Starting /dee2/code/volunteer_pipeline.sh SRR5031090
    current disk space = 160491339776
    free memory = 73956880 
SRR5031090 SRAfilesize
9b1a7bd3f6535301d2059e1921b97d93  SRR5031090.sra
SRR5031090.sra file validated
SRR5031090 is single end
SRR5031090 is conventional basespace
SRR5031090 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031090_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	53
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.76975	31.0	31.0	34.0	30.0	34.0
2	32.3065	33.0	31.0	34.0	31.0	34.0
3	32.3085	33.0	31.0	34.0	30.0	34.0
4	36.0865	37.0	35.0	37.0	35.0	37.0
5	36.059	37.0	35.0	37.0	35.0	37.0
6	35.99225	37.0	35.0	37.0	35.0	37.0
7	35.724	37.0	35.0	37.0	35.0	37.0
8	35.5785	37.0	35.0	37.0	33.0	37.0
9	36.9645	39.0	37.0	39.0	33.0	39.0
10	36.492	39.0	35.0	39.0	32.0	39.0
11	37.2965	39.0	37.0	39.0	34.0	39.0
12	37.5895	39.0	37.0	39.0	35.0	39.0
13	37.403	39.0	37.0	39.0	35.0	39.0
14	38.35225	40.0	38.0	41.0	34.0	41.0
15	36.70775	39.0	36.0	41.0	27.0	41.0
16	36.94375	38.0	36.0	40.0	32.0	41.0
17	36.9015	39.0	36.0	40.0	31.0	41.0
18	38.13125	40.0	37.0	41.0	34.0	41.0
19	38.574	40.0	38.0	41.0	35.0	41.0
20	38.0725	40.0	38.0	41.0	34.0	41.0
21	38.4215	40.0	38.0	41.0	34.0	41.0
22	36.79425	39.0	36.0	40.0	30.0	41.0
23	37.518	39.0	37.0	40.0	32.0	41.0
24	36.71425	39.0	36.0	40.0	30.0	41.0
25	37.80375	39.0	37.0	41.0	32.0	41.0
26	37.8425	40.0	37.0	41.0	33.0	41.0
27	37.846	40.0	37.0	41.0	33.0	41.0
28	38.04425	40.0	38.0	41.0	33.0	41.0
29	37.7385	40.0	38.0	41.0	32.0	41.0
30	38.4365	40.0	38.0	41.0	34.0	41.0
31	38.318	40.0	38.0	41.0	34.0	41.0
32	38.568	40.0	38.0	41.0	35.0	41.0
33	38.429	40.0	38.0	41.0	34.0	41.0
34	37.7465	40.0	37.0	41.0	31.0	41.0
35	37.34	40.0	36.0	41.0	30.0	41.0
36	33.28925	35.0	30.0	40.0	23.0	41.0
37	35.0525	37.0	33.0	39.0	30.0	40.0
38	36.3855	38.0	35.0	40.0	30.0	40.0
39	36.59475	38.0	35.0	40.0	31.0	40.0
40	36.80575	39.0	36.0	40.0	31.0	41.0
41	36.96625	39.0	36.0	40.0	31.0	41.0
42	36.718	39.0	36.0	40.0	30.0	41.0
43	36.9575	39.0	36.0	40.0	31.0	41.0
44	36.43075	39.0	35.0	40.0	30.0	41.0
45	36.13125	38.0	35.0	40.0	30.0	41.0
46	36.19125	39.0	35.0	40.0	30.0	41.0
47	35.18275	38.0	33.0	40.0	26.0	41.0
48	36.39125	39.0	35.0	40.0	30.0	41.0
49	36.70675	39.0	36.0	41.0	31.0	41.0
50	34.8055	38.0	34.0	40.0	28.0	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
5	1.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	1.0
14	0.0
15	2.0
16	2.0
17	0.0
18	1.0
19	5.0
20	4.0
21	2.0
22	12.0
23	5.0
24	3.0
25	7.0
26	15.0
27	18.0
28	31.0
29	38.0
30	60.0
31	92.0
32	88.0
33	160.0
34	208.0
35	324.0
36	510.0
37	766.0
38	1063.0
39	582.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.13892365456821	26.082603254067582	44.80600750938674	17.972465581977474
2	25.531382845711427	28.382095523880967	18.27956989247312	27.806951737934483
3	23.75	16.900000000000002	22.975	36.375
4	35.475	29.975	13.125	21.425
5	21.25	35.05	30.125	13.575000000000001
6	27.325	15.55	39.675	17.45
7	15.825	20.95	21.85	41.375
8	23.3	29.175	17.45	30.075000000000003
9	22.225	32.05	25.874999999999996	19.85
10	23.125	16.55	27.6	32.725
11	35.875	12.825000000000001	16.675	34.625
12	18.15	18.5	31.4	31.95
13	30.025000000000002	14.05	36.6	19.325
14	33.4	24.825	19.475	22.3
15	34.599999999999994	14.85	31.25	19.3
16	20.724999999999998	16.2	22.825	40.25
17	31.85	19.625	33.475	15.049999999999999
18	32.0	15.125	28.175	24.7
19	36.775000000000006	16.1	30.9	16.225
20	44.3	15.7	25.55	14.45
21	24.474999999999998	25.25	25.124999999999996	25.15
22	33.375	11.35	41.199999999999996	14.075
23	23.549999999999997	12.55	44.75	19.15
24	46.0	11.600000000000001	29.9	12.5
25	47.65	22.725	17.224999999999998	12.4
