Starting /dee2/code/volunteer_pipeline.sh SRR5030978
    current disk space = 160583385088
    free memory = 56709288 
SRR5030978 SRAfilesize
6ea822f913674d4bd6bdbd2a6b2072f9  SRR5030978.sra
SRR5030978.sra file validated
SRR5030978 is single end
SRR5030978 is conventional basespace
SRR5030978 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030978_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	32.5065	34.0	31.0	34.0	31.0	34.0
2	32.81975	34.0	31.0	34.0	31.0	34.0
3	32.7865	34.0	31.0	34.0	31.0	34.0
4	36.30125	37.0	37.0	37.0	35.0	37.0
5	36.1575	37.0	37.0	37.0	35.0	37.0
6	35.9505	37.0	35.0	37.0	35.0	37.0
7	36.02825	37.0	35.0	37.0	35.0	37.0
8	36.0975	37.0	36.0	37.0	35.0	37.0
9	37.84525	39.0	38.0	39.0	35.0	39.0
10	37.955	39.0	39.0	39.0	35.0	39.0
11	37.8415	39.0	38.0	39.0	35.0	39.0
12	37.85275	39.0	38.0	39.0	35.0	39.0
13	37.77425	39.0	38.0	39.0	35.0	39.0
14	39.08825	41.0	38.0	41.0	35.0	41.0
15	39.24	41.0	39.0	41.0	36.0	41.0
16	39.24775	40.0	39.0	41.0	36.0	41.0
17	39.33925	41.0	39.0	41.0	36.0	41.0
18	39.311	41.0	39.0	41.0	36.0	41.0
19	39.13125	40.0	39.0	41.0	36.0	41.0
20	39.1135	40.0	39.0	41.0	36.0	41.0
21	39.06425	40.0	39.0	41.0	35.0	41.0
22	39.10425	40.0	39.0	41.0	36.0	41.0
23	38.858	40.0	38.0	41.0	35.0	41.0
24	39.0055	40.0	38.0	41.0	36.0	41.0
25	39.00275	40.0	39.0	41.0	35.0	41.0
26	38.76975	40.0	38.0	41.0	35.0	41.0
27	38.763	40.0	38.0	41.0	35.0	41.0
28	38.53175	40.0	38.0	41.0	34.0	41.0
29	37.8225	40.0	38.0	41.0	32.0	41.0
30	38.11375	40.0	38.0	41.0	33.0	41.0
31	38.24	40.0	38.0	41.0	33.0	41.0
32	38.112	40.0	38.0	41.0	33.0	41.0
33	38.27825	40.0	38.0	41.0	34.0	41.0
34	38.32125	40.0	38.0	41.0	34.0	41.0
35	37.83475	40.0	38.0	41.0	33.0	41.0
36	37.474	40.0	37.0	41.0	31.0	41.0
37	37.10125	39.0	37.0	41.0	31.0	41.0
38	37.391	39.0	37.0	41.0	31.0	41.0
39	37.61325	39.0	37.0	41.0	33.0	41.0
40	37.63225	40.0	37.0	41.0	33.0	41.0
41	37.6	40.0	37.0	41.0	33.0	41.0
42	37.794	40.0	37.0	41.0	33.0	41.0
43	37.82825	40.0	37.0	41.0	33.0	41.0
44	37.678	40.0	37.0	41.0	33.0	41.0
45	37.43675	39.0	37.0	41.0	33.0	41.0
46	36.87275	39.0	36.0	41.0	31.0	41.0
47	36.591	39.0	35.0	41.0	30.0	41.0
48	36.23775	39.0	35.0	41.0	29.0	41.0
49	36.408	39.0	35.0	41.0	30.0	41.0
50	35.83725	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
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	3.0
18	1.0
19	2.0
20	5.0
21	1.0
22	2.0
23	4.0
24	9.0
25	7.0
26	16.0
27	12.0
28	25.0
29	30.0
30	41.0
31	79.0
32	94.0
33	104.0
34	140.0
35	202.0
36	263.0
37	460.0
38	857.0
39	1641.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.756567425569177	26.319739804853644	48.386289717287966	16.537403052289218
2	22.400000000000002	27.800000000000004	20.5	29.299999999999997
3	24.975	18.45	22.85	33.725
4	32.775	27.775	15.024999999999999	24.425
5	22.88072018004501	37.15928982245561	28.307076769192296	11.652913228307076
6	34.2	14.899999999999999	34.5	16.400000000000002
7	15.275	22.675	22.925	39.125
8	25.825	27.875	15.725	30.575000000000003
9	21.375	34.0	28.349999999999998	16.275000000000002
10	22.425	20.825	28.125	28.625
11	31.0	10.424999999999999	18.625	39.95
12	17.5	16.225	31.525	34.75
13	31.75	16.825000000000003	31.874999999999996	19.55
14	30.9	30.325000000000003	20.625	18.15
15	35.05	22.575	28.125	14.249999999999998
16	21.05	18.75	22.725	37.475
17	28.1	21.475	37.5	12.925
