Starting /dee2/code/volunteer_pipeline.sh SRR5030878
    current disk space = 160665878528
    free memory = 73954504 
SRR5030878 SRAfilesize
b02fb188bb5f16419ac604fdf094bc3b  SRR5030878.sra
SRR5030878.sra file validated
SRR5030878 is single end
SRR5030878 is conventional basespace
SRR5030878 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030878_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	32.30525	33.0	31.0	34.0	30.0	34.0
2	32.65325	34.0	31.0	34.0	31.0	34.0
3	32.71475	34.0	31.0	34.0	31.0	34.0
4	36.2025	37.0	35.0	37.0	35.0	37.0
5	36.1675	37.0	35.0	37.0	35.0	37.0
6	35.93	37.0	35.0	37.0	35.0	37.0
7	36.05025	37.0	35.0	37.0	35.0	37.0
8	36.06675	37.0	35.0	37.0	35.0	37.0
9	37.9	39.0	38.0	39.0	35.0	39.0
10	37.91775	39.0	38.0	39.0	35.0	39.0
11	37.75575	39.0	38.0	39.0	35.0	39.0
12	37.868	39.0	38.0	39.0	35.0	39.0
13	37.8735	39.0	38.0	39.0	35.0	39.0
14	39.25025	41.0	39.0	41.0	36.0	41.0
15	39.26675	41.0	39.0	41.0	36.0	41.0
16	39.2045	40.0	39.0	41.0	36.0	41.0
17	39.3035	41.0	39.0	41.0	36.0	41.0
18	39.25625	41.0	39.0	41.0	36.0	41.0
19	39.215	40.0	39.0	41.0	36.0	41.0
20	39.16025	40.0	39.0	41.0	36.0	41.0
21	39.112	40.0	39.0	41.0	36.0	41.0
22	39.07275	40.0	39.0	41.0	36.0	41.0
23	39.076	40.0	39.0	41.0	36.0	41.0
24	38.32975	40.0	38.0	41.0	34.0	41.0
25	38.584	40.0	38.0	41.0	34.0	41.0
26	38.657	40.0	38.0	41.0	34.0	41.0
27	38.65	40.0	38.0	41.0	35.0	41.0
28	38.64425	40.0	38.0	41.0	34.0	41.0
29	38.357	40.0	38.0	41.0	33.0	41.0
30	38.02175	40.0	38.0	41.0	33.0	41.0
31	38.436	40.0	38.0	41.0	34.0	41.0
32	38.649	40.0	38.0	41.0	35.0	41.0
33	36.96475	40.0	37.0	41.0	30.0	41.0
34	36.324	40.0	36.0	41.0	28.0	41.0
35	33.1705	38.0	32.0	40.0	15.0	41.0
36	30.43875	37.0	23.0	40.0	8.0	41.0
37	30.67125	37.0	25.0	39.0	8.0	41.0
38	32.716	37.0	31.0	40.0	16.0	41.0
39	32.2385	37.0	31.0	40.0	9.0	41.0
40	32.818	38.0	32.0	40.0	9.0	41.0
41	30.98425	36.0	28.0	40.0	2.0	41.0
42	32.1295	37.0	31.0	40.0	2.0	41.0
43	31.177	37.0	30.0	40.0	2.0	41.0
44	31.64425	37.0	31.0	40.0	2.0	41.0
45	29.90025	37.0	27.0	40.0	2.0	41.0
46	27.78125	35.0	19.0	39.0	2.0	40.0
47	27.596	34.0	21.0	39.0	2.0	41.0
48	28.04275	35.0	23.0	39.0	2.0	41.0
49	26.5415	34.0	2.0	39.0	2.0	41.0
50	23.1035	31.0	2.0	37.0	2.0	40.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
12	1.0
13	0.0
14	0.0
15	2.0
16	1.0
17	0.0
18	3.0
19	8.0
20	6.0
21	12.0
22	16.0
23	26.0
24	36.0
25	59.0
26	87.0
27	145.0
28	65.0
29	104.0
30	140.0
31	150.0
32	190.0
33	197.0
34	228.0
35	277.0
36	348.0
37	462.0
38	698.0
39	739.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	14.321482223335003	23.960941412118178	43.23985978968452	18.477716574862292
2	27.85	23.5	20.1	28.549999999999997
3	22.175	21.15	23.425	33.25
4	31.900000000000002	27.075	16.45	24.575
5	23.5	38.85	24.099999999999998	13.55
6	28.075	16.475	37.1	18.35
7	20.275000000000002	21.55	24.875	33.300000000000004
8	26.674999999999997	28.775000000000002	18.425	26.125
9	19.625	31.225	31.924999999999997	17.224999999999998
10	24.425	22.900000000000002	28.4	24.275
11	37.65	15.174999999999999	14.524999999999999	32.65
12	19.950000000000003	22.125	26.325	31.6
13	26.275	20.825	33.85	19.05
14	26.625	27.35	24.05	21.975
15	33.2	23.775	25.674999999999997	17.349999999999998
16	21.3	20.474999999999998	23.525	34.699999999999996
17	25.6	23.775	34.075	16.55
18	23.25	19.5	29.925	27.325
19	35.475	15.35	31.275	17.9
20	38.625	17.075000000000003	29.049999999999997	15.25
21	25.874999999999996	19.725	29.049999999999997	25.35
22	29.95	14.374999999999998	41.875	13.8
23	26.85	15.5	38.6	19.05
24	47.125	15.049999999999999	24.325	13.5
25	43.45	24.099999999999998	15.825	16.625
26	28.599999999999998	37.025000000000006	16.625	17.75
27	17.65	40.45	22.525000000000002	19.375
28	16.6	25.174999999999997	39.45	18.775