26	31.825	39.75	14.875	13.55
27	20.925	42.3	22.0	14.774999999999999
28	16.0	25.674999999999997	41.875	16.45
29	15.35	13.175	51.575	19.900000000000002
30	13.775	7.449999999999999	35.099999999999994	43.675000000000004
31	14.399999999999999	5.8500000000000005	45.95	33.800000000000004
32	27.325	7.2749999999999995	22.400000000000002	43.0
33	46.949999999999996	13.075000000000001	14.35	25.624999999999996
34	55.775	11.450000000000001	15.725	17.05
35	64.525	9.65	16.675	9.15
36	44.9	8.9	33.475	12.725
37	44.45	13.950000000000001	20.599999999999998	21.0
38	24.9	19.625	13.475000000000001	42.0
39	16.1	23.599999999999998	11.600000000000001	48.699999999999996
40	14.625	44.55	13.850000000000001	26.974999999999998
41	22.725	44.4	9.125	23.75
42	41.949999999999996	30.225	14.35	13.475000000000001
43	46.275	29.45	9.975000000000001	14.299999999999999
44	33.0	41.925000000000004	7.575	17.5
45	20.5	45.775	14.124999999999998	19.6
46	15.65	27.200000000000003	16.425	40.725
47	10.025	17.974999999999998	37.0	35.0
48	12.325	13.600000000000001	20.45	53.625
49	13.900000000000002	21.05	14.825	50.224999999999994
50	19.075	33.675	13.025	34.225
>>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	0.0
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	1.0
28	2.0
29	1.0
30	0.0
31	2.5
32	5.0
33	6.5
34	8.0
35	11.0
36	14.0
37	15.5
38	17.0
39	22.0
40	27.0
41	38.5
42	50.0
43	62.0
44	74.0
45	109.0
46	144.0
47	230.5
48	317.0
49	401.5
50	486.0
51	685.5
52	885.0
53	695.5
54	506.0
55	559.5
56	613.0
57	488.0
58	363.0
59	246.0
60	129.0
61	92.5
62	56.0
63	95.0
64	134.0
65	100.5
66	67.0
67	46.5
68	26.0
69	20.5
70	15.0
71	34.5
72	54.0
73	29.0
74	4.0
75	3.0
76	2.0
77	1.5
78	1.0
79	0.5
80	0.0
81	0.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.125
2	0.025
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	44.675
#Duplication Level	Percentage of deduplicated	Percentage of total
1	77.72803581421377	34.725
2	9.7929490766648	8.75
3	4.141018466703973	5.55
4	2.0705092333519866	3.6999999999999997
5	1.119194180190263	2.5
6	0.8953553441522105	2.4
7	0.7274762171236709	2.275
8	0.44767767207610526	1.6
9	0.22383883603805263	0.8999999999999999
>10	2.3503077783995523	17.299999999999997
>50	0.33575825405707893	9.425
>100	0.16787912702853947	10.875
>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	185	4.625	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	125	3.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	125	3.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAG	78	1.95	RNA PCR Primer, Index 2 (97% over 35bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	78	1.95	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	65	1.625	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	54	1.35	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	51	1.275	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	51	1.275	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	42	1.05	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	27	0.675	RNA PCR Primer, Index 1 (96% over 30bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTC	26	0.65	RNA PCR Primer, Index 14 (100% over 44bp)
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	24	0.6	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGC	20	0.5	RNA PCR Primer, Index 14 (100% over 50bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGT	19	0.475	RNA PCR Primer, Index 8 (97% over 36bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAG	17	0.42500000000000004	RNA PCR Primer, Index 2 (97% over 35bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	17	0.42500000000000004	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	15	0.375	No Hit
