Starting /dee2/code/volunteer_pipeline.sh SRR5031107
    current disk space = 160471498752
    free memory = 73934704 
SRR5031107 SRAfilesize
6a76dfdfe2a10671728f29c45e2abcd3  SRR5031107.sra
SRR5031107.sra file validated
SRR5031107 is single end
SRR5031107 is conventional basespace
SRR5031107 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031107_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	31.9395	31.0	31.0	34.0	30.0	34.0
2	32.39025	33.0	31.0	34.0	31.0	34.0
3	32.38	33.0	31.0	34.0	31.0	34.0
4	36.14225	37.0	35.0	37.0	35.0	37.0
5	36.1055	37.0	35.0	37.0	35.0	37.0
6	35.96375	37.0	35.0	37.0	35.0	37.0
7	35.78675	37.0	35.0	37.0	35.0	37.0
8	35.623	37.0	35.0	37.0	33.0	37.0
9	36.808	39.0	37.0	39.0	33.0	39.0
10	36.465	39.0	35.0	39.0	32.0	39.0
11	37.2745	39.0	37.0	39.0	34.0	39.0
12	37.58475	39.0	37.0	39.0	35.0	39.0
13	37.383	39.0	37.0	39.0	34.0	39.0
14	38.3155	40.0	38.0	41.0	33.0	41.0
15	36.703	39.0	36.0	41.0	27.0	41.0
16	36.374	38.0	35.0	40.0	30.0	41.0
17	36.407	39.0	36.0	40.0	30.0	41.0
18	37.90875	39.0	37.0	41.0	33.0	41.0
19	38.679	40.0	38.0	41.0	35.0	41.0
20	38.45175	40.0	38.0	41.0	34.0	41.0
21	38.62125	40.0	38.0	41.0	34.0	41.0
22	37.418	39.0	37.0	40.0	32.0	41.0
23	37.91125	39.0	37.0	40.0	34.0	41.0
24	37.41575	39.0	37.0	40.0	32.0	41.0
25	38.306	40.0	38.0	41.0	34.0	41.0
26	38.3155	40.0	38.0	41.0	34.0	41.0
27	38.403	40.0	38.0	41.0	34.0	41.0
28	38.5425	40.0	38.0	41.0	34.0	41.0
29	38.532	40.0	38.0	41.0	34.0	41.0
30	38.74475	40.0	38.0	41.0	34.0	41.0
31	38.81225	40.0	38.0	41.0	35.0	41.0
32	38.88825	40.0	38.0	41.0	35.0	41.0
33	38.904	40.0	39.0	41.0	35.0	41.0
34	38.268	40.0	38.0	41.0	33.0	41.0
35	37.2465	40.0	35.0	41.0	30.0	41.0
36	32.8585	35.0	30.0	39.0	23.0	41.0
37	34.91125	37.0	33.0	39.0	30.0	40.0
38	36.2975	38.0	35.0	39.0	31.0	40.0
39	36.683	38.0	36.0	40.0	31.0	40.0
40	37.15425	39.0	37.0	40.0	33.0	41.0
41	37.54625	40.0	37.0	40.0	32.0	41.0
42	37.537	40.0	37.0	41.0	33.0	41.0
43	37.428	40.0	37.0	41.0	32.0	41.0
44	36.46875	39.0	35.0	40.0	30.0	41.0
45	36.75775	39.0	36.0	40.0	31.0	41.0
46	36.986	39.0	37.0	40.0	31.0	41.0
47	36.07375	39.0	35.0	40.0	29.0	41.0
48	37.18475	40.0	37.0	40.0	32.0	41.0
49	37.373	40.0	37.0	41.0	33.0	41.0
50	35.496	38.0	34.0	40.0	29.0	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
14	1.0
15	0.0
16	1.0
17	4.0
18	0.0
19	2.0
20	4.0
21	2.0
22	6.0
23	6.0
24	6.0
25	9.0
26	18.0
27	25.0
28	26.0
29	30.0
30	44.0
31	61.0
32	110.0
33	108.0
34	192.0
35	267.0
36	460.0
37	778.0
38	1166.0
39	674.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	6.3	26.05	55.875	11.774999999999999
2	22.428035043804755	29.46182728410513	16.896120150187734	31.214017521902377
3	24.5	22.400000000000002	19.375	33.725
4	32.625	29.825000000000003	11.675	25.874999999999996
5	22.05	40.300000000000004	28.475	9.175
6	34.949999999999996	14.299999999999999	37.675	13.075000000000001
7	11.425	23.549999999999997	23.775	41.25
8	26.150000000000002	30.049999999999997	12.975	30.825000000000003
9	21.2	37.85	28.4	12.55
10	19.950000000000003	22.15	29.4	28.499999999999996
11	32.6	7.775	16.7	42.925000000000004
12	15.15	16.125	31.900000000000002	36.825
13	32.45	14.875	33.074999999999996	19.6
14	33.95	30.2	22.125	13.725000000000001
15	37.574999999999996	18.35	27.725	16.35
