Starting /dee2/code/volunteer_pipeline.sh SRR5030841
    current disk space = 160655835136
    free memory = 73941824 
SRR5030841 SRAfilesize
dc4ed86542403c28f18af63afa3b9d0d  SRR5030841.sra
SRR5030841.sra file validated
SRR5030841 is single end
SRR5030841 is conventional basespace
SRR5030841 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030841_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	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.50125	34.0	31.0	34.0	31.0	34.0
2	32.6855	34.0	31.0	34.0	31.0	34.0
3	32.80775	34.0	31.0	34.0	31.0	34.0
4	36.21925	37.0	37.0	37.0	35.0	37.0
5	36.238	37.0	37.0	37.0	35.0	37.0
6	36.06325	37.0	35.0	37.0	35.0	37.0
7	36.02625	37.0	35.0	37.0	35.0	37.0
8	36.1335	37.0	36.0	37.0	35.0	37.0
9	37.8645	39.0	38.0	39.0	35.0	39.0
10	37.94625	39.0	38.0	39.0	35.0	39.0
11	37.80725	39.0	38.0	39.0	35.0	39.0
12	37.82175	39.0	38.0	39.0	35.0	39.0
13	37.7335	39.0	38.0	39.0	35.0	39.0
14	39.21175	41.0	39.0	41.0	36.0	41.0
15	39.10025	40.0	38.0	41.0	36.0	41.0
16	39.12575	40.0	38.0	41.0	36.0	41.0
17	39.30525	41.0	39.0	41.0	36.0	41.0
18	39.28625	41.0	39.0	41.0	36.0	41.0
19	39.0985	41.0	39.0	41.0	36.0	41.0
20	39.11175	41.0	39.0	41.0	36.0	41.0
21	39.1435	40.0	39.0	41.0	36.0	41.0
22	39.2035	41.0	39.0	41.0	36.0	41.0
23	39.04	40.0	39.0	41.0	36.0	41.0
24	38.7385	40.0	39.0	41.0	35.0	41.0
25	39.00575	41.0	39.0	41.0	35.0	41.0
26	39.06375	41.0	39.0	41.0	35.0	41.0
27	39.08975	41.0	39.0	41.0	36.0	41.0
28	38.86575	40.0	39.0	41.0	35.0	41.0
29	38.1915	40.0	38.0	41.0	33.0	41.0
30	38.58625	40.0	38.0	41.0	34.0	41.0
31	38.7625	40.0	38.0	41.0	35.0	41.0
32	38.9935	40.0	39.0	41.0	35.0	41.0
33	38.3545	40.0	38.0	41.0	34.0	41.0
34	38.2915	40.0	38.0	41.0	33.0	41.0
35	37.9555	40.0	38.0	41.0	33.0	41.0
36	33.82	38.0	30.0	40.0	21.0	41.0
37	35.64825	38.0	34.0	40.0	30.0	41.0
38	36.94275	39.0	37.0	40.0	31.0	41.0
39	37.0835	39.0	37.0	40.0	31.0	41.0
40	37.01625	39.0	37.0	40.0	31.0	41.0
41	37.00325	39.0	37.0	41.0	31.0	41.0
42	37.30575	40.0	37.0	41.0	32.0	41.0
43	36.86375	39.0	36.0	41.0	31.0	41.0
44	36.9975	40.0	37.0	41.0	31.0	41.0
45	36.72325	39.0	36.0	41.0	30.0	41.0
46	34.83025	38.0	34.0	40.0	24.0	41.0
47	35.5555	38.0	35.0	40.0	28.0	41.0
48	36.1155	39.0	36.0	40.0	30.0	41.0
49	34.90725	39.0	35.0	40.0	26.0	41.0
50	30.3575	34.0	27.0	38.0	2.0	40.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
14	1.0
15	1.0
16	0.0
17	3.0
18	2.0
19	4.0
20	2.0
21	4.0
22	7.0
23	7.0
24	10.0
25	21.0
26	18.0
27	34.0
28	34.0
29	38.0
30	49.0
31	70.0
32	69.0
33	126.0
34	148.0
35	225.0
36	283.0
37	548.0
38	944.0
39	1352.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.553776888444222	22.436218109054526	58.10405202601301	11.905952976488244
2	21.075	26.825	19.725	32.375
3	27.35	20.1	22.775000000000002	29.775000000000002
4	30.4	29.025000000000002	13.325000000000001	27.250000000000004
5	19.675	45.475	24.0	10.85
6	36.075	16.625	33.1	14.2
7	14.35	20.275000000000002	26.3	39.074999999999996
8	24.775	31.2	12.725	31.3
9	22.425	35.975	29.175	12.425
10	22.15	21.15	31.3	25.4
11	27.250000000000004	10.424999999999999	18.025	44.3
12	15.299999999999999	16.875	33.975	33.85
13	33.275	21.7	28.575	16.45
14	31.85	34.075	19.725	14.35
15	35.95898974743686	24.90622655663916	25.6064016004001	13.528382095523881
16	16.8	22.625	19.775000000000002	40.8
17	19.375	20.025000000000002	45.2	15.4
