Starting /dee2/code/volunteer_pipeline.sh SRR5031050
    current disk space = 160529448960
    free memory = 73935288 
SRR5031050 SRAfilesize
a5418be7d6997672f2a667534eff887d  SRR5031050.sra
SRR5031050.sra file validated
SRR5031050 is single end
SRR5031050 is conventional basespace
SRR5031050 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031050_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	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.36725	33.0	31.0	34.0	31.0	34.0
2	32.5905	34.0	31.0	34.0	31.0	34.0
3	32.62575	34.0	31.0	34.0	31.0	34.0
4	36.1845	37.0	35.0	37.0	35.0	37.0
5	36.095	37.0	35.0	37.0	35.0	37.0
6	35.7725	37.0	35.0	37.0	33.0	37.0
7	35.951	37.0	35.0	37.0	35.0	37.0
8	35.7655	37.0	35.0	37.0	33.0	37.0
9	37.48675	39.0	37.0	39.0	35.0	39.0
10	37.752	39.0	37.0	39.0	35.0	39.0
11	37.67625	39.0	37.0	39.0	35.0	39.0
12	37.6055	39.0	37.0	39.0	35.0	39.0
13	37.618	39.0	37.0	39.0	35.0	39.0
14	39.05225	40.0	38.0	41.0	36.0	41.0
15	39.0485	40.0	38.0	41.0	35.0	41.0
16	38.964	40.0	38.0	41.0	35.0	41.0
17	38.8155	40.0	38.0	41.0	34.0	41.0
18	38.9825	40.0	38.0	41.0	35.0	41.0
19	38.5705	40.0	38.0	41.0	34.0	41.0
20	38.84325	40.0	38.0	41.0	35.0	41.0
21	38.72725	40.0	38.0	41.0	34.0	41.0
22	38.93925	40.0	39.0	41.0	35.0	41.0
23	38.78425	40.0	38.0	41.0	35.0	41.0
24	38.85425	40.0	38.0	41.0	35.0	41.0
25	39.07225	41.0	39.0	41.0	35.0	41.0
26	38.66825	40.0	38.0	41.0	34.0	41.0
27	38.718	40.0	38.0	41.0	34.0	41.0
28	38.78325	40.0	38.0	41.0	35.0	41.0
29	38.42025	40.0	38.0	41.0	34.0	41.0
30	38.36025	40.0	38.0	41.0	33.0	41.0
31	38.48325	40.0	38.0	41.0	34.0	41.0
32	38.55675	40.0	38.0	41.0	34.0	41.0
33	38.5885	40.0	38.0	41.0	34.0	41.0
34	38.6075	40.0	38.0	41.0	34.0	41.0
35	38.54625	40.0	38.0	41.0	34.0	41.0
36	38.13725	40.0	38.0	41.0	33.0	41.0
37	37.7535	40.0	37.0	41.0	32.0	41.0
38	36.8905	40.0	36.0	41.0	30.0	41.0
39	37.23575	40.0	37.0	41.0	31.0	41.0
40	37.67675	40.0	37.0	41.0	33.0	41.0
41	37.888	40.0	38.0	41.0	33.0	41.0
42	38.116	40.0	38.0	41.0	33.0	41.0
43	38.33125	40.0	38.0	41.0	34.0	41.0
44	38.04925	40.0	38.0	41.0	33.0	41.0
45	38.003	40.0	38.0	41.0	33.0	41.0
46	37.9885	40.0	38.0	41.0	33.0	41.0
47	37.5735	40.0	37.0	41.0	32.0	41.0
48	37.0185	40.0	36.0	41.0	31.0	41.0
49	37.3115	40.0	37.0	41.0	32.0	41.0
50	36.79475	40.0	36.0	41.0	31.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
14	1.0
15	0.0
16	1.0
17	0.0
18	1.0
19	0.0
20	2.0
21	5.0
22	2.0
23	8.0
24	5.0
25	10.0
26	15.0
27	20.0
28	24.0
29	34.0
30	58.0
31	60.0
32	80.0
33	109.0
34	158.0
35	171.0
36	252.0
37	426.0
38	645.0
39	1913.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.2749999999999995	23.075000000000003	56.974999999999994	12.675
2	22.876472062139815	27.31145076421949	22.099724379854674	27.712352793786017
3	17.575	18.275	18.2	45.95
4	26.775	36.625	13.075000000000001	23.525
5	22.650000000000002	35.65	29.75	11.95
6	37.15	14.05	37.7	11.1
7	12.6	26.5	23.95	36.95
8	25.1	40.300000000000004	13.850000000000001	20.75
9	17.775	39.95	29.175	13.100000000000001
10	18.125	21.65	26.275	33.95
11	31.7	11.525	13.600000000000001	43.175000000000004
12	16.375	15.15	23.9	44.574999999999996
13	20.025000000000002	20.474999999999998	40.125	19.375
14	38.3	22.975	26.55	12.174999999999999
15	39.875	20.200000000000003	28.849999999999998	11.075
16	12.174999999999999	27.800000000000004	21.224999999999998	38.800000000000004
17	24.3	24.6	37.625	13.475000000000001
18	27.900000000000002	18.925	28.499999999999996	24.675
19	37.574999999999996	13.900000000000002	29.925	18.6
20	52.0	15.125	22.375	10.5
21	21.3	25.474999999999998	24.65	28.575
22	31.225	11.475	50.224999999999994	7.074999999999999
23	23.95	11.65	52.37500000000001	12.025
24	54.0	12.425	28.525	5.050000000000001
25	59.150000000000006	21.175	12.425	7.249999999999999
26	30.099999999999998	51.2	10.8	7.9
27	12.65	57.025000000000006	21.7	8.625
28	8.125	27.375	53.0	11.5
29	8.75	10.4	63.65	17.2
30	8.15	4.324999999999999	39.1	48.425000000000004
31	11.275	3.8249999999999997	49.275000000000006	35.625
32	23.974999999999998	4.625	23.45	47.949999999999996
33	57.550000000000004	5.8500000000000005	12.6	24.0
34	70.95	4.9	12.0	12.15
35	72.225	5.55	16.475	5.75
36	42.425000000000004	6.0	40.875	10.7
37	48.425000000000004	7.9750000000000005	23.1	20.5
38	25.1	12.725	10.525	51.65
39	12.8	21.2	7.175	58.825
40	11.450000000000001	52.1	7.9750000000000005	28.475
41	21.65	57.975	6.175	14.2
42	52.87500000000001	32.275	8.425	6.425
43	60.275	26.3	5.35	8.075000000000001
44	32.5	51.324999999999996	4.9	11.275
45	14.7	58.475	10.575	16.25
46	9.4	28.249999999999996	15.825	46.525
47	7.000000000000001	11.725	42.55	38.725
48	8.35	9.775	22.75	59.12500000000001
49	10.65	17.275	10.725	61.35
50	16.35	41.6	9.675	32.375
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.5
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	0.0
28	0.0
29	1.0
30	2.0
31	4.5
32	7.0
33	8.0
34	9.0
35	12.5
36	16.0
37	21.0
38	26.0
39	27.5
40	29.0
41	32.0
42	35.0
43	77.5
44	120.0
45	186.5
46	253.0
47	437.5
48	622.0
49	606.5
50	591.0
51	804.0
52	1017.0
53	688.5
54	360.0
55	354.5
56	349.0
57	323.0
58	297.0
59	183.0
60	69.0
61	48.0
62	27.0
63	54.0
64	81.0
65	56.0
66	31.0
67	18.5
68	6.0
69	9.0
70	12.0
71	22.0
72	32.0
73	17.0
74	2.0
75	1.5
76	1.0
77	1.0
78	1.0
79	2.0
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	0.0
2	0.22499999999999998
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	34.699999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.49567723342939	25.85
2	10.590778097982708	7.35
