38.0	41.0	35.0	41.0
29	38.88975	40.0	38.0	41.0	35.0	41.0
30	38.6075	40.0	38.0	41.0	34.0	41.0
31	38.9105	40.0	38.0	41.0	35.0	41.0
32	39.11975	40.0	39.0	41.0	35.0	41.0
33	37.87525	40.0	38.0	41.0	33.0	41.0
34	37.45925	40.0	38.0	41.0	31.0	41.0
35	32.57325	38.0	31.0	40.0	15.0	41.0
36	28.8105	37.0	15.0	40.0	8.0	41.0
37	28.818	35.0	22.0	39.0	6.0	40.0
38	31.8155	37.0	30.0	39.0	12.0	40.0
39	30.886	37.0	27.0	40.0	2.0	41.0
40	32.249	37.0	31.0	40.0	2.0	41.0
41	29.6685	36.0	25.0	40.0	2.0	41.0
42	31.637	37.0	30.0	40.0	2.0	41.0
43	29.649	36.0	26.0	40.0	2.0	41.0
44	30.94825	37.0	30.0	40.0	2.0	41.0
45	28.1715	36.0	18.0	40.0	2.0	41.0
46	25.79675	33.0	2.0	39.0	2.0	41.0
47	26.18575	34.0	2.0	39.0	2.0	41.0
48	27.076	35.0	2.0	40.0	2.0	41.0
49	25.1485	34.0	2.0	40.0	2.0	41.0
50	22.00675	29.0	2.0	38.0	2.0	40.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
15	2.0
16	1.0
17	1.0
18	1.0
19	1.0
20	12.0
21	19.0
22	16.0
23	32.0
24	45.0
25	63.0
26	94.0
27	188.0
28	66.0
29	120.0
30	168.0
31	209.0
32	159.0
33	174.0
34	218.0
35	300.0
36	309.0
37	394.0
38	568.0
39	840.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.404702351175589	23.536768384192097	54.777388694347174	12.281140570285142
2	23.525	26.825	23.875	25.775
3	16.7	19.950000000000003	19.325	44.025
4	24.95	37.225	14.099999999999998	23.724999999999998
5	21.55	38.7	28.849999999999998	10.9
6	35.3	16.075	38.425	10.2
7	15.2	23.35	26.674999999999997	34.775
8	25.275	41.825	13.850000000000001	19.05
9	16.0	42.225	30.925000000000004	10.85
10	19.975	19.175	28.125	32.725
11	33.074999999999996	12.575	13.125	41.225
12	15.725	17.299999999999997	23.175	43.8
13	18.875	22.8	38.824999999999996	19.5
14	38.2	22.975	25.374999999999996	13.450000000000001
15	38.275	19.675	29.349999999999998	12.7
16	12.975	26.125	22.3	38.6
17	25.275	24.375	37.5	12.85
18	28.925	19.825	27.575	23.674999999999997
19	36.975	14.374999999999998	31.900000000000002	16.75
20	50.0	15.950000000000001	22.35	11.700000000000001
21	21.2	26.900000000000002	23.599999999999998	28.299999999999997
22	32.074999999999996	11.700000000000001	48.6	7.625
23	23.3	14.35	49.475	12.875
24	50.849999999999994	12.325	29.849999999999998	6.9750000000000005
25	56.55	20.275000000000002	14.35	8.825
26	31.55	47.85	10.525	10.075000000000001
27	13.950000000000001	55.00000000000001	21.8	9.25
28	9.25	29.7	49.65	11.4
29	8.200000000000001	12.7	62.125	16.975
30	8.35	5.75	41.099999999999994	44.800000000000004
31	11.4	4.6	48.199999999999996	35.8
32	23.150000000000002	4.875	25.95	46.025
33	54.074999999999996	6.3	13.125	26.5
34	68.35	6.05	11.825	13.775
35	65.425	6.6000000000000005	18.825	9.15
36	69.0	6.65	14.224999999999998	10.125
37	40.775	8.774999999999999	24.5	25.95
38	26.825	11.35	13.125	48.699999999999996
39	14.575	24.725	7.7	53.0
40	11.924999999999999	49.425000000000004	9.5	29.15
41	26.150000000000002	50.675000000000004	8.9	14.274999999999999
42	52.2	32.225	8.0	7.575
43	53.449999999999996	30.95	7.6	8.0
44	33.0	50.55	5.5	10.95
45	16.650000000000002	52.625	7.75	22.975
46	8.75	31.974999999999998	25.6	33.675
47	7.95	14.2	34.475	43.375
48	8.425	9.8	24.825	56.95
49	11.175	23.575	12.125	53.125
50	32.425	23.7	8.225	35.65
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.5
2	1.0
3	0.5
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	1.0
16	2.0
17	1.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.5
28	1.0
29	3.5
30	6.0
31	7.0
32	8.0
33	16.0
34	24.0
35	34.0
36	44.0
37	49.5
38	55.0
39	55.5
40	56.0
41	49.0
42	42.0
43	69.0
44	96.0
45	160.0
46	224.0
47	301.5
48	379.0
49	499.5
50	620.0
51	784.0
52	948.0
53	743.0
54	538.0
55	433.5
56	329.0
57	297.0
58	265.0
59	199.0
60	133.0
61	98.5
62	64.0
63	72.0
64	80.0
65	55.0
66	30.0
67	20.0
68	10.0
69	10.0
70	10.0
71	17.0
72	24.0
73	13.5
74	3.0
75	3.0
76	3.0
77	1.5
78	0.0
79	1.5
80	3.0
81	2.0
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	0.05
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	50.275000000000006
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.40775733465937	40.425
2	7.558428642466435	7.6
3	3.82894082545997	5.775
4	1.9890601690701142	4.0
5	1.3426156141223273	3.375
6	0.8453505718547987	2.55
7	0.8950770760815515	3.15
8	0.5469915464942815	2.1999999999999997
9	0.19890601690701143	0.8999999999999999
>10	2.2376926902038785	21.575
>50	0.09945300845350571	3.675
>100	0.04972650422675286	4.775
>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
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	191	4.775	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	93	2.325	RNA PCR Primer, Index 1 (96% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	54	1.35	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	30	0.75	RNA PCR Primer, Index 1 (96% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	29	0.7250000000000001	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	15	0.375	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	14	0.35000000000000003	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCGTATGC	13	0.325	RNA PCR Primer, Index 46 (100% over 50bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	12	0.3	RNA PCR Primer, Index 1 (95% over 23bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTC	12	0.3	RNA PCR Primer, Index 46 (100% over 44bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	10	0.25	RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	9	0.22499999999999998	No Hit
