Starting /dee2/code/volunteer_pipeline.sh SRR5031066
    current disk space = 160511279104
    free memory = 73946352 
SRR5031066 SRAfilesize
599f6908c26ce3dfbedadb2c5854f505  SRR5031066.sra
SRR5031066.sra file validated
SRR5031066 is single end
SRR5031066 is conventional basespace
SRR5031066 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031066_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	32.331	33.0	31.0	34.0	31.0	34.0
2	32.5625	34.0	31.0	34.0	31.0	34.0
3	32.6625	34.0	31.0	34.0	31.0	34.0
4	36.14475	37.0	37.0	37.0	35.0	37.0
5	35.94325	37.0	35.0	37.0	35.0	37.0
6	35.88	37.0	35.0	37.0	35.0	37.0
7	35.988	37.0	35.0	37.0	35.0	37.0
8	35.81025	37.0	35.0	37.0	35.0	37.0
9	37.48	39.0	37.0	39.0	34.0	39.0
10	37.689	39.0	37.0	39.0	35.0	39.0
11	37.628	39.0	37.0	39.0	35.0	39.0
12	37.57825	39.0	37.0	39.0	35.0	39.0
13	37.663	39.0	37.0	39.0	35.0	39.0
14	39.003	40.0	38.0	41.0	35.0	41.0
15	38.997	40.0	38.0	41.0	35.0	41.0
16	39.00025	40.0	38.0	41.0	35.0	41.0
17	38.8575	40.0	38.0	41.0	35.0	41.0
18	39.02875	40.0	38.0	41.0	35.0	41.0
19	38.5495	40.0	38.0	41.0	34.0	41.0
20	38.684	40.0	38.0	41.0	34.0	41.0
21	38.72625	40.0	38.0	41.0	34.0	41.0
22	38.91075	40.0	38.0	41.0	35.0	41.0
23	38.5895	40.0	38.0	41.0	34.0	41.0
24	38.6385	40.0	38.0	41.0	34.0	41.0
25	38.881	40.0	38.0	41.0	35.0	41.0
26	38.645	40.0	38.0	41.0	34.0	41.0
27	38.57725	40.0	38.0	41.0	34.0	41.0
28	38.53225	40.0	38.0	41.0	34.0	41.0
29	38.123	40.0	38.0	41.0	33.0	41.0
30	37.827	40.0	37.0	41.0	32.0	41.0
31	38.20125	40.0	38.0	41.0	33.0	41.0
32	38.20925	40.0	38.0	41.0	33.0	41.0
33	38.19425	40.0	38.0	41.0	33.0	41.0
34	38.28825	40.0	38.0	41.0	34.0	41.0
35	38.2985	40.0	38.0	41.0	34.0	41.0
36	37.81225	40.0	37.0	41.0	33.0	41.0
37	37.3675	40.0	37.0	41.0	31.0	41.0
38	36.7315	39.0	36.0	40.0	30.0	41.0
39	37.079	39.0	37.0	41.0	31.0	41.0
40	37.26425	39.0	37.0	41.0	31.0	41.0
41	37.47525	40.0	37.0	41.0	32.0	41.0
42	37.83525	40.0	37.0	41.0	33.0	41.0
43	38.14425	40.0	38.0	41.0	34.0	41.0
44	37.9225	40.0	37.0	41.0	33.0	41.0
45	37.808	40.0	37.0	41.0	33.0	41.0
46	37.60675	40.0	37.0	41.0	33.0	41.0
47	36.8285	40.0	36.0	41.0	30.0	41.0
48	36.44925	39.0	35.0	41.0	30.0	41.0
49	36.5825	39.0	35.0	41.0	31.0	41.0
50	36.084	39.0	35.0	41.0	30.0	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	0.0
17	3.0
18	1.0
19	4.0
20	5.0
21	6.0
22	9.0
23	7.0
24	9.0
25	8.0
26	8.0
27	25.0
28	28.0
29	34.0
30	42.0
31	61.0
32	80.0
33	121.0
34	193.0
35	185.0
36	292.0
37	441.0
38	739.0
39	1698.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	13.175	25.15	43.525000000000006	18.15
2	25.344008006004504	26.09457092819615	18.939204403302476	29.622216662496875
3	23.225	17.75	21.75	37.275000000000006
4	33.975	29.95	14.475	21.6
5	21.75	37.35	26.525	14.374999999999998
6	28.95	15.425	37.375	18.25
7	19.8	19.85	19.55	40.8
8	20.925	27.925	21.2	29.95
9	25.45	30.975	24.85	18.725
10	23.075000000000003	20.275000000000002	29.275000000000002	27.375
11	35.275	12.375	16.275000000000002	36.075
12	17.125	21.3	30.85	30.725
13	27.750000000000004	16.175	34.849999999999994	21.224999999999998
14	29.275000000000002	29.575000000000003	19.85	21.3
15	35.925000000000004	24.175	25.1	14.799999999999999
16	21.675	19.3	22.175	36.85
17	29.125	23.799999999999997	33.975	13.100000000000001
18	27.250000000000004	15.325	30.25	27.175
19	37.075	14.924999999999999	31.25	16.75
20	43.9	16.0	26.6	13.5
21	27.275	22.875	22.325	27.525
22	32.800000000000004	14.45	40.65	12.1
23	24.85	14.274999999999999	41.4	19.475
24	47.699999999999996	15.950000000000001	26.6	9.75
25	46.225	24.7	17.05	12.025
26	28.075	40.849999999999994	15.375	15.7
27	18.2	42.475	23.1	16.225
28	14.224999999999998	24.175	42.1	19.5
29	17.175	14.325	50.625	17.875
30	11.875	8.475000000000001	33.95	45.7
31	15.375	5.8999999999999995	45.775	32.95
32	28.7	6.65	23.65	41.0
33	48.5	12.8	15.950000000000001	22.75
34	55.275	8.35	18.975	17.4
35	62.224999999999994	8.525	18.375	10.875
36	43.275000000000006	10.174999999999999	32.525	14.025000000000002
37	42.65	14.674999999999999	21.5	21.175
38	25.374999999999996	19.400000000000002	13.350000000000001	41.875
39	17.05	21.9	15.55	45.5
