Starting /dee2/code/volunteer_pipeline.sh SRR5030911
    current disk space = 160649461760
    free memory = 73931908 
SRR5030911 SRAfilesize
bba10293c108050f59c97e47da84114f  SRR5030911.sra
SRR5030911.sra file validated
SRR5030911 is single end
SRR5030911 is conventional basespace
SRR5030911 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030911_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	51
>>END_MODULE
>>Per base sequence quality	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.288	33.0	31.0	34.0	31.0	34.0
2	32.74475	34.0	31.0	34.0	31.0	34.0
3	32.6875	34.0	31.0	34.0	31.0	34.0
4	36.1595	37.0	35.0	37.0	35.0	37.0
5	36.216	37.0	37.0	37.0	35.0	37.0
6	35.88825	37.0	35.0	37.0	33.0	37.0
7	36.04825	37.0	35.0	37.0	35.0	37.0
8	36.17275	37.0	35.0	37.0	35.0	37.0
9	37.86575	39.0	38.0	39.0	35.0	39.0
10	37.84625	39.0	38.0	39.0	35.0	39.0
11	37.86525	39.0	38.0	39.0	35.0	39.0
12	37.872	39.0	38.0	39.0	35.0	39.0
13	37.86725	39.0	38.0	39.0	35.0	39.0
14	39.35375	41.0	39.0	41.0	36.0	41.0
15	39.3665	41.0	39.0	41.0	36.0	41.0
16	39.19275	40.0	39.0	41.0	36.0	41.0
17	39.34225	41.0	39.0	41.0	36.0	41.0
18	39.31175	41.0	39.0	41.0	36.0	41.0
19	39.038	40.0	39.0	41.0	36.0	41.0
20	39.2345	40.0	39.0	41.0	36.0	41.0
21	39.193	41.0	39.0	41.0	36.0	41.0
22	39.33075	41.0	39.0	41.0	36.0	41.0
23	39.21875	40.0	39.0	41.0	36.0	41.0
24	38.43575	40.0	38.0	41.0	34.0	41.0
25	38.837	40.0	39.0	41.0	35.0	41.0
26	38.84325	40.0	38.0	41.0	35.0	41.0
27	38.89425	40.0	39.0	41.0	35.0	41.0
28	38.8995	40.0	39.0	41.0	35.0	41.0
29	38.966	41.0	39.0	41.0	35.0	41.0
30	38.7985	40.0	39.0	41.0	35.0	41.0
31	39.129	41.0	39.0	41.0	36.0	41.0
32	39.26775	41.0	39.0	41.0	36.0	41.0
33	38.0175	40.0	38.0	41.0	33.0	41.0
34	37.2965	40.0	38.0	41.0	31.0	41.0
35	32.26325	38.0	30.0	40.0	8.0	41.0
36	28.0785	36.0	15.0	40.0	8.0	41.0
37	28.15375	35.0	19.0	39.0	6.0	40.0
38	31.36975	36.0	29.0	39.0	7.0	40.0
39	30.54775	36.0	26.0	40.0	2.0	41.0
40	31.97625	37.0	31.0	40.0	2.0	41.0
41	29.39075	35.0	23.0	40.0	2.0	41.0
42	31.57325	37.0	31.0	40.0	2.0	41.0
43	29.38875	36.0	24.0	40.0	2.0	41.0
44	30.71575	37.0	30.0	40.0	2.0	41.0
45	27.58675	35.0	9.0	40.0	2.0	41.0
46	25.7395	33.0	2.0	39.0	2.0	41.0
47	26.058	34.0	2.0	39.0	2.0	41.0
48	26.93075	35.0	2.0	40.0	2.0	41.0
49	24.88725	34.0	2.0	40.0	2.0	41.0
50	22.09	29.0	2.0	39.0	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
15	1.0
16	2.0
17	2.0
18	5.0
19	4.0
20	8.0
21	13.0
22	19.0
23	31.0
24	43.0
25	60.0
26	111.0
27	181.0
28	76.0
29	129.0
30	154.0
31	222.0
32	196.0
33	180.0
34	213.0
35	257.0
36	282.0
37	392.0
38	547.0
39	872.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.986980470706059	22.984476715072606	57.41111667501252	11.617426139208813
2	24.725	26.85	22.625	25.8
3	16.025	20.200000000000003	20.45	43.325
4	26.325	37.55	14.174999999999999	21.95
5	22.725	37.9	28.999999999999996	10.375
6	34.75	15.75	39.2	10.299999999999999
7	13.850000000000001	24.625	25.3	36.225
8	24.875	42.675000000000004	13.575000000000001	18.875
9	15.725	40.65	32.550000000000004	11.075
10	18.725	21.75	27.750000000000004	31.775
11	34.050000000000004	11.525	12.65	41.775
12	14.299999999999999	18.275	24.925	42.5
13	19.325	21.3	39.75	19.625
14	39.45	21.45	27.200000000000003	11.899999999999999
15	40.125	20.150000000000002	27.725	12.0
16	12.375	25.474999999999998	22.1	40.050000000000004
17	24.425	24.875	38.15	12.55