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	8	0.2	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	8	0.2	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	8	0.2	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	7	0.17500000000000002	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	7	0.17500000000000002	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	7	0.17500000000000002	No Hit
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	7	0.17500000000000002	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	6	0.15	RNA PCR Primer, Index 1 (95% over 23bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	6	0.15	RNA PCR Primer, Index 3 (100% over 34bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	6	0.15	RNA PCR Primer, Index 5 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	6	0.15	RNA PCR Primer, Index 5 (97% over 35bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCC	6	0.15	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	6	0.15	No Hit
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	6	0.15	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	5	0.125	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	5	0.125	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCAA	5	0.125	RNA PCR Primer, Index 1 (96% over 26bp)
ATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGCCGCGCC	5	0.125	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	5	0.125	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	5	0.125	No Hit
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGAGGTAGTAGGTTGCATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACCCCA	5	0.125	RNA PCR Primer, Index 1 (95% over 24bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	5	0.125	No Hit
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	5	0.125	No Hit
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGAATTCTCGGGTGC	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CTTAATGATGATTGTCTGTTTGATTGCTTGATGCAATGTGAAAACCACAT	5	0.125	No Hit
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>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	0.35	0.0	0.0	0.0
2	0.0	0.35	0.0	0.0	0.0
3	0.0	0.375	0.0	0.0	0.0
4	0.0	0.4	0.0	0.0	0.0
5	0.0	0.4	0.0	0.0	0.0
6	0.0	0.475	0.0	0.0	0.0
7	0.0	0.9	0.0	0.0	0.0
8	0.0	1.05	0.0	0.0	0.0
9	0.0	1.075	0.0	0.0	0.0
10	0.0	1.225	0.0	0.0	0.0
11	0.0	1.35	0.0	0.0	0.0
12	0.0	1.4	0.0	0.0	0.0
13	0.0	1.6	0.0	0.0	0.0
14	0.0	1.85	0.0	0.0	0.0
15	0.0	1.95	0.0	0.0	0.0
16	0.0	2.45	0.0	0.0	0.0
17	0.0	3.05	0.0	0.0	0.0
18	0.0	3.65	0.0	0.0	0.0
19	0.0	4.025	0.0	0.0	0.0
20	0.0	4.75	0.0	0.0	0.0
21	0.0	8.575	0.0	0.0	0.0
22	0.0	19.0	0.0	0.0	0.0
23	0.0	51.2	0.0	0.0	0.0
24	0.0	68.6	0.0	0.0	0.0
25	0.0	74.85	0.0	0.0	0.0
26	0.0	75.8	0.0	0.0	0.0
27	0.0	76.075	0.0	0.0	0.0
28	0.0	76.45	0.0	0.0	0.0
29	0.0	76.525	0.0	0.0	0.0
30	0.0	77.0	0.0	0.0	0.0
31	0.0	77.55	0.0	0.0	0.0
32	0.0	78.3	0.0	0.0	0.0
33	0.0	79.15	0.0	0.0	0.0
34	0.0	80.8	0.0	0.0	0.0
35	0.0	81.725	0.0	0.0	0.0
36	0.0	82.075	0.0	0.0	0.0
37	0.0	82.7	0.0	0.0	0.0
38	0.0	82.925	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACATTCA	40	5.315087E-9	44.000004	2
CTTGGCT	20	6.952051E-4	44.000004	16
AGGCTTG	20	6.952051E-4	44.000004	18
AACATTC	40	5.315087E-9	44.000004	1
AACGCTG	30	1.9515464E-6	44.0	8
AAGTAAT	55	0.0	44.0	4
TCAAGTA	55	0.0	44.0	2
ACGCTGT	30	1.9515464E-6	44.0	9
ATCCAGG	55	0.0	44.0	9
TTCAAGT	55	0.0	44.0	1
TTCAACG	30	1.9515464E-6	44.0	5
CGGGGCC	30	1.9515464E-6	44.0	32
AGGATAG	55	0.0	44.0	13
ATAGGCT	50	1.4551915E-11	44.0	16
GAGCTTG	30	1.9515464E-6	44.0	13
GGATCCG	30	1.9515464E-6	44.0	3
CCGTCTG	30	1.9515464E-6	44.0	7
TCGGATC	30	1.9515464E-6	44.0	1
CATTCAA	35	1.02281774E-7	44.0	3
TCAACGC	30	1.9515464E-6	44.0	6
>>END_MODULE
Read 346240 spots for SRR5030927.sra
Written 346240 spots for SRR5030927.sra
Read 346240 spots for SRR5030927.sra
Written 346240 spots for SRR5030927.sra
Read 346240 spots for SRR5030927.sra
Written 346240 spots for SRR5030927.sra
Read 346240 spots for SRR5030927.sra
Written 346240 spots for SRR5030927.sra
Read 346240 spots for SRR5030927.sra
Written 346240 spots for SRR5030927.sra
Read 346240 spots for SRR5030927.sra
Written 346240 spots for SRR5030927.sra
Read 346240 spots for SRR5030927.sra
Written 346240 spots for SRR5030927.sra
Read 346240 spots for SRR5030927.sra
Written 346240 spots for SRR5030927.sra
Read 346240 spots for SRR5030927.sra
Written 346240 spots for SRR5030927.sra
Read 346240 spots for SRR5030927.sra
Written 346240 spots for SRR5030927.sra
Read 346245 spots for SRR5030927.sra
Written 346245 spots for SRR5030927.sra
Read 346240 spots for SRR5030927.sra
Written 346240 spots for SRR5030927.sra
SRR ids: ['SRR5030927.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_jr1dzkf6
SRR5030927.sra spots: 4154885
blocks: [[1, 346240], [346241, 692480], [692481, 1038720], [1038721, 1384960], [1384961, 1731200], [1731201, 2077440], [2077441, 2423680], [2423681, 2769920], [2769921, 3116160], [3116161, 3462400], [3462401, 3808640], [3808641, 4154885]]
SRR5030927 file size 719054
SRR5030927 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030927 SRR5030927_1.fastq
Input file:	SRR5030927_1.fastq
trimmed:	SRR5030927-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 06:46:19 2020 >> started