16	18.05	18.125	22.525000000000002	41.3
17	25.25	21.525	38.9	14.325
18	25.7	16.75	30.4	27.150000000000002
19	36.199999999999996	14.099999999999998	32.275	17.424999999999997
20	49.025	11.700000000000001	27.474999999999998	11.799999999999999
21	21.025	20.5	30.675	27.800000000000004
22	28.4	9.2	52.125	10.274999999999999
23	27.275	11.125	50.74999999999999	10.85
24	56.55	11.175	25.474999999999998	6.800000000000001
25	54.37499999999999	25.6	13.675	6.35
26	26.35	53.525	12.6	7.5249999999999995
27	13.25	52.25	25.85	8.649999999999999
28	8.0	24.275	55.45	12.275
29	8.6	10.25	60.724999999999994	20.424999999999997
30	7.875	4.675	39.15	48.3
31	12.45	3.225	49.5	34.825
32	29.425	4.324999999999999	19.650000000000002	46.6
33	61.525	5.800000000000001	12.025	20.65
34	69.55	5.1499999999999995	12.65	12.65
35	68.8	5.575	19.375	6.25
36	44.525	5.325	37.95	12.2
37	49.225	7.55	18.0	25.224999999999998
38	21.4	13.950000000000001	10.0	54.65
39	13.0	25.7	7.1499999999999995	54.15
40	13.05	55.025	6.6000000000000005	25.324999999999996
41	26.3	53.7	6.0	14.000000000000002
42	55.15	30.599999999999998	6.35	7.9
43	55.55	31.775	4.625	8.05
44	27.575	55.425000000000004	4.8500000000000005	12.15
45	14.75	54.50000000000001	10.7	20.05
46	8.075000000000001	25.275	19.325	47.325
47	5.5	13.775	41.0	39.725
48	6.3	11.774999999999999	18.7	63.224999999999994
49	10.825	21.125	11.0	57.05
50	18.85	41.125	10.274999999999999	29.75
>>END_MODULE
>>Per sequence GC content	warn
#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	0.5
20	1.0
21	0.5
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	1.5
32	3.0
33	4.0
34	5.0
35	10.0
36	15.0
37	16.0
38	17.0
39	13.5
40	10.0
41	23.5
42	37.0
43	72.0
44	107.0
45	144.0
46	181.0
47	304.0
48	427.0
49	543.5
50	660.0
51	823.5
52	987.0
53	731.5
54	476.0
55	504.0
56	532.0
57	405.0
58	278.0
59	185.0
60	92.0
61	64.0
62	36.0
63	51.5
64	67.0
65	45.0
66	23.0
67	17.5
68	12.0
69	10.0
70	8.0
71	16.0
72	24.0
73	13.0
74	2.0
75	1.0
76	0.0
77	0.0
78	0.0
79	0.0
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	0.0
2	0.125
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	38.800000000000004
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.51546391752578	29.299999999999997
2	9.858247422680412	7.6499999999999995
3	4.252577319587629	4.95
4	2.7061855670103094	4.2
5	1.2886597938144329	2.5
6	1.2242268041237114	2.85
7	0.6443298969072164	1.7500000000000002
8	0.6443298969072164	2.0
9	0.3221649484536082	1.125
>10	2.899484536082474	20.275000000000002
>50	0.3221649484536082	8.875
>100	0.3221649484536082	14.524999999999999
>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	135	3.375	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	119	2.9749999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	112	2.8000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	108	2.7	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	107	2.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	88	2.1999999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	75	1.875	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	73	1.825	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	55	1.