Starting /dee2/code/volunteer_pipeline.sh SRR5030874
    current disk space = 160654802944
    free memory = 73950568 
SRR5030874 SRAfilesize
cb1a720bc9d2e6975c078e5d5a295aea  SRR5030874.sra
SRR5030874.sra file validated
SRR5030874 is single end
SRR5030874 is conventional basespace
SRR5030874 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030874_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	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.375	33.0	31.0	34.0	31.0	34.0
2	32.78625	34.0	31.0	34.0	31.0	34.0
3	32.8225	34.0	31.0	34.0	31.0	34.0
4	36.30375	37.0	37.0	37.0	35.0	37.0
5	36.247	37.0	37.0	37.0	35.0	37.0
6	36.045	37.0	35.0	37.0	35.0	37.0
7	36.14	37.0	35.0	37.0	35.0	37.0
8	36.1755	37.0	36.0	37.0	35.0	37.0
9	37.93125	39.0	38.0	39.0	35.0	39.0
10	37.92825	39.0	38.0	39.0	35.0	39.0
11	37.84075	39.0	38.0	39.0	35.0	39.0
12	37.96025	39.0	38.0	39.0	35.0	39.0
13	37.9	39.0	38.0	39.0	35.0	39.0
14	39.35	41.0	39.0	41.0	36.0	41.0
15	39.44075	41.0	39.0	41.0	36.0	41.0
16	39.31075	41.0	39.0	41.0	36.0	41.0
17	39.3595	41.0	39.0	41.0	36.0	41.0
18	39.26275	41.0	39.0	41.0	36.0	41.0
19	39.1075	40.0	39.0	41.0	36.0	41.0
20	39.19825	40.0	39.0	41.0	36.0	41.0
21	39.22075	41.0	39.0	41.0	36.0	41.0
22	39.24625	41.0	39.0	41.0	36.0	41.0
23	39.17425	40.0	39.0	41.0	36.0	41.0
24	38.40775	40.0	38.0	41.0	34.0	41.0
25	38.6275	40.0	38.0	41.0	34.0	41.0
26	38.535	40.0	38.0	41.0	34.0	41.0
27	38.696	40.0	38.0	41.0	34.0	41.0
28	38.63675	40.0	38.0	41.0	34.0	41.0
29	38.35925	40.0	38.0	41.0	34.0	41.0
30	38.11775	40.0	38.0	41.0	33.0	41.0
31	38.557	40.0	38.0	41.0	34.0	41.0
32	38.7645	40.0	38.0	41.0	35.0	41.0
33	36.99675	40.0	37.0	41.0	30.0	41.0
34	36.20175	39.0	36.0	41.0	28.0	41.0
35	32.745	38.0	31.0	40.0	15.0	41.0
36	29.8525	37.0	23.0	40.0	8.0	41.0
37	30.04775	36.0	24.0	39.0	7.0	41.0
38	32.30925	37.0	30.0	40.0	15.0	41.0
39	31.8125	37.0	30.0	40.0	8.0	41.0
40	32.34675	37.0	31.0	40.0	7.0	41.0
41	30.41825	36.0	26.0	40.0	2.0	41.0
42	31.75375	37.0	30.0	40.0	2.0	41.0
43	30.254	37.0	26.0	40.0	2.0	41.0
44	31.19475	37.0	30.0	40.0	2.0	41.0
45	29.3295	37.0	26.0	40.0	2.0	41.0
46	27.148	35.0	14.0	39.0	2.0	41.0
47	27.02575	34.0	13.0	39.0	2.0	41.0
48	27.4655	35.0	7.0	39.0	2.0	41.0
49	25.7475	34.0	2.0	39.0	2.0	41.0
50	22.7585	30.0	2.0	38.0	2.0	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	2.0
15	2.0
16	3.0
17	2.0
18	5.0
19	3.0
20	10.0
21	15.0
22	19.0
23	28.0
24	44.0
25	64.0
26	92.0
27	149.0
28	80.0
29	92.0
30	162.0
31	161.0
32	166.0
33	163.0
34	222.0
35	295.0
36	359.0
37	424.0
38	665.0
39	773.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.146255947908841	25.41948409717005	43.451039318807915	18.9832206361132
2	26.700000000000003	25.374999999999996	20.474999999999998	27.450000000000003
3	23.275000000000002	20.125	21.675	34.925
4	31.6	26.3	16.55	25.55
5	22.325	38.25	26.625	12.8
6	30.599999999999998	16.325	36.825	16.25
7	20.025000000000002	20.424999999999997	24.325	35.225
8	25.674999999999997	30.425	17.875	26.025
9	20.5	32.375	29.725	17.4
10	22.925	21.2	29.599999999999998	26.275
11	36.9	14.674999999999999	14.524999999999999	33.900000000000006
12	17.925	23.225	28.125	30.725
13	27.125	18.925	33.525	20.424999999999997
14	27.85	27.750000000000004	23.974999999999998	20.424999999999997
15	32.0	24.55	26.200000000000003	17.25
16	20.974999999999998	20.424999999999997	23.075000000000003	35.525
17	24.825	23.625	34.300000000000004	17.25
18	24.25	18.9	31.15	25.7
19	34.525	14.924999999999999	31.874999999999996	18.675
20	39.425	16.925	28.7	14.95
21	26.900000000000002	21.275	25.424999999999997	26.400000000000002
22	31.075000000000003	13.4	42.475	13.05
23	26.1	14.7	41.425	17.775
24	47.0	14.025000000000002	25.8	13.175