18	26.25	17.599999999999998	28.95	27.200000000000003
19	36.525	13.700000000000001	30.775000000000002	19.0
20	44.074999999999996	15.6	27.375	12.950000000000001
21	24.65	20.325	27.775	27.250000000000004
22	28.425	12.35	48.525	10.7
23	28.225	12.475	44.175	15.125
24	51.075	15.299999999999999	25.5	8.125
25	48.8	25.2	15.049999999999999	10.95
26	28.249999999999996	46.475	14.774999999999999	10.5
27	16.55	45.85	25.025	12.575
28	13.0	22.900000000000002	49.125	14.975
29	12.025	12.125	55.7	20.150000000000002
30	12.35	6.675000000000001	35.825	45.15
31	15.65	5.2749999999999995	45.300000000000004	33.775
32	29.299999999999997	6.5	20.4	43.8
33	54.325	9.425	13.475000000000001	22.775000000000002
34	61.425	8.55	16.025	14.000000000000002
35	62.949999999999996	7.675	19.375	10.0
36	41.65	7.875	36.449999999999996	14.025000000000002
37	44.35	10.525	19.175	25.95
38	22.8	17.5	12.2	47.5
39	15.125	25.15	9.775	49.95
40	15.85	48.625	11.4	24.125
41	25.25	47.875	9.0	17.875
42	48.325	29.225	11.325000000000001	11.125
43	49.875	29.825000000000003	9.075	11.225
44	29.299999999999997	48.25	8.175	14.274999999999999
45	16.85	49.0	13.450000000000001	20.7
46	12.225	24.55	19.125	44.1
47	8.5	15.425	39.7	36.375
48	9.75	12.55	19.875	57.825
49	12.45	20.05	15.6	51.9
50	18.125	36.05	14.149999999999999	31.674999999999997
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.5
12	1.0
13	0.5
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	1.0
26	1.0
27	0.5
28	0.0
29	1.0
30	2.0
31	8.0
32	14.0
33	12.5
34	11.0
35	13.5
36	16.0
37	23.5
38	31.0
39	27.0
40	23.0
41	32.5
42	42.0
43	63.0
44	84.0
45	122.5
46	161.0
47	299.0
48	437.0
49	559.0
50	681.0
51	788.5
52	896.0
53	664.0
54	432.0
55	483.0
56	534.0
57	392.0
58	250.0
59	179.0
60	108.0
61	81.0
62	54.0
63	74.0
64	94.0
65	63.0
66	32.0
67	25.5
68	19.0
69	21.0
70	23.0
71	34.0
72	45.0
73	24.5
74	4.0
75	3.0
76	2.0
77	1.0
78	0.0
79	0.0
80	0.0
81	1.0
82	2.0
83	1.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.075
2	0.0
3	0.0
4	0.0
5	0.025
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	38.75
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.77419354838709	29.75
2	9.161290322580646	7.1
3	4.129032258064516	4.8
4	2.3870967741935485	3.6999999999999997
5	0.8387096774193548	1.625
6	1.4838709677419355	3.45
7	0.5161290322580645	1.4000000000000001
8	0.5161290322580645	1.6
9	0.3225806451612903	1.125
>10	3.225806451612903	22.325
>50	0.3225806451612903	8.025
>100	0.3225806451612903	15.1
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	163	4.075	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	119	2.9749999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	112	2.8000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	106	2.65	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	104	2.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	93	2.325	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	67	1.675	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	56	1.4000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	53	1.325	RNA PCR Primer, Index 5 (97% over 35bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	52	1.3	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	50	1.25	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	38	0.95	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTC	26	0.65	RNA PCR Primer, Index 45 (100% over 44bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	21	0.525	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	19	0.475	RNA PCR Primer, Index 1 (100% over 31bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGC	16	0.4	RNA PCR Primer, Index 45 (100% over 50bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	12	0.3	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	10	0.25	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	10	0.25	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	8	0.2	RNA PCR Primer, Index 3 (100% over 34bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	7	0.17500000000000002	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTG	7	0.17500000000000002	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	6	0.15	RNA PCR Primer, Index 3 (100% over 34bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	6	0.15	RNA PCR Primer, Index 5 (97% over 35bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	6	0.15	No Hit
ATCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCAT	6	0.15	RNA PCR Primer, Index 42 (97% over 37bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTAT	6	0.15	RNA PCR Primer, Index 45 (100% over 48bp)
TATTGCACTCGTCCCGGCCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGCACTCCAGTCACTC	6	0.15	RNA PCR Primer, Index 45 (97% over 35bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCACGGGGTCGGCGGCGATGTCGGTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CAAAGAATTCTCCTTTTGGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGCATTCTCGGGTGCC	5	0.125	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	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	0.425	0.0	0.0	0.0
2	0.0	0.45	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	0.725	0.0	0.0	0.0
6	0.0	0.875	0.0	0.0	0.0
7	0.0	1.7	0.0	0.0	0.0
8	0.0	1.825	0.0	0.0	0.0
9	0.0	1.9	0.0	0.0	0.0
10	0.0	2.125	0.0	0.0	0.0
11	0.0	2.525	0.0	0.0	0.0
12	0.0	2.8	0.0	0.0	0.0
13	0.0	3.125	0.0	0.0	0.0
14	0.0	3.725	0.0	0.0	0.0
15	0.0	4.1	0.0	0.0	0.0
16	0.0	6.175	0.0	0.0	0.0
17	0.0	7.025	0.0	0.0	0.0
18	0.0	8.7	0.0	0.0	0.0
19	0.0	9.175	0.0	0.0	0.0
20	0.0	10.6	0.0	0.0	0.0
21	0.0	16.425	0.0	0.0	0.0
22	0.0	28.725	0.0	0.0	0.0
23	0.0	58.075	0.0	0.0	0.0
24	0.0	70.225	0.0	0.0	0.0
25	0.0	75.675	0.0	0.0	0.0
26	0.0	77.4	0.0	0.0	0.0
27	0.0	78.225	0.0	0.0	0.0
28	0.0	78.875	0.0	0.0	0.0
29	0.0	79.775	0.0	0.0	0.0
30	0.0	80.425	0.0	0.0	0.0
31	0.0	81.275	0.0	0.0	0.0
32	0.0	82.15	0.0	0.0	0.0
33	0.0	83.4	0.0	0.0	0.0
34	0.0	85.7	0.0	0.0	0.0
35	0.0	86.775	0.0	0.0	0.0
36	0.0	87.675	0.0	0.0	0.0
37	0.0	88.525	0.0	0.0	0.0
38	0.0	89.075	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	20	6.952051E-4	44.000004	8
GGTGAGT	20	6.952051E-4	44.000004	17
ACGCTGT	20	6.952051E-4	44.000004	9
CCTGTTG	20	6.952051E-4	44.000004	18
TTCAACG	20	6.952051E-4	44.000004	5
TCGGTGA	20	6.952051E-4	44.000004	15
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
ACCTGTT	20	6.952051E-4	44.000004	17
CTTGGTG	20	6.952051E-4	44.000004	16
ACATTCA	20	6.952051E-4	44.000004	2
GCTGTCG	20	6.952051E-4	44.000004	11
CGGTGAG	20	6.952051E-4	44.000004	16
GCTTGGT	20	6.952051E-4	44.000004	15
TTGGTGG	20	6.952051E-4	44.000004	17
GGTGGAA	20	6.952051E-4	44.000004	19
CTGTCGG	20	6.952051E-4	44.000004	12
TGGTGGA	20	6.952051E-4	44.000004	18
