Starting /dee2/code/volunteer_pipeline.sh SRR5030879
    current disk space = 160664633344
    free memory = 73913612 
SRR5030879 SRAfilesize
ef7c1596928f2283ddc8506af9877a7a  SRR5030879.sra
SRR5030879.sra file validated
SRR5030879 is single end
SRR5030879 is conventional basespace
SRR5030879 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030879_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	32.3355	33.0	31.0	34.0	31.0	34.0
2	32.71425	34.0	31.0	34.0	31.0	34.0
3	32.7725	34.0	31.0	34.0	31.0	34.0
4	36.24575	37.0	37.0	37.0	35.0	37.0
5	36.1655	37.0	37.0	37.0	35.0	37.0
6	35.919	37.0	35.0	37.0	35.0	37.0
7	36.072	37.0	35.0	37.0	35.0	37.0
8	36.119	37.0	36.0	37.0	35.0	37.0
9	37.85825	39.0	38.0	39.0	35.0	39.0
10	37.88775	39.0	38.0	39.0	35.0	39.0
11	37.8025	39.0	38.0	39.0	35.0	39.0
12	37.897	39.0	38.0	39.0	35.0	39.0
13	37.81475	39.0	38.0	39.0	35.0	39.0
14	39.1415	41.0	39.0	41.0	36.0	41.0
15	39.19725	41.0	39.0	41.0	36.0	41.0
16	39.16075	40.0	39.0	41.0	36.0	41.0
17	39.255	41.0	39.0	41.0	36.0	41.0
18	39.24725	41.0	39.0	41.0	36.0	41.0
19	39.04425	40.0	39.0	41.0	36.0	41.0
20	39.0515	40.0	39.0	41.0	35.0	41.0
21	39.14725	40.0	39.0	41.0	36.0	41.0
22	39.065	41.0	39.0	41.0	35.0	41.0
23	39.11425	40.0	39.0	41.0	36.0	41.0
24	38.4735	40.0	38.0	41.0	34.0	41.0
25	38.72425	40.0	38.0	41.0	35.0	41.0
26	38.6945	40.0	38.0	41.0	35.0	41.0
27	38.6705	40.0	38.0	41.0	34.0	41.0
28	38.598	40.0	38.0	41.0	34.0	41.0
29	38.38125	40.0	38.0	41.0	34.0	41.0
30	38.04725	40.0	38.0	41.0	33.0	41.0
31	38.4965	40.0	38.0	41.0	34.0	41.0
32	38.70125	40.0	38.0	41.0	35.0	41.0
33	36.69125	40.0	36.0	41.0	29.0	41.0
34	36.151	39.0	36.0	41.0	27.0	41.0
35	32.43625	37.0	30.0	40.0	15.0	41.0
36	29.9185	37.0	23.0	40.0	8.0	41.0
37	29.98525	36.0	25.0	39.0	6.0	40.0
38	32.2955	37.0	30.0	39.0	15.0	41.0
39	31.8065	37.0	30.0	40.0	8.0	41.0
40	32.61875	37.0	32.0	40.0	8.0	41.0
41	30.422	36.0	26.0	40.0	2.0	41.0
42	31.77025	37.0	31.0	40.0	2.0	41.0
43	30.22425	37.0	26.0	40.0	2.0	41.0
44	30.93725	37.0	30.0	40.0	2.0	41.0
45	29.097	36.0	24.0	40.0	2.0	41.0
46	26.98875	35.0	13.0	39.0	2.0	41.0
47	26.85825	34.0	13.0	39.0	2.0	41.0
48	27.18	35.0	2.0	39.0	2.0	41.0
49	25.60575	34.0	2.0	39.0	2.0	41.0
50	21.9485	29.0	2.0	37.0	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
9	1.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	1.0
16	0.0
17	1.0
18	4.0
19	11.0
20	12.0
21	18.0
22	21.0
23	30.0
24	45.0
25	53.0
26	94.0
27	148.0
28	67.0
29	109.0
30	146.0
31	206.0
32	165.0
33	183.0
34	236.0
35	257.0
36	339.0
37	456.0
38	681.0
39	716.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.95971978984238	25.74430823117338	42.60695521641231	18.689016762571928
2	25.7	24.925	21.15	28.225
3	22.7	21.349999999999998	22.125	33.825
4	31.025000000000002	27.175	16.5	25.3
5	21.875	40.150000000000006	24.9	13.075000000000001
6	29.5	17.5	36.1	16.900000000000002
7	20.5	19.775000000000002	25.75	33.975
8	26.025	30.125	17.4	26.450000000000003
9	19.5	32.85	31.674999999999997	15.975
10	25.3	21.175	30.099999999999998	23.425
11	35.85	15.375	14.899999999999999	33.875
12	18.35	23.325000000000003	28.549999999999997	29.775000000000002
13	27.725	19.975	31.95	20.349999999999998
14	26.924999999999997	28.675	23.45	20.95
15	32.725	24.975	24.95	17.349999999999998
16	20.525	21.25	24.375	33.85
17	23.599999999999998	25.074999999999996	34.875	16.45
18	22.375	19.475	31.7	26.450000000000003
19	34.849999999999994	15.625	30.85	18.675
20	38.074999999999996	17.8	28.499999999999996	15.625
21	24.925	21.55	25.7	27.825
22	29.475	13.975000000000001	41.9	14.649999999999999
23	26.025	14.625	40.125	19.225
24	47.449999999999996	14.475	24.6	13.475000000000001
25	44.4	23.35	16.25	16.0
26	27.400000000000002	39.75	15.15	17.7
27	17.175	42.125	22.575	18.125
28	15.825	23.625	42.15	18.4
29	15.6	14.399999999999999	50.849999999999994	19.15