25	46.625	23.325000000000003	16.425	13.625000000000002
26	27.900000000000002	39.35	15.7	17.05
27	17.599999999999998	43.15	20.9	18.35
28	15.5	24.65	41.725	18.125
29	15.15	14.649999999999999	52.6	17.599999999999998
30	11.5	9.175	34.775	44.55
31	16.55	7.449999999999999	44.3	31.7
32	28.349999999999998	7.249999999999999	23.5	40.9
33	46.650000000000006	13.175	15.075	25.1
34	54.37499999999999	8.7	18.75	18.175
35	57.025000000000006	8.7	19.725	14.549999999999999
36	60.275	10.45	16.0	13.275
37	37.625	15.15	21.8	25.424999999999997
38	26.025	18.175	14.2	41.6
39	18.8	24.45	13.900000000000002	42.85
40	18.375	42.35	14.7	24.575
41	25.775	41.725	12.9	19.6
42	44.025	29.9	14.799999999999999	11.275
43	42.525	33.725	10.674999999999999	13.075000000000001
44	32.1	43.15	10.45	14.299999999999999
45	21.625	43.725	12.174999999999999	22.475
46	16.7	29.9	22.875	30.525000000000002
47	11.600000000000001	17.45	33.375	37.574999999999996
48	15.225	12.975	22.5	49.3
49	16.05	23.75	15.575	44.625
50	29.875	23.674999999999997	11.325000000000001	35.125
>>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	0.5
20	1.0
21	0.5
22	0.0
23	0.0
24	0.0
25	1.5
26	3.0
27	5.5
28	8.0
29	5.0
30	2.0
31	6.0
32	10.0
33	14.5
34	19.0
35	37.5
36	56.0
37	78.0
38	100.0
39	93.5
40	87.0
41	82.0
42	77.0
43	108.5
44	140.0
45	174.0
46	208.0
47	233.0
48	258.0
49	351.5
50	445.0
51	614.5
52	784.0
53	619.5
54	455.0
55	429.0
56	403.0
57	345.5
58	288.0
59	232.5
60	177.0
61	142.5
62	108.0
63	151.0
64	194.0
65	122.5
66	51.0
67	33.0
68	15.0
69	18.0
70	21.0
71	44.5
72	68.0
73	39.5
74	11.0
75	6.0
76	1.0
77	0.5
78	0.0
79	4.0
80	8.0
81	5.0
82	2.0
83	1.0
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	0.17500000000000002
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	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	warn
#Total Deduplicated Percentage	51.949999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.70259865255053	41.925000000000004
2	8.325312800769971	8.649999999999999
3	3.4167468719923004	5.325
4	1.4436958614051971	3.0
5	1.395572666025024	3.6249999999999996
6	0.6737247353224254	2.1
7	0.4812319538017324	1.7500000000000002
8	0.28873917228103946	1.2
9	0.4812319538017324	2.25
>10	2.6948989412897015	24.175
>50	0.0	0.0
>100	0.0962463907603465	6.0
>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	121	3.025	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	119	2.9749999999999996	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	43	1.075	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	38	0.95	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	35	0.8750000000000001	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (96% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	27	0.675	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAG	22	0.5499999999999999	RNA PCR Primer, Index 2 (97% over 35bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	21	0.525	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	19	0.475	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	18	0.44999999999999996	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	18	0.44999999999999996	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	17	0.42500000000000004	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	17	0.42500000000000004	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	16	0.4	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	15	0.375	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 27bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	14	0.35000000000000003	No Hit
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	14	0.35000000000000003	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	14	0.35000000000000003	No Hit