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	42	1.05	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	35	0.8750000000000001	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	25	0.625	RNA PCR Primer, Index 7 (100% over 35bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	24	0.6	RNA PCR Primer, Index 1 (100% over 33bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGC	15	0.375	RNA PCR Primer, Index 31 (100% over 50bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	10	0.25	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATCGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTC	9	0.22499999999999998	RNA PCR Primer, Index 31 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	8	0.2	RNA PCR Primer, Index 2 (100% over 34bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGGCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (96% over 30bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	7	0.17500000000000002	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
TTCAAGTAATCCCGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	6	0.15	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	5	0.125	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTACATCTGGCTCCTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAC	5	0.125	RNA PCR Primer, Index 30 (100% over 36bp)
CAACGGAATCCCAACAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTCTAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	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	0.55	0.0	0.0	0.0
2	0.0	0.55	0.0	0.0	0.0
3	0.0	0.65	0.0	0.0	0.0
4	0.0	0.725	0.0	0.0	0.0
5	0.0	0.85	0.0	0.0	0.0
6	0.0	0.925	0.0	0.0	0.0
7	0.0	1.25	0.0	0.0	0.0
8	0.0	1.35	0.0	0.0	0.0
9	0.0	1.375	0.0	0.0	0.0
10	0.0	1.55	0.0	0.0	0.0
11	0.0	1.775	0.0	0.0	0.0
12	0.0	1.9	0.0	0.0	0.0
13	0.0	2.15	0.0	0.0	0.0
14	0.0	2.3	0.0	0.0	0.0
15	0.0	2.75	0.0	0.0	0.0
16	0.0	3.825	0.0	0.0	0.0
17	0.0	4.325	0.0	0.0	0.0
18	0.0	5.475	0.0	0.0	0.0
19	0.0	5.825	0.0	0.0	0.0
20	0.0	6.8	0.0	0.0	0.0
21	0.0	12.35	0.0	0.0	0.0
22	0.0	27.075	0.0	0.0	0.0
23	0.0	62.25	0.0	0.0	0.0
24	0.0	76.375	0.0	0.0	0.0
25	0.0	82.475	0.0	0.0	0.0
26	0.0	83.775	0.0	0.0	0.0
27	0.0	84.475	0.0	0.0	0.0
28	0.0	84.95	0.0	0.0	0.0
29	0.0	85.5	0.0	0.0	0.0
30	0.0	85.925	0.0	0.0	0.0
31	0.0	86.775	0.0	0.0	0.0
32	0.0	87.3	0.0	0.0	0.0
33	0.0	88.05	0.0	0.0	0.0
34	0.0	89.675	0.0	0.0	0.0
35	0.0	90.375	0.0	0.0	0.0
36	0.0	90.825	0.0	0.0	0.0
37	0.0	91.2	0.0	0.0	0.0
38	0.0	91.45	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	20	6.952051E-4	44.000004	8
TGTTGGA	20	6.952051E-4	44.000004	20
TGCACTC	20	6.952051E-4	44.000004	4
GAGGTAG	40	5.315087E-9	44.000004	2
ACTCGTC	20	6.952051E-4	44.000004	7
GGTGAGT	20	6.952051E-4	44.000004	17
AAGTAAT	20	6.952051E-4	44.000004	4
GTTGAAG	20	6.952051E-4	44.000004	10
TCAAGTA	20	6.952051E-4	44.000004	2
TTGCACT	20	6.952051E-4	44.000004	3
ACGCTGT	20	6.952051E-4	44.000004	9
CAGTTGA	20	6.952051E-4	44.000004	8
CCAGTTG	20	6.952051E-4	44.000004	7
TTCAAGT	20	6.952051E-4	44.000004	1
TTCAACG	20	6.952051E-4	44.000004	5
CCCGGCC	20	6.952051E-4	44.000004	13
ATAGGCT	20	6.952051E-4	44.000004	16
GGATCCG	40	5.315087E-9	44.000004	3
CCGTCTG	40	5.315087E-9	44.000004	7
TCGGATC	40	5.315087E-9	44.000004	1
>>END_MODULE
Read 142358 spots for SRR5031107.sra
Written 142358 spots for SRR5031107.sra