18	23.400000000000002	19.625	29.925	27.05
19	37.775	13.450000000000001	30.55	18.224999999999998
20	43.025000000000006	14.45	28.7	13.825000000000001
21	21.45	17.05	30.425	31.075000000000003
22	27.725	12.825000000000001	50.1	9.35
23	28.499999999999996	13.15	46.375	11.975
24	54.225	14.424999999999999	23.974999999999998	7.375
25	51.525	25.650000000000002	14.099999999999998	8.725
26	25.6	50.8	14.35	9.25
27	15.25	49.75	26.025	8.975
28	10.2	24.05	52.325	13.425
29	8.825	12.7	59.150000000000006	19.325
30	9.15	5.8999999999999995	37.35	47.599999999999994
31	14.224999999999998	5.25	47.825	32.7
32	28.525	6.05	19.825	45.6
33	59.824999999999996	6.2	12.55	21.425
34	66.475	5.7	14.95	12.875
35	65.625	6.3	18.85	9.225
36	43.025000000000006	7.1499999999999995	36.225	13.600000000000001
37	47.175	8.649999999999999	18.6	25.575
38	21.224999999999998	15.375	11.475	51.925
39	14.95	26.25	7.3999999999999995	51.4
40	15.5	53.125	7.925	23.45
41	26.650000000000002	51.15	6.825	15.375
42	53.800000000000004	30.275000000000002	6.9750000000000005	8.95
43	51.725	33.75	6.325	8.200000000000001
44	26.474999999999998	54.025	5.6000000000000005	13.900000000000002
45	15.475	52.47500000000001	12.4	19.650000000000002
46	8.825	26.900000000000002	19.425	44.85
47	6.2	15.825	40.125	37.85
48	7.9	13.4	18.3	60.4
49	13.225000000000001	21.125	12.275	53.37499999999999
50	19.15	39.375	12.75	28.725
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.5
18	1.0
19	0.5
20	0.0
21	1.0
22	2.0
23	1.0
24	0.0
25	1.0
26	2.0
27	1.5
28	1.0
29	2.5
30	4.0
31	6.5
32	9.0
33	13.5
34	18.0
35	23.0
36	28.0
37	32.5
38	37.0
39	41.5
40	46.0
41	43.0
42	40.0
43	72.0
44	104.0
45	164.5
46	225.0
47	370.0
48	515.0
49	643.0
50	771.0
51	801.5
52	832.0
53	611.0
54	390.0
55	435.5
56	481.0
57	356.0
58	231.0
59	151.5
60	72.0
61	58.0
62	44.0
63	54.0
64	64.0
65	41.5
66	19.0
67	16.0
68	13.0
69	13.0
70	13.0
71	20.0
72	27.0
73	16.0
74	5.0
75	3.0
76	1.0
77	1.5
78	2.0
79	1.0
80	0.0
81	1.0
82	2.0
83	1.5
84	1.0
85	0.5
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	0.05
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	0.025
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	38.625
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.11650485436893	29.4
2	9.06148867313916	7.000000000000001
3	4.983818770226537	5.775
4	2.071197411003236	3.2
5	1.3592233009708738	2.625
6	0.7119741100323626	1.6500000000000001
7	0.6472491909385114	1.7500000000000002
8	0.6472491909385114	2.0
9	0.517799352750809	1.7999999999999998
>10	3.300970873786408	23.65
>50	0.3236245954692557	8.525
>100	0.2588996763754045	12.625
>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	148	3.6999999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	145	3.6249999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	108	2.7	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	104	2.6	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	68	1.7000000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	59	1.4749999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	53	1.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGC	28	0.7000000000000001	RNA PCR Primer, Index 6 (100% over 50bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	25	0.625	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	23	0.575	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 30bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTC	20	0.5	RNA PCR Primer, Index 6 (100% over 44bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGC	18	0.44999999999999996	RNA PCR Primer, Index 5 (97% over 35bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCAGTGCACTACAGAACTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	10	0.25	No Hit