18	28.549999999999997	18.525	28.675	24.25
19	35.175	14.274999999999999	33.2	17.349999999999998
20	50.449999999999996	16.400000000000002	21.975	11.175
21	19.900000000000002	25.75	26.125	28.225
22	31.75	10.775	50.025	7.449999999999999
23	23.849999999999998	13.15	51.625	11.375
24	53.449999999999996	11.325000000000001	28.525	6.7
25	57.475	20.925	14.05	7.55
26	29.375	50.64999999999999	12.049999999999999	7.925
27	13.275	56.05	21.875	8.799999999999999
28	7.7	28.075	52.97500000000001	11.25
29	7.3	11.65	62.74999999999999	18.3
30	7.675	5.575	40.8	45.95
31	11.325000000000001	3.5249999999999995	48.55	36.6
32	24.375	4.15	24.775	46.7
33	57.05	5.800000000000001	12.375	24.775
34	72.0	4.625	10.274999999999999	13.100000000000001
35	66.2	5.775	19.75	8.275
36	70.325	6.6000000000000005	13.5	9.575
37	41.4	8.625	23.65	26.325
38	25.75	11.075	11.450000000000001	51.725
39	13.975000000000001	24.6	7.3	54.125
40	12.25	52.425	6.925000000000001	28.4
41	27.224999999999998	52.25	7.074999999999999	13.450000000000001
42	53.0	32.9	6.9	7.199999999999999
43	53.87499999999999	32.675	5.800000000000001	7.6499999999999995
44	31.025000000000002	51.775000000000006	5.925	11.275
45	15.4	51.2	7.75	25.650000000000002
46	8.725	30.5	26.400000000000002	34.375
47	7.124999999999999	13.450000000000001	34.050000000000004	45.375
48	8.225	10.05	23.05	58.675
49	10.825	25.324999999999996	10.75	53.1
50	33.175	26.150000000000002	8.3	32.375
>>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	0.0
18	0.0
19	0.5
20	1.0
21	0.5
22	0.0
23	0.0
24	0.0
25	0.5
26	1.0
27	1.0
28	1.0
29	1.0
30	1.0
31	4.5
32	8.0
33	14.5
34	21.0
35	22.0
36	23.0
37	38.5
38	54.0
39	49.5
40	45.0
41	46.5
42	48.0
43	74.5
44	101.0
45	179.0
46	257.0
47	337.5
48	418.0
49	522.0
50	626.0
51	793.0
52	960.0
53	724.5
54	489.0
55	405.5
56	322.0
57	321.5
58	321.0
59	219.0
60	117.0
61	84.5
62	52.0
63	63.0
64	74.0
65	42.5
66	11.0
67	6.5
68	2.0
69	7.5
70	13.0
71	18.0
72	23.0
73	12.5
74	2.0
75	1.0
76	0.0
77	0.5
78	1.0
79	4.0
80	7.0
81	4.0
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	fail
#Total Deduplicated Percentage	49.15
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.9766022380468	39.800000000000004
2	7.8331637843336726	7.7
3	2.8484231943031535	4.2
4	1.9837232960325535	3.9
5	1.119023397761953	2.75
6	1.0681586978636826	3.15
7	0.40691759918616477	1.4000000000000001
8	0.4577822990844354	1.7999999999999998
9	0.3560528992878942	1.575
>10	2.797558494404883	25.15
>50	0.10172939979654119	3.775
>100	0.050864699898270596	4.8
>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	192	4.8	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	97	2.4250000000000003	RNA PCR Primer, Index 1 (96% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	54	1.35	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	42	1.05	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	38	0.95	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	31	0.775	RNA PCR Primer, Index 1 (96% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	31	0.775	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (96% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	25	0.625	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (96% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 27bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	13	0.325	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	13	0.325	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	11	0.27499999999999997	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (95% over 23bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	10	0.25	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	10	0.25	RNA PCR Primer, Index 1 (100% over 33bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	10	0.25	No Hit