Read 142358 spots for SRR5031107.sra
Written 142358 spots for SRR5031107.sra
Read 142358 spots for SRR5031107.sra
Written 142358 spots for SRR5031107.sra
Read 142358 spots for SRR5031107.sra
Written 142358 spots for SRR5031107.sra
Read 142358 spots for SRR5031107.sra
Written 142358 spots for SRR5031107.sra
Read 142358 spots for SRR5031107.sra
Written 142358 spots for SRR5031107.sra
Read 142358 spots for SRR5031107.sra
Written 142358 spots for SRR5031107.sra
Read 142358 spots for SRR5031107.sra
Written 142358 spots for SRR5031107.sra
Read 142358 spots for SRR5031107.sra
Written 142358 spots for SRR5031107.sra
Read 142358 spots for SRR5031107.sra
Written 142358 spots for SRR5031107.sra
Read 142358 spots for SRR5031107.sra
Written 142358 spots for SRR5031107.sra
Read 142365 spots for SRR5031107.sra
Written 142365 spots for SRR5031107.sra
SRR ids: ['SRR5031107.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ax_n72fg
SRR5031107.sra spots: 1708303
blocks: [[1, 142358], [142359, 284716], [284717, 427074], [427075, 569432], [569433, 711790], [711791, 854148], [854149, 996506], [996507, 1138864], [1138865, 1281222], [1281223, 1423580], [1423581, 1565938], [1565939, 1708303]]
SRR5031107 file size 295015
SRR5031107 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031107 SRR5031107_1.fastq
Input file:	SRR5031107_1.fastq
trimmed:	SRR5031107-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 07:25:15 2020 >> started

Wed Mar  4 07:25:16 2020 >> done (1.208s)
1708303 reads processed; of these:
    109 ( 0.01%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
1708189 (99.99%) reads available; of these:
 136918 ( 8.02%) trimmed reads available after processing
1571271 (91.98%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     36	  0.00%
 19	     70	  0.00%
 20	    114	  0.01%
 21	    203	  0.01%
 22	    341	  0.02%
 23	    347	  0.02%
 24	    372	  0.02%
 25	    453	  0.03%
 26	    296	  0.02%
 27	    395	  0.02%
 28	    503	  0.03%
 29	   1158	  0.07%
 30	    456	  0.03%
 31	    507	  0.03%
 32	    663	  0.04%
 33	   1517	  0.09%
 34	   1983	  0.12%
 35	   5241	  0.31%
 36	   3093	  0.18%
 37	   2711	  0.16%
 38	   2295	  0.13%
 39	   2531	  0.15%
 40	   3060	  0.18%
 41	   3306	  0.19%
 42	   4132	  0.24%
 43	   6811	  0.40%
 44	   6996	  0.41%
 45	   8721	  0.51%
 46	  10524	  0.62%
 47	  10201	  0.60%
 48	  31073	  1.82%
 49	  26809	  1.57%
 50	1571271	 91.98%
1708189 reads passed initial QC


criterion=sequence-density
sequence-density=91.70
sequence-density-rank=1
fanout-score=20.11
fanout-score-rank=2
prefix-density=92.65
prefix-fanout=19.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGCC


criterion=fanout-score
sequence-density=3.97
sequence-density-rank=3
fanout-score=64.79
fanout-score-rank=1
prefix-density=92.80
prefix-fanout=2.8
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGCC -o SRR5031107 -
Input file:	STDIN
trimmed:	SRR5031107-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGCC
-- 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 07:25:28 2020 >> started

Wed Mar  4 07:25:31 2020 >> done (2.758s)
1671055 reads processed; of these:
  84003 ( 5.03%) short reads filtered out after trimming by size control