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	13	0.325	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	13	0.325	No Hit
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	13	0.325	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	12	0.3	RNA PCR Primer, Index 1 (96% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTC	12	0.3	RNA PCR Primer, Index 13 (100% over 44bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	12	0.3	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 33bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	11	0.27499999999999997	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	11	0.27499999999999997	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	11	0.27499999999999997	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	10	0.25	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	10	0.25	No Hit
ACGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	10	0.25	No Hit
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	10	0.25	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	10	0.25	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	9	0.22499999999999998	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGC	9	0.22499999999999998	RNA PCR Primer, Index 13 (100% over 50bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	9	0.22499999999999998	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ACGCACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTC	8	0.2	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	8	0.2	No Hit
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	8	0.2	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	7	0.17500000000000002	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	6	0.15	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGAAGAAAGGT	6	0.15	No Hit
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTGGTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	6	0.15	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	5	0.125	No Hit
CTGGGCTACACATTTTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	5	0.125	RNA PCR Primer, Index 1 (100% over 34bp)
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	5	0.125	No Hit
CGCACGGGGTCGGCGGCGATGTCGGTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGCCGCGCC	5	0.125	No Hit
GTCTGATGATGAGCCCATTGCCCTGAGCTCTTGTGATGCTGGCTTCAAAG	5	0.125	No Hit
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	5	0.125	RNA PCR Primer, Index 1 (100% over 34bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	5	0.125	RNA PCR Primer, Index 1 (100% over 32bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	5	0.125	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAATGGAATTCTCG	5	0.125	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
>>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	0.3	0.0	0.0	0.0
2	0.0	0.3	0.0	0.0	0.0
3	0.0	0.325	0.0	0.0	0.0
4	0.0	0.325	0.0	0.0	0.0
5	0.0	0.4	0.0	0.0	0.0
6	0.0	0.475	0.0	0.0	0.0
7	0.0	0.85	0.0	0.0	0.0
8	0.0	0.925	0.0	0.0	0.0
9	0.0	1.075	0.0	0.0	0.0
10	0.0	1.225	0.0	0.0	0.0
11	0.0	1.375	0.0	0.0	0.0
12	0.0	1.625	0.0	0.0	0.0
13	0.0	1.875	0.0	0.0	0.0
14	0.0	2.05	0.0	0.0	0.0
15	0.0	2.45	0.0	0.0	0.0
16	0.0	3.325	0.0	0.0	0.0
17	0.0	3.975	0.0	0.0	0.0
18	0.0	4.825	0.0	0.0	0.0
19	0.0	5.225	0.0	0.0	0.0
20	0.0	6.325	0.0	0.0	0.0
21	0.0	10.525	0.0	0.0	0.0
22	0.0	18.75	0.0	0.0	0.0
23	0.0	42.425	0.0	0.0	0.0
24	0.0	54.35	0.0	0.0	0.0
25	0.0	60.0	0.0	0.0	0.0
26	0.0	61.45	0.0	0.0	0.0
27	0.0	61.9	0.0	0.0	0.0
28	0.0	62.325	0.0	0.0	0.0
29	0.0	62.6	0.0	0.0	0.0
30	0.0	62.95	0.0	0.0	0.0
31	0.0	63.45	0.0	0.0	0.0
32	0.0	64.45	0.0	0.0	0.0
33	0.0	65.275	0.0	0.0	0.0
34	0.0	69.575	0.0	0.0	0.0
35	0.0	70.625	0.0	0.0	0.0
36	0.0	71.425	0.0	0.0	0.0