ATTCAAC	20	6.952051E-4	44.000004	4
GTCGGTG	20	6.952051E-4	44.000004	14
>>END_MODULE
Read 222787 spots for SRR5030978.sra
Written 222787 spots for SRR5030978.sra
Read 222787 spots for SRR5030978.sra
Written 222787 spots for SRR5030978.sra
Read 222787 spots for SRR5030978.sra
Written 222787 spots for SRR5030978.sra
Read 222787 spots for SRR5030978.sra
Written 222787 spots for SRR5030978.sra
Read 222787 spots for SRR5030978.sra
Written 222787 spots for SRR5030978.sra
Read 222787 spots for SRR5030978.sra
Written 222787 spots for SRR5030978.sra
Read 222787 spots for SRR5030978.sra
Written 222787 spots for SRR5030978.sra
Read 222787 spots for SRR5030978.sra
Written 222787 spots for SRR5030978.sra
Read 222787 spots for SRR5030978.sra
Written 222787 spots for SRR5030978.sra
Read 222787 spots for SRR5030978.sra
Written 222787 spots for SRR5030978.sra
Read 222787 spots for SRR5030978.sra
Written 222787 spots for SRR5030978.sra
Read 222798 spots for SRR5030978.sra
Written 222798 spots for SRR5030978.sra
SRR ids: ['SRR5030978.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_muc5r3g1
SRR5030978.sra spots: 2673455
blocks: [[1, 222787], [222788, 445574], [445575, 668361], [668362, 891148], [891149, 1113935], [1113936, 1336722], [1336723, 1559509], [1559510, 1782296], [1782297, 2005083], [2005084, 2227870], [2227871, 2450657], [2450658, 2673455]]
SRR5030978 file size 462296
SRR5030978 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030978 SRR5030978_1.fastq
Input file:	SRR5030978_1.fastq
trimmed:	SRR5030978-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 06:58:30 2020 >> started

Wed Mar  4 06:58:32 2020 >> done (1.770s)
2673455 reads processed; of these:
    181 ( 0.01%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
2673269 (99.99%) reads available; of these:
 167113 ( 6.25%) trimmed reads available after processing
2506156 (93.75%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     51	  0.00%
 19	     58	  0.00%
 20	    132	  0.00%
 21	    177	  0.01%
 22	    308	  0.01%
 23	    326	  0.01%
 24	    382	  0.01%
 25	    534	  0.02%
 26	    435	  0.02%
 27	    593	  0.02%
 28	    734	  0.03%
 29	    909	  0.03%
 30	    677	  0.03%
 31	    688	  0.03%
 32	    799	  0.03%
 33	   1123	  0.04%
 34	   1412	  0.05%
 35	   2489	  0.09%
 36	   2320	  0.09%
 37	   2482	  0.09%
 38	   2556	  0.10%
 39	   2713	  0.10%
 40	   3094	  0.12%
 41	   3440	  0.13%
 42	   4644	  0.17%
 43	   6347	  0.24%
 44	   8378	  0.31%
 45	  10182	  0.38%
 46	  15948	  0.60%
 47	  17704	  0.66%
 48	  30692	  1.15%
 49	  44786	  1.68%
 50	2506156	 93.75%
2673269 reads passed initial QC


criterion=sequence-density
sequence-density=89.19
sequence-density-rank=1
fanout-score=20.10
fanout-score-rank=1
prefix-density=90.82
prefix-fanout=19.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC


criterion=fanout-score
sequence-density=89.19
sequence-density-rank=1
fanout-score=20.10
fanout-score-rank=1
prefix-density=90.82
prefix-fanout=19.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC -o SRR5030978 -
Input file:	STDIN
trimmed:	SRR5030978-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC
-- 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 06:58:46 2020 >> started

Wed Mar  4 06:58:50 2020 >> done (4.172s)