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	9	0.22499999999999998	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	8	0.2	No Hit
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	8	0.2	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	8	0.2	No Hit
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
TTTGGCAATGGTAGAACTCACATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGGCAATGGTAGAACTCACTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	7	0.17500000000000002	No Hit
TTTGGCAATGGTAGAACTCACACCTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	6	0.15	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
TAACAGTCTACAGCCATGGTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	6	0.15	No Hit
TAAGGCACGCGGTGAATGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	5	0.125	No Hit
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	5	0.125	No Hit
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CTAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
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)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	5	0.125	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	5	0.125	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>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	0.775	0.0	0.0	0.0
2	0.0	0.775	0.0	0.0	0.0
3	0.0	0.8	0.0	0.0	0.0
4	0.0	0.825	0.0	0.0	0.0
5	0.0	0.85	0.0	0.0	0.0
6	0.0	0.975	0.0	0.0	0.0
7	0.0	1.6	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	2.025	0.0	0.0	0.0
11	0.0	2.175	0.0	0.0	0.0
12	0.0	2.425	0.0	0.0	0.0
13	0.0	2.725	0.0	0.0	0.0
14	0.0	2.925	0.0	0.0	0.0
15	0.0	3.25	0.0	0.0	0.0
16	0.0	4.15	0.0	0.0	0.0
17	0.0	4.775	0.0	0.0	0.0
18	0.0	5.875	0.0	0.0	0.0
19	0.0	6.6	0.0	0.0	0.0
20	0.0	7.8	0.0	0.0	0.0
21	0.0	14.5	0.0	0.0	0.0
22	0.0	27.825	0.0	0.0	0.0
23	0.0	60.875	0.0	0.0	0.0
24	0.0	73.225	0.0	0.0	0.0
25	0.0	79.5	0.0	0.0	0.0
26	0.0	81.025	0.0	0.0	0.0
27	0.0	81.6	0.0	0.0	0.0
28	0.0	82.2	0.0	0.0	0.0
29	0.0	82.7	0.0	0.0	0.0
30	0.0	83.025	0.0	0.0	0.0
31	0.0	83.5	0.0	0.0	0.0
32	0.0	84.475	0.0	0.0	0.0
33	0.0	85.1	0.0	0.0	0.0
34	0.0	86.375	0.0	0.0	0.0
35	0.0	86.875	0.0	0.0	0.0
36	0.0	87.1	0.0	0.0	0.0
37	0.0	87.4	0.0	0.0	0.0
38	0.0	87.625	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CATTCAA	40	5.315087E-9	44.000004	3
ACATTCA	40	5.315087E-9	44.000004	2
GCTTGGC	20	6.952051E-4	44.000004	15
ATTCAAC	40	5.315087E-9	44.000004	4
AACATTC	40	5.315087E-9	44.000004	1
ACTGTTG	25	3.6958358E-5	44.0	18
AACGCTG	30	1.9515464E-6	44.0	8
AAGTAAT	35	1.02281774E-7	44.0	4
GTTGAAG	25	3.6958358E-5	44.0	10
TCAAGTA	35	1.02281774E-7	44.0	2
ACGCTGT	30	1.9515464E-6	44.0	9
AATCCAG	35	1.02281774E-7	44.0	8
CAGTTGA	25	3.6958358E-5	44.0	8
ATCCAGG	35	1.02281774E-7	44.0	9
AACTGTT	25	3.6958358E-5	44.0	17
TTCAAGT	35	1.02281774E-7	44.0	1
TTCAACG	30	1.9515464E-6	44.0	5
AGGATAG	35	1.02281774E-7	44.0	13
ATAGGCT	35	1.02281774E-7	44.0	16
GAGCTTG	30	1.9515464E-6	44.0	13