29	17.7	13.575000000000001	49.925000000000004	18.8
30	14.000000000000002	10.299999999999999	33.175	42.525
31	15.6	9.575	41.949999999999996	32.875
32	30.049999999999997	8.85	23.125	37.974999999999994
33	44.725	14.224999999999998	15.5	25.55
34	51.87500000000001	9.2	20.05	18.875
35	54.125	10.125	19.925	15.825
36	57.99999999999999	11.0	16.425	14.575
37	34.675	16.2	22.95	26.174999999999997
38	26.700000000000003	19.175	13.175	40.949999999999996
39	19.175	24.875	15.675	40.275
40	19.125	40.400000000000006	16.150000000000002	24.325
41	25.974999999999998	40.225	13.925	19.875
42	43.025000000000006	28.749999999999996	16.650000000000002	11.575000000000001
43	41.875	30.25	13.600000000000001	14.274999999999999
44	30.425	41.8	10.875	16.900000000000002
45	22.05	43.0	13.425	21.525
46	17.95	28.675	23.799999999999997	29.575000000000003
47	13.825000000000001	16.525000000000002	33.550000000000004	36.1
48	15.825	13.200000000000001	23.474999999999998	47.5
49	16.45	23.25	16.625	43.675000000000004
50	27.500000000000004	23.925	13.950000000000001	34.625
>>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	0.5
14	1.0
15	0.5
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	3.0
28	6.0
29	5.5
30	5.0
31	9.0
32	13.0
33	18.0
34	23.0
35	40.0
36	57.0
37	74.5
38	92.0
39	91.0
40	90.0
41	86.0
42	82.0
43	109.5
44	137.0
45	186.5
46	236.0
47	250.0
48	264.0
49	360.0
50	456.0
51	584.0
52	712.0
53	604.0
54	496.0
55	449.5
56	403.0
57	349.5
58	296.0
59	222.5
60	149.0
61	117.0
62	85.0
63	152.0
64	219.0
65	136.0
66	53.0
67	36.0
68	19.0
69	24.0
70	29.0
71	42.0
72	55.0
73	30.5
74	6.0
75	6.0
76	6.0
77	5.0
78	4.0
79	3.5
80	3.0
81	3.0
82	3.0
83	1.5
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	51.275000000000006
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.83861530960506	41.449999999999996
2	7.80107264748903	8.0
3	3.1204290589956116	4.8
4	1.999024865919064	4.1000000000000005
5	1.023890784982935	2.625
6	0.7801072647489029	2.4
7	0.5850804485616773	2.1
8	0.48756704046806437	2.0
9	0.29254022428083865	1.35
>10	2.9741589468551926	25.8
>50	0.04875670404680643	2.125
>100	0.04875670404680643	3.25
>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
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	130	3.25	No Hit
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	85	2.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	50	1.25	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	47	1.175	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	31	0.775	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	31	0.775	RNA PCR Primer, Index 1 (100% over 30bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	28	0.7000000000000001	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	24	0.6	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	24	0.6	RNA PCR Primer, Index 7 (97% over 35bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAATCGATCTCGTATGC	21	0.525	RNA PCR Primer, Index 42 (100% over 50bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	21	0.525	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	20	0.5	RNA PCR Primer, Index 1 (100% over 33bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	19	0.475	No Hit
