Starting /dee2/code/volunteer_pipeline.sh SRR5030957
    current disk space = 160590331904
    free memory = 1048127832 
SRR5030957 SRAfilesize
361a70eb6072391a68a9dba4df9e691c  SRR5030957.sra
SRR5030957.sra file validated
SRR5030957 is single end
SRR5030957 is conventional basespace
SRR5030957 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030957_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	32.36475	33.0	31.0	34.0	31.0	34.0
2	32.74225	34.0	31.0	34.0	31.0	34.0
3	32.81675	34.0	31.0	34.0	31.0	34.0
4	36.297	37.0	37.0	37.0	35.0	37.0
5	36.225	37.0	37.0	37.0	35.0	37.0
6	35.985	37.0	35.0	37.0	35.0	37.0
7	36.107	37.0	35.0	37.0	35.0	37.0
8	36.171	37.0	36.0	37.0	35.0	37.0
9	37.96	39.0	38.0	39.0	35.0	39.0
10	37.9315	39.0	38.0	39.0	35.0	39.0
11	37.817	39.0	38.0	39.0	35.0	39.0
12	37.8835	39.0	38.0	39.0	35.0	39.0
13	37.912	39.0	38.0	39.0	35.0	39.0
14	39.242	41.0	39.0	41.0	36.0	41.0
15	39.31925	41.0	39.0	41.0	36.0	41.0
16	39.233	40.0	39.0	41.0	36.0	41.0
17	39.35475	41.0	39.0	41.0	36.0	41.0
18	39.288	41.0	39.0	41.0	36.0	41.0
19	39.09075	40.0	39.0	41.0	36.0	41.0
20	39.25125	40.0	39.0	41.0	36.0	41.0
21	39.21875	40.0	39.0	41.0	36.0	41.0
22	39.22425	41.0	39.0	41.0	36.0	41.0
23	39.175	40.0	39.0	41.0	36.0	41.0
24	38.5575	40.0	38.0	41.0	34.0	41.0
25	38.80775	40.0	38.0	41.0	35.0	41.0
26	38.75525	40.0	38.0	41.0	35.0	41.0
27	38.79825	40.0	38.0	41.0	35.0	41.0
28	38.752	40.0	38.0	41.0	35.0	41.0
29	38.4835	40.0	38.0	41.0	34.0	41.0
30	38.29675	40.0	38.0	41.0	34.0	41.0
31	38.6475	40.0	38.0	41.0	34.0	41.0
32	38.91725	40.0	39.0	41.0	35.0	41.0
33	37.46625	40.0	38.0	41.0	32.0	41.0
34	36.51025	40.0	37.0	41.0	29.0	41.0
35	32.4615	38.0	30.0	40.0	10.0	41.0
36	29.47225	37.0	18.0	40.0	8.0	41.0
37	29.449	35.0	22.0	39.0	6.0	41.0
38	32.1465	37.0	30.0	39.0	12.0	41.0
39	31.5135	37.0	30.0	40.0	7.0	41.0
40	32.5715	37.0	32.0	40.0	2.0	41.0
41	30.06325	36.0	26.0	40.0	2.0	41.0
42	31.7435	37.0	30.0	40.0	2.0	41.0
43	30.17675	37.0	26.0	40.0	2.0	41.0
44	31.00775	37.0	30.0	40.0	2.0	41.0
45	28.66375	36.0	23.0	40.0	2.0	41.0
46	26.688	34.0	8.0	39.0	2.0	41.0
47	26.62525	34.0	8.0	39.0	2.0	41.0
48	27.15725	35.0	2.0	39.0	2.0	41.0
49	25.34525	34.0	2.0	39.0	2.0	41.0
50	22.36425	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
9	1.0
10	0.0
11	0.0
12	0.0
13	0.0
14	1.0
15	0.0
16	0.0
17	4.0
18	6.0
19	5.0
20	6.0
21	15.0
22	22.0
23	21.0
24	40.0
25	59.0
26	105.0
27	170.0
28	63.0
29	122.0
30	161.0
31	164.0
32	171.0
33	213.0
34	218.0
35	267.0
36	305.0
37	436.0
38	606.0
39	819.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.116675012518778	26.189283925888834	48.29744616925388	14.396594892338507
2	25.45	28.275	20.974999999999998	25.3
3	23.200000000000003	19.425	23.425	33.95
4	31.1	32.85	13.850000000000001	22.2
5	22.125	38.074999999999996	27.250000000000004	12.55
6	26.900000000000002	18.5	42.15	12.45
7	19.975	20.849999999999998	21.349999999999998	37.824999999999996
8	24.099999999999998	34.025	15.075	26.8
9	20.349999999999998	33.85	31.924999999999997	13.875000000000002
10	23.9	18.775	30.55	26.775
11	36.9	15.0	13.3	34.8
12	15.875	22.925	29.825000000000003	31.374999999999996
13	25.374999999999996	18.925	34.225	21.475
14	30.5	27.55	24.175	17.775
15	33.900000000000006	22.6	27.375	16.125
16	17.424999999999997	20.625	23.425	38.525
17	25.25	24.725	34.849999999999994	15.174999999999999
18	26.1	16.525000000000002	32.65	24.725
19	32.275	16.025	34.025	17.675
20	44.125	17.125	23.549999999999997	15.2
21	22.15	23.7	26.3	27.85
22	30.8	12.5	45.45	11.25
23	25.924999999999997	14.299999999999999	43.275000000000006	16.5
24	47.825	14.6	26.6	10.975
25	49.375	23.35	15.725	11.55
26	29.799999999999997	43.475	14.7	12.025
27	17.1	46.0	23.599999999999998	13.3
28	12.950000000000001	26.625	45.775	14.649999999999999
29	10.875	14.875	55.7	18.55
30	10.625	8.6	37.8	42.975
31	15.35	6.9	44.45	33.300000000000004
32	27.525	7.324999999999999	23.45	41.699999999999996
33	51.025	9.425	15.575	23.974999999999998
34	59.550000000000004	7.5249999999999995	15.925	17.0
35	58.5	7.75	21.099999999999998	12.65
36	62.7	9.375	14.149999999999999	13.775
37	38.1	12.174999999999999	21.975	27.750000000000004