40	17.1	41.85	15.5	25.55
41	22.375	43.85	11.575000000000001	22.2
42	42.675000000000004	29.225	15.725	12.375
43	48.3	27.525	10.325	13.850000000000001
44	33.675	42.275	8.475000000000001	15.575
45	22.925	44.95	15.225	16.900000000000002
46	18.7	25.174999999999997	17.675	38.45
47	12.375	15.6	38.1	33.925
48	14.725	12.950000000000001	21.475	50.849999999999994
49	14.7	17.5	15.35	52.449999999999996
50	16.650000000000002	33.525	15.275	34.55
>>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	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	0.5
26	0.0
27	0.0
28	0.0
29	1.5
30	3.0
31	7.0
32	11.0
33	10.0
34	9.0
35	13.0
36	17.0
37	30.5
38	44.0
39	46.5
40	49.0
41	49.0
42	49.0
43	75.0
44	101.0
45	116.5
46	132.0
47	259.5
48	387.0
49	455.5
50	524.0
51	690.5
52	857.0
53	652.0
54	447.0
55	507.5
56	568.0
57	430.5
58	293.0
59	189.5
60	86.0
61	70.5
62	55.0
63	147.5
64	240.0
65	138.0
66	36.0
67	23.5
68	11.0
69	13.5
70	16.0
71	33.5
72	51.0
73	29.5
74	8.0
75	4.5
76	1.0
77	1.5
78	2.0
79	2.0
80	2.0
81	1.0
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	0.075
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	39.975
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.17198248905565	30.049999999999997
2	10.318949343339586	8.25
3	4.752970606629144	5.7
4	2.7517198248905568	4.3999999999999995
5	1.5009380863039399	3.0
6	0.37523452157598497	0.8999999999999999
7	1.0006253908692933	2.8000000000000003
8	0.18761726078799248	0.6
9	0.37523452157598497	1.35
>10	3.0644152595372107	21.375
>50	0.18761726078799248	5.35
>100	0.31269543464665417	16.225
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	167	4.175	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	149	3.7249999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	120	3.0	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	108	2.7	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	105	2.625	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	94	2.35	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	68	1.7000000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	52	1.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	49	1.225	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	27	0.675	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	26	0.65	RNA PCR Primer, Index 1 (100% over 26bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	25	0.625	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCT	22	0.5499999999999999	RNA PCR Primer, Index 1 (97% over 35bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	19	0.475	RNA PCR Primer, Index 1 (100% over 33bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	18	0.44999999999999996	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTC	18	0.44999999999999996	RNA PCR Primer, Index 38 (100% over 44bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGC	17	0.42500000000000004	RNA PCR Primer, Index 38 (100% over 50bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	13	0.325	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	13	0.325	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	12	0.3	RNA PCR Primer, Index 1 (100% over 31bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	12	0.3	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	11	0.27499999999999997	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 25bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	11	0.27499999999999997	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	11	0.27499999999999997	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	11	0.27499999999999997	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	10	0.25	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	9	0.22499999999999998	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	9	0.22499999999999998	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	8	0.2	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
CGCACGGGGTCGGCGGCGATGTCGGTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
GAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
GGAATACCGGGTGCTGTAGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACGCACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTC	7	0.17500000000000002	No Hit
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGCC	5	0.125	No Hit
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACCCTGTAGATCCGAATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
ATTGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
TATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTCTCGGGTGCC	5	0.125	No Hit
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTTGG	5	0.125	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGAATTGTGGCTGGACATCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TACCCTGTAGAACCGAATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTACTTGATGATAGTAAAAGATCTGATGTGGAATTCTCGGGTGCCAAGGA	5	0.125	RNA PCR Primer, Index 1 (100% over 22bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
>>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	0.425	0.0	0.0	0.0
2	0.0	0.45	0.0	0.0	0.0
3	0.0	0.475	0.0	0.0	0.0
4	0.0	0.475	0.0	0.0	0.0
5	0.0	0.525	0.0	0.0	0.0
6	0.0	0.7	0.0	0.0	0.0
7	0.0	1.175	0.0	0.0	0.0
8	0.0	1.4	0.0	0.0	0.0
9	0.0	1.475	0.0	0.0	0.0
10	0.0	1.675	0.0	0.0	0.0
11	0.0	1.95	0.0	0.0	0.0
12	0.0	2.275	0.0	0.0	0.0
13	0.0	2.7	0.0	0.0	0.0
14	0.0	2.925	0.0	0.0	0.0
15	0.0	3.45	0.0	0.0	0.0
16	0.0	4.6	0.0	0.0	0.0
17	0.0	5.225	0.0	0.0	0.0
18	0.0	6.325	0.0	0.0	0.0
19	0.0	7.0	0.0	0.0	0.0
20	0.0	7.925	0.0	0.0	0.0
21	0.0	12.875	0.0	0.0	0.0
22	0.0	21.9	0.0	0.0	0.0
23	0.0	46.875	0.0	0.0	0.0
24	0.0	58.925	0.0	0.0	0.0
25	0.0	64.975	0.0	0.0	0.0
26	0.0	67.05	0.0	0.0	0.0
27	0.0	67.95	0.0	0.0	0.0
28	0.0	68.625	0.0	0.0	0.0
29	0.0	69.425	0.0	0.0	0.0
30	0.0	69.975	0.0	0.0	0.0
31	0.0	70.875	0.0	0.0	0.0
32	0.0	72.5	0.0	0.0	0.0
33	0.0	74.0	0.0	0.0	0.0
34	0.0	79.875	0.0	0.0	0.0
35	0.0	81.75	0.0	0.0	0.0
36	0.0	82.8	0.0	0.0	0.0
37	0.0	84.525	0.0	0.0	0.0
38	0.0	85.275	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTAGAAT	20	6.952051E-4	44.000004	18
TGGTTCA	20	6.952051E-4	44.000004	8
CTGAGCT	40	5.315087E-9	44.000004	11
TGGTAGA	20	6.952051E-4	44.000004	16
CGCCTGC	20	6.952051E-4	44.000004	28
CCTAACT	20	6.952051E-4	44.000004	11
AGTGGTA	20	6.952051E-4	44.000004	14
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
GGTTCAG	20	6.952051E-4	44.000004	9
CATTCAA	20	6.952051E-4	44.000004	3
GTTCAGT	20	6.952051E-4	44.000004	10
CGGATCC	40	5.315087E-9	44.000004	2
AGAATTC	20	6.952051E-4	44.000004	20
AACTTGT	20	6.952051E-4	44.000004	14
TCAGTGG	20	6.952051E-4	44.000004	12
TAACTTG	20	6.952051E-4	44.000004	13
CTAACTT	20	6.952051E-4	44.000004	12
>>END_MODULE
Read 311719 spots for SRR5031066.sra
Written 311719 spots for SRR5031066.sra
Read 311719 spots for SRR5031066.sra
Written 311719 spots for SRR5031066.sra
Read 311719 spots for SRR5031066.sra
Written 311719 spots for SRR5031066.sra
Read 311719 spots for SRR5031066.sra
Written 311719 spots for SRR5031066.sra
Read 311719 spots for SRR5031066.sra
Written 311719 spots for SRR5031066.sra
Read 311719 spots for SRR5031066.sra
Written 311719 spots for SRR5031066.sra
Read 311719 spots for SRR5031066.sra
Written 311719 spots for SRR5031066.sra
Read 311719 spots for SRR5031066.sra
Written 311719 spots for SRR5031066.sra
Read 311719 spots for SRR5031066.sra
Written 311719 spots for SRR5031066.sra
Read 311719 spots for SRR5031066.sra
Written 311719 spots for SRR5031066.sra
Read 311719 spots for SRR5031066.sra
Written 311719 spots for SRR5031066.sra
Read 311721 spots for SRR5031066.sra
Written 311721 spots for SRR5031066.sra
SRR ids: ['SRR5031066.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_9kiuyj99
SRR5031066.sra spots: 3740630
blocks: [[1, 311719], [311720, 623438], [623439, 935157], [935158, 1246876], [1246877, 1558595], [1558596, 1870314], [1870315, 2182033], [2182034, 2493752], [2493753, 2805471], [2805472, 3117190], [3117191, 3428909], [3428910, 3740630]]
SRR5031066 file size 647275
SRR5031066 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031066 SRR5031066_1.fastq
Input file:	SRR5031066_1.fastq
trimmed:	SRR5031066-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 07:17:05 2020 >> started

