Starting /dee2/code/volunteer_pipeline.sh SRR5030883
    current disk space = 160632979456
    free memory = 73951688 
SRR5030883 SRAfilesize
612f79fe94ddf8d9008b4762000181cd  SRR5030883.sra
SRR5030883.sra file validated
SRR5030883 is single end
SRR5030883 is conventional basespace
SRR5030883 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030883_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	32.41775	33.0	31.0	34.0	31.0	34.0
2	32.747	34.0	31.0	34.0	31.0	34.0
3	32.709	34.0	31.0	34.0	31.0	34.0
4	36.2915	37.0	37.0	37.0	35.0	37.0
5	36.3195	37.0	37.0	37.0	35.0	37.0
6	36.12625	37.0	36.0	37.0	35.0	37.0
7	36.1405	37.0	35.0	37.0	35.0	37.0
8	36.18525	37.0	36.0	37.0	35.0	37.0
9	37.9615	39.0	38.0	39.0	35.0	39.0
10	37.90675	39.0	38.0	39.0	35.0	39.0
11	37.76475	39.0	38.0	39.0	35.0	39.0
12	37.73525	39.0	38.0	39.0	35.0	39.0
13	37.79	39.0	38.0	39.0	35.0	39.0
14	39.202	41.0	39.0	41.0	36.0	41.0
15	39.169	41.0	39.0	41.0	36.0	41.0
16	39.18075	40.0	39.0	41.0	36.0	41.0
17	39.13925	40.0	39.0	41.0	36.0	41.0
18	39.30525	41.0	39.0	41.0	36.0	41.0
19	39.16875	41.0	39.0	41.0	36.0	41.0
20	39.058	41.0	39.0	41.0	36.0	41.0
21	39.123	41.0	39.0	41.0	36.0	41.0
22	39.242	41.0	39.0	41.0	36.0	41.0
23	39.299	41.0	39.0	41.0	36.0	41.0
24	38.45425	40.0	38.0	41.0	34.0	41.0
25	38.48025	40.0	38.0	41.0	34.0	41.0
26	38.70275	40.0	38.0	41.0	34.0	41.0
27	38.901	40.0	38.0	41.0	35.0	41.0
28	38.63025	40.0	38.0	41.0	34.0	41.0
29	38.143	40.0	38.0	41.0	33.0	41.0
30	38.2605	40.0	38.0	41.0	33.0	41.0
31	38.74475	40.0	38.0	41.0	34.0	41.0
32	38.9405	40.0	38.0	41.0	35.0	41.0
33	37.8285	40.0	38.0	41.0	32.0	41.0
34	37.78875	40.0	37.0	41.0	31.0	41.0
35	37.53275	40.0	37.0	41.0	32.0	41.0
36	33.1665	38.0	30.0	40.0	17.0	41.0
37	35.47675	38.0	33.0	40.0	30.0	41.0
38	37.0435	39.0	37.0	40.0	32.0	41.0
39	37.0945	39.0	36.0	40.0	32.0	41.0
40	37.2975	39.0	37.0	40.0	32.0	41.0
41	36.97375	39.0	36.0	40.0	31.0	41.0
42	37.00975	39.0	36.0	40.0	31.0	41.0
43	37.22025	39.0	37.0	41.0	32.0	41.0
44	37.264	39.0	37.0	41.0	32.0	41.0
45	36.936	39.0	36.0	40.0	31.0	41.0
46	34.38725	38.0	33.0	40.0	24.0	41.0
47	35.37975	38.0	34.0	40.0	28.0	41.0
48	35.66725	38.0	35.0	40.0	30.0	41.0
49	34.72475	38.0	34.0	40.0	28.0	41.0
50	30.942	34.0	29.0	38.0	17.0	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
18	2.0
19	4.0
20	4.0
21	4.0
22	3.0
23	9.0
24	9.0
25	15.0
26	24.0
27	19.0
28	35.0
29	38.0
30	56.0
31	72.0
32	91.0
33	124.0
34	175.0
35	208.0
36	309.0
37	552.0
38	1075.0
39	1172.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.64629258517034	24.799599198396795	46.09218436873748	18.46192384769539
2	22.675	25.15	20.75	31.424999999999997
3	24.187093546773387	18.734367183591797	21.335667833916958	35.74287143571786
4	31.6	27.700000000000003	15.950000000000001	24.75
5	21.375	40.925	25.474999999999998	12.225
6	33.15	16.0	35.099999999999994	15.75
7	19.175	20.674999999999997	23.225	36.925000000000004
8	24.825	28.999999999999996	17.4	28.775000000000002
9	21.775	33.050000000000004	28.449999999999996	16.725
10	22.775000000000002	21.275	30.975	24.975
11	32.425	13.15	15.975	38.45
12	16.375	20.849999999999998	29.25	33.525
13	29.15	19.425	31.324999999999996	20.1
14	28.275	31.474999999999998	21.825	18.425
15	35.099999999999994	24.8	24.95	15.15
16	19.85	21.45	22.925	35.775
17	23.799999999999997	22.75	38.574999999999996	14.875
18	23.175	19.950000000000003	30.65	26.224999999999998
19	37.85	13.8	29.9	18.45
20	41.349999999999994	17.275	27.725	13.65
21	25.45	19.275000000000002	25.575	29.7
22	28.925	13.65	44.5	12.925
23	27.250000000000004	13.925	41.875	16.950000000000003