38	26.400000000000002	14.224999999999998	14.149999999999999	45.225
39	18.25	25.650000000000002	10.975	45.125
40	17.325	45.300000000000004	11.175	26.200000000000003
41	28.975	42.8	11.35	16.875
42	48.275	31.175000000000004	10.299999999999999	10.25
43	45.525	35.05	9.3	10.125
44	30.349999999999998	47.4	8.575000000000001	13.675
45	19.525000000000002	44.05	11.05	25.374999999999996
46	13.100000000000001	29.95	26.05	30.9
47	9.8	17.775	31.45	40.975
48	10.575	14.6	22.650000000000002	52.175000000000004
49	13.65	26.275	14.325	45.75
50	30.7	25.124999999999996	11.924999999999999	32.25
>>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	0.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	1.0
26	1.0
27	2.0
28	3.0
29	2.5
30	2.0
31	7.5
32	13.0
33	23.5
34	34.0
35	48.0
36	62.0
37	81.0
38	100.0
39	80.0
40	60.0
41	67.5
42	75.0
43	104.5
44	134.0
45	180.0
46	226.0
47	278.0
48	330.0
49	406.5
50	483.0
51	647.0
52	811.0
53	658.0
54	505.0
55	449.5
56	394.0
57	352.0
58	310.0
59	232.0
60	154.0
61	121.0
62	88.0
63	92.5
64	97.0
65	64.5
66	32.0
67	22.0
68	12.0
69	13.5
70	15.0
71	30.0
72	45.0
73	25.0
74	5.0
75	3.5
76	2.0
77	2.5
78	3.0
79	2.0
80	1.0
81	1.0
82	1.0
83	0.5
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.15
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	53.27499999999999
#Duplication Level	Percentage of deduplicated	Percentage of total
1	81.37024870952605	43.35
2	8.775222900046927	9.35
3	2.721726888784608	4.35
4	1.2200844673862037	2.6
5	0.8446738620366024	2.25
6	0.8446738620366024	2.7
7	0.6100422336931018	2.275
8	0.5631159080244017	2.4
9	0.4692632566870014	2.25
>10	2.534021586109808	24.925
>50	0.0	0.0
>100	0.04692632566870014	3.55
>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	142	3.55	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	42	1.05	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	40	1.0	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	40	1.0	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	38	0.95	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	31	0.775	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	18	0.44999999999999996	No Hit
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAT	15	0.375	RNA PCR Primer, Index 1 (100% over 35bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	15	0.375	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	14	0.35000000000000003	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	13	0.325	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	13	0.325	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	13	0.325	No Hit
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	13	0.325	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	12	0.3	No Hit
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	12	0.3	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	11	0.27499999999999997	No Hit
TTTGGCAATGGTAGAACTCACACCGTGGAATTCTCGGGTGCCAAGGAACT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 25bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGC	10	0.25	RNA PCR Primer, Index 1 (100% over 50bp)
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	10	0.25	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	9	0.22499999999999998	No Hit
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	9	0.22499999999999998	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 25bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	9	0.22499999999999998	No Hit
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCC	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 27bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	8	0.2	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	8	0.2	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	8	0.2	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	8	0.2	No Hit