Wed Mar  4 07:17:07 2020 >> done (1.902s)
3740630 reads processed; of these:
    481 ( 0.01%) short reads filtered out after trimming by size control
     14 ( 0.00%) empty reads filtered out after trimming by size control
3740135 (99.99%) reads available; of these:
 203235 ( 5.43%) trimmed reads available after processing
3536900 (94.57%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    138	  0.00%
 19	    118	  0.00%
 20	    248	  0.01%
 21	    329	  0.01%
 22	    525	  0.01%
 23	    650	  0.02%
 24	    700	  0.02%
 25	    859	  0.02%
 26	    736	  0.02%
 27	    924	  0.02%
 28	   1070	  0.03%
 29	   1834	  0.05%
 30	   1061	  0.03%
 31	   1277	  0.03%
 32	   1421	  0.04%
 33	   1734	  0.05%
 34	   1868	  0.05%
 35	   3804	  0.10%
 36	   3429	  0.09%
 37	   3717	  0.10%
 38	   3697	  0.10%
 39	   3833	  0.10%
 40	   4084	  0.11%
 41	   4328	  0.12%
 42	   5444	  0.15%
 43	   8296	  0.22%
 44	  11546	  0.31%
 45	  14642	  0.39%
 46	  21744	  0.58%
 47	  25823	  0.69%
 48	  35482	  0.95%
 49	  37874	  1.01%
 50	3536900	 94.57%
3740135 reads passed initial QC


