Starting /dee2/code/volunteer_pipeline.sh SRR5030997
    current disk space = 160568737792
    free memory = 73937784 
SRR5030997 SRAfilesize
14ad58f8fd5c50fd2ebea812be24bb9e  SRR5030997.sra
SRR5030997.sra file validated
SRR5030997 is single end
SRR5030997 is conventional basespace
SRR5030997 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030997_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	32.33725	33.0	31.0	34.0	31.0	34.0
2	32.60575	34.0	31.0	34.0	31.0	34.0
3	32.60225	34.0	31.0	34.0	31.0	34.0
4	36.161	37.0	35.0	37.0	35.0	37.0
5	36.10775	37.0	35.0	37.0	35.0	37.0
6	35.892	37.0	35.0	37.0	33.0	37.0
7	35.81175	37.0	35.0	37.0	35.0	37.0
8	35.89325	37.0	35.0	37.0	35.0	37.0
9	37.55625	39.0	37.0	39.0	35.0	39.0
10	37.55775	39.0	37.0	39.0	35.0	39.0
11	37.3685	39.0	37.0	39.0	34.0	39.0
12	37.6235	39.0	37.0	39.0	35.0	39.0
13	37.60325	39.0	37.0	39.0	35.0	39.0
14	38.967	40.0	38.0	41.0	35.0	41.0
15	38.90275	40.0	38.0	41.0	35.0	41.0
16	39.0195	40.0	38.0	41.0	35.0	41.0
17	39.09725	40.0	38.0	41.0	36.0	41.0
18	38.97925	41.0	38.0	41.0	35.0	41.0
19	38.732	40.0	38.0	41.0	34.0	41.0
20	38.812	40.0	38.0	41.0	35.0	41.0
21	38.8745	40.0	38.0	41.0	35.0	41.0
22	38.86825	40.0	38.0	41.0	35.0	41.0
23	38.704	40.0	38.0	41.0	34.0	41.0
24	38.82125	40.0	38.0	41.0	35.0	41.0
25	39.02725	40.0	39.0	41.0	35.0	41.0
26	38.90225	40.0	38.0	41.0	35.0	41.0
27	39.0415	40.0	39.0	41.0	35.0	41.0
28	38.84725	40.0	38.0	41.0	35.0	41.0
29	38.4285	40.0	38.0	41.0	34.0	41.0
30	38.33275	40.0	38.0	41.0	34.0	41.0
31	38.57325	40.0	38.0	41.0	34.0	41.0
32	38.56175	40.0	38.0	41.0	34.0	41.0
33	38.173	40.0	38.0	41.0	33.0	41.0
34	38.217	40.0	38.0	41.0	33.0	41.0
35	37.9575	40.0	37.0	41.0	33.0	41.0
36	37.6895	40.0	37.0	41.0	33.0	41.0
37	37.325	39.0	37.0	41.0	31.0	41.0
38	37.05325	39.0	36.0	41.0	31.0	41.0
39	37.5465	40.0	37.0	41.0	32.0	41.0
40	37.73175	40.0	37.0	41.0	33.0	41.0
41	37.96025	40.0	37.0	41.0	33.0	41.0
42	37.759	40.0	37.0	41.0	33.0	41.0
43	37.86125	40.0	37.0	41.0	33.0	41.0
44	37.85575	40.0	37.0	41.0	33.0	41.0
45	37.83525	40.0	37.0	41.0	33.0	41.0
46	37.6245	40.0	37.0	41.0	33.0	41.0
47	36.94025	40.0	36.0	41.0	31.0	41.0
48	36.75375	40.0	35.0	41.0	31.0	41.0
49	36.836	40.0	36.0	41.0	31.0	41.0
50	36.22175	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
13	1.0
14	0.0
15	2.0
16	0.0
17	0.0
18	3.0
19	2.0
20	2.0
21	4.0
22	3.0
23	3.0
24	7.0
25	9.0
26	14.0
27	26.0
28	24.0
29	38.0
30	43.0
31	65.0
32	71.0
33	107.0
34	164.0
35	185.0
36	285.0
37	472.0
38	792.0
39	1678.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.225	24.725	50.5	15.55
2	23.816679188580014	25.77009767092412	18.80791384923616	31.605309291259704
3	24.025	20.9	24.349999999999998	30.725
4	33.875	26.25	14.899999999999999	24.975
5	21.5	40.325	26.75	11.425
6	35.025	16.55	33.425	15.0
7	16.125	20.349999999999998	23.75	39.775
8	26.150000000000002	26.75	16.825000000000003	30.275000000000002
9	22.2	33.175	27.825	16.8
10	21.7	22.875	27.775	27.650000000000002
11	31.225	9.375	18.025	41.375
12	15.7	18.725	31.75	33.825
13	32.824999999999996	17.05	31.15	18.975
14	31.1	32.5	19.25	17.150000000000002
15	35.6	24.65	25.3	14.45
16	19.025	18.8	24.224999999999998	37.95
17	24.025	22.5	39.025	14.45
18	25.4	17.925	28.249999999999996	28.425
19	35.35	13.950000000000001	31.900000000000002	18.8
20	41.55	16.1	28.15	14.2
21	24.925	19.8	27.3	27.975
22	29.125	13.65	46.050000000000004	11.175
23	27.85	13.725000000000001	42.05	16.375
24	51.475	14.7	25.900000000000002	7.925
25	48.85	25.55	15.75	9.85
26	27.775	45.574999999999996	15.0	11.65
27	16.375	45.375	24.575	13.675
28	11.75	24.7	47.05	16.5
29	12.75	14.424999999999999	53.925	18.9
30	10.35	7.825	35.725	46.1
31	14.374999999999998	5.4	45.5	34.725
32	29.299999999999997	5.925	21.475	43.3
33	53.974999999999994	7.35	14.575	24.099999999999998
34	60.699999999999996	7.375	16.475	15.45
35	63.625	6.4750000000000005	19.675	10.225
36	43.125	8.3	35.0	13.575000000000001
37	46.125	11.3	19.25	23.325000000000003
38	23.075000000000003	17.45	13.225000000000001	46.25
39	17.150000000000002	23.974999999999998	11.325000000000001	47.55
40	16.35	47.025	11.725	24.9
41	25.4	46.85	10.075000000000001	17.675
42	47.275	29.45	11.425	11.85
43	50.775000000000006	29.675	8.450000000000001	11.1
44	32.15	47.175	7.3999999999999995	13.275
45	21.25	47.675	12.525	18.55
46	14.799999999999999	25.525	18.7	40.975
47	10.225	16.5	37.75	35.525
48	11.450000000000001	13.025	20.225	55.300000000000004
49	14.45	19.55	14.549999999999999	51.449999999999996
50	18.925	35.949999999999996	14.224999999999998	30.9
>>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	0.5
12	1.0
13	1.0
14	1.0
15	1.0
16	1.0
17	0.5
18	0.0
19	0.0
20	0.0
21	0.5
22	1.0
23	1.0
24	1.0
25	2.0
26	3.0
27	2.0
28	1.0
29	3.0
30	5.0
31	7.0
32	9.0
33	9.0
34	9.0
35	14.5
36	20.0
37	20.0
38	20.0
39	32.0
40	44.0
41	40.5
42	37.0
43	75.5
44	114.0
45	148.0
46	182.0
47	291.5
48	401.0
49	556.5
50	712.0
51	810.5
52	909.0
53	649.0
54	389.0
55	441.0
56	493.0
57	361.0
58	229.0
59	145.0
60	61.0
61	54.5
62	48.0
63	83.0
64	118.0
65	77.0
66	36.0
67	26.5
68	17.0
69	26.0
70	35.0
71	62.5
72	90.0
73	49.5
74	9.0
75	5.0
76	1.0
77	0.5
78	0.0
79	1.0
80	2.0
81	1.5
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	0.17500000000000002
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	39.324999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.09663064208519	29.925
2	10.616656071201525	8.35
3	3.877940241576605	4.575
4	2.0343293070565798	3.2
5	1.3986013986013985	2.75
6	0.8900190718372537	2.1
7	0.44500953591862685	1.225
8	0.5721551176096631	1.7999999999999998
9	0.5085823267641449	1.7999999999999998
>10	2.9879211697393515	23.1
>50	0.44500953591862685	14.674999999999999
>100	0.12714558169103624	6.5
>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
