Starting /dee2/code/volunteer_pipeline.sh SRR5030994
    current disk space = 160568426496
    free memory = 73946176 
SRR5030994 SRAfilesize
785b59aaf95f3b93602c0cfbf35bd027  SRR5030994.sra
SRR5030994.sra file validated
SRR5030994 is single end
SRR5030994 is conventional basespace
SRR5030994 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030994_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	32.282	33.0	31.0	34.0	31.0	34.0
2	32.467	34.0	31.0	34.0	31.0	34.0
3	32.50925	34.0	31.0	34.0	31.0	34.0
4	36.14525	37.0	35.0	37.0	35.0	37.0
5	36.0175	37.0	35.0	37.0	35.0	37.0
6	35.8275	37.0	35.0	37.0	33.0	37.0
7	35.85925	37.0	35.0	37.0	35.0	37.0
8	35.9675	37.0	35.0	37.0	35.0	37.0
9	37.59625	39.0	37.0	39.0	35.0	39.0
10	37.58925	39.0	37.0	39.0	35.0	39.0
11	37.08275	39.0	37.0	39.0	33.0	39.0
12	37.52175	39.0	37.0	39.0	34.0	39.0
13	37.53175	39.0	37.0	39.0	34.0	39.0
14	38.905	40.0	38.0	41.0	35.0	41.0
15	38.85675	40.0	38.0	41.0	35.0	41.0
16	38.84125	40.0	38.0	41.0	34.0	41.0
17	38.95075	40.0	38.0	41.0	35.0	41.0
18	38.86725	40.0	38.0	41.0	35.0	41.0
19	38.8465	40.0	38.0	41.0	35.0	41.0
20	38.747	40.0	38.0	41.0	34.0	41.0
21	38.849	40.0	38.0	41.0	35.0	41.0
22	38.74025	40.0	38.0	41.0	35.0	41.0
23	38.49325	40.0	38.0	41.0	34.0	41.0
24	38.83	40.0	38.0	41.0	35.0	41.0
25	38.89525	40.0	38.0	41.0	35.0	41.0
26	38.815	40.0	38.0	41.0	35.0	41.0
27	38.89525	40.0	38.0	41.0	35.0	41.0
28	38.664	40.0	38.0	41.0	34.0	41.0
29	38.40775	40.0	38.0	41.0	33.0	41.0
30	38.3905	40.0	38.0	41.0	34.0	41.0
31	38.456	40.0	38.0	41.0	34.0	41.0
32	38.5235	40.0	38.0	41.0	34.0	41.0
33	38.158	40.0	38.0	41.0	33.0	41.0
34	38.06375	40.0	38.0	41.0	33.0	41.0
35	37.89475	40.0	38.0	41.0	33.0	41.0
36	37.704	40.0	37.0	41.0	33.0	41.0
37	36.988	39.0	36.0	41.0	31.0	41.0
38	37.175	39.0	36.0	41.0	31.0	41.0
39	37.6985	40.0	37.0	41.0	33.0	41.0
40	37.8075	40.0	37.0	41.0	33.0	41.0
41	37.71125	40.0	37.0	41.0	33.0	41.0
42	37.47425	40.0	37.0	41.0	32.0	41.0
43	37.37775	40.0	37.0	41.0	32.0	41.0
44	37.5215	40.0	37.0	41.0	33.0	41.0
45	37.5505	40.0	37.0	41.0	33.0	41.0
46	37.3935	40.0	37.0	41.0	33.0	41.0
47	36.637	40.0	35.0	41.0	30.0	41.0
48	36.53625	39.0	35.0	41.0	30.0	41.0
49	36.695	40.0	35.0	41.0	31.0	41.0
50	35.8935	39.0	34.0	41.0	29.0	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	1.0
16	1.0
17	0.0
18	1.0
19	5.0
20	0.0
21	4.0
22	5.0
23	6.0
24	9.0
25	12.0
26	15.0
27	23.0
28	25.0
29	41.0
30	57.0
31	63.0
32	85.0
33	121.0
34	139.0
35	196.0
36	295.0
37	471.0
38	763.0
39	1661.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.25	25.374999999999996	45.85	17.525
2	25.571464456166794	25.445867872393872	20.57272042200452	28.409947249434815
3	23.674999999999997	20.95	23.05	32.324999999999996
4	33.550000000000004	26.75	16.55	23.150000000000002
5	23.425	38.75	25.174999999999997	12.65
6	33.2	15.975	33.074999999999996	17.75
7	17.599999999999998	22.05	23.175	37.175000000000004
8	25.85	28.275	17.875	28.000000000000004
9	21.825	31.900000000000002	27.775	18.5
10	22.225	24.05	27.6	26.125
11	32.0	11.85	18.25	37.9
12	17.525	18.65	30.825000000000003	33.0
13	30.3	18.525	32.925	18.25
14	29.25	29.875	20.925	19.950000000000003
15	34.625	24.675	25.825	14.875
16	20.625	19.15	25.3	34.925
17	25.650000000000002	22.125	36.525	15.7
18	25.674999999999997	19.175	27.525	27.625
19	37.574999999999996	14.899999999999999	28.675	18.85
20	41.825	17.175	27.500000000000004	13.5
21	25.15	20.175	26.424999999999997	28.249999999999996
22	29.175	13.325000000000001	45.625	11.875
23	26.85	13.575000000000001	41.625	17.95
24	50.449999999999996	14.475	24.474999999999998	10.6