37	0.0	72.2	0.0	0.0	0.0
38	0.0	72.55	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CGCGACC	20	6.952051E-4	44.000004	1
GCGACCT	20	6.952051E-4	44.000004	2
GCGACCC	20	6.952051E-4	44.000004	22
GGCGACC	20	6.952051E-4	44.000004	21
GTGAGTT	20	6.952051E-4	44.000004	18
CGTGGCG	20	6.952051E-4	44.000004	18
ATCAGAC	20	6.952051E-4	44.000004	12
AGACGTG	20	6.952051E-4	44.000004	15
GACGTGG	20	6.952051E-4	44.000004	16
TCAGACG	20	6.952051E-4	44.000004	13
CTCAGAT	20	6.952051E-4	44.000004	7
CCTCAGA	20	6.952051E-4	44.000004	6
CAGACGT	20	6.952051E-4	44.000004	14
GATCAGA	20	6.952051E-4	44.000004	11
ACCTCAG	20	6.952051E-4	44.000004	5
GTGGCGA	20	6.952051E-4	44.000004	19
TGGCGAC	20	6.952051E-4	44.000004	20
GACCTCA	20	6.952051E-4	44.000004	4
AGATCAG	20	6.952051E-4	44.000004	10
CGACCTC	20	6.952051E-4	44.000004	3
>>END_MODULE
Read 250919 spots for SRR5030874.sra
Written 250919 spots for SRR5030874.sra
Read 250919 spots for SRR5030874.sra
Written 250919 spots for SRR5030874.sra
Read 250919 spots for SRR5030874.sra
Written 250919 spots for SRR5030874.sra
Read 250919 spots for SRR5030874.sra
Written 250919 spots for SRR5030874.sra
Read 250919 spots for SRR5030874.sra
Written 250919 spots for SRR5030874.sra
Read 250919 spots for SRR5030874.sra
Written 250919 spots for SRR5030874.sra
Read 250919 spots for SRR5030874.sra
Written 250919 spots for SRR5030874.sra
Read 250919 spots for SRR5030874.sra
Written 250919 spots for SRR5030874.sra
Read 250919 spots for SRR5030874.sra
Written 250919 spots for SRR5030874.sra
Read 250919 spots for SRR5030874.sra
Written 250919 spots for SRR5030874.sra
Read 250919 spots for SRR5030874.sra
Written 250919 spots for SRR5030874.sra
Read 250927 spots for SRR5030874.sra
Written 250927 spots for SRR5030874.sra
SRR ids: ['SRR5030874.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_y9my9dxc
SRR5030874.sra spots: 3011036
blocks: [[1, 250919], [250920, 501838], [501839, 752757], [752758, 1003676], [1003677, 1254595], [1254596, 1505514], [1505515, 1756433], [1756434, 2007352], [2007353, 2258271], [2258272, 2509190], [2509191, 2760109], [2760110, 3011036]]
SRR5030874 file size 520803
SRR5030874 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030874 SRR5030874_1.fastq
Input file:	SRR5030874_1.fastq
trimmed:	SRR5030874-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 06:34:13 2020 >> started

Wed Mar  4 06:34:16 2020 >> done (2.839s)
3011036 reads processed; of these:
    181 ( 0.01%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
3010846 (99.99%) reads available; of these:
 351323 (11.67%) trimmed reads available after processing
2659523 (88.33%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     49	  0.00%
 19	     64	  0.00%
 20	    111	  0.00%
 21	    173	  0.01%
 22	    322	  0.01%
 23	    439	  0.01%
 24	    482	  0.02%
 25	    623	  0.02%
 26	    469	  0.02%
 27	    637	  0.02%
 28	    863	  0.03%
 29	   1231	  0.04%
 30	    908	  0.03%
 31	   1286	  0.04%
 32	   3429	  0.11%
 33	   9460	  0.31%
 34	  22636	  0.75%
 35	   5169	  0.17%
 36	   6101	  0.20%
 37	   3462	  0.11%
 38	   6888	  0.23%
 39	   6956	  0.23%
 40	  12446	  0.41%
 41	   7022	  0.23%
 42	  17420	  0.58%
 43	   8244	  0.27%
 44	  32009	  1.06%
 45	  22435	  0.75%
 46	  22027	  0.73%
 47	  23396	  0.78%
 48	  61869	  2.05%
 49	  72697	  2.41%
 50	2659523	 88.33%
3010846 reads passed initial QC


criterion=sequence-density
sequence-density=72.02
sequence-density-rank=1
fanout-score=21.81
fanout-score-rank=2
prefix-density=74.72
prefix-fanout=21.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCC


criterion=fanout-score
sequence-density=3.02
sequence-density-rank=2
fanout-score=76.57