Wed Mar  4 06:46:22 2020 >> done (2.621s)
4154885 reads processed; of these:
    191 ( 0.00%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
4154688 (100.00%) reads available; of these:
 503803 (12.13%) trimmed reads available after processing
3650885 (87.87%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     49	  0.00%
 19	     96	  0.00%
 20	    154	  0.00%
 21	    211	  0.01%
 22	    461	  0.01%
 23	    552	  0.01%
 24	    511	  0.01%
 25	    648	  0.02%
 26	    582	  0.01%
 27	    726	  0.02%
 28	   1009	  0.02%
 29	   1945	  0.05%
 30	   1134	  0.03%
 31	   1568	  0.04%
 32	   3766	  0.09%
 33	  12229	  0.29%
 34	  40992	  0.99%
 35	   9297	  0.22%
 36	  10928	  0.26%
 37	   4691	  0.11%
 38	  10619	  0.26%
 39	   8010	  0.19%
 40	  18498	  0.45%
 41	   9570	  0.23%
 42	  27410	  0.66%
 43	  10217	  0.25%
 44	  56534	  1.36%
 45	  29397	  0.71%
 46	  23559	  0.57%
 47	  25257	  0.61%
 48	  95066	  2.29%
 49	  98117	  2.36%
 50	3650885	 87.87%
4154688 reads passed initial QC


