Starting /dee2/code/volunteer_pipeline.sh SRR5030967
    current disk space = 160596115456
    free memory = 1048241912 
SRR5030967 SRAfilesize
ec0fa810ae3ad2afa7df5e71ba50ef73  SRR5030967.sra
SRR5030967.sra file validated
SRR5030967 is single end
SRR5030967 is conventional basespace
SRR5030967 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030967_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	32.354	33.0	31.0	34.0	31.0	34.0
2	32.7645	34.0	31.0	34.0	31.0	34.0
3	32.79325	34.0	31.0	34.0	31.0	34.0
4	36.2485	37.0	37.0	37.0	35.0	37.0
5	36.2105	37.0	37.0	37.0	35.0	37.0
6	36.018	37.0	35.0	37.0	35.0	37.0
7	36.1745	37.0	35.0	37.0	35.0	37.0
8	36.15125	37.0	36.0	37.0	35.0	37.0
9	37.9215	39.0	38.0	39.0	35.0	39.0
10	38.01425	39.0	39.0	39.0	35.0	39.0
11	37.92125	39.0	38.0	39.0	35.0	39.0
12	37.95075	39.0	38.0	39.0	35.0	39.0
13	37.903	39.0	38.0	39.0	35.0	39.0
14	39.3135	41.0	39.0	41.0	36.0	41.0
15	39.3035	41.0	39.0	41.0	36.0	41.0
16	39.237	40.0	39.0	41.0	36.0	41.0
17	39.30275	41.0	39.0	41.0	36.0	41.0
18	39.3445	41.0	39.0	41.0	36.0	41.0
19	38.947	40.0	38.0	41.0	35.0	41.0
20	39.19725	40.0	39.0	41.0	36.0	41.0
21	39.22125	40.0	39.0	41.0	36.0	41.0
22	39.206	41.0	39.0	41.0	36.0	41.0
23	39.1535	40.0	39.0	41.0	36.0	41.0
24	38.4795	40.0	38.0	41.0	34.0	41.0
25	38.699	40.0	38.0	41.0	34.0	41.0
26	38.7375	40.0	38.0	41.0	35.0	41.0
27	38.7815	40.0	38.0	41.0	35.0	41.0
28	38.80475	40.0	38.0	41.0	35.0	41.0
29	38.79025	40.0	38.0	41.0	35.0	41.0
30	38.4355	40.0	38.0	41.0	34.0	41.0
31	38.823	40.0	38.0	41.0	35.0	41.0
32	38.98	40.0	38.0	41.0	35.0	41.0
33	37.5125	40.0	38.0	41.0	32.0	41.0
34	36.91575	40.0	37.0	41.0	30.0	41.0
35	32.9965	38.0	31.0	40.0	15.0	41.0
36	29.53025	37.0	18.0	40.0	8.0	41.0
37	30.07375	36.0	24.0	39.0	7.0	41.0
38	32.523	37.0	31.0	40.0	15.0	41.0
39	31.966	37.0	30.0	40.0	8.0	41.0
40	32.5835	37.0	32.0	40.0	7.0	41.0
41	30.65725	36.0	27.0	40.0	2.0	41.0
42	32.269	37.0	31.0	40.0	2.0	41.0
43	30.864	37.0	28.0	40.0	2.0	41.0
44	31.86275	38.0	31.0	40.0	2.0	41.0
45	29.89825	37.0	26.0	40.0	2.0	41.0
46	27.9045	35.0	18.0	39.0	2.0	41.0
47	28.1285	35.0	22.0	39.0	2.0	41.0
48	28.83425	36.0	26.0	40.0	2.0	41.0
49	26.76175	35.0	2.0	40.0	2.0	41.0
50	23.088	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
12	1.0
13	0.0
14	2.0
15	1.0
16	0.0
17	2.0
18	2.0
19	4.0
20	6.0
21	11.0
22	27.0
23	34.0
24	45.0
25	64.0
26	90.0
27	143.0
28	57.0
29	94.0
30	144.0
31	145.0
32	139.0
33	156.0
34	226.0
35	277.0
36	366.0
37	456.0
38	681.0
39	827.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.550100200400802	26.728456913827653	44.81462925851704	15.90681362725451
2	23.375	27.250000000000004	21.175	28.199999999999996
3	22.8	18.775	24.025	34.4
4	30.675	30.099999999999998	15.525	23.7
5	21.325	37.425000000000004	27.825	13.425
6	26.05	18.725	40.6	14.625
7	20.45	19.875	22.6	37.075
8	24.975	32.725	15.2	27.1
9	21.525	34.949999999999996	29.4	14.124999999999998
10	23.775	17.775	30.125	28.325
11	37.175000000000004	14.649999999999999	14.424999999999999	33.75
12	15.775	22.5	28.975	32.75
13	24.95	18.875	33.4	22.775000000000002
14	28.975	29.175	23.599999999999998	18.25
15	33.375	21.7	27.425	17.5
16	17.299999999999997	20.974999999999998	24.45	37.275000000000006
17	27.150000000000002	23.549999999999997	33.324999999999996	15.975
18	26.674999999999997	16.925	33.475	22.925
19	31.85	16.400000000000002	34.125	17.625
20	42.5	17.325	23.724999999999998	16.45
21	22.675	23.775	26.224999999999998	27.325
22	30.099999999999998	15.625	42.075	12.2
23	24.725	15.25	43.45	16.575