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (95% over 23bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	7	0.17500000000000002	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	7	0.17500000000000002	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CTTAATGATGATTGTCTGTTTGATTGCTTGATGCAATGTGAAAACCACAT	7	0.17500000000000002	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	6	0.15	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	6	0.15	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGGG	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGC	6	0.15	RNA PCR Primer, Index 1 (96% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	6	0.15	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	6	0.15	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	6	0.15	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	6	0.15	No Hit
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
AACATTCATTGCTGTCGGTGGGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	5	0.125	RNA PCR Primer, Index 1 (100% over 32bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGTGCCAAGGAACTCCAG	5	0.125	No Hit
ATTCTGTGATGACTTTACCAAATGACTTTCGTTCTTCTGAGTTTGCTGAA	5	0.125	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	5	0.125	No Hit
AGCAGCATTGTACAGGGCTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	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	0.275	0.0	0.0	0.0
2	0.0	0.3	0.0	0.0	0.0
3	0.0	0.35	0.0	0.0	0.0
4	0.0	0.4	0.0	0.0	0.0
5	0.0	0.45	0.0	0.0	0.0
6	0.0	0.525	0.0	0.0	0.0
7	0.0	0.9	0.0	0.0	0.0
8	0.0	0.975	0.0	0.0	0.0
9	0.0	1.05	0.0	0.0	0.0
10	0.0	1.15	0.0	0.0	0.0
11	0.0	1.225	0.0	0.0	0.0
12	0.0	1.375	0.0	0.0	0.0
13	0.0	1.525	0.0	0.0	0.0
14	0.0	1.8	0.0	0.0	0.0
15	0.0	2.2	0.0	0.0	0.0
16	0.0	3.075	0.0	0.0	0.0
17	0.0	3.525	0.0	0.0	0.0
18	0.0	4.375	0.0	0.0	0.0
19	0.0	4.875	0.0	0.0	0.0
20	0.0	5.625	0.0	0.0	0.0
21	0.0	10.6	0.0	0.0	0.0
22	0.0	21.15	0.0	0.0	0.0
23	0.0	47.3	0.0	0.0	0.0
24	0.0	60.625	0.0	0.0	0.0
25	0.0	66.875	0.0	0.0	0.0
26	0.0	68.825	0.0	0.0	0.0
27	0.0	69.575	0.0	0.0	0.0
28	0.0	70.125	0.0	0.0	0.0
29	0.0	70.325	0.0	0.0	0.0
30	0.0	70.75	0.0	0.0	0.0
31	0.0	71.6	0.0	0.0	0.0
32	0.0	72.45	0.0	0.0	0.0
33	0.0	73.325	0.0	0.0	0.0
34	0.0	75.525	0.0	0.0	0.0
35	0.0	76.275	0.0	0.0	0.0
36	0.0	76.625	0.0	0.0	0.0
37	0.0	77.3	0.0	0.0	0.0
38	0.0	77.825	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACATTCA	40	5.315087E-9	44.000004	2
CTTGGCT	20	6.952051E-4	44.000004	16
GCTGTCG	40	5.315087E-9	44.000004	11
GCTTGGC	20	6.952051E-4	44.000004	15
CTGTCGG	40	5.315087E-9	44.000004	12
GTCGGTG	40	5.315087E-9	44.000004	14
AACATTC	40	5.315087E-9	44.000004	1
TGTCGGT	40	5.315087E-9	44.000004	13
AACGCTG	30	1.9515464E-6	44.0	8
GAGGTAG	25	3.6958358E-5	44.0	2
GGTGAGT	30	1.9515464E-6	44.0	17
ACGCTGT	30	1.9515464E-6	44.0	9
TTCAACG	30	1.9515464E-6	44.0	5
TCGGTGA	30	1.9515464E-6	44.0	15
GAGCTTG	30	1.9515464E-6	44.0	13
GGATCCG	30	1.9515464E-6	44.0	3
CCGTCTG	30	1.9515464E-6	44.0	7
TCGGATC	30	1.9515464E-6	44.0	1
CATTCAA	30	1.9515464E-6	44.0	3
TCAACGC	30	1.9515464E-6	44.0	6
>>END_MODULE
Read 54946 spots for SRR5030957.sra
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SRR ids: ['SRR5030957.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_bspkqrty
SRR5030957.sra spots: 2637451
blocks: [[1, 54946], [54947, 109892], [109893, 164838], [164839, 219784], [219785, 274730], [274731, 329676], [329677, 384622], [384623, 439568], [439569, 494514], [494515, 549460], [549461, 604406], [604407, 659352], [659353, 714298], [714299, 769244], [769245, 824190], [824191, 879136], [879137, 934082], [934083, 989028], [989029, 1043974], [1043975, 1098920], [1098921, 1153866], [1153867, 1208812], [1208813, 1263758], [1263759, 1318704], [1318705, 1373650], [1373651, 1428596], [1428597, 1483542], [1483543, 1538488], [1538489, 1593434], [1593435, 1648380], [1648381, 1703326], [1703327, 1758272], [1758273, 1813218], [1813219, 1868164], [1868165, 1923110], [1923111, 1978056], [1978057, 2033002], [2033003, 2087948], [2087949, 2142894], [2142895, 2197840], [2197841, 2252786], [2252787, 2307732], [2307733, 2362678], [2362679, 2417624], [2417625, 2472570], [2472571, 2527516], [2527517, 2582462], [2582463, 2637451]]
SRR5030957 file size 456051
SRR5030957 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5030957 SRR5030957_1.fastq
Input file:	SRR5030957_1.fastq
trimmed:	SRR5030957-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 06:53:30 2020 >> started