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	146	3.65	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	114	2.85	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	98	2.45	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	95	2.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	91	2.275	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	88	2.1999999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	79	1.975	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	73	1.825	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	63	1.575	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	50	1.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	46	1.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	36	0.8999999999999999	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	32	0.8	RNA PCR Primer, Index 1 (97% over 35bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	27	0.675	RNA PCR Primer, Index 1 (100% over 33bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	27	0.675	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGC	24	0.6	RNA PCR Primer, Index 17 (100% over 50bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	19	0.475	RNA PCR Primer, Index 1 (100% over 30bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	19	0.475	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	15	0.375	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTC	15	0.375	RNA PCR Primer, Index 17 (100% over 44bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	14	0.35000000000000003	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	13	0.325	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	11	0.27499999999999997	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	10	0.25	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	10	0.25	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	9	0.22499999999999998	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 31bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	9	0.22499999999999998	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	8	0.2	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
TTCAAGTAATCCAGGATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	6	0.15	No Hit
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	6	0.15	No Hit
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CTAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGGCAATGGTAGAACTCACACCGTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
CAACGGAATCCCAAAAGCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTATTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.675	0.0	0.0	0.0
2	0.0	0.7	0.0	0.0	0.0
3	0.0	0.8	0.0	0.0	0.0
4	0.0	0.85	0.0	0.0	0.0
5	0.0	0.875	0.0	0.0	0.0
6	0.0	0.925	0.0	0.0	0.0
7	0.0	1.475	0.0	0.0	0.0
8	0.0	1.625	0.0	0.0	0.0
9	0.0	1.65	0.0	0.0	0.0
10	0.0	1.8	0.0	0.0	0.0
11	0.0	1.975	0.0	0.0	0.0
12	0.0	2.175	0.0	0.0	0.0
13	0.0	2.45	0.0	0.0	0.0
14	0.0	2.6	0.0	0.0	0.0
15	0.0	2.925	0.0	0.0	0.0
16	0.0	4.225	0.0	0.0	0.0
17	0.0	4.675	0.0	0.0	0.0
18	0.0	5.775	0.0	0.0	0.0
19	0.0	6.175	0.0	0.0	0.0
20	0.0	7.3	0.0	0.0	0.0
21	0.0	12.65	0.0	0.0	0.0
22	0.0	24.125	0.0	0.0	0.0
23	0.0	51.75	0.0	0.0	0.0
24	0.0	63.825	0.0	0.0	0.0
25	0.0	69.95	0.0	0.0	0.0
26	0.0	71.875	0.0	0.0	0.0
27	0.0	72.85	0.0	0.0	0.0
28	0.0	73.325	0.0	0.0	0.0
29	0.0	73.85	0.0	0.0	0.0
30	0.0	74.05	0.0	0.0	0.0
31	0.0	74.925	0.0	0.0	0.0
32	0.0	76.025	0.0	0.0	0.0
33	0.0	77.575	0.0	0.0	0.0
34	0.0	80.775	0.0	0.0	0.0
35	0.0	82.3	0.0	0.0	0.0
36	0.0	83.075	0.0	0.0	0.0
37	0.0	83.925	0.0	0.0	0.0
38	0.0	84.5	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
ACGCTGT	20	6.952051E-4	44.000004	9
TTCAACG	20	6.952051E-4	44.000004	5
GGTCTCT	20	6.952051E-4	44.000004	13
CTCTTTT	20	6.952051E-4	44.000004	16
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
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
CGGATCC	40	5.315087E-9	44.000004	2
GGATAGG	20	6.952051E-4	44.000004	14
GTCTCTT	20	6.952051E-4	44.000004	14
GATCCGT	40	5.315087E-9	44.000004	4
GCTTGGT	20	6.952051E-4	44.000004	15
TCTCTTT	20	6.952051E-4	44.000004	15
TCCGTCT	40	5.315087E-9	44.000004	6
ATCCGTC	40	5.315087E-9	44.000004	5
CGGTCTC	20	6.952051E-4	44.000004	12
>>END_MODULE
Read 170120 spots for SRR5030997.sra
Written 170120 spots for SRR5030997.sra
Read 170120 spots for SRR5030997.sra
Written 170120 spots for SRR5030997.sra
Read 170120 spots for SRR5030997.sra
Written 170120 spots for SRR5030997.sra
Read 170120 spots for SRR5030997.sra
Written 170120 spots for SRR5030997.sra
Read 170120 spots for SRR5030997.sra
Written 170120 spots for SRR5030997.sra
Read 170120 spots for SRR5030997.sra
Written 170120 spots for SRR5030997.sra
Read 170120 spots for SRR5030997.sra
Written 170120 spots for SRR5030997.sra
Read 170120 spots for SRR5030997.sra
Written 170120 spots for SRR5030997.sra
Read 170123 spots for SRR5030997.sra
Written 170123 spots for SRR5030997.sra
Read 170120 spots for SRR5030997.sra
Written 170120 spots for SRR5030997.sra
Read 170120 spots for SRR5030997.sra
Written 170120 spots for SRR5030997.sra
Read 170120 spots for SRR5030997.sra
Written 170120 spots for SRR5030997.sra
SRR ids: ['SRR5030997.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_7vs9o6jz
SRR5030997.sra spots: 2041443
blocks: [[1, 170120], [170121, 340240], [340241, 510360], [510361, 680480], [680481, 850600], [850601, 1020720], [1020721, 1190840], [1190841, 1360960], [1360961, 1531080], [1531081, 1701200], [1701201, 1871320], [1871321, 2041443]]
SRR5030997 file size 352756
SRR5030997 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030997 SRR5030997_1.fastq
Input file:	SRR5030997_1.fastq
trimmed:	SRR5030997-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 07:02:32 2020 >> started