3	3.674351585014409	3.8249999999999997
4	2.7377521613832854	3.8
5	1.3688760806916427	2.375
6	0.9365994236311239	1.95
7	0.792507204610951	1.925
8	0.792507204610951	2.1999999999999997
9	0.5763688760806917	1.7999999999999998
>10	3.5302593659942363	24.675
>50	0.21613832853025938	4.925
>100	0.2881844380403458	19.325
>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
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	279	6.9750000000000005	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	192	4.8	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	154	3.85	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	148	3.6999999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	71	1.775	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	62	1.55	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	45	1.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	40	1.0	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	38	0.95	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	19	0.475	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 33bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	11	0.27499999999999997	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	10	0.25	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	10	0.25	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	10	0.25	No Hit
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	9	0.22499999999999998	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	8	0.2	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTC	8	0.2	RNA PCR Primer, Index 22 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCG	8	0.2	RNA PCR Primer, Index 2 (100% over 35bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACTGGACTTGGAGTCAGAAGGCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGC	7	0.17500000000000002	RNA PCR Primer, Index 22 (100% over 50bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	5	0.125	RNA PCR Primer, Index 2 (100% over 34bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTAAGGCACGCGGTGAATGCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGAGGAGCTCACAGTCTAGTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
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	0.2	0.0	0.0	0.0
2	0.0	0.225	0.0	0.0	0.0
3	0.0	0.25	0.0	0.0	0.0
4	0.0	0.275	0.0	0.0	0.0
5	0.0	0.275	0.0	0.0	0.0
6	0.0	0.325	0.0	0.0	0.0
7	0.0	0.6	0.0	0.0	0.0
8	0.0	0.675	0.0	0.0	0.0
9	0.0	0.8	0.0	0.0	0.0
10	0.0	0.95	0.0	0.0	0.0
11	0.0	1.125	0.0	0.0	0.0
12	0.0	1.275	0.0	0.0	0.0
13	0.0	1.475	0.0	0.0	0.0
14	0.0	1.675	0.0	0.0	0.0
15	0.0	2.0	0.0	0.0	0.0
16	0.0	2.675	0.0	0.0	0.0
17	0.0	3.075	0.0	0.0	0.0
18	0.0	4.1	0.0	0.0	0.0
19	0.0	4.4	0.0	0.0	0.0
20	0.0	5.275	0.0	0.0	0.0
21	0.0	10.125	0.0	0.0	0.0
22	0.0	21.325	0.0	0.0	0.0
23	0.0	57.05	0.0	0.0	0.0
24	0.0	75.0	0.0	0.0	0.0
25	0.0	81.0	0.0	0.0	0.0
26	0.0	81.875	0.0	0.0	0.0
27	0.0	82.4	0.0	0.0	0.0
28	0.0	83.025	0.0	0.0	0.0
29	0.0	83.625	0.0	0.0	0.0
30	0.0	84.125	0.0	0.0	0.0
31	0.0	84.775	0.0	0.0	0.0
32	0.0	85.9	0.0	0.0	0.0
33	0.0	86.875	0.0	0.0	0.0
34	0.0	89.175	0.0	0.0	0.0
35	0.0	90.1	0.0	0.0	0.0
36	0.0	90.75	0.0	0.0	0.0
37	0.0	91.475	0.0	0.0	0.0
38	0.0	91.775	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGAGACC	20	6.952051E-4	44.000004	5
CTGAGAC	20	6.952051E-4	44.000004	4
CTTTAAC	20	6.952051E-4	44.000004	12
AGTAGGT	40	5.315087E-9	44.000004	7
CCTGAGA	20	6.952051E-4	44.000004	3
CTTGGCT	40	5.315087E-9	44.000004	16
TAACCTG	20	6.952051E-4	44.000004	15
TAGTAGG	40	5.315087E-9	44.000004	6
ACCCTTT	20	6.952051E-4	44.000004	9
CCTTTAA	20	6.952051E-4	44.000004	11
CCCTGAG	20	6.952051E-4	44.000004	2
GCTTGGC	45	2.728484E-10	44.000004	15
AGGTTGT	40	5.315087E-9	44.000004	10
TTGGCTT	20	6.952051E-4	44.000004	17
GTAGGTT	40	5.315087E-9	44.000004	8
GACCCTT	20	6.952051E-4	44.000004	8
AGACCCT	20	6.952051E-4	44.000004	7
CCCTTTA	20	6.952051E-4	44.000004	10
TTAACCT	20	6.952051E-4	44.000004	14
TTTAACC	20	6.952051E-4	44.000004	13
>>END_MODULE
Read 357340 spots for SRR5031050.sra
Written 357340 spots for SRR5031050.sra
Read 357340 spots for SRR5031050.sra
Written 357340 spots for SRR5031050.sra
Read 357340 spots for SRR5031050.sra
Written 357340 spots for SRR5031050.sra
Read 357340 spots for SRR5031050.sra
Written 357340 spots for SRR5031050.sra
Read 357340 spots for SRR5031050.sra
Written 357340 spots for SRR5031050.sra
Read 357340 spots for SRR5031050.sra
Written 357340 spots for SRR5031050.sra
Read 357340 spots for SRR5031050.sra
Written 357340 spots for SRR5031050.sra
Read 357342 spots for SRR5031050.sra
Written 357342 spots for SRR5031050.sra
Read 357340 spots for SRR5031050.sra
Written 357340 spots for SRR5031050.sra
Read 357340 spots for SRR5031050.sra
Written 357340 spots for SRR5031050.sra
Read 357340 spots for SRR5031050.sra
Written 357340 spots for SRR5031050.sra
Read 357340 spots for SRR5031050.sra
Written 357340 spots for SRR5031050.sra
SRR ids: ['SRR5031050.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_yyw4fldq
SRR5031050.sra spots: 4288082
blocks: [[1, 357340], [357341, 714680], [714681, 1072020], [1072021, 1429360], [1429361, 1786700], [1786701, 2144040], [2144041, 2501380], [2501381, 2858720], [2858721, 3216060], [3216061, 3573400], [3573401, 3930740], [3930741, 4288082]]
SRR5031050 file size 742165
SRR5031050 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031050 SRR5031050_1.fastq
Input file:	SRR5031050_1.fastq
trimmed:	SRR5031050-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 07:13:38 2020 >> started