30	12.25	9.625	33.800000000000004	44.324999999999996
31	16.3	8.125	44.55	31.025000000000002
32	29.099999999999998	8.375	22.175	40.35
33	46.949999999999996	13.600000000000001	15.4	24.05
34	52.949999999999996	9.625	18.35	19.075
35	52.949999999999996	9.55	22.45	15.049999999999999
36	59.050000000000004	10.8	16.1	14.05
37	36.0	14.274999999999999	22.375	27.35
38	25.874999999999996	16.575	15.024999999999999	42.525
39	19.5	25.525	14.05	40.925
40	18.875	42.65	15.525	22.95
41	27.625	39.7	14.825	17.849999999999998
42	45.75	27.224999999999998	15.55	11.475
43	41.199999999999996	32.5	13.100000000000001	13.200000000000001
44	30.5	43.85	10.025	15.625
45	21.625	41.925000000000004	13.575000000000001	22.875
46	17.25	27.3	24.9	30.55
47	13.575000000000001	16.85	33.275	36.3
48	16.75	13.225000000000001	21.925	48.1
49	18.175	24.075	14.774999999999999	42.975
50	32.300000000000004	20.849999999999998	13.450000000000001	33.4
>>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	1.0
14	2.0
15	1.0
16	0.0
17	0.0
18	0.0
19	1.0
20	2.0
21	1.0
22	0.0
23	0.5
24	1.0
25	0.5
26	0.0
27	1.5
28	3.0
29	4.5
30	6.0
31	11.0
32	16.0
33	19.5
34	23.0
35	50.5
36	78.0
37	99.0
38	120.0
39	110.0
40	100.0
41	89.0
42	78.0
43	105.0
44	132.0
45	177.5
46	223.0
47	241.5
48	260.0
49	338.5
50	417.0
51	549.5
52	682.0
53	581.5
54	481.0
55	451.0
56	421.0
57	379.5
58	338.0
59	251.0
60	164.0
61	135.5
62	107.0
63	137.5
64	168.0
65	100.5
66	33.0
67	30.0
68	27.0
69	29.5
70	32.0
71	44.0
72	56.0
73	35.0
74	14.0
75	7.5
76	1.0
77	1.5
78	2.0
79	6.5
80	11.0
81	6.5
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	0.075
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	52.775000000000006
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.57792515395548	42.525
2	8.100426338228328	8.55
3	3.4107058266224537	5.4
4	1.7053529133112268	3.5999999999999996
5	1.0421601136901941	2.75
6	1.1369019422074846	3.5999999999999996
7	0.5684509711037423	2.1
8	0.37896731406916156	1.6
9	0.23685457129322599	1.125
>10	2.747513027001421	24.0
>50	0.047370914258645196	2.225
>100	0.047370914258645196	2.5250000000000004
>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	101	2.5250000000000004	No Hit
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	89	2.225	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	39	0.975	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (96% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	28	0.7000000000000001	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	23	0.575	RNA PCR Primer, Index 1 (100% over 33bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	22	0.5499999999999999	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	21	0.525	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	21	0.525	RNA PCR Primer, Index 1 (100% over 30bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGC	20	0.5	RNA PCR Primer, Index 20 (100% over 50bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	19	0.475	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	19	0.475	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	18	0.44999999999999996	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	18	0.44999999999999996	RNA PCR Primer, Index 1 (97% over 35bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	17	0.42500000000000004	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	17	0.42500000000000004	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	16	0.4	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	16	0.4	No Hit
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	16	0.4	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	16	0.4	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	15	0.375	No Hit