25	47.349999999999994	25.275	16.3	11.075
26	28.599999999999998	44.375	13.0	14.025000000000002
27	17.65	43.8	23.65	14.899999999999999
28	12.85	23.474999999999998	46.975	16.7
29	14.975	13.675	51.449999999999996	19.900000000000002
30	12.975	8.0	35.099999999999994	43.925
31	15.4	6.5	44.775	33.324999999999996
32	28.675	7.124999999999999	21.025	43.175000000000004
33	50.324999999999996	11.5	15.25	22.925
34	57.4	9.575	16.900000000000002	16.125
35	60.75000000000001	7.6	20.849999999999998	10.8
36	42.6	8.525	35.925000000000004	12.950000000000001
37	42.875	13.0	20.65	23.474999999999998
38	23.474999999999998	16.775000000000002	13.825000000000001	45.925
39	17.525	23.75	12.3	46.425
40	16.3	45.75	14.099999999999998	23.849999999999998
41	24.5	44.824999999999996	11.825	18.85
42	46.675	26.724999999999998	15.325	11.275
43	48.449999999999996	27.650000000000002	10.925	12.975
44	31.95	44.95	9.15	13.950000000000001
45	20.849999999999998	45.95	13.3	19.900000000000002
46	15.9	25.95	19.125	39.025
47	11.600000000000001	15.950000000000001	38.725	33.725
48	13.950000000000001	11.95	20.424999999999997	53.675
49	13.350000000000001	21.525	15.5	49.625
50	20.225	35.699999999999996	13.125	30.95
>>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	0.5
10	1.0
11	0.5
12	0.0
13	0.5
14	1.0
15	0.5
16	0.0
17	1.5
18	3.0
19	1.5
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	1.0
28	2.0
29	3.0
30	4.0
31	10.0
32	16.0
33	18.0
34	20.0
35	22.0
36	24.0
37	29.0
38	34.0
39	40.0
40	46.0
41	52.5
42	59.0
43	87.0
44	115.0
45	159.5
46	204.0
47	323.5
48	443.0
49	535.5
50	628.0
51	702.0
52	776.0
53	613.5
54	451.0
55	454.5
56	458.0
57	352.0
58	246.0
59	160.0
60	74.0
61	67.0
62	60.0
63	106.0
64	152.0
65	95.5
66	39.0
67	28.0
68	17.0
69	27.5
70	38.0
71	56.5
72	75.0
73	39.5
74	4.0
75	3.5
76	3.0
77	3.5
78	4.0
79	3.0
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	0.475
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	41.349999999999994
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.84401451027811	31.775
2	10.217654171704957	8.450000000000001
3	3.6275695284159615	4.5
4	1.995163240628779	3.3000000000000003
5	1.3905683192261185	2.875
6	1.2091898428053205	3.0
7	1.1487303506650544	3.325
8	0.12091898428053204	0.4
9	0.5441354292623942	2.025
>10	2.357920193470375	19.75
>50	0.3022974607013301	8.7
>100	0.24183796856106407	11.899999999999999
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	140	3.5000000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	128	3.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	105	2.625	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	103	2.5749999999999997	No Hit
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	96	2.4	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	76	1.9	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	66	1.6500000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	58	1.4500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	52	1.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	40	1.0	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAG	33	0.8250000000000001	RNA PCR Primer, Index 2 (97% over 35bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	30	0.75	RNA PCR Primer, Index 1 (100% over 26bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	29	0.7250000000000001	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	25	0.625	RNA PCR Primer, Index 1 (100% over 33bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	22	0.5499999999999999	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	19	0.475	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTC	19	0.475	RNA PCR Primer, Index 14 (100% over 44bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	13	0.325	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	12	0.3	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	12	0.3	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	11	0.27499999999999997	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGC	11	0.27499999999999997	RNA PCR Primer, Index 14 (100% over 50bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
ATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTCTCGGGTGCCA	10	0.25	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 31bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	7	0.17500000000000002	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 34bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CAAAGAATTCTCCTTTTGGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	7	0.17500000000000002	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTAT	7	0.17500000000000002	RNA PCR Primer, Index 14 (100% over 48bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	7	0.17500000000000002	No Hit
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	6	0.15	No Hit
AGAAATGCGGATATGGGACTGAGATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	6	0.15	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	6	0.15	No Hit
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	6	0.15	No Hit
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	6	0.15	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	6	0.15	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	5	0.125	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCCAGGAACTCCAGTCACAG	5	0.125	RNA PCR Primer, Index 13 (97% over 35bp)
GAATGTTGCTCGGTGAACCCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	5	0.125	RNA PCR Primer, Index 1 (100% over 34bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	5	0.125	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGT	5	0.125	RNA PCR Primer, Index 8 (97% over 36bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
TTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCG	5	0.125	RNA PCR Primer, Index 14 (100% over 45bp)
ATCATGATGGGCTCCTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
ATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTCTCGGGT	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.375	0.0	0.0	0.0
2	0.0	0.375	0.0	0.0	0.0
3	0.0	0.575	0.0	0.0	0.0
4	0.0	0.6	0.0	0.0	0.0
5	0.0	0.675	0.0	0.0	0.0
6	0.0	0.85	0.0	0.0	0.0
7	0.0	1.525	0.0	0.0	0.0
8	0.0	1.725	0.0	0.0	0.0
9	0.0	1.825	0.0	0.0	0.0
10	0.0	1.975	0.0	0.0	0.0
11	0.0	2.15	0.0	0.0	0.0
12	0.0	2.5	0.0	0.0	0.0
13	0.0	2.65	0.0	0.0	0.0
14	0.0	2.775	0.0	0.0	0.0
15	0.0	3.375	0.0	0.0	0.0
16	0.0	4.9	0.0	0.0	0.0
17	0.0	5.675	0.0	0.0	0.0
18	0.0	6.725	0.0	0.0	0.0
19	0.0	7.15	0.0	0.0	0.0
20	0.0	8.225	0.0	0.0	0.0
21	0.0	11.975	0.0	0.0	0.0
22	0.0	23.15	0.0	0.0	0.0
23	0.0	49.55	0.0	0.0	0.0
24	0.0	60.725	0.0	0.0	0.0
25	0.0	66.525	0.0	0.0	0.0
26	0.0	67.825	0.0	0.0	0.0
27	0.0	68.525	0.0	0.0	0.0
28	0.0	69.575	0.0	0.0	0.0
29	0.0	70.5	0.0	0.0	0.0
30	0.0	71.15	0.0	0.0	0.0
31	0.0	72.075	0.0	0.0	0.0
32	0.0	73.25	0.0	0.0	0.0
33	0.0	74.575	0.0	0.0	0.0
34	0.0	78.875	0.0	0.0	0.0
35	0.0	80.3	0.0	0.0	0.0
36	0.0	81.35	0.0	0.0	0.0
37	0.0	82.675	0.0	0.0	0.0
38	0.0	83.475	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACTGTTG	20	6.952051E-4	44.000004	18
GTTGAAG	20	6.952051E-4	44.000004	10
CAGTTGA	20	6.952051E-4	44.000004	8
CTGAGCT	20	6.952051E-4	44.000004	11
CCAGTTG	20	6.952051E-4	44.000004	7
AACTGTT	20	6.952051E-4	44.000004	17