fanout-score-rank=1
prefix-density=74.28
prefix-fanout=3.1
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCC -o SRR5030874 -
Input file:	STDIN
trimmed:	SRR5030874-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCC
-- 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 06:34:40 2020 >> started

Wed Mar  4 06:34:48 2020 >> done (8.401s)
2928357 reads processed; of these:
 131113 ( 4.48%) short reads filtered out after trimming by size control
  19087 ( 0.65%) empty reads filtered out after trimming by size control
2778157 (94.87%) reads available; of these:
2240491 (80.65%) trimmed reads available after processing
 537666 (19.35%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  17438	  0.63%
 19	  23868	  0.86%
 20	 105477	  3.80%
 21	 250365	  9.01%
 22	 690359	 24.85%
 23	 346805	 12.48%
 24	 153666	  5.53%
 25	  42010	  1.51%
 26	  22278	  0.80%
 27	  18795	  0.68%
 28	  20261	  0.73%
 29	  17073	  0.61%
 30	  23495	  0.85%
 31	  31758	  1.14%
 32	  29802	  1.07%
 33	 128657	  4.63%
 34	  35751	  1.29%
 35	  26824	  0.97%
 36	  37848	  1.36%
 37	  16357	  0.59%
 38	  18885	  0.68%
 39	  18656	  0.67%
 40	  27553	  0.99%
 41	  32108	  1.16%
 42	  39023	  1.40%
 43	  26990	  0.97%
 44	  25397	  0.91%
 45	  29701	  1.07%
 46	  24893	  0.90%
 47	  20930	  0.75%
 48	   8299	  0.30%
 49	  15639	  0.56%
 50	 451196	 16.24%


criterion=sequence-density
sequence-density=6.32
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.53
sequence-density-rank=29
fanout-score=11.01
fanout-score-rank=1
prefix-density=5.85
prefix-fanout=1.0
sequence=TGAGCTTGGCTATTT
                                 Started job on |	Mar 04 06:35:18
                             Started mapping on |	Mar 04 06:35:19
                                    Finished on |	Mar 04 06:35:42
       Mapping speed, Million of reads per hour |	447.75

                          Number of input reads |	2860646
                      Average input read length |	30
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1482199
                        Uniquely mapped reads % |	51.81%
                          Average mapped length |	29.70
                       Number of splices: Total |	1909
            Number of splices: Annotated (sjdb) |	276
                       Number of splices: GT/AG |	1784
                       Number of splices: GC/AG |	26
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	99
                      Mismatch rate per base, % |	0.23%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.33
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	865189
             % of reads mapped to multiple loci |	30.24%
        Number of reads mapped to too many loci |	76645
             % of reads mapped to too many loci |	2.68%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	14.71%
                     % of reads unmapped: other |	0.56%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	513258	513258	513258
N_multimapping	865189	865189	865189
N_noFeature	79847	98158	1115436
N_ambiguous	808744	496210	16592
UnstrandedReadsAssigned:593608 PositiveStrandReadsAssigned:887831 NegativeStrandReadsAssigned:350171
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030874 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: SRR5030874-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,860,646 reads, 642,678 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,126 rounds

 109283 SRR5030874.ke.tsv
  52636 SRR5030874.se.tsv
 161919 total
==> SRR5030874.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

==> SRR5030874.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030874 completed mapping pipeline successfully