   8750 ( 0.52%) empty reads filtered out after trimming by size control
1578302 (94.45%) reads available; of these:
1539078 (97.51%) trimmed reads available after processing
  39224 ( 2.49%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   9561	  0.61%
 19	  20003	  1.27%
 20	 107528	  6.81%
 21	 239552	 15.18%
 22	 585348	 37.09%
 23	 260946	 16.53%
 24	 109526	  6.94%
 25	  26551	  1.68%
 26	  12903	  0.82%
 27	  10039	  0.64%
 28	  10288	  0.65%
 29	   7775	  0.49%
 30	  10835	  0.69%
 31	  11483	  0.73%
 32	  15021	  0.95%
 33	  30693	  1.94%
 34	  10651	  0.67%
 35	   7266	  0.46%
 36	   8188	  0.52%
 37	   4296	  0.27%
 38	   4452	  0.28%
 39	   3966	  0.25%
 40	   5981	  0.38%
 41	   7131	  0.45%
 42	   7765	  0.49%
 43	   5057	  0.32%
 44	   3615	  0.23%
 45	   4860	  0.31%
 46	   3285	  0.21%
 47	   2433	  0.15%
 48	    441	  0.03%
 49	    645	  0.04%
 50	  30218	  1.91%


criterion=sequence-density
sequence-density=9.53
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=0.49
sequence-density-rank=32
fanout-score=22.68
fanout-score-rank=1
prefix-density=11.00
prefix-fanout=1.0
sequence=CTGAGCTTGGCA
                                 Started job on |	Mar 04 07:25:51
                             Started mapping on |	Mar 04 07:25:52
                                    Finished on |	Mar 04 07:26:18
       Mapping speed, Million of reads per hour |	223.68

                          Number of input reads |	1615436
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	852200
                        Uniquely mapped reads % |	52.75%
                          Average mapped length |	23.05
                       Number of splices: Total |	3474
            Number of splices: Annotated (sjdb) |	813
                       Number of splices: GT/AG |	3418
                       Number of splices: GC/AG |	33
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	22
                      Mismatch rate per base, % |	0.36%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.74
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	626232
             % of reads mapped to multiple loci |	38.77%
        Number of reads mapped to too many loci |	21696
             % of reads mapped to too many loci |	1.34%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	6.57%
                     % of reads unmapped: other |	0.57%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	137004	137004	137004
N_multimapping	626232	626232	626232
N_noFeature	44211	50300	571029
N_ambiguous	491612	241220	5056
UnstrandedReadsAssigned:316377 PositiveStrandReadsAssigned:560680 NegativeStrandReadsAssigned:276115
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031107 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: SRR5031107-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,615,436 reads, 422,770 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,032 rounds

 109283 SRR5031107.ke.tsv
  52636 SRR5031107.se.tsv
 161919 total
==> SRR5031107.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

==> SRR5031107.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031107 completed mapping pipeline successfully