GAGCTTG	20	6.952051E-4	44.000004	13
GGATCCG	20	6.952051E-4	44.000004	3
CCGTCTG	20	6.952051E-4	44.000004	7
TCGGATC	20	6.952051E-4	44.000004	1
CGGATCC	20	6.952051E-4	44.000004	2
GAAGAAC	20	6.952051E-4	44.000004	13
AGAACTG	20	6.952051E-4	44.000004	15
GTGAGTT	20	6.952051E-4	44.000004	18
GAGTTGG	20	6.952051E-4	44.000004	20
GCTGCCA	20	6.952051E-4	44.000004	3
GAACTGT	20	6.952051E-4	44.000004	16
GATCCGT	20	6.952051E-4	44.000004	4
AGGCTTG	20	6.952051E-4	44.000004	18
TGAAGAA	20	6.952051E-4	44.000004	12
>>END_MODULE
Read 318884 spots for SRR5030994.sra
Written 318884 spots for SRR5030994.sra
Read 318884 spots for SRR5030994.sra
Written 318884 spots for SRR5030994.sra
Read 318884 spots for SRR5030994.sra
Written 318884 spots for SRR5030994.sra
Read 318884 spots for SRR5030994.sra
Written 318884 spots for SRR5030994.sra
Read 318884 spots for SRR5030994.sra
Written 318884 spots for SRR5030994.sra
Read 318884 spots for SRR5030994.sra
Written 318884 spots for SRR5030994.sra
Read 318884 spots for SRR5030994.sra
Written 318884 spots for SRR5030994.sra
Read 318884 spots for SRR5030994.sra
Written 318884 spots for SRR5030994.sra
Read 318888 spots for SRR5030994.sra
Written 318888 spots for SRR5030994.sra
Read 318884 spots for SRR5030994.sra
Written 318884 spots for SRR5030994.sra
Read 318884 spots for SRR5030994.sra
Written 318884 spots for SRR5030994.sra
Read 318884 spots for SRR5030994.sra
Written 318884 spots for SRR5030994.sra
SRR ids: ['SRR5030994.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_sozz7yk2
SRR5030994.sra spots: 3826612
blocks: [[1, 318884], [318885, 637768], [637769, 956652], [956653, 1275536], [1275537, 1594420], [1594421, 1913304], [1913305, 2232188], [2232189, 2551072], [2551073, 2869956], [2869957, 3188840], [3188841, 3507724], [3507725, 3826612]]
SRR5030994 file size 662175
SRR5030994 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030994 SRR5030994_1.fastq
Input file:	SRR5030994_1.fastq
trimmed:	SRR5030994-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 07:01:38 2020 >> started

Wed Mar  4 07:01:40 2020 >> done (1.907s)
3826612 reads processed; of these:
    273 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
3826333 (99.99%) reads available; of these:
 219321 ( 5.73%) trimmed reads available after processing
3607012 (94.27%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     86	  0.00%
 19	    114	  0.00%
 20	    206	  0.01%
 21	    229	  0.01%
 22	    409	  0.01%
 23	    454	  0.01%
 24	    507	  0.01%
 25	    775	  0.02%
 26	    611	  0.02%
 27	    796	  0.02%
 28	    933	  0.02%
 29	   1330	  0.03%
 30	   1145	  0.03%
 31	   1099	  0.03%
 32	   1368	  0.04%
 33	   1747	  0.05%
 34	   2022	  0.05%
 35	   3955	  0.10%
 36	   3524	  0.09%
 37	   3909	  0.10%
 38	   4136	  0.11%
 39	   4366	  0.11%
 40	   4723	  0.12%
 41	   4959	  0.13%
 42	   5922	  0.15%
 43	   8460	  0.22%
 44	  11617	  0.30%
 45	  15248	  0.40%
 46	  22202	  0.58%
 47	  25415	  0.66%
 48	  38160	  1.00%
 49	  48894	  1.28%
 50	3607012	 94.27%
3826333 reads passed initial QC


criterion=sequence-density
sequence-density=83.33
sequence-density-rank=1
fanout-score=20.61
fanout-score-rank=1
prefix-density=85.85
prefix-fanout=20.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC


criterion=fanout-score
sequence-density=83.33
sequence-density-rank=1
fanout-score=20.61
fanout-score-rank=1
prefix-density=85.85
prefix-fanout=20.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC -o SRR5030994 -
Input file:	STDIN