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 31bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	12	0.3	No Hit
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	11	0.27499999999999997	No Hit
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCCAGGAACTCCAGTCACAGTTCCATCTC	10	0.25	RNA PCR Primer, Index 14 (97% over 44bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	10	0.25	RNA PCR Primer, Index 1 (100% over 34bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTAT	10	0.25	RNA PCR Primer, Index 14 (100% over 48bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGACTTCTCGGGTGCCAAGGAACTCCAGTCAC	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 33bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCCGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	8	0.2	No Hit
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	7	0.17500000000000002	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 34bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CGCTAAACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGG	7	0.17500000000000002	Illumina Small RNA Adapter 2 (100% over 21bp)
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTT	7	0.17500000000000002	RNA PCR Primer, Index 8 (97% over 37bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CATGCTCAATAGGATTACGCTGAGGCCCTGGAATTCTCGGGTGCCAAGGA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 22bp)
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	6	0.15	No Hit
TGGAATTCTCGGGTGCCAAGGCACTCCAGTCACAGTTCCATCTCGTATGC	6	0.15	RNA PCR Primer, Index 14 (98% over 50bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTC	6	0.15	RNA PCR Primer, Index 14 (100% over 38bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	6	0.15	No Hit
TCCCTGAGACCCTACCTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTG	6	0.15	No Hit
AAGCTGCCAGTTGACGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGACTTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (96% over 31bp)
CTCAATAGGATTACGCTGAGGCCCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTTGTCCCGGCCTGTATTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	5	0.125	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGACTTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (96% over 26bp)
AACATTCATTGCTGTCGGTGGGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AGAAATGCGGATATGGGACTGAGATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGACCCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGGTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>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	0.775	0.0	0.0	0.0
2	0.0	0.875	0.0	0.0	0.0
3	0.0	1.275	0.0	0.0	0.0
4	0.0	1.4	0.0	0.0	0.0
5	0.0	1.5	0.0	0.0	0.0
6	0.0	1.8	0.0	0.0	0.0
7	0.0	3.0	0.0	0.0	0.0
8	0.0	3.25	0.0	0.0	0.0
9	0.0	3.3	0.0	0.0	0.0
10	0.0	3.625	0.0	0.0	0.0
11	0.0	4.0	0.0	0.0	0.0
12	0.0	4.3	0.0	0.0	0.0
13	0.0	4.8	0.0	0.0	0.0
14	0.0	5.35	0.0	0.0	0.0
15	0.0	6.425	0.0	0.0	0.0
16	0.0	9.575	0.0	0.0	0.0
17	0.0	10.7	0.0	0.0	0.0
18	0.0	12.625	0.0	0.0	0.0
19	0.0	13.2	0.0	0.0	0.0
20	0.0	13.95	0.0	0.0	0.0
21	0.0	17.6	0.0	0.0	0.0
22	0.0	26.775	0.0	0.0	0.0
23	0.0	52.15	0.0	0.0	0.0
24	0.0	64.95	0.0	0.0	0.0
25	0.0	71.1	0.0	0.0	0.0
26	0.0	72.525	0.0	0.0	0.0
27	0.0	73.625	0.0	0.0	0.0
28	0.0	74.325	0.0	0.0	0.0
29	0.0	75.175	0.0	0.0	0.0
30	0.0	76.025	0.0	0.0	0.0
31	0.0	76.7	0.0	0.0	0.0
32	0.0	77.95	0.0	0.0	0.0
33	0.0	78.75	0.0	0.0	0.0
34	0.0	82.75	0.0	0.0	0.0
35	0.0	83.975	0.0	0.0	0.0
36	0.0	85.15	0.0	0.0	0.0
37	0.0	86.225	0.0	0.0	0.0
38	0.0	86.725	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	40	5.315087E-9	44.000004	8