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	18	0.44999999999999996	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	17	0.42500000000000004	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	14	0.35000000000000003	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	14	0.35000000000000003	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAATCGATCTC	13	0.325	RNA PCR Primer, Index 42 (100% over 44bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	13	0.325	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	13	0.325	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	12	0.3	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	12	0.3	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	11	0.27499999999999997	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	10	0.25	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	10	0.25	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	10	0.25	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	10	0.25	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	10	0.25	No Hit
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	9	0.22499999999999998	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	9	0.22499999999999998	No Hit
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	9	0.22499999999999998	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	8	0.2	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	8	0.2	No Hit
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	8	0.2	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	8	0.2	No Hit
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAA	8	0.2	RNA PCR Primer, Index 3 (97% over 36bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
CTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCTA	7	0.17500000000000002	No Hit
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 24bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	7	0.17500000000000002	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	6	0.15	No Hit
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	6	0.15	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	6	0.15	No Hit
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCC	6	0.15	No Hit
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	6	0.15	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	6	0.15	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GAGCAATGATGACCCCAACATGCCATCTGAGTGGCTTTGCTGAAATCCAG	6	0.15	No Hit
GGTCCATGATGAAGCCCATTATCAGTGGACATCTATGGATGAGAAATGCG	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TACCATGATGATAACATAGTTCAGCAGACTTAACTCTGATGAACAATCAT	5	0.125	No Hit
ATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGCCGCGCC	5	0.125	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAT	5	0.125	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAATTCCA	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	5	0.125	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	5	0.125	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	5	0.125	No Hit
AAGAAAGATTGCAAGAACTGCTAATTCTGGAATTCTCGGGTGCCAAGGAA	5	0.125	RNA PCR Primer, Index 1 (100% over 23bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTCAATGATGAAAACCCAATGTCATGAAGAAAAGTGATGACATAAAATTC	5	0.125	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.65	0.0	0.0	0.0
2	0.0	0.65	0.0	0.0	0.0
3	0.0	0.7	0.0	0.0	0.0
4	0.0	0.7	0.0	0.0	0.0
5	0.0	0.7	0.0	0.0	0.0
6	0.0	0.725	0.0	0.0	0.0
7	0.0	1.2	0.0	0.0	0.0
8	0.0	1.35	0.0	0.0	0.0
9	0.0	1.425	0.0	0.0	0.0
10	0.0	1.725	0.0	0.0	0.0
11	0.0	1.9	0.0	0.0	0.0
12	0.0	2.15	0.0	0.0	0.0
13	0.0	2.375	0.0	0.0	0.0
14	0.0	2.6	0.0	0.0	0.0
15	0.0	3.15	0.0	0.0	0.0
16	0.0	4.325	0.0	0.0	0.0
17	0.0	4.925	0.0	0.0	0.0
18	0.0	6.125	0.0	0.0	0.0
19	0.0	6.7	0.0	0.0	0.0
20	0.0	7.475	0.0	0.0	0.0
21	0.0	11.875	0.0	0.0	0.0
22	0.0	20.475	0.0	0.0	0.0
23	0.0	41.85	0.0	0.0	0.0
24	0.0	53.075	0.0	0.0	0.0
25	0.0	57.4	0.0	0.0	0.0
26	0.0	58.55	0.0	0.0	0.0
27	0.0	59.425	0.0	0.0	0.0
28	0.0	60.25	0.0	0.0	0.0
29	0.0	60.475	0.0	0.0	0.0
30	0.0	60.925	0.0	0.0	0.0
31	0.0	61.675	0.0	0.0	0.0
32	0.0	62.45	0.0	0.0	0.0
33	0.0	63.25	0.0	0.0	0.0
34	0.0	68.275	0.0	0.0	0.0
35	0.0	69.375	0.0	0.0	0.0
36	0.0	69.95	0.0	0.0	0.0
37	0.0	70.975	0.0	0.0	0.0