trimmed:	SRR5030994-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCC
-- 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 07:01:57 2020 >> started

Wed Mar  4 07:02:01 2020 >> done (4.032s)
3735230 reads processed; of these:
 274280 ( 7.34%) short reads filtered out after trimming by size control
  13776 ( 0.37%) empty reads filtered out after trimming by size control
3447174 (92.29%) reads available; of these:
3238759 (93.95%) trimmed reads available after processing
 208415 ( 6.05%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  21088	  0.61%
 19	  40695	  1.18%
 20	 182210	  5.29%
 21	 389198	 11.29%
 22	1007704	 29.23%
 23	 448420	 13.01%
 24	 208369	  6.04%
 25	  58591	  1.70%
 26	  32986	  0.96%
 27	  28539	  0.83%
 28	  31775	  0.92%
 29	  24107	  0.70%
 30	  32638	  0.95%
 31	  38143	  1.11%
 32	  47034	  1.36%
 33	 137597	  3.99%
 34	  51112	  1.48%
 35	  40708	  1.18%
 36	  46414	  1.35%
 37	  25216	  0.73%
 38	  26252	  0.76%
 39	  26335	  0.76%
 40	  37539	  1.09%
 41	  50824	  1.47%
 42	  58621	  1.70%
 43	  42363	  1.23%
 44	  31828	  0.92%
 45	  39659	  1.15%
 46	  32246	  0.94%
 47	  24595	  0.71%
 48	   2389	  0.07%
 49	   4236	  0.12%
 50	 177743	  5.16%


criterion=sequence-density
sequence-density=5.98
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=47
fanout-score=30.12
fanout-score-rank=1
prefix-density=0.07
prefix-fanout=2.2
sequence=TTTGCTGAAGGAGGCAGAGGCAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTTAA
                                 Started job on |	Mar 04 07:02:22
                             Started mapping on |	Mar 04 07:02:22
                                    Finished on |	Mar 04 07:02:47
       Mapping speed, Million of reads per hour |	509.51

                          Number of input reads |	3538277
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1799802
                        Uniquely mapped reads % |	50.87%
                          Average mapped length |	25.47
                       Number of splices: Total |	2176
            Number of splices: Annotated (sjdb) |	570
                       Number of splices: GT/AG |	2050
                       Number of splices: GC/AG |	23
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	102
                      Mismatch rate per base, % |	0.23%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.76
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.07
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1184115
             % of reads mapped to multiple loci |	33.47%
        Number of reads mapped to too many loci |	100946
             % of reads mapped to too many loci |	2.85%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.03%
                     % of reads unmapped: other |	0.78%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	554360	554360	554360
N_multimapping	1184115	1184115	1184115
N_noFeature	104087	130720	1244844
N_ambiguous	1001624	528202	23965
UnstrandedReadsAssigned:694091 PositiveStrandReadsAssigned:1140880 NegativeStrandReadsAssigned:530993
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030994 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: SRR5030994-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,538,277 reads, 867,229 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,164 rounds

 109283 SRR5030994.ke.tsv
  52636 SRR5030994.se.tsv
 161919 total
==> SRR5030994.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

==> SRR5030994.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030994 completed mapping pipeline successfully
