Starting /dee2/code/volunteer_pipeline.sh SRR5030923
    current disk space = 160632045568
    free memory = 73927336 
SRR5030923 SRAfilesize
703714d7d95a3d971ce5170c56d87649  SRR5030923.sra
SRR5030923.sra file validated
SRR5030923 is single end
SRR5030923 is conventional basespace
SRR5030923 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030923_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	32.4135	34.0	31.0	34.0	31.0	34.0
2	32.777	34.0	31.0	34.0	31.0	34.0
3	32.74325	34.0	31.0	34.0	31.0	34.0
4	36.21325	37.0	37.0	37.0	35.0	37.0
5	36.2925	37.0	37.0	37.0	35.0	37.0
6	35.908	37.0	35.0	37.0	35.0	37.0
7	36.12	37.0	35.0	37.0	35.0	37.0
8	36.1835	37.0	36.0	37.0	35.0	37.0
9	37.868	39.0	38.0	39.0	35.0	39.0
10	37.92525	39.0	38.0	39.0	35.0	39.0
11	37.93525	39.0	38.0	39.0	35.0	39.0
12	37.9425	39.0	38.0	39.0	35.0	39.0
13	37.97225	39.0	38.0	39.0	35.0	39.0
14	39.411	41.0	39.0	41.0	36.0	41.0
15	39.4375	41.0	39.0	41.0	36.0	41.0
16	39.16125	40.0	39.0	41.0	36.0	41.0
17	39.37225	41.0	39.0	41.0	36.0	41.0
18	39.3225	41.0	39.0	41.0	36.0	41.0
19	39.187	40.0	39.0	41.0	36.0	41.0
20	39.29375	41.0	39.0	41.0	36.0	41.0
21	39.30475	41.0	39.0	41.0	36.0	41.0
22	39.49875	41.0	39.0	41.0	37.0	41.0
23	39.36575	41.0	39.0	41.0	36.0	41.0
24	38.54875	40.0	38.0	41.0	34.0	41.0
25	38.955	40.0	39.0	41.0	36.0	41.0
26	38.9165	40.0	38.0	41.0	35.0	41.0
27	38.87625	40.0	39.0	41.0	35.0	41.0
28	38.94075	40.0	39.0	41.0	35.0	41.0
29	39.0955	41.0	39.0	41.0	35.0	41.0
30	38.838	40.0	38.0	41.0	35.0	41.0
31	39.0785	41.0	39.0	41.0	35.0	41.0
32	39.2545	41.0	39.0	41.0	36.0	41.0
33	37.824	40.0	38.0	41.0	33.0	41.0
34	37.168	40.0	38.0	41.0	30.0	41.0
35	32.139	38.0	30.0	40.0	8.0	41.0
36	28.49025	37.0	15.0	40.0	8.0	41.0
37	28.4575	35.0	20.0	39.0	6.0	40.0
38	31.531	36.0	30.0	39.0	8.0	40.0
39	30.7565	37.0	27.0	40.0	2.0	41.0
40	32.02575	37.0	31.0	40.0	2.0	41.0
41	29.3945	36.0	24.0	40.0	2.0	41.0
42	31.3355	37.0	30.0	40.0	2.0	41.0
43	29.44475	36.0	25.0	40.0	2.0	41.0
44	30.686	37.0	30.0	40.0	2.0	41.0
45	27.80475	36.0	15.0	40.0	2.0	41.0
46	25.82	33.0	2.0	39.0	2.0	41.0
47	25.9675	34.0	2.0	39.0	2.0	41.0
48	26.89675	35.0	2.0	40.0	2.0	41.0
49	24.7865	34.0	2.0	40.0	2.0	41.0
50	21.68175	28.0	2.0	38.0	2.0	40.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
15	2.0
16	0.0
17	1.0
18	0.0
19	2.0
20	13.0
21	11.0
22	22.0
23	32.0
24	51.0
25	57.0
26	106.0
27	180.0
28	88.0
29	115.0
30	161.0
31	195.0
32	175.0
33	165.0
34	233.0
35	277.0
36	323.0
37	370.0
38	556.0
39	865.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.571535955900776	21.42320220496116	56.75269356051115	12.25256827862691
2	24.775	24.975	23.625	26.625
3	18.5	19.400000000000002	20.375	41.725
4	26.025	36.575	14.774999999999999	22.625
5	21.349999999999998	39.525	27.150000000000002	11.975
6	35.325	16.125	38.074999999999996	10.475
7	16.225	23.974999999999998	25.6	34.2
8	24.95	40.699999999999996	14.174999999999999	20.175
9	17.75	40.050000000000004	31.674999999999997	10.525
10	21.275	19.900000000000002	28.050000000000004	30.775000000000002
11	30.55	14.075	14.299999999999999	41.075
12	16.675	17.125	24.65	41.55
13	19.7	24.2	35.625	20.474999999999998
14	36.475	24.55	26.125	12.85
15	40.075	21.2	26.450000000000003	12.275
16	12.45	27.224999999999998	21.85	38.475
17	22.95	23.825	39.125	14.099999999999998
18	27.800000000000004	20.575	27.925	23.7
19	38.3	14.099999999999998	30.349999999999998	17.25
20	47.775	17.849999999999998	22.975	11.4
21	22.075	24.575	25.2	28.15
22	30.55	11.95	49.325	8.175
23	23.775	14.499999999999998	47.825	13.900000000000002
24	51.275000000000006	13.675	27.450000000000003	7.6
25	55.05	21.65	14.649999999999999	8.649999999999999
26	29.95	47.425	12.4	10.225
27	13.900000000000002	52.800000000000004	23.0	10.299999999999999
28	9.375	28.249999999999996	50.2	12.174999999999999
29	8.450000000000001	12.55	60.85	18.15
30	8.799999999999999	6.4	38.925	45.875
31	13.475000000000001	5.625	46.35	34.55
32	23.7	6.275	23.799999999999997	46.225
33	54.2	6.575	13.975000000000001	25.25
34	67.05	6.1	12.775	14.075
35	63.0	6.2	20.424999999999997	10.375
36	66.75	7.725	13.625000000000002	11.899999999999999
37	40.725	9.75	22.3	27.224999999999998
38	24.474999999999998	12.8	14.000000000000002	48.725
39	17.150000000000002	25.624999999999996	7.775	49.45
40	13.375	49.975	9.6	27.05
41	27.425	48.449999999999996	9.55	14.575
42	51.575	31.825	8.125	8.475000000000001
43	51.475	32.125	7.95	8.450000000000001
44	30.925000000000004	50.224999999999994	6.625	12.225
45	17.5	49.175000000000004	9.075	24.25
46	9.55	30.775000000000002	26.650000000000002	33.025
47	8.5	15.15	33.15	43.2
48	9.525	10.625	22.900000000000002	56.95
49	12.85	25.1	12.425	49.625