criterion=sequence-density
sequence-density=81.43
sequence-density-rank=1
fanout-score=18.52
fanout-score-rank=3
prefix-density=83.84
prefix-fanout=18.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCGTATGCC


criterion=fanout-score
sequence-density=1.43
sequence-density-rank=12
fanout-score=517.41
fanout-score-rank=1
prefix-density=83.12
prefix-fanout=8.9
sequence=GGAATTCTCGGTGCCAAGGA
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -t 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCGTATGCC -o SRR5030927 -
Input file:	STDIN
trimmed:	SRR5030927-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCGTATGCC
-- 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 06:46:39 2020 >> started

Wed Mar  4 06:46:46 2020 >> done (6.411s)
4053354 reads processed; of these:
 135796 ( 3.35%) short reads filtered out after trimming by size control
  17869 ( 0.44%) empty reads filtered out after trimming by size control
3899689 (96.21%) reads available; of these:
3434494 (88.07%) trimmed reads available after processing
 465195 (11.93%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  20257	  0.52%
 19	  38561	  0.99%
 20	 153922	  3.95%
 21	 420536	 10.78%
 22	1292416	 33.14%
 23	 689319	 17.68%
 24	 245995	  6.31%
 25	  41289	  1.06%
 26	  20373	  0.52%
 27	  19560	  0.50%
 28	  21976	  0.56%
 29	  18066	  0.46%
 30	  28906	  0.74%
 31	  36317	  0.93%
 32	  40498	  1.04%
 33	  70813	  1.82%
 34	  31973	  0.82%
 35	  20576	  0.53%
 36	  29954	  0.77%
 37	  14736	  0.38%
 38	  19030	  0.49%
 39	  17405	  0.45%
 40	  27466	  0.70%
 41	  30957	  0.79%
 42	  38791	  0.99%
 43	  25169	  0.65%
 44	  27295	  0.70%
 45	  25455	  0.65%
 46	  21091	  0.54%
 47	  16131	  0.41%
 48	   8675	  0.22%
 49	  14496	  0.37%
 50	 371685	  9.53%


criterion=sequence-density
sequence-density=6.26
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=21
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.44
sequence-density-rank=32
fanout-score=10.20
fanout-score-rank=1
prefix-density=0.83
prefix-fanout=5.3
sequence=GGAATTCTCGGGGCCCAGG
                                 Started job on |	Mar 04 06:47:24
                             Started mapping on |	Mar 04 06:47:24
                                    Finished on |	Mar 04 06:47:51
       Mapping speed, Million of reads per hour |	533.47

                          Number of input reads |	4001023
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1981375
                        Uniquely mapped reads % |	49.52%
                          Average mapped length |	27.26
                       Number of splices: Total |	1948
            Number of splices: Annotated (sjdb) |	188
                       Number of splices: GT/AG |	1722
                       Number of splices: GC/AG |	33
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	192
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.26
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.11
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1599870
             % of reads mapped to multiple loci |	39.99%
        Number of reads mapped to too many loci |	77186
             % of reads mapped to too many loci |	1.93%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.03%
                     % of reads unmapped: other |	0.54%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	419778	419778	419778
N_multimapping	1599870	1599870	1599870
N_noFeature	80915	97886	1592270
N_ambiguous	1053199	724591	13513
UnstrandedReadsAssigned:847261 PositiveStrandReadsAssigned:1158898 NegativeStrandReadsAssigned:375592
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030927 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: SRR5030927-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,001,023 reads, 787,563 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 625 rounds

 109283 SRR5030927.ke.tsv
  52636 SRR5030927.se.tsv
 161919 total
==> SRR5030927.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

==> SRR5030927.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030927 completed mapping pipeline successfully