GAGGTAG	20	6.952051E-4	44.000004	2
ACGCTGT	40	5.315087E-9	44.000004	9
CTGAGCT	40	5.315087E-9	44.000004	11
TTCAACG	40	5.315087E-9	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
TCGGATC	40	5.315087E-9	44.000004	1
CATTCAA	40	5.315087E-9	44.000004	3
TCAACGC	40	5.315087E-9	44.000004	6
CGGATCC	40	5.315087E-9	44.000004	2
ACATTCA	45	2.728484E-10	44.000004	2
GAGTTGG	20	6.952051E-4	44.000004	20
GCTGTCG	40	5.315087E-9	44.000004	11
GATCCGT	40	5.315087E-9	44.000004	4
TGAGGTA	20	6.952051E-4	44.000004	1
TTGGCTT	20	6.952051E-4	44.000004	17
TCCGTCT	40	5.315087E-9	44.000004	6
ATCCGTC	40	5.315087E-9	44.000004	5
>>END_MODULE
Read 116308 spots for SRR5031090.sra
Written 116308 spots for SRR5031090.sra
Read 116308 spots for SRR5031090.sra
Written 116308 spots for SRR5031090.sra
Read 116308 spots for SRR5031090.sra
Written 116308 spots for SRR5031090.sra
Read 116308 spots for SRR5031090.sra
Written 116308 spots for SRR5031090.sra
Read 116308 spots for SRR5031090.sra
Written 116308 spots for SRR5031090.sra
Read 116313 spots for SRR5031090.sra
Written 116313 spots for SRR5031090.sra
Read 116308 spots for SRR5031090.sra
Written 116308 spots for SRR5031090.sra
Read 116308 spots for SRR5031090.sra
Written 116308 spots for SRR5031090.sra
Read 116308 spots for SRR5031090.sra
Written 116308 spots for SRR5031090.sra
Read 116308 spots for SRR5031090.sra
Written 116308 spots for SRR5031090.sra
Read 116308 spots for SRR5031090.sra
Written 116308 spots for SRR5031090.sra
Read 116308 spots for SRR5031090.sra
Written 116308 spots for SRR5031090.sra
SRR ids: ['SRR5031090.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_iy1kx7ww
SRR5031090.sra spots: 1395701
blocks: [[1, 116308], [116309, 232616], [232617, 348924], [348925, 465232], [465233, 581540], [581541, 697848], [697849, 814156], [814157, 930464], [930465, 1046772], [1046773, 1163080], [1163081, 1279388], [1279389, 1395701]]
SRR5031090 file size 240843
SRR5031090 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031090 SRR5031090_1.fastq
Input file:	SRR5031090_1.fastq
trimmed:	SRR5031090-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 07:21:56 2020 >> started

Wed Mar  4 07:21:57 2020 >> done (1.052s)
1395701 reads processed; of these:
    129 ( 0.01%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
1395567 (99.99%) reads available; of these:
 117584 ( 8.43%) trimmed reads available after processing
1277983 (91.57%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     38	  0.00%
 19	     66	  0.00%
 20	    104	  0.01%
 21	    125	  0.01%
 22	    221	  0.02%
 23	    295	  0.02%
 24	    304	  0.02%
 25	    437	  0.03%
 26	    312	  0.02%
 27	    374	  0.03%
 28	    448	  0.03%
 29	    675	  0.05%
 30	    507	  0.04%
 31	    558	  0.04%
 32	    691	  0.05%
 33	   1129	  0.08%
 34	   1637	  0.12%
 35	   3847	  0.28%
 36	   2587	  0.19%
 37	   2269	  0.16%
 38	   2408	  0.17%
 39	   2745	  0.20%
 40	   2920	  0.21%
 41	   3396	  0.24%
 42	   3453	  0.25%
 43	   5363	  0.38%
 44	   6156	  0.44%
 45	   8430	  0.60%
 46	  11344	  0.81%
 47	   8996	  0.64%
 48	  21143	  1.52%
 49	  24606	  1.76%
 50	1277983	 91.57%
1395567 reads passed initial QC


criterion=sequence-density
sequence-density=88.43
sequence-density-rank=1
fanout-score=18.85
fanout-score-rank=2
prefix-density=89.23
prefix-fanout=18.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC


criterion=fanout-score
sequence-density=3.26
sequence-density-rank=3
fanout-score=87.60
fanout-score-rank=1
prefix-density=89.88
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC -o SRR5031090 -
Input file:	STDIN