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	15	0.375	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTC	13	0.325	RNA PCR Primer, Index 20 (100% over 44bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	13	0.325	RNA PCR Primer, Index 1 (96% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	13	0.325	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	12	0.3	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	12	0.3	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	11	0.27499999999999997	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	11	0.27499999999999997	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	10	0.25	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	10	0.25	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (95% over 23bp)
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	9	0.22499999999999998	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	9	0.22499999999999998	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	9	0.22499999999999998	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	8	0.2	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	8	0.2	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	8	0.2	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCTA	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	7	0.17500000000000002	No Hit
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	7	0.17500000000000002	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAATTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (95% over 23bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	7	0.17500000000000002	No Hit
AACCAGTGATGTGATGATTCTGCCAAATGATACAAAGTGATATCACCTTT	7	0.17500000000000002	No Hit
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	7	0.17500000000000002	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGC	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 29bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	6	0.15	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	6	0.15	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGGG	6	0.15	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGTGCCAAGGAACTCCAG	6	0.15	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATT	6	0.15	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTA	6	0.15	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTTCTGTGATGAGGCTCTGGAATGTGCGCTGGGCACAGCGCCCGAGAGAG	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
GGTCCATGATGAAGCCCATTATCAGTGGACATCTATGGATGAGAAATGCG	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	5	0.125	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	5	0.125	No Hit
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCA	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
ATACCCGTCGCCGCGCTCTCCCTCTCCCCCCGTCCGCCTCCCGGGCGGGC	5	0.125	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GAAGGATCATTATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGC	5	0.125	RNA PCR Primer, Index 20 (100% over 38bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	5	0.125	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.55	0.0	0.0	0.0
2	0.0	0.575	0.0	0.0	0.0
3	0.0	0.625	0.0	0.0	0.0
4	0.0	0.625	0.0	0.0	0.0
5	0.0	0.7	0.0	0.0	0.0
6	0.0	0.7	0.0	0.0	0.0
7	0.0	1.125	0.0	0.0	0.0
8	0.0	1.3	0.0	0.0	0.0
9	0.0	1.375	0.0	0.0	0.0
10	0.0	1.55	0.0	0.0	0.0
11	0.0	1.6	0.0	0.0	0.0
12	0.0	1.8	0.0	0.0	0.0
13	0.0	2.05	0.0	0.0	0.0
14	0.0	2.35	0.0	0.0	0.0
15	0.0	2.675	0.0	0.0	0.0
16	0.0	3.5	0.0	0.0	0.0
17	0.0	3.775	0.0	0.0	0.0
18	0.0	4.7	0.0	0.0	0.0
19	0.0	5.15	0.0	0.0	0.0
20	0.0	5.575	0.0	0.0	0.0
21	0.0	9.425	0.0	0.0	0.0
22	0.0	17.75	0.0	0.0	0.0
23	0.0	41.1	0.0	0.0	0.0
24	0.0	51.35	0.0	0.0	0.0
25	0.0	56.15	0.0	0.0	0.0
26	0.0	57.5	0.0	0.0	0.0
27	0.0	58.25	0.0	0.0	0.0
28	0.0	58.8	0.0	0.0	0.0
29	0.0	59.025	0.0	0.0	0.0
30	0.0	59.55	0.0	0.0	0.0
31	0.0	60.375	0.0	0.0	0.0
32	0.0	61.3	0.0	0.0	0.0
33	0.0	62.125	0.0	0.0	0.0