Wed Mar  4 07:02:33 2020 >> done (1.316s)
2041443 reads processed; of these:
    164 ( 0.01%) short reads filtered out after trimming by size control
      4 ( 0.00%) empty reads filtered out after trimming by size control
2041275 (99.99%) reads available; of these:
 122230 ( 5.99%) trimmed reads available after processing
1919045 (94.01%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     52	  0.00%
 19	     76	  0.00%
 20	    119	  0.01%
 21	    144	  0.01%
 22	    247	  0.01%
 23	    287	  0.01%
 24	    316	  0.02%
 25	    410	  0.02%
 26	    351	  0.02%
 27	    514	  0.03%
 28	    589	  0.03%
 29	    845	  0.04%
 30	    603	  0.03%
 31	    701	  0.03%
 32	    783	  0.04%
 33	    999	  0.05%
 34	   1130	  0.06%
 35	   2073	  0.10%
 36	   1926	  0.09%
 37	   2151	  0.11%
 38	   2102	  0.10%
 39	   2253	  0.11%
 40	   2506	  0.12%
 41	   2581	  0.13%
 42	   3299	  0.16%
 43	   4899	  0.24%
 44	   6472	  0.32%
 45	   8244	  0.40%
 46	  11719	  0.57%
 47	  13949	  0.68%
 48	  21725	  1.06%
 49	  28165	  1.38%
 50	1919045	 94.01%
2041275 reads passed initial QC