Wed Mar  4 07:13:40 2020 >> done (2.362s)
4288082 reads processed; of these:
    371 ( 0.01%) short reads filtered out after trimming by size control
     11 ( 0.00%) empty reads filtered out after trimming by size control
4287700 (99.99%) reads available; of these:
 214240 ( 5.00%) trimmed reads available after processing
4073460 (95.00%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     91	  0.00%
 19	    104	  0.00%
 20	    197	  0.00%
 21	    293	  0.01%
 22	    514	  0.01%
 23	    576	  0.01%
 24	    569	  0.01%
 25	    784	  0.02%
 26	    596	  0.01%
 27	    769	  0.02%
 28	    918	  0.02%
 29	   1621	  0.04%
 30	    895	  0.02%
 31	    966	  0.02%
 32	    996	  0.02%
 33	   1332	  0.03%
 34	   1860	  0.04%
 35	   3990	  0.09%
 36	   3219	  0.08%
 37	   3629	  0.08%
 38	   3203	  0.07%
 39	   3550	  0.08%
 40	   4235	  0.10%
 41	   4476	  0.10%
 42	   5829	  0.14%
 43	   8449	  0.20%
 44	  11613	  0.27%
 45	  15060	  0.35%
 46	  19952	  0.47%
 47	  27837	  0.65%
 48	  43951	  1.03%
 49	  42166	  0.98%
 50	4073460	 95.00%
4287700 reads passed initial QC