34	0.0	66.175	0.0	0.0	0.0
35	0.0	67.375	0.0	0.0	0.0
36	0.0	68.15	0.0	0.0	0.0
37	0.0	69.425	0.0	0.0	0.0
38	0.0	70.025	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CTTGGCT	20	6.952051E-4	44.000004	16
GGGGGCC	45	2.728484E-10	44.000004	33
GGCTTGG	20	6.952051E-4	44.000004	19
GGCCAAG	40	5.315087E-9	44.000004	36
GCTTGGC	20	6.952051E-4	44.000004	15
GGGGCCA	45	2.728484E-10	44.000004	34
CTGTTGG	20	6.952051E-4	44.000004	19
GGGCCAA	40	5.315087E-9	44.000004	35
AACGCTG	25	3.6958358E-5	44.0	8
GGTGAGT	25	3.6958358E-5	44.0	17
ACGCTGT	25	3.6958358E-5	44.0	9
CTGAGCT	30	1.9515464E-6	44.0	11
AGCTTGG	30	1.9515464E-6	44.0	14
TCTAGCT	25	3.6958358E-5	44.0	11
TTCAACG	25	3.6958358E-5	44.0	5
CGGGGGC	50	1.4551915E-11	44.0	32
ATCTAGC	25	3.6958358E-5	44.0	10
TTATCTA	25	3.6958358E-5	44.0	8
TCGGTGA	25	3.6958358E-5	44.0	15
TAGCTGT	25	3.6958358E-5	44.0	13
>>END_MODULE
Read 219458 spots for SRR5030879.sra
Written 219458 spots for SRR5030879.sra
Read 219458 spots for SRR5030879.sra
Written 219458 spots for SRR5030879.sra
Read 219458 spots for SRR5030879.sra
Written 219458 spots for SRR5030879.sra
Read 219458 spots for SRR5030879.sra
Written 219458 spots for SRR5030879.sra
Read 219458 spots for SRR5030879.sra
Written 219458 spots for SRR5030879.sra
Read 219458 spots for SRR5030879.sra
Written 219458 spots for SRR5030879.sra
Read 219458 spots for SRR5030879.sra
Written 219458 spots for SRR5030879.sra
Read 219458 spots for SRR5030879.sra
Written 219458 spots for SRR5030879.sra
Read 219458 spots for SRR5030879.sra
Written 219458 spots for SRR5030879.sra
Read 219458 spots for SRR5030879.sra
Written 219458 spots for SRR5030879.sra
Read 219458 spots for SRR5030879.sra
Written 219458 spots for SRR5030879.sra
Read 219458 spots for SRR5030879.sra
Written 219458 spots for SRR5030879.sra
SRR ids: ['SRR5030879.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_vgjydolu
SRR5030879.sra spots: 2633496
blocks: [[1, 219458], [219459, 438916], [438917, 658374], [658375, 877832], [877833, 1097290], [1097291, 1316748], [1316749, 1536206], [1536207, 1755664], [1755665, 1975122], [1975123, 2194580], [2194581, 2414038], [2414039, 2633496]]
SRR5030879 file size 455363
SRR5030879 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030879 SRR5030879_1.fastq
Input file:	SRR5030879_1.fastq
trimmed:	SRR5030879-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 06:34:51 2020 >> started

Wed Mar  4 06:34:53 2020 >> done (2.773s)
2633496 reads processed; of these:
    160 ( 0.01%) short reads filtered out after trimming by size control
      4 ( 0.00%) empty reads filtered out after trimming by size control
2633332 (99.99%) reads available; of these:
 334891 (12.72%) trimmed reads available after processing
2298441 (87.28%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     42	  0.00%
 19	     52	  0.00%
 20	    113	  0.00%
 21	    153	  0.01%
 22	    244	  0.01%
 23	    346	  0.01%
 24	    405	  0.02%
 25	    541	  0.02%
 26	    440	  0.02%
 27	    597	  0.02%
 28	    858	  0.03%
 29	   1153	  0.04%
 30	   1007	  0.04%
 31	   1357	  0.05%
 32	   3628	  0.14%
 33	   8979	  0.34%
 34	  18986	  0.72%
 35	   4708	  0.18%
 36	   5409	  0.21%
 37	   3222	  0.12%
 38	   6178	  0.23%
 39	   6505	  0.25%
 40	  11369	  0.43%
 41	   6661	  0.25%
 42	  16241	  0.62%
 43	   8152	  0.31%
 44	  30194	  1.15%
 45	  21606	  0.82%
 46	  21814	  0.83%
 47	  22891	  0.87%
 48	  56792	  2.16%
 49	  74248	  2.82%
 50	2298441	 87.28%
2633332 reads passed initial QC


criterion=sequence-density
sequence-density=70.10
sequence-density-rank=1
fanout-score=21.61
fanout-score-rank=3
prefix-density=73.33
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCC


criterion=fanout-score
sequence-density=1.68
sequence-density-rank=7
fanout-score=421.38
fanout-score-rank=1