criterion=sequence-density
sequence-density=83.32
sequence-density-rank=1
fanout-score=21.41
fanout-score-rank=1
prefix-density=85.18
prefix-fanout=20.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCC


criterion=fanout-score
sequence-density=83.32
sequence-density-rank=1
fanout-score=21.41
fanout-score-rank=1
prefix-density=85.18
prefix-fanout=20.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCC -o SRR5030997 -
Input file:	STDIN
trimmed:	SRR5030997-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCC
-- 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 07:02:46 2020 >> started

Wed Mar  4 07:02:49 2020 >> done (3.106s)
1992673 reads processed; of these:
 107652 ( 5.40%) short reads filtered out after trimming by size control
  11602 ( 0.58%) empty reads filtered out after trimming by size control
1873419 (94.02%) reads available; of these:
1758846 (93.88%) trimmed reads available after processing
 114573 ( 6.12%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  10675	  0.57%
 19	  21368	  1.14%
 20	 109194	  5.83%
 21	 237074	 12.65%
 22	 566243	 30.23%
 23	 259741	 13.86%
 24	 126824	  6.77%
 25	  33532	  1.79%
 26	  17539	  0.94%
 27	  13335	  0.71%
 28	  14894	  0.80%
 29	  11077	  0.59%
 30	  15820	  0.84%
 31	  21478	  1.15%
 32	  25922	  1.38%
 33	  56896	  3.04%
 34	  21085	  1.13%
 35	  15779	  0.84%
 36	  18053	  0.96%
 37	  10184	  0.54%
 38	  11055	  0.59%
 39	  10661	  0.57%
 40	  16944	  0.90%
 41	  22334	  1.19%
 42	  27089	  1.45%
 43	  18599	  0.99%
 44	  13369	  0.71%
 45	  20642	  1.10%
 46	  14763	  0.79%
 47	  10411	  0.56%
 48	   1237	  0.07%
 49	   2287	  0.12%
 50	  97315	  5.19%


criterion=sequence-density
sequence-density=6.52
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=36
fanout-score=304.87
fanout-score-rank=1
prefix-density=2.24
prefix-fanout=1.8
sequence=TTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:03:10
                             Started mapping on |	Mar 04 07:03:10
                                    Finished on |	Mar 04 07:03:36
       Mapping speed, Million of reads per hour |	266.13

                          Number of input reads |	1922021
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1008874
                        Uniquely mapped reads % |	52.49%
                          Average mapped length |	24.70
                       Number of splices: Total |	1449
            Number of splices: Annotated (sjdb) |	377
                       Number of splices: GT/AG |	1380
                       Number of splices: GC/AG |	20
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	47
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.85
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.02
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	637004
             % of reads mapped to multiple loci |	33.14%
        Number of reads mapped to too many loci |	41795
             % of reads mapped to too many loci |	2.17%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.52%
                     % of reads unmapped: other |	0.67%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	276143	276143	276143
N_multimapping	637004	637004	637004
N_noFeature	49672	62572	695846
N_ambiguous	558609	288669	9284
UnstrandedReadsAssigned:400593 PositiveStrandReadsAssigned:657633 NegativeStrandReadsAssigned:303744
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030997 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: SRR5030997-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,922,021 reads, 482,796 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,099 rounds

 109283 SRR5030997.ke.tsv
  52636 SRR5030997.se.tsv
 161919 total
==> SRR5030997.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

==> SRR5030997.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030997 completed mapping pipeline successfully