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGC	9	0.22499999999999998	RNA PCR Primer, Index 9 (100% over 50bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	9	0.22499999999999998	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	8	0.2	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACCCCG	8	0.2	RNA PCR Primer, Index 1 (95% over 24bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	8	0.2	RNA PCR Primer, Index 1 (96% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	7	0.17500000000000002	No Hit
CAGCAGCACACTGTGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	6	0.15	RNA PCR Primer, Index 1 (95% over 23bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
AGAGGTAGTAGGTTGCATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	6	0.15	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	6	0.15	No Hit
AGCAGCATTGTACAGGGCTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	5	0.125	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	5	0.125	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	5	0.125	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGCCCAAGGAATCCCG	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
GATACCCGTCGCCGCGCTCTCCCTCTCCCCCCGTCCGCCTCCCGGGCGGG	5	0.125	No Hit
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
>>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	0.25	0.0	0.0	0.0
2	0.0	0.275	0.0	0.0	0.0
3	0.0	0.3	0.0	0.0	0.0
4	0.0	0.3	0.0	0.0	0.0
5	0.0	0.35	0.0	0.0	0.0
6	0.0	0.375	0.0	0.0	0.0
7	0.0	0.525	0.0	0.0	0.0
8	0.0	0.55	0.0	0.0	0.0
9	0.0	0.625	0.0	0.0	0.0
10	0.0	0.75	0.0	0.0	0.0
11	0.0	0.875	0.0	0.0	0.0
12	0.0	1.175	0.0	0.0	0.0
13	0.0	1.45	0.0	0.0	0.0
14	0.0	1.625	0.0	0.0	0.0
15	0.0	2.15	0.0	0.0	0.0
16	0.0	2.575	0.0	0.0	0.0
17	0.0	3.1	0.0	0.0	0.0
18	0.0	3.8	0.0	0.0	0.0
19	0.0	4.275	0.0	0.0	0.0
20	0.0	5.35	0.0	0.0	0.0
21	0.0	9.6	0.0	0.0	0.0
22	0.0	21.3	0.0	0.0	0.0
23	0.0	55.825	0.0	0.0	0.0
24	0.0	73.3	0.0	0.0	0.0
25	0.0	79.35	0.0	0.0	0.0
26	0.0	80.375	0.0	0.0	0.0
27	0.0	80.625	0.0	0.0	0.0
28	0.0	80.825	0.0	0.0	0.0
29	0.0	81.05	0.0	0.0	0.0
30	0.0	81.325	0.0	0.0	0.0
31	0.0	81.775	0.0	0.0	0.0
32	0.0	82.6	0.0	0.0	0.0
33	0.0	83.575	0.0	0.0	0.0
34	0.0	85.075	0.0	0.0	0.0
35	0.0	85.7	0.0	0.0	0.0
36	0.0	86.15	0.0	0.0	0.0
37	0.0	86.55	0.0	0.0	0.0
38	0.0	86.775	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTAGATT	20	6.952051E-4	44.000004	8
ACAGTGA	20	6.952051E-4	44.000004	3
ACCGGTC	20	6.952051E-4	44.000004	10
AACGCTG	65	0.0	44.000004	8
GAGGTAG	40	5.315087E-9	44.000004	2
GGTGAGT	65	0.0	44.000004	17
ACGCTGT	65	0.0	44.000004	9
AACCGGT	20	6.952051E-4	44.000004	9
AATTCCG	20	6.952051E-4	44.000004	44
AGTAGAT	20	6.952051E-4	44.000004	7
TTCAACG	65	0.0	44.000004	5
GGTCTCT	20	6.952051E-4	44.000004	13
GAGCTTG	45	2.728484E-10	44.000004	13
GGATCCG	45	2.728484E-10	44.000004	3
CCGTCTG	45	2.728484E-10	44.000004	7
TCGGATC	45	2.728484E-10	44.000004	1
CATTCAA	65	0.0	44.000004	3
TCAACGC	65	0.0	44.000004	6