24	50.74999999999999	14.799999999999999	24.224999999999998	10.225
25	47.025	24.975	15.325	12.675
26	27.55	42.775	14.549999999999999	15.125
27	17.349999999999998	44.95	23.225	14.475
28	13.375	23.525	45.300000000000004	17.8
29	14.299999999999999	13.200000000000001	53.75	18.75
30	11.175	9.275	33.575	45.975
31	15.950000000000001	7.875	44.625	31.55
32	28.775000000000002	7.725	22.275	41.225
33	50.5	12.950000000000001	14.05	22.5
34	55.800000000000004	9.325	18.2	16.675
35	59.9	8.1	19.05	12.950000000000001
36	44.3	10.025	31.900000000000002	13.775
37	43.15	12.65	21.099999999999998	23.1
38	24.55	17.224999999999998	13.125	45.1
39	17.05	24.125	13.05	45.775
40	16.975	45.225	14.374999999999998	23.425
41	24.5	46.25	12.075	17.175
42	46.325	27.1	14.975	11.600000000000001
43	48.225	28.549999999999997	11.774999999999999	11.450000000000001
44	30.95	46.25	9.25	13.55
45	19.75	49.45	13.525	17.275
46	15.375	27.400000000000002	19.650000000000002	37.574999999999996
47	11.899999999999999	16.225	38.95	32.925
48	13.200000000000001	13.8	21.625	51.37500000000001
49	14.649999999999999	19.650000000000002	15.725	49.975
50	18.25	35.525	15.8	30.425
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.5
10	1.0
11	0.5
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.5
18	1.0
19	0.5
20	0.0
21	0.5
22	1.0
23	0.5
24	0.0
25	0.5
26	1.0
27	2.0
28	3.0
29	3.5
30	4.0
31	14.0
32	24.0
33	20.0
34	16.0
35	32.5
36	49.0
37	61.0
38	73.0
39	75.5
40	78.0
41	72.5
42	67.0
43	91.0
44	115.0
45	172.5
46	230.0
47	307.0
48	384.0
49	468.0
50	552.0
51	676.0
52	800.0
53	615.5
54	431.0
55	452.0
56	473.0
57	376.5
58	280.0
59	178.0
60	76.0
61	58.5
62	41.0
63	99.5
64	158.0
65	97.0
66	36.0
67	23.0
68	10.0
69	17.5
70	25.0
71	38.0
72	51.0
73	30.0
74	9.0
75	6.0
76	3.0
77	2.5
78	2.0
79	3.0
80	4.0
81	3.0
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	0.2
2	0.0
3	0.05
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	40.825
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.87262706674831	30.975
2	9.736680955296999	7.95
3	3.7966932026944273	4.65
4	2.9393753827311695	4.8
5	1.2859767299448868	2.625
6	0.8573178199632578	2.1
7	0.9185548071034906	2.625
8	0.6736068585425597	2.1999999999999997
9	0.5511328842620943	2.025
>10	2.8169014084507045	21.325
>50	0.3674219228413962	10.65
>100	0.1837109614206981	8.075000000000001
>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	112	2.8000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	110	2.75	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	101	2.5250000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	86	2.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	79	1.975	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	78	1.95	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	74	1.8499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	58	1.4500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	51	1.275	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	48	1.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	35	0.8750000000000001	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	31	0.775	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	24	0.6	No Hit
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	21	0.525	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (96% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	17	0.42500000000000004	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAC	16	0.4	RNA PCR Primer, Index 5 (100% over 35bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	14	0.35000000000000003	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	14	0.35000000000000003	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	13	0.325	No Hit