24	47.775	14.85	26.450000000000003	10.925
25	48.6	22.15	17.075000000000003	12.174999999999999
26	28.599999999999998	41.875	14.625	14.899999999999999
27	17.424999999999997	45.574999999999996	22.775000000000002	14.224999999999998
28	13.100000000000001	26.625	44.224999999999994	16.05
29	12.425	14.85	54.825	17.9
30	11.15	9.0	35.9	43.95
31	15.15	7.375	43.824999999999996	33.650000000000006
32	25.974999999999998	8.25	23.95	41.825
33	49.675000000000004	10.45	15.35	24.525
34	57.675	8.375	15.85	18.099999999999998
35	57.15	8.825	20.925	13.100000000000001
36	57.49999999999999	11.0	18.025	13.475000000000001
37	39.75	13.075000000000001	22.175	25.0
38	26.1	14.45	15.55	43.9
39	19.3	24.65	11.325000000000001	44.725
40	17.8	44.525	12.15	25.525
41	26.150000000000002	44.125	12.825000000000001	16.900000000000002
42	47.8	29.25	11.225	11.725
43	46.2	31.574999999999996	11.774999999999999	10.45
44	30.45	45.65	9.575	14.325
45	19.650000000000002	46.575	12.825000000000001	20.95
46	13.700000000000001	29.75	23.35	33.2
47	12.049999999999999	17.299999999999997	33.4	37.25
48	11.875	13.625000000000002	22.375	52.125
49	15.575	22.900000000000002	15.45	46.075
50	28.449999999999996	26.85	12.975	31.724999999999998
>>END_MODULE
>>Per sequence GC content	warn
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	1.5
26	2.0
27	3.0
28	4.0
29	3.5
30	3.0
31	12.5
32	22.0
33	24.5
34	27.0
35	51.5
36	76.0
37	81.5
38	87.0
39	80.5
40	74.0
41	79.0
42	84.0
43	107.5
44	131.0
45	175.0
46	219.0
47	270.0
48	321.0
49	402.5
50	484.0
51	649.0
52	814.0
53	626.5
54	439.0
55	425.0
56	411.0
57	369.0
58	327.0
59	233.5
60	140.0
61	112.5
62	85.0
63	95.5
64	106.0
65	70.5
66	35.0
67	24.0
68	13.0
69	24.5
70	36.0
71	42.0
72	48.0
73	25.5
74	3.0
75	2.0
76	1.0
77	1.0
78	1.0
79	3.5
80	6.0
81	3.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.2
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	53.125
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.14117647058823	42.575
2	8.894117647058824	9.45
3	3.011764705882353	4.8
4	2.023529411764706	4.3
5	1.035294117647059	2.75
6	1.1294117647058823	3.5999999999999996
7	0.7058823529411765	2.625
8	0.1411764705882353	0.6
9	0.2352941176470588	1.125
>10	2.635294117647059	24.55
>50	0.0	0.0
>100	0.047058823529411764	3.6249999999999996
>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	145	3.6249999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	41	1.0250000000000001	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	40	1.0	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCT	20	0.5	RNA PCR Primer, Index 1 (97% over 35bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	17	0.42500000000000004	No Hit
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	17	0.42500000000000004	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	16	0.4	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (96% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (96% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	15	0.375	No Hit
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 33bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGC	14	0.35000000000000003	RNA PCR Primer, Index 12 (100% over 50bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	13	0.325	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	13	0.325	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	12	0.3	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	11	0.27499999999999997	No Hit