Wed Mar  4 06:53:31 2020 >> done (1.664s)
2637451 reads processed; of these:
    138 ( 0.01%) short reads filtered out after trimming by size control
     10 ( 0.00%) empty reads filtered out after trimming by size control
2637303 (99.99%) reads available; of these:
 317599 (12.04%) trimmed reads available after processing
2319704 (87.96%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     43	  0.00%
 19	     71	  0.00%
 20	    109	  0.00%
 21	    141	  0.01%
 22	    238	  0.01%
 23	    321	  0.01%
 24	    355	  0.01%
 25	    521	  0.02%
 26	    444	  0.02%
 27	    507	  0.02%
 28	    693	  0.03%
 29	   1174	  0.04%
 30	    841	  0.03%
 31	   1124	  0.04%
 32	   3033	  0.12%
 33	   9025	  0.34%
 34	  21563	  0.82%
 35	   5142	  0.19%
 36	   5658	  0.21%
 37	   3155	  0.12%
 38	   6172	  0.23%
 39	   5625	  0.21%
 40	  11739	  0.45%
 41	   6119	  0.23%
 42	  16239	  0.62%
 43	   7530	  0.29%
 44	  33215	  1.26%
 45	  18462	  0.70%
 46	  17192	  0.65%
 47	  19679	  0.75%
 48	  57291	  2.17%
 49	  64178	  2.43%
 50	2319704	 87.96%
2637303 reads passed initial QC