CGGATCC	45	2.728484E-10	44.000004	2
GATTGTA	20	6.952051E-4	44.000004	11
>>END_MODULE
Read 295264 spots for SRR5030911.sra
Written 295264 spots for SRR5030911.sra
Read 295264 spots for SRR5030911.sra
Written 295264 spots for SRR5030911.sra
Read 295264 spots for SRR5030911.sra
Written 295264 spots for SRR5030911.sra
Read 295264 spots for SRR5030911.sra
Written 295264 spots for SRR5030911.sra
Read 295264 spots for SRR5030911.sra
Written 295264 spots for SRR5030911.sra
Read 295264 spots for SRR5030911.sra
Written 295264 spots for SRR5030911.sra
Read 295264 spots for SRR5030911.sra
Written 295264 spots for SRR5030911.sra
Read 295264 spots for SRR5030911.sra
Written 295264 spots for SRR5030911.sra
Read 295265 spots for SRR5030911.sra
Written 295265 spots for SRR5030911.sra
Read 295264 spots for SRR5030911.sra
Written 295264 spots for SRR5030911.sra
Read 295264 spots for SRR5030911.sra
Written 295264 spots for SRR5030911.sra
Read 295264 spots for SRR5030911.sra
Written 295264 spots for SRR5030911.sra
SRR ids: ['SRR5030911.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_vsvxt9lp
SRR5030911.sra spots: 3543169
blocks: [[1, 295264], [295265, 590528], [590529, 885792], [885793, 1181056], [1181057, 1476320], [1476321, 1771584], [1771585, 2066848], [2066849, 2362112], [2362113, 2657376], [2657377, 2952640], [2952641, 3247904], [3247905, 3543169]]
SRR5030911 file size 613035
SRR5030911 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030911 SRR5030911_1.fastq
Input file:	SRR5030911_1.fastq
trimmed:	SRR5030911-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 06:42:54 2020 >> started

Wed Mar  4 06:42:57 2020 >> done (2.260s)
3543169 reads processed; of these:
    147 ( 0.00%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
3543013 (100.00%) reads available; of these:
 416342 (11.75%) trimmed reads available after processing
3126671 (88.25%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     47	  0.00%
 19	     62	  0.00%
 20	    129	  0.00%
 21	    175	  0.00%
 22	    323	  0.01%
 23	    437	  0.01%
 24	    321	  0.01%
 25	    457	  0.01%
 26	    410	  0.01%
 27	    569	  0.02%
 28	    736	  0.02%
 29	   1490	  0.04%
 30	    838	  0.02%
 31	   1130	  0.03%
 32	   3139	  0.09%
 33	  10780	  0.30%
 34	  36076	  1.02%
 35	   8095	  0.23%
 36	   9689	  0.27%
 37	   4010	  0.11%
 38	   8940	  0.25%
 39	   6587	  0.19%
 40	  15218	  0.43%
 41	   8245	  0.23%
 42	  22895	  0.65%
 43	   8380	  0.24%
 44	  48781	  1.38%
 45	  24232	  0.68%
 46	  18006	  0.51%
 47	  20161	  0.57%
 48	  79719	  2.25%
 49	  76265	  2.15%
 50	3126671	 88.25%
3543013 reads passed initial QC


criterion=sequence-density
sequence-density=85.38
sequence-density-rank=1
fanout-score=17.83
fanout-score-rank=2
prefix-density=87.66
prefix-fanout=17.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC


criterion=fanout-score
sequence-density=5.06
sequence-density-rank=2
fanout-score=47.65
fanout-score-rank=1
prefix-density=87.67
prefix-fanout=2.8
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC -o SRR5030911 -
Input file:	STDIN
trimmed:	SRR5030911-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC
-- 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 06:43:13 2020 >> started

Wed Mar  4 06:43:17 2020 >> done (4.385s)
3460617 reads processed; of these:
 105713 ( 3.05%) short reads filtered out after trimming by size control
  14086 ( 0.41%) empty reads filtered out after trimming by size control
3340818 (96.54%) reads available; of these:
3036466 (90.89%) trimmed reads available after processing
 304352 ( 9.11%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  18002	  0.54%
 19	  35550	  1.06%
 20	 146502	  4.39%
 21	 410356	 12.28%
 22	1165081	 34.87%
 23	 627298	 18.78%
 24	 210580	  6.30%
 25	  31791	  0.95%
 26	  15038	  0.45%
 27	  15145	  0.45%
 28	  16742	  0.50%
 29	  14034	  0.42%
 30	  22810	  0.68%
 31	  26490	  0.79%
 32	  29831	  0.89%
 33	  51802	  1.55%
 34	  26482	  0.79%
 35	  17001	  0.51%
 36	  27430	  0.82%
 37	  10670	  0.32%
 38	  13565	  0.41%
 39	  12288	  0.37%
 40	  17430	  0.52%
 41	  20343	  0.61%
 42	  26094	  0.78%
 43	  16508	  0.49%
 44	  18996	  0.57%
 45	  16543	  0.50%
 46	  13340	  0.40%
 47	  11330	  0.34%
 48	   5514	  0.17%
 49	   8882	  0.27%
 50	 241350	  7.22%


criterion=sequence-density
sequence-density=5.09
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=22
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.46
sequence-density-rank=31
fanout-score=9.49
fanout-score-rank=1
prefix-density=0.85
prefix-fanout=5.1
sequence=GGAATTCTCGGGGCCCAGG
                                 Started job on |	Mar 04 06:43:38
                             Started mapping on |	Mar 04 06:43:39
                                    Finished on |	Mar 04 06:44:04
       Mapping speed, Million of reads per hour |	492.94

                          Number of input reads |	3423214
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1632313
                        Uniquely mapped reads % |	47.68%
                          Average mapped length |	25.82
                       Number of splices: Total |	1502
            Number of splices: Annotated (sjdb) |	191
                       Number of splices: GT/AG |	1326
                       Number of splices: GC/AG |	23
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	152
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.33
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.19
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1471477
             % of reads mapped to multiple loci |	42.99%
        Number of reads mapped to too many loci |	51773
             % of reads mapped to too many loci |	1.51%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.40%
                     % of reads unmapped: other |	0.41%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	319424	319424	319424
N_multimapping	1471477	1471477	1471477
N_noFeature	63097	75483	1274594
N_ambiguous	873140	563850	11013
UnstrandedReadsAssigned:696076 PositiveStrandReadsAssigned:992980 NegativeStrandReadsAssigned:346706
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5030911 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: SRR5030911-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,423,214 reads, 662,603 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,106 rounds

 109283 SRR5030911.ke.tsv
  52636 SRR5030911.se.tsv
 161919 total
==> SRR5030911.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

==> SRR5030911.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	2
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030911 completed mapping pipeline successfully