38	0.0	71.525	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CTCTTTT	20	6.952051E-4	44.000004	16
GTGAGTT	20	6.952051E-4	44.000004	18
ACATTCA	40	5.315087E-9	44.000004	2
GCTGTCG	40	5.315087E-9	44.000004	11
GAACCGG	20	6.952051E-4	44.000004	8
AGTGAAC	20	6.952051E-4	44.000004	5
AGGTTGT	20	6.952051E-4	44.000004	10
GTGAACC	20	6.952051E-4	44.000004	6
CTGTCGG	40	5.315087E-9	44.000004	12
TGAACCG	20	6.952051E-4	44.000004	7
TCACAGT	20	6.952051E-4	44.000004	1
CACAGTG	20	6.952051E-4	44.000004	2
TGAGTTG	20	6.952051E-4	44.000004	19
CAGTGAA	20	6.952051E-4	44.000004	4
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	35	1.02281774E-7	44.0	8
GAGGTAG	30	1.9515464E-6	44.0	2
GGTGAGT	30	1.9515464E-6	44.0	17
>>END_MODULE
Read 249381 spots for SRR5030878.sra
Written 249381 spots for SRR5030878.sra
Read 249381 spots for SRR5030878.sra
Written 249381 spots for SRR5030878.sra
Read 249381 spots for SRR5030878.sra
Written 249381 spots for SRR5030878.sra
Read 249381 spots for SRR5030878.sra
Written 249381 spots for SRR5030878.sra
Read 249381 spots for SRR5030878.sra
Written 249381 spots for SRR5030878.sra
Read 249381 spots for SRR5030878.sra
Written 249381 spots for SRR5030878.sra
Read 249381 spots for SRR5030878.sra
Written 249381 spots for SRR5030878.sra
Read 249381 spots for SRR5030878.sra
Written 249381 spots for SRR5030878.sra
Read 249381 spots for SRR5030878.sra
Written 249381 spots for SRR5030878.sra
Read 249381 spots for SRR5030878.sra
Written 249381 spots for SRR5030878.sra
Read 249381 spots for SRR5030878.sra
Written 249381 spots for SRR5030878.sra
Read 249383 spots for SRR5030878.sra
Written 249383 spots for SRR5030878.sra
SRR ids: ['SRR5030878.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_zmlm4mjc
SRR5030878.sra spots: 2992574
blocks: [[1, 249381], [249382, 498762], [498763, 748143], [748144, 997524], [997525, 1246905], [1246906, 1496286], [1496287, 1745667], [1745668, 1995048], [1995049, 2244429], [2244430, 2493810], [2493811, 2743191], [2743192, 2992574]]
SRR5030878 file size 517603
SRR5030878 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030878 SRR5030878_1.fastq
Input file:	SRR5030878_1.fastq
trimmed:	SRR5030878-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 06:34:21 2020 >> started

Wed Mar  4 06:34:23 2020 >> done (1.652s)
2992574 reads processed; of these:
    180 ( 0.01%) short reads filtered out after trimming by size control
      7 ( 0.00%) empty reads filtered out after trimming by size control
2992387 (99.99%) reads available; of these:
 345740 (11.55%) trimmed reads available after processing
2646647 (88.45%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     56	  0.00%
 19	     63	  0.00%
 20	    136	  0.00%
 21	    191	  0.01%
 22	    268	  0.01%
 23	    408	  0.01%
 24	    400	  0.01%
 25	    625	  0.02%
 26	    505	  0.02%
 27	    664	  0.02%
 28	    884	  0.03%
 29	   1268	  0.04%
 30	    932	  0.03%
 31	   1366	  0.05%
 32	   3369	  0.11%
 33	   9818	  0.33%
 34	  21733	  0.73%
 35	   5560	  0.19%
 36	   6136	  0.21%
 37	   3706	  0.12%
 38	   6912	  0.23%
 39	   6805	  0.23%
 40	  12202	  0.41%
 41	   7304	  0.24%
 42	  16015	  0.54%
 43	   8248	  0.28%
 44	  31210	  1.04%
 45	  21969	  0.73%
 46	  22527	  0.75%
 47	  23671	  0.79%
 48	  58570	  1.96%
 49	  72219	  2.41%
 50	2646647	 88.45%
2992387 reads passed initial QC


criterion=sequence-density
sequence-density=71.49
sequence-density-rank=1
fanout-score=21.26
fanout-score-rank=2
prefix-density=73.97
prefix-fanout=20.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAATCGATCTCGTATGCC


criterion=fanout-score
sequence-density=2.91
sequence-density-rank=2
fanout-score=79.34
fanout-score-rank=1
prefix-density=73.45
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAATCGATCTCGTATGCC -o SRR5030878 -