trimmed:	SRR5031090-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC
-- 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 07:22:08 2020 >> started

Wed Mar  4 07:22:10 2020 >> done (2.403s)
1364206 reads processed; of these:
 168090 (12.32%) short reads filtered out after trimming by size control
  13213 ( 0.97%) empty reads filtered out after trimming by size control
1182903 (86.71%) reads available; of these:
1134775 (95.93%) trimmed reads available after processing
  48128 ( 4.07%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   9768	  0.83%
 19	  19128	  1.62%
 20	  68981	  5.83%
 21	 131040	 11.08%
 22	 354622	 29.98%
 23	 186756	 15.79%
 24	  86857	  7.34%
 25	  24765	  2.09%
 26	  13800	  1.17%
 27	  11264	  0.95%
 28	  11308	  0.96%
 29	   8440	  0.71%
 30	  11845	  1.00%
 31	  20597	  1.74%
 32	  14267	  1.21%
 33	  54444	  4.60%
 34	  16156	  1.37%
 35	  13599	  1.15%
 36	  15320	  1.30%
 37	   6837	  0.58%
 38	   6448	  0.55%
 39	   5350	  0.45%
 40	   5941	  0.50%
 41	   7629	  0.64%
 42	   8015	  0.68%
 43	   6194	  0.52%
 44	   4966	  0.42%
 45	   7584	  0.64%
 46	   6166	  0.52%
 47	   4459	  0.38%
 48	    592	  0.05%
 49	    633	  0.05%
 50	  39132	  3.31%


criterion=sequence-density
sequence-density=11.37
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=13
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=2.38
sequence-density-rank=3
fanout-score=18.16
fanout-score-rank=1
prefix-density=2.41
prefix-fanout=18.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGC
                                 Started job on |	Mar 04 07:22:28
                             Started mapping on |	Mar 04 07:22:29
                                    Finished on |	Mar 04 07:22:52
       Mapping speed, Million of reads per hour |	190.06

                          Number of input reads |	1214264
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	602023
                        Uniquely mapped reads % |	49.58%
                          Average mapped length |	24.14
                       Number of splices: Total |	1608
            Number of splices: Annotated (sjdb) |	287
                       Number of splices: GT/AG |	1559
                       Number of splices: GC/AG |	27
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	22
                      Mismatch rate per base, % |	0.35%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.78
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.11
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	437528
             % of reads mapped to multiple loci |	36.03%
        Number of reads mapped to too many loci |	29702
             % of reads mapped to too many loci |	2.45%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.48%
                     % of reads unmapped: other |	1.46%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	174713	174713	174713
N_multimapping	437528	437528	437528
N_noFeature	45475	52010	404260
N_ambiguous	320422	142003	4783
UnstrandedReadsAssigned:236126 PositiveStrandReadsAssigned:408010 NegativeStrandReadsAssigned:192980
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031090 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: SRR5031090-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,214,264 reads, 271,720 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,059 rounds

 109283 SRR5031090.ke.tsv
  52636 SRR5031090.se.tsv
 161919 total
==> SRR5031090.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

==> SRR5031090.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031090 completed mapping pipeline successfully