criterion=sequence-density
sequence-density=76.25
sequence-density-rank=1
fanout-score=21.59
fanout-score-rank=3
prefix-density=79.07
prefix-fanout=20.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC


criterion=fanout-score
sequence-density=1.67
sequence-density-rank=5
fanout-score=437.57
fanout-score-rank=1
prefix-density=78.18
prefix-fanout=9.4
sequence=GGAATTCTCGGTGCCAAGGA
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -t 48 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC -o SRR5030957 -
Input file:	STDIN
trimmed:	SRR5030957-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC
-- 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 06:53:50 2020 >> started

Wed Mar  4 06:53:55 2020 >> done (4.336s)
2568802 reads processed; of these:
 116498 ( 4.54%) short reads filtered out after trimming by size control
  12347 ( 0.48%) empty reads filtered out after trimming by size control
2439957 (94.98%) reads available; of these:
2057604 (84.33%) trimmed reads available after processing
 382353 (15.67%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  16047	  0.66%
 19	  20290	  0.83%
 20	 110127	  4.51%
 21	 262821	 10.77%
 22	 683977	 28.03%
 23	 341352	 13.99%
 24	 154903	  6.35%
 25	  41223	  1.69%
 26	  20890	  0.86%
 27	  17347	  0.71%
 28	  17683	  0.72%
 29	  15206	  0.62%
 30	  19148	  0.78%
 31	  25285	  1.04%
 32	  26084	  1.07%
 33	  56225	  2.30%
 34	  22775	  0.93%
 35	  16589	  0.68%
 36	  20403	  0.84%
 37	  12666	  0.52%
 38	  14457	  0.59%
 39	  14691	  0.60%
 40	  22712	  0.93%
 41	  24625	  1.01%
 42	  30573	  1.25%
 43	  20469	  0.84%
 44	  19828	  0.81%
 45	  23137	  0.95%
 46	  18575	  0.76%
 47	  15401	  0.63%
 48	   6109	  0.25%
 49	  11088	  0.45%
 50	 317251	 13.00%


criterion=sequence-density
sequence-density=2.84
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=AAGCTGCCAGTTGAAGAACTGTTGGAATTCTC


criterion=fanout-score
sequence-density=0.52
sequence-density-rank=26
fanout-score=13.47
fanout-score-rank=1
prefix-density=7.05
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 06:54:35
                             Started mapping on |	Mar 04 06:54:35
                                    Finished on |	Mar 04 06:55:01
       Mapping speed, Million of reads per hour |	347.32

                          Number of input reads |	2508458
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1388689
                        Uniquely mapped reads % |	55.36%
                          Average mapped length |	28.10
                       Number of splices: Total |	1467
            Number of splices: Annotated (sjdb) |	213
                       Number of splices: GT/AG |	1345
                       Number of splices: GC/AG |	35
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	86
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.28
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.13
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	777265
             % of reads mapped to multiple loci |	30.99%
        Number of reads mapped to too many loci |	49958
             % of reads mapped to too many loci |	1.99%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.84%
                     % of reads unmapped: other |	0.82%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	342504	342504	342504
N_multimapping	777265	777265	777265
N_noFeature	62240	79901	997538
N_ambiguous	752178	407394	11398
UnstrandedReadsAssigned:574271 PositiveStrandReadsAssigned:901394 NegativeStrandReadsAssigned:379753
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030957 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: SRR5030957-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,508,458 reads, 604,762 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,055 rounds

 109283 SRR5030957.ke.tsv
  52636 SRR5030957.se.tsv
 161919 total
==> SRR5030957.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

==> SRR5030957.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030957 completed mapping pipeline successfully