Input file:	STDIN
trimmed:	SRR5030878-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAATCGATCTCGTATGCC
-- 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 06:34:37 2020 >> started

Wed Mar  4 06:34:40 2020 >> done (3.230s)
2909265 reads processed; of these:
 158518 ( 5.45%) short reads filtered out after trimming by size control
  22664 ( 0.78%) empty reads filtered out after trimming by size control
2728083 (93.77%) reads available; of these:
2190961 (80.31%) trimmed reads available after processing
 537122 (19.69%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  15990	  0.59%
 19	  24398	  0.89%
 20	 104551	  3.83%
 21	 243236	  8.92%
 22	 651456	 23.88%
 23	 314909	 11.54%
 24	 148287	  5.44%
 25	  42726	  1.57%
 26	  23031	  0.84%
 27	  19986	  0.73%
 28	  21080	  0.77%
 29	  16940	  0.62%
 30	  23251	  0.85%
 31	  26728	  0.98%
 32	  30182	  1.11%
 33	 148849	  5.46%
 34	  35960	  1.32%
 35	  27165	  1.00%
 36	  38491	  1.41%
 37	  17255	  0.63%
 38	  18869	  0.69%
 39	  19705	  0.72%
 40	  27636	  1.01%
 41	  33962	  1.24%
 42	  41750	  1.53%
 43	  29433	  1.08%
 44	  26750	  0.98%
 45	  29933	  1.10%
 46	  25713	  0.94%
 47	  22228	  0.81%
 48	   8192	  0.30%
 49	  15252	  0.56%
 50	 454189	 16.65%


criterion=sequence-density
sequence-density=5.22
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=0.51
sequence-density-rank=27
fanout-score=11.11
fanout-score-rank=1
prefix-density=5.68
prefix-fanout=1.0
sequence=TGAGCTTGGCTATTT
                                 Started job on |	Mar 04 06:35:02
                             Started mapping on |	Mar 04 06:35:03
                                    Finished on |	Mar 04 06:35:25
       Mapping speed, Million of reads per hour |	460.02

                          Number of input reads |	2811205
                      Average input read length |	31
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1448607
                        Uniquely mapped reads % |	51.53%
                          Average mapped length |	29.99
                       Number of splices: Total |	1724
            Number of splices: Annotated (sjdb) |	245
                       Number of splices: GT/AG |	1603
                       Number of splices: GC/AG |	16
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	104
                      Mismatch rate per base, % |	0.25%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.28
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.09
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	821015
             % of reads mapped to multiple loci |	29.21%
        Number of reads mapped to too many loci |	86073
             % of reads mapped to too many loci |	3.06%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	15.60%
                     % of reads unmapped: other |	0.61%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	541583	541583	541583
N_multimapping	821015	821015	821015
N_noFeature	76837	96597	1095682
N_ambiguous	778229	480716	17220
UnstrandedReadsAssigned:593541 PositiveStrandReadsAssigned:871294 NegativeStrandReadsAssigned:335705
Dataset is classified unstranded
MeadianReadLen=24 20thPercentileLength=22 echo kmer=19
SRR5030878 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: SRR5030878-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,811,205 reads, 630,320 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,119 rounds

 109283 SRR5030878.ke.tsv
  52636 SRR5030878.se.tsv
 161919 total
==> SRR5030878.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

==> SRR5030878.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030878 completed mapping pipeline successfully