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	12	0.3	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	11	0.27499999999999997	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	10	0.25	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	10	0.25	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	10	0.25	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGC	9	0.22499999999999998	RNA PCR Primer, Index 8 (100% over 50bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTC	9	0.22499999999999998	RNA PCR Primer, Index 8 (100% over 44bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	9	0.22499999999999998	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	9	0.22499999999999998	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	8	0.2	RNA PCR Primer, Index 1 (100% over 32bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	8	0.2	No Hit
CTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCTA	8	0.2	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	7	0.17500000000000002	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	7	0.17500000000000002	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	7	0.17500000000000002	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	7	0.17500000000000002	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	7	0.17500000000000002	No Hit
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	6	0.15	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	6	0.15	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGTCCATGATGAAGCCCATTATCAGTGGACATCTATGGATGAGAAATGCG	6	0.15	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CGCACGGGGTCGGCGGCGATGTCGGTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	5	0.125	No Hit
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATGGAAT	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	5	0.125	No Hit
CAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTTGGAATT	5	0.125	No Hit
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	5	0.125	No Hit
GGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCTTTGGAATT	5	0.125	No Hit
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.225	0.0	0.0	0.0
2	0.0	0.225	0.0	0.0	0.0
3	0.0	0.25	0.0	0.0	0.0
4	0.0	0.25	0.0	0.0	0.0
5	0.0	0.3	0.0	0.0	0.0
6	0.0	0.325	0.0	0.0	0.0
7	0.0	0.65	0.0	0.0	0.0
8	0.0	0.85	0.0	0.0	0.0
9	0.0	0.95	0.0	0.0	0.0
10	0.0	1.175	0.0	0.0	0.0
11	0.0	1.175	0.0	0.0	0.0
12	0.0	1.425	0.0	0.0	0.0
13	0.0	1.675	0.0	0.0	0.0
14	0.0	1.9	0.0	0.0	0.0
15	0.0	2.175	0.0	0.0	0.0
16	0.0	3.025	0.0	0.0	0.0
17	0.0	3.675	0.0	0.0	0.0
18	0.0	4.475	0.0	0.0	0.0
19	0.0	5.2	0.0	0.0	0.0
20	0.0	5.925	0.0	0.0	0.0
21	0.0	10.6	0.0	0.0	0.0
22	0.0	20.675	0.0	0.0	0.0
23	0.0	47.125	0.0	0.0	0.0
24	0.0	58.5	0.0	0.0	0.0
25	0.0	63.55	0.0	0.0	0.0
26	0.0	65.05	0.0	0.0	0.0
27	0.0	65.825	0.0	0.0	0.0
28	0.0	66.425	0.0	0.0	0.0
29	0.0	67.05	0.0	0.0	0.0
30	0.0	67.35	0.0	0.0	0.0
31	0.0	67.85	0.0	0.0	0.0
32	0.0	68.6	0.0	0.0	0.0
33	0.0	69.575	0.0	0.0	0.0
34	0.0	73.2	0.0	0.0	0.0
35	0.0	74.425	0.0	0.0	0.0
36	0.0	75.275	0.0	0.0	0.0
37	0.0	76.3	0.0	0.0	0.0
38	0.0	76.75	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
ACGCTGT	20	6.952051E-4	44.000004	9
TTCAACG	20	6.952051E-4	44.000004	5
ACCCGTA	20	6.952051E-4	44.000004	2
TCAACGC	20	6.952051E-4	44.000004	6
CCGTAGA	20	6.952051E-4	44.000004	4
CCCGTAG	20	6.952051E-4	44.000004	3
GCTGTCG	20	6.952051E-4	44.000004	11
CAACGCT	20	6.952051E-4	44.000004	7
CGCTGTC	20	6.952051E-4	44.000004	10