2613863 reads processed; of these:
 226936 ( 8.68%) short reads filtered out after trimming by size control
  15278 ( 0.58%) empty reads filtered out after trimming by size control
2371649 (90.73%) reads available; of these:
2298876 (96.93%) trimmed reads available after processing
  72773 ( 3.07%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  16579	  0.70%
 19	  33922	  1.43%
 20	 152179	  6.42%
 21	 307984	 12.99%
 22	 775148	 32.68%
 23	 341207	 14.39%
 24	 153388	  6.47%
 25	  40698	  1.72%
 26	  22127	  0.93%
 27	  18565	  0.78%
 28	  20738	  0.87%
 29	  15085	  0.64%
 30	  22120	  0.93%
 31	  26691	  1.13%
 32	  31109	  1.31%
 33	  68564	  2.89%
 34	  30666	  1.29%
 35	  23921	  1.01%
 36	  26986	  1.14%
 37	  13194	  0.56%
 38	  13209	  0.56%
 39	  12695	  0.54%
 40	  18487	  0.78%
 41	  24374	  1.03%
 42	  27423	  1.16%
 43	  19313	  0.81%
 44	  13531	  0.57%
 45	  17556	  0.74%
 46	  13930	  0.59%
 47	   9628	  0.41%
 48	    706	  0.03%
 49	   1378	  0.06%
 50	  58548	  2.47%


criterion=sequence-density
sequence-density=7.35
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.54
sequence-density-rank=28
fanout-score=13.84
fanout-score-rank=1
prefix-density=7.42
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 06:59:11
                             Started mapping on |	Mar 04 06:59:11
                                    Finished on |	Mar 04 06:59:37
       Mapping speed, Million of reads per hour |	336.61

                          Number of input reads |	2431055
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1288169
                        Uniquely mapped reads % |	52.99%
                          Average mapped length |	23.97
                       Number of splices: Total |	1330
            Number of splices: Annotated (sjdb) |	277
                       Number of splices: GT/AG |	1279
                       Number of splices: GC/AG |	13
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	37
                      Mismatch rate per base, % |	0.17%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.79
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.15
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	854283
             % of reads mapped to multiple loci |	35.14%
        Number of reads mapped to too many loci |	53163
             % of reads mapped to too many loci |	2.19%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.99%
                     % of reads unmapped: other |	0.69%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	288603	288603	288603
N_multimapping	854283	854283	854283
N_noFeature	60928	74617	882001
N_ambiguous	732251	381193	11090
UnstrandedReadsAssigned:494990 PositiveStrandReadsAssigned:832359 NegativeStrandReadsAssigned:395078
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030978 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: SRR5030978-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,431,055 reads, 619,547 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,126 rounds

 109283 SRR5030978.ke.tsv
  52636 SRR5030978.se.tsv
 161919 total
==> SRR5030978.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

==> SRR5030978.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030978 completed mapping pipeline successfully