>>END_MODULE
Read 253786 spots for SRR5030841.sra
Written 253786 spots for SRR5030841.sra
Read 253786 spots for SRR5030841.sra
Written 253786 spots for SRR5030841.sra
Read 253786 spots for SRR5030841.sra
Written 253786 spots for SRR5030841.sra
Read 253786 spots for SRR5030841.sra
Written 253786 spots for SRR5030841.sra
Read 253786 spots for SRR5030841.sra
Written 253786 spots for SRR5030841.sra
Read 253786 spots for SRR5030841.sra
Written 253786 spots for SRR5030841.sra
Read 253786 spots for SRR5030841.sra
Written 253786 spots for SRR5030841.sra
Read 253786 spots for SRR5030841.sra
Written 253786 spots for SRR5030841.sra
Read 253786 spots for SRR5030841.sra
Written 253786 spots for SRR5030841.sra
Read 253786 spots for SRR5030841.sra
Written 253786 spots for SRR5030841.sra
Read 253786 spots for SRR5030841.sra
Written 253786 spots for SRR5030841.sra
Read 253789 spots for SRR5030841.sra
Written 253789 spots for SRR5030841.sra
SRR ids: ['SRR5030841.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_h7vwlsvn
SRR5030841.sra spots: 3045435
blocks: [[1, 253786], [253787, 507572], [507573, 761358], [761359, 1015144], [1015145, 1268930], [1268931, 1522716], [1522717, 1776502], [1776503, 2030288], [2030289, 2284074], [2284075, 2537860], [2537861, 2791646], [2791647, 3045435]]
SRR5030841 file size 526764
SRR5030841 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030841 SRR5030841_1.fastq
Input file:	SRR5030841_1.fastq
trimmed:	SRR5030841-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 06:25:53 2020 >> started

Wed Mar  4 06:25:55 2020 >> done (1.628s)
3045435 reads processed; of these:
    138 ( 0.00%) short reads filtered out after trimming by size control
      8 ( 0.00%) empty reads filtered out after trimming by size control
3045289 (100.00%) reads available; of these:
 167295 ( 5.49%) trimmed reads available after processing
2877994 (94.51%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     44	  0.00%
 19	     41	  0.00%
 20	    133	  0.00%
 21	    155	  0.01%
 22	    294	  0.01%
 23	    351	  0.01%
 24	    317	  0.01%
 25	    424	  0.01%
 26	    343	  0.01%
 27	    446	  0.01%
 28	    606	  0.02%
 29	    869	  0.03%
 30	    652	  0.02%
 31	    764	  0.03%
 32	    725	  0.02%
 33	   1053	  0.03%
 34	   3107	  0.10%
 35	   2398	  0.08%
 36	   1838	  0.06%
 37	   1947	  0.06%
 38	   2266	  0.07%
 39	   2527	  0.08%
 40	   2826	  0.09%
 41	   2888	  0.09%
 42	   4463	  0.15%
 43	   5237	  0.17%
 44	  10642	  0.35%
 45	  12660	  0.42%
 46	  11396	  0.37%
 47	  16396	  0.54%
 48	  36613	  1.20%
 49	  42874	  1.41%
 50	2877994	 94.51%
3045289 reads passed initial QC


criterion=sequence-density
sequence-density=87.21
sequence-density-rank=1
fanout-score=19.20
fanout-score-rank=1
prefix-density=87.89
prefix-fanout=19.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC


criterion=fanout-score
sequence-density=87.21
sequence-density-rank=1
fanout-score=19.20
fanout-score-rank=1
prefix-density=87.89
prefix-fanout=19.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC -o SRR5030841 -
Input file:	STDIN
trimmed:	SRR5030841-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC
-- 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 06:26:09 2020 >> started

Wed Mar  4 06:26:13 2020 >> done (4.100s)