prefix-density=72.29
prefix-fanout=9.8
sequence=GGAATTCTCGGTGCCAAGGA
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCC -o SRR5030879 -
Input file:	STDIN
trimmed:	SRR5030879-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCC
-- 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 06:35:13 2020 >> started

Wed Mar  4 06:35:20 2020 >> done (6.790s)
2559154 reads processed; of these:
 105889 ( 4.14%) short reads filtered out after trimming by size control
  13992 ( 0.55%) empty reads filtered out after trimming by size control
2439273 (95.32%) reads available; of these:
1942444 (79.63%) trimmed reads available after processing
 496829 (20.37%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  14039	  0.58%
 19	  20434	  0.84%
 20	  94855	  3.89%
 21	 216210	  8.86%
 22	 584121	 23.95%
 23	 287133	 11.77%
 24	 130824	  5.36%
 25	  36717	  1.51%
 26	  19831	  0.81%
 27	  17254	  0.71%
 28	  18482	  0.76%
 29	  15665	  0.64%
 30	  20577	  0.84%
 31	  23487	  0.96%
 32	  26433	  1.08%
 33	 117061	  4.80%
 34	  32584	  1.34%
 35	  25732	  1.05%
 36	  36675	  1.50%
 37	  15322	  0.63%
 38	  17413	  0.71%
 39	  17605	  0.72%
 40	  25299	  1.04%
 41	  30008	  1.23%
 42	  37640	  1.54%
 43	  25564	  1.05%
 44	  24930	  1.02%
 45	  26692	  1.09%
 46	  22795	  0.93%
 47	  19052	  0.78%
 48	   7905	  0.32%
 49	  14998	  0.61%
 50	 415936	 17.05%


criterion=sequence-density
sequence-density=5.21
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=0.47
sequence-density-rank=28
fanout-score=12.61
fanout-score-rank=1
prefix-density=5.94
prefix-fanout=1.0
sequence=TGAGCTTGGCTATT
                                 Started job on |	Mar 04 06:35:52
                             Started mapping on |	Mar 04 06:35:53
                                    Finished on |	Mar 04 06:36:16
       Mapping speed, Million of reads per hour |	393.41

                          Number of input reads |	2513451
                      Average input read length |	31
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1303689
                        Uniquely mapped reads % |	51.87%
                          Average mapped length |	30.19
                       Number of splices: Total |	1523
            Number of splices: Annotated (sjdb) |	211
                       Number of splices: GT/AG |	1396
                       Number of splices: GC/AG |	27
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	99
                      Mismatch rate per base, % |	0.26%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.33
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.13
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	749211
             % of reads mapped to multiple loci |	29.81%
        Number of reads mapped to too many loci |	68124
             % of reads mapped to too many loci |	2.71%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	15.10%
                     % of reads unmapped: other |	0.51%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	460551	460551	460551
N_multimapping	749211	749211	749211
N_noFeature	69763	87055	979155
N_ambiguous	703803	428781	17505
UnstrandedReadsAssigned:530123 PositiveStrandReadsAssigned:787853 NegativeStrandReadsAssigned:307029
Dataset is classified unstranded
MeadianReadLen=24 20thPercentileLength=22 echo kmer=19
SRR5030879 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: SRR5030879-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,513,451 reads, 575,593 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,117 rounds

 109283 SRR5030879.ke.tsv
  52636 SRR5030879.se.tsv
 161919 total
==> SRR5030879.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

==> SRR5030879.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030879 completed mapping pipeline successfully