criterion=sequence-density
sequence-density=85.08
sequence-density-rank=1
fanout-score=22.21
fanout-score-rank=1
prefix-density=87.86
prefix-fanout=21.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGCC


criterion=fanout-score
sequence-density=85.08
sequence-density-rank=1
fanout-score=22.21
fanout-score-rank=1
prefix-density=87.86
prefix-fanout=21.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGCC -o SRR5031066 -
Input file:	STDIN
trimmed:	SRR5031066-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGCC
-- 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 07:17:23 2020 >> started

Wed Mar  4 07:17:27 2020 >> done (4.030s)
3653155 reads processed; of these:
 205457 ( 5.62%) short reads filtered out after trimming by size control
  15780 ( 0.43%) empty reads filtered out after trimming by size control
3431918 (93.94%) reads available; of these:
3260983 (95.02%) trimmed reads available after processing
 170935 ( 4.98%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  23262	  0.68%
 19	  33879	  0.99%
 20	 172564	  5.03%
 21	 345190	 10.06%
 22	 958873	 27.94%
 23	 460531	 13.42%
 24	 211692	  6.17%
 25	  66716	  1.94%
 26	  34114	  0.99%
 27	  29126	  0.85%
 28	  30346	  0.88%
 29	  26116	  0.76%
 30	  37830	  1.10%
 31	  73041	  2.13%
 32	  47971	  1.40%
 33	 206478	  6.02%
 34	  66694	  1.94%
 35	  54959	  1.60%
 36	  64282	  1.87%
 37	  24621	  0.72%
 38	  31425	  0.92%
 39	  24974	  0.73%
 40	  35021	  1.02%
 41	  39035	  1.14%
 42	  44851	  1.31%
 43	  32252	  0.94%
 44	  27176	  0.79%
 45	  33459	  0.97%
 46	  25353	  0.74%
 47	  21971	  0.64%
 48	   1710	  0.05%
 49	   2278	  0.07%
 50	 144128	  4.20%


criterion=sequence-density
sequence-density=3.16
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCT


criterion=fanout-score
sequence-density=0.48
sequence-density-rank=31
fanout-score=17.75
fanout-score-rank=1
prefix-density=8.47
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:17:48
                             Started mapping on |	Mar 04 07:17:49
                                    Finished on |	Mar 04 07:18:12
       Mapping speed, Million of reads per hour |	550.78

                          Number of input reads |	3518898
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1744959
                        Uniquely mapped reads % |	49.59%
                          Average mapped length |	24.99
                       Number of splices: Total |	2450
            Number of splices: Annotated (sjdb) |	429
                       Number of splices: GT/AG |	2341
                       Number of splices: GC/AG |	22
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	87
                      Mismatch rate per base, % |	0.23%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.72
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.02
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1137554
             % of reads mapped to multiple loci |	32.33%
        Number of reads mapped to too many loci |	145235
             % of reads mapped to too many loci |	4.13%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.10%
                     % of reads unmapped: other |	1.86%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	636385	636385	636385
N_multimapping	1137554	1137554	1137554
N_noFeature	124322	147517	1156526
N_ambiguous	942938	421963	20248
UnstrandedReadsAssigned:677699 PositiveStrandReadsAssigned:1175479 NegativeStrandReadsAssigned:568185
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031066 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: SRR5031066-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,518,898 reads, 905,882 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,209 rounds

 109283 SRR5031066.ke.tsv
  52636 SRR5031066.se.tsv
 161919 total
==> SRR5031066.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

==> SRR5031066.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031066 completed mapping pipeline successfully