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 32bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	11	0.27499999999999997	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	10	0.25	No Hit
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	10	0.25	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	10	0.25	RNA PCR Primer, Index 1 (96% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	10	0.25	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	10	0.25	No Hit
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	10	0.25	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	9	0.22499999999999998	No Hit
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTC	7	0.17500000000000002	RNA PCR Primer, Index 12 (100% over 44bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	7	0.17500000000000002	No Hit
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	7	0.17500000000000002	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	7	0.17500000000000002	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	6	0.15	No Hit
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	6	0.15	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	6	0.15	RNA PCR Primer, Index 2 (100% over 34bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	6	0.15	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TGCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTG	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	6	0.15	No Hit
ATTCTGTGATGACTTTACCAAATGACTTTCGTTCTTCTGAGTTTGCTGAA	6	0.15	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTT	6	0.15	RNA PCR Primer, Index 12 (100% over 36bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	6	0.15	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	6	0.15	No Hit
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
CTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	5	0.125	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	5	0.125	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCAGCATCAGTGATTTTGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCC	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
CTAGACTGAGGCTCCTTGAGGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	5	0.125	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	5	0.125	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	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	0.4	0.0	0.0	0.0
2	0.0	0.425	0.0	0.0	0.0
3	0.0	0.55	0.0	0.0	0.0
4	0.0	0.575	0.0	0.0	0.0
5	0.0	0.575	0.0	0.0	0.0
6	0.0	0.65	0.0	0.0	0.0
7	0.0	0.875	0.0	0.0	0.0
8	0.0	1.0	0.0	0.0	0.0
9	0.0	1.075	0.0	0.0	0.0
10	0.0	1.1	0.0	0.0	0.0
11	0.0	1.175	0.0	0.0	0.0
12	0.0	1.275	0.0	0.0	0.0
13	0.0	1.5	0.0	0.0	0.0
14	0.0	1.775	0.0	0.0	0.0
15	0.0	2.35	0.0	0.0	0.0
16	0.0	3.2	0.0	0.0	0.0
17	0.0	3.8	0.0	0.0	0.0
18	0.0	4.55	0.0	0.0	0.0
19	0.0	5.3	0.0	0.0	0.0
20	0.0	5.775	0.0	0.0	0.0
21	0.0	10.15	0.0	0.0	0.0
22	0.0	19.225	0.0	0.0	0.0
23	0.0	45.225	0.0	0.0	0.0
24	0.0	57.4	0.0	0.0	0.0
25	0.0	63.15	0.0	0.0	0.0
26	0.0	64.75	0.0	0.0	0.0
27	0.0	65.375	0.0	0.0	0.0
28	0.0	66.075	0.0	0.0	0.0
29	0.0	66.35	0.0	0.0	0.0
30	0.0	66.85	0.0	0.0	0.0
31	0.0	67.55	0.0	0.0	0.0
32	0.0	68.65	0.0	0.0	0.0
33	0.0	69.825	0.0	0.0	0.0
34	0.0	71.85	0.0	0.0	0.0
35	0.0	72.825	0.0	0.0	0.0
36	0.0	73.375	0.0	0.0	0.0
37	0.0	74.2	0.0	0.0	0.0
38	0.0	74.55	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CTGAGCT	40	5.315087E-9	44.000004	11
AGCTTGG	40	5.315087E-9	44.000004	14
GAGCTTG	40	5.315087E-9	44.000004	13
GGATCCG	40	5.315087E-9	44.000004	3
CCGTCTG	40	5.315087E-9	44.000004	7
TCGGATC	40	5.315087E-9	44.000004	1
CGGATCC	40	5.315087E-9	44.000004	2