criterion=sequence-density
sequence-density=91.08
sequence-density-rank=1
fanout-score=17.97
fanout-score-rank=1
prefix-density=92.70
prefix-fanout=17.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCC


criterion=fanout-score
sequence-density=91.08
sequence-density-rank=1
fanout-score=17.97
fanout-score-rank=1
prefix-density=92.70
prefix-fanout=17.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCC -o SRR5031050 -
Input file:	STDIN
trimmed:	SRR5031050-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCC
-- 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 07:13:59 2020 >> started

Wed Mar  4 07:14:06 2020 >> done (6.768s)
4194489 reads processed; of these:
 150807 ( 3.60%) short reads filtered out after trimming by size control
  11560 ( 0.28%) empty reads filtered out after trimming by size control
4032122 (96.13%) reads available; of these:
3920201 (97.22%) trimmed reads available after processing
 111921 ( 2.78%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  20855	  0.52%
 19	  42815	  1.06%
 20	 186679	  4.63%
 21	 487577	 12.09%
 22	1535986	 38.09%
 23	 749659	 18.59%
 24	 249099	  6.18%
 25	  44133	  1.09%
 26	  21279	  0.53%
 27	  21566	  0.53%
 28	  24214	  0.60%
 29	  19797	  0.49%
 30	  33060	  0.82%
 31	  46047	  1.14%
 32	  43204	  1.07%
 33	  79362	  1.97%
 34	  40374	  1.00%
 35	  30363	  0.75%
 36	  35550	  0.88%
 37	  16860	  0.42%
 38	  19916	  0.49%
 39	  16722	  0.41%
 40	  22514	  0.56%
 41	  28968	  0.72%
 42	  30886	  0.77%
 43	  22719	  0.56%
 44	  17671	  0.44%
 45	  20868	  0.52%
 46	  15632	  0.39%
 47	  11303	  0.28%
 48	   1148	  0.03%
 49	   1663	  0.04%
 50	  93633	  2.32%


criterion=sequence-density
sequence-density=7.18
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=24
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.37
sequence-density-rank=31
fanout-score=16.50
fanout-score-rank=1
prefix-density=6.13
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 07:14:28
                             Started mapping on |	Mar 04 07:14:29
                                    Finished on |	Mar 04 07:14:55
       Mapping speed, Million of reads per hour |	571.20

                          Number of input reads |	4125333
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1964350
                        Uniquely mapped reads % |	47.62%
                          Average mapped length |	23.88
                       Number of splices: Total |	2318
            Number of splices: Annotated (sjdb) |	289
                       Number of splices: GT/AG |	2111
                       Number of splices: GC/AG |	26
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	180
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.73
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1807243
             % of reads mapped to multiple loci |	43.81%
        Number of reads mapped to too many loci |	70910
             % of reads mapped to too many loci |	1.72%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	6.33%
                     % of reads unmapped: other |	0.53%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	353740	353740	353740
N_multimapping	1807243	1807243	1807243
N_noFeature	93545	109812	1509901
N_ambiguous	1059562	673057	12490
UnstrandedReadsAssigned:811243 PositiveStrandReadsAssigned:1181481 NegativeStrandReadsAssigned:441959
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031050 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: SRR5031050-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,125,333 reads, 839,037 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,172 rounds

 109283 SRR5031050.ke.tsv
  52636 SRR5031050.se.tsv
 161919 total
==> SRR5031050.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

==> SRR5031050.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031050 completed mapping pipeline successfully