2976078 reads processed; of these:
 154316 ( 5.19%) short reads filtered out after trimming by size control
  22807 ( 0.77%) empty reads filtered out after trimming by size control
2798955 (94.05%) reads available; of these:
2595931 (92.75%) trimmed reads available after processing
 203024 ( 7.25%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  16960	  0.61%
 19	  31852	  1.14%
 20	 192419	  6.87%
 21	 436395	 15.59%
 22	 966214	 34.52%
 23	 383853	 13.71%
 24	 181698	  6.49%
 25	  42978	  1.54%
 26	  20167	  0.72%
 27	  14856	  0.53%
 28	  14190	  0.51%
 29	   9590	  0.34%
 30	  16453	  0.59%
 31	  23759	  0.85%
 32	  19596	  0.70%
 33	  41113	  1.47%
 34	  15706	  0.56%
 35	  12497	  0.45%
 36	  14111	  0.50%
 37	   9008	  0.32%
 38	   8960	  0.32%
 39	   9664	  0.35%
 40	  13044	  0.47%
 41	  19965	  0.71%
 42	  23803	  0.85%
 43	  16960	  0.61%
 44	  13914	  0.50%
 45	  18251	  0.65%
 46	  12847	  0.46%
 47	  10021	  0.36%
 48	   2123	  0.08%
 49	   6853	  0.24%
 50	 179135	  6.40%


criterion=sequence-density
sequence-density=5.29
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=22
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.03
sequence-density-rank=40
fanout-score=53.82
fanout-score-rank=1
prefix-density=1.42
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:26:31
                             Started mapping on |	Mar 04 06:26:32
                                    Finished on |	Mar 04 06:26:58
       Mapping speed, Million of reads per hour |	397.13

                          Number of input reads |	2868166
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1684523
                        Uniquely mapped reads % |	58.73%
                          Average mapped length |	25.12
                       Number of splices: Total |	1029
            Number of splices: Annotated (sjdb) |	147
                       Number of splices: GT/AG |	977
                       Number of splices: GC/AG |	11
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	39
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.50
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.07
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	944603
             % of reads mapped to multiple loci |	32.93%
        Number of reads mapped to too many loci |	36550
             % of reads mapped to too many loci |	1.27%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	6.68%
                     % of reads unmapped: other |	0.38%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	239040	239040	239040
N_multimapping	944603	944603	944603
N_noFeature	61603	73955	1166006
N_ambiguous	947172	491501	14929
UnstrandedReadsAssigned:675748 PositiveStrandReadsAssigned:1119067 NegativeStrandReadsAssigned:503588
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030841 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: SRR5030841-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,868,166 reads, 798,190 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 816 rounds

 109283 SRR5030841.ke.tsv
  52636 SRR5030841.se.tsv
 161919 total
==> SRR5030841.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

==> SRR5030841.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030841 completed mapping pipeline successfully