GATCCGT	40	5.315087E-9	44.000004	4
TGAGGTA	20	6.952051E-4	44.000004	1
TCCGTCT	40	5.315087E-9	44.000004	6
ATCCGTC	40	5.315087E-9	44.000004	5
TGAGCTT	40	5.315087E-9	44.000004	12
CGTCTGA	40	5.315087E-9	44.000004	8
AACGCTG	35	1.02281774E-7	44.0	8
GAGGTAG	25	3.6958358E-5	44.0	2
GGTGAGT	25	3.6958358E-5	44.0	17
TTCAACG	35	1.02281774E-7	44.0	5
TCGGTGA	30	1.9515464E-6	44.0	15
CATTCAA	35	1.02281774E-7	44.0	3
TCAACGC	35	1.02281774E-7	44.0	6
>>END_MODULE
Read 76579 spots for SRR5030967.sra
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SRR ids: ['SRR5030967.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd__wwt0765
SRR5030967.sra spots: 3675814
blocks: [[1, 76579], [76580, 153158], [153159, 229737], [229738, 306316], [306317, 382895], [382896, 459474], [459475, 536053], [536054, 612632], [612633, 689211], [689212, 765790], [765791, 842369], [842370, 918948], [918949, 995527], [995528, 1072106], [1072107, 1148685], [1148686, 1225264], [1225265, 1301843], [1301844, 1378422], [1378423, 1455001], [1455002, 1531580], [1531581, 1608159], [1608160, 1684738], [1684739, 1761317], [1761318, 1837896], [1837897, 1914475], [1914476, 1991054], [1991055, 2067633], [2067634, 2144212], [2144213, 2220791], [2220792, 2297370], [2297371, 2373949], [2373950, 2450528], [2450529, 2527107], [2527108, 2603686], [2603687, 2680265], [2680266, 2756844], [2756845, 2833423], [2833424, 2910002], [2910003, 2986581], [2986582, 3063160], [3063161, 3139739], [3139740, 3216318], [3216319, 3292897], [3292898, 3369476], [3369477, 3446055], [3446056, 3522634], [3522635, 3599213], [3599214, 3675814]]
SRR5030967 file size 636025
SRR5030967 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5030967 SRR5030967_1.fastq
Input file:	SRR5030967_1.fastq
trimmed:	SRR5030967-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):	32
Wed Mar  4 06:55:58 2020 >> started

Wed Mar  4 06:56:00 2020 >> done (2.176s)
3675814 reads processed; of these:
    181 ( 0.00%) short reads filtered out after trimming by size control
     13 ( 0.00%) empty reads filtered out after trimming by size control
3675620 (99.99%) reads available; of these:
 423117 (11.51%) trimmed reads available after processing
3252503 (88.49%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     82	  0.00%
 19	     67	  0.00%
 20	    139	  0.00%
 21	    179	  0.00%
 22	    361	  0.01%
 23	    493	  0.01%
 24	    485	  0.01%
 25	    643	  0.02%
 26	    516	  0.01%
 27	    761	  0.02%
 28	   1024	  0.03%
 29	   1576	  0.04%
 30	   1178	  0.03%
 31	   1620	  0.04%
 32	   4083	  0.11%
 33	  13256	  0.36%
 34	  32791	  0.89%
 35	   7385	  0.20%
 36	   7549	  0.21%
 37	   4607	  0.13%
 38	   8473	  0.23%
 39	   7843	  0.21%
 40	  14060	  0.38%
 41	   8283	  0.23%
 42	  19630	  0.53%
 43	   9745	  0.27%
 44	  40043	  1.09%
 45	  25263	  0.69%
 46	  22690	  0.62%
 47	  26672	  0.73%
 48	  75659	  2.06%
 49	  85961	  2.34%
 50	3252503	 88.49%
3675620 reads passed initial QC


criterion=sequence-density
sequence-density=73.87
sequence-density-rank=1
fanout-score=21.34
fanout-score-rank=2
prefix-density=76.73
prefix-fanout=20.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCC


criterion=fanout-score
sequence-density=3.23
sequence-density-rank=2
fanout-score=72.30
fanout-score-rank=1
prefix-density=76.15
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 48 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCC -o SRR5030967 -
Input file:	STDIN
trimmed:	SRR5030967-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCC
-- 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):	32
Wed Mar  4 06:56:18 2020 >> started

Wed Mar  4 06:56:24 2020 >> done (5.429s)
3576279 reads processed; of these:
 163105 ( 4.56%) short reads filtered out after trimming by size control
  18656 ( 0.52%) empty reads filtered out after trimming by size control
3394518 (94.92%) reads available; of these:
2807078 (82.69%) trimmed reads available after processing
 587440 (17.31%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  21185	  0.62%
 19	  28149	  0.83%
 20	 168516	  4.96%
 21	 343002	 10.10%
 22	 912419	 26.88%
 23	 430727	 12.69%
 24	 206901	  6.10%
 25	  57033	  1.68%
 26	  29811	  0.88%
 27	  23431	  0.69%
 28	  25154	  0.74%
 29	  20010	  0.59%
 30	  26631	  0.78%
 31	  33638	  0.99%
 32	  35684	  1.05%
 33	  78935	  2.33%
 34	  34956	  1.03%
 35	  26807	  0.79%
 36	  33009	  0.97%
 37	  19349	  0.57%
 38	  22050	  0.65%
 39	  21908	  0.65%
 40	  36550	  1.08%
 41	  39443	  1.16%
 42	  48661	  1.43%
 43	  32195	  0.95%
 44	  29703	  0.88%
 45	  38004	  1.12%
 46	  29967	  0.88%
 47	  22473	  0.66%
 48	   9099	  0.27%
 49	  16669	  0.49%
 50	 492449	 14.51%


criterion=sequence-density
sequence-density=2.58
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=12
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.67
sequence-density-rank=20
fanout-score=11.32
fanout-score-rank=1
prefix-density=7.52
prefix-fanout=1.0
sequence=TGAGCTTGGCTAT
                                 Started job on |	Mar 04 06:57:05
                             Started mapping on |	Mar 04 06:57:06
                                    Finished on |	Mar 04 06:57:38
       Mapping speed, Million of reads per hour |	393.06

                          Number of input reads |	3493859
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2006807
                        Uniquely mapped reads % |	57.44%
                          Average mapped length |	28.73
                       Number of splices: Total |	2159
            Number of splices: Annotated (sjdb) |	334
                       Number of splices: GT/AG |	2003
                       Number of splices: GC/AG |	27
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	127
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.28
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.11
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	996924
             % of reads mapped to multiple loci |	28.53%
        Number of reads mapped to too many loci |	72090
             % of reads mapped to too many loci |	2.06%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.09%
                     % of reads unmapped: other |	0.88%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	490128	490128	490128
N_multimapping	996924	996924	996924
N_noFeature	83178	109284	1424701
N_ambiguous	1087395	574128	17901
UnstrandedReadsAssigned:836234 PositiveStrandReadsAssigned:1323395 NegativeStrandReadsAssigned:564205
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030967 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: SRR5030967-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,493,859 reads, 856,333 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,119 rounds

 109283 SRR5030967.ke.tsv
  52636 SRR5030967.se.tsv
 161919 total
==> SRR5030967.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

==> SRR5030967.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030967 completed mapping pipeline successfully