ACTGTTG	30	1.9515464E-6	44.0	18
GTTGAAG	30	1.9515464E-6	44.0	10
CCAGTTG	30	1.9515464E-6	44.0	7
AACTGTT	30	1.9515464E-6	44.0	17
CATTCAA	25	3.6958358E-5	44.0	3
GAAGAAC	30	1.9515464E-6	44.0	13
AGAACTG	30	1.9515464E-6	44.0	15
GCCAGTT	30	1.9515464E-6	44.0	6
ACATTCA	25	3.6958358E-5	44.0	2
GCTGCCA	30	1.9515464E-6	44.0	3
>>END_MODULE
Read 214741 spots for SRR5030883.sra
Written 214741 spots for SRR5030883.sra
Read 214741 spots for SRR5030883.sra
Written 214741 spots for SRR5030883.sra
Read 214741 spots for SRR5030883.sra
Written 214741 spots for SRR5030883.sra
Read 214741 spots for SRR5030883.sra
Written 214741 spots for SRR5030883.sra
Read 214741 spots for SRR5030883.sra
Written 214741 spots for SRR5030883.sra
Read 214741 spots for SRR5030883.sra
Written 214741 spots for SRR5030883.sra
Read 214741 spots for SRR5030883.sra
Written 214741 spots for SRR5030883.sra
Read 214741 spots for SRR5030883.sra
Written 214741 spots for SRR5030883.sra
Read 214741 spots for SRR5030883.sra
Written 214741 spots for SRR5030883.sra
Read 214741 spots for SRR5030883.sra
Written 214741 spots for SRR5030883.sra
Read 214752 spots for SRR5030883.sra
Written 214752 spots for SRR5030883.sra
Read 214741 spots for SRR5030883.sra
Written 214741 spots for SRR5030883.sra
SRR ids: ['SRR5030883.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_o_wum6bd
SRR5030883.sra spots: 2576903
blocks: [[1, 214741], [214742, 429482], [429483, 644223], [644224, 858964], [858965, 1073705], [1073706, 1288446], [1288447, 1503187], [1503188, 1717928], [1717929, 1932669], [1932670, 2147410], [2147411, 2362151], [2362152, 2576903]]
SRR5030883 file size 445556
SRR5030883 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030883 SRR5030883_1.fastq
Input file:	SRR5030883_1.fastq
trimmed:	SRR5030883-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 06:36:12 2020 >> started

Wed Mar  4 06:36:13 2020 >> done (1.406s)
2576903 reads processed; of these:
    156 ( 0.01%) short reads filtered out after trimming by size control
      7 ( 0.00%) empty reads filtered out after trimming by size control
2576740 (99.99%) reads available; of these:
 196847 ( 7.64%) trimmed reads available after processing
2379893 (92.36%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     45	  0.00%
 19	     62	  0.00%
 20	    114	  0.00%
 21	    135	  0.01%
 22	    272	  0.01%
 23	    316	  0.01%
 24	    366	  0.01%
 25	    419	  0.02%
 26	    328	  0.01%
 27	    478	  0.02%
 28	    570	  0.02%
 29	    845	  0.03%
 30	    642	  0.02%
 31	    865	  0.03%
 32	   1170	  0.05%
 33	   2040	  0.08%
 34	   6372	  0.25%
 35	   3354	  0.13%
 36	   2488	  0.10%
 37	   2378	  0.09%
 38	   3730	  0.14%
 39	   3359	  0.13%
 40	   5077	  0.20%
 41	   3836	  0.15%
 42	   6002	  0.23%
 43	   5311	  0.21%
 44	  13960	  0.54%
 45	  14193	  0.55%
 46	  13747	  0.53%
 47	  15669	  0.61%
 48	  38749	  1.50%
 49	  49955	  1.94%
 50	2379893	 92.36%
2576740 reads passed initial QC


criterion=sequence-density
sequence-density=76.01
sequence-density-rank=1
fanout-score=20.35
fanout-score-rank=2
prefix-density=78.50
prefix-fanout=19.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC


criterion=fanout-score
sequence-density=2.31
sequence-density-rank=5
fanout-score=102.84
fanout-score-rank=1
prefix-density=77.93
prefix-fanout=3.1
sequence=GAATTCTCGGGGGCCAAGGAACT
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -t 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC -o SRR5030883 -
Input file:	STDIN
trimmed:	SRR5030883-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC
-- 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 06:36:26 2020 >> started

Wed Mar  4 06:36:28 2020 >> done (2.657s)
2509812 reads processed; of these:
 119205 ( 4.75%) short reads filtered out after trimming by size control
   7436 ( 0.30%) empty reads filtered out after trimming by size control
2383171 (94.95%) reads available; of these:
2031318 (85.24%) trimmed reads available after processing
 351853 (14.76%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  13503	  0.57%
 19	  22240	  0.93%
 20	 119760	  5.03%
 21	 262233	 11.00%
 22	 665950	 27.94%
 23	 282217	 11.84%
 24	 119095	  5.00%
 25	  32194	  1.35%
 26	  16695	  0.70%
 27	  14243	  0.60%
 28	  14716	  0.62%
 29	  11875	  0.50%
 30	  18659	  0.78%
 31	  22651	  0.95%
 32	  23849	  1.00%
 33	 101283	  4.25%
 34	  28188	  1.18%
 35	  21244	  0.89%
 36	  26540	  1.11%
 37	  13728	  0.58%
 38	  14676	  0.62%
 39	  15481	  0.65%
 40	  23039	  0.97%
 41	  28500	  1.20%
 42	  33059	  1.39%
 43	  25048	  1.05%
 44	  20625	  0.87%
 45	  26254	  1.10%
 46	  21799	  0.91%
 47	  19652	  0.82%
 48	   4140	  0.17%
 49	  10861	  0.46%
 50	 309174	 12.97%


criterion=sequence-density
sequence-density=5.20
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.56
sequence-density-rank=21
fanout-score=13.09
fanout-score-rank=1
prefix-density=7.34
prefix-fanout=1.0
sequence=TGAGCTTGGCTATTT
                                 Started job on |	Mar 04 06:36:50
                             Started mapping on |	Mar 04 06:36:50
                                    Finished on |	Mar 04 06:37:13
       Mapping speed, Million of reads per hour |	383.49

                          Number of input reads |	2450099
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1328803
                        Uniquely mapped reads % |	54.23%
                          Average mapped length |	28.36
                       Number of splices: Total |	1257
            Number of splices: Annotated (sjdb) |	278
                       Number of splices: GT/AG |	1156
                       Number of splices: GC/AG |	14
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	86
                      Mismatch rate per base, % |	0.24%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.51
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.12
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	734448
             % of reads mapped to multiple loci |	29.98%
        Number of reads mapped to too many loci |	70908
             % of reads mapped to too many loci |	2.89%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.42%
                     % of reads unmapped: other |	0.47%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	386848	386848	386848
N_multimapping	734448	734448	734448
N_noFeature	68320	85511	950123
N_ambiguous	736517	410030	17667
UnstrandedReadsAssigned:523966 PositiveStrandReadsAssigned:833262 NegativeStrandReadsAssigned:361013
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030883 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: SRR5030883-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,450,099 reads, 636,442 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,114 rounds

 109283 SRR5030883.ke.tsv
  52636 SRR5030883.se.tsv
 161919 total
==> SRR5030883.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

==> SRR5030883.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	2
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030883 completed mapping pipeline successfully