50	33.691845922961484	24.137068534267133	7.453726863431716	34.71735867933967
>>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	1.0
10	2.0
11	1.5
12	1.0
13	0.5
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	1.0
20	2.0
21	1.0
22	0.0
23	0.0
24	0.0
25	0.5
26	1.0
27	0.5
28	0.0
29	1.0
30	2.0
31	6.0
32	10.0
33	13.5
34	17.0
35	26.5
36	36.0
37	50.0
38	64.0
39	53.5
40	43.0
41	49.0
42	55.0
43	79.5
44	104.0
45	190.0
46	276.0
47	342.5
48	409.0
49	507.0
50	605.0
51	739.5
52	874.0
53	685.0
54	496.0
55	423.0
56	350.0
57	321.5
58	293.0
59	203.0
60	113.0
61	88.0
62	63.0
63	78.5
64	94.0
65	63.5
66	33.0
67	24.0
68	15.0
69	13.5
70	12.0
71	17.5
72	23.0
73	13.5
74	4.0
75	2.0
76	0.0
77	0.5
78	1.0
79	1.5
80	2.0
81	1.0
82	0.0
83	0.0
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	0.22499999999999998
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	0.05
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	52.175000000000004
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.40249161475802	41.949999999999996
2	8.576904647819838	8.95
3	3.689506468615237	5.775
4	1.2937230474365118	2.7
5	1.3416387158600862	3.5000000000000004
6	0.6229036895064686	1.95
7	0.6708193579300431	2.45
8	0.7187350263536176	3.0
9	0.3833253473885961	1.7999999999999998
>10	2.156205079060853	20.825
>50	0.09583133684714902	3.45
>100	0.04791566842357451	3.65
>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	146	3.65	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	85	2.125	RNA PCR Primer, Index 1 (96% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	53	1.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	38	0.95	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	33	0.8250000000000001	RNA PCR Primer, Index 1 (96% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	28	0.7000000000000001	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGC	19	0.475	RNA PCR Primer, Index 5 (100% over 50bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	18	0.44999999999999996	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	15	0.375	RNA PCR Primer, Index 1 (96% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTC	14	0.35000000000000003	RNA PCR Primer, Index 5 (100% over 44bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	11	0.27499999999999997	No Hit
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	11	0.27499999999999997	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	10	0.25	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	10	0.25	No Hit
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (95% over 23bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAC	9	0.22499999999999998	RNA PCR Primer, Index 5 (100% over 35bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	8	0.2	No Hit
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	8	0.2	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	8	0.2	RNA PCR Primer, Index 1 (100% over 33bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	8	0.2	RNA PCR Primer, Index 1 (96% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (95% over 23bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	7	0.17500000000000002	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	7	0.17500000000000002	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	7	0.17500000000000002	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	6	0.15	No Hit
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	6	0.15	No Hit
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	6	0.15	No Hit
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	6	0.15	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	5	0.125	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTGTGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAATTCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATCCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	5	0.125	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	5	0.125	No Hit
AACATTCAACCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
GAGCAATGATGACCCCAACATGCCATCTGAGTGGCTTTGCTGAAATCCAG	5	0.125	No Hit
>>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	0.5	0.0	0.0	0.0
2	0.0	0.5	0.0	0.0	0.0
3	0.0	0.575	0.0	0.0	0.0
4	0.0	0.575	0.0	0.0	0.0
5	0.0	0.6	0.0	0.0	0.0
6	0.0	0.6	0.0	0.0	0.0
7	0.0	1.0	0.0	0.0	0.0
8	0.0	1.05	0.0	0.0	0.0
9	0.0	1.15	0.0	0.0	0.0
10	0.0	1.2	0.0	0.0	0.0
11	0.0	1.4	0.0	0.0	0.0
12	0.0	1.5	0.0	0.0	0.0
13	0.0	1.675	0.0	0.0	0.0
14	0.0	1.925	0.0	0.0	0.0
15	0.0	2.05	0.0	0.0	0.0
16	0.0	2.525	0.0	0.0	0.0
17	0.0	3.05	0.0	0.0	0.0
18	0.0	3.65	0.0	0.0	0.0
19	0.0	3.925	0.0	0.0	0.0
20	0.0	4.975	0.0	0.0	0.0
21	0.0	9.5	0.0	0.0	0.0
22	0.0	20.275	0.0	0.0	0.0
23	0.0	52.275	0.0	0.0	0.0
24	0.0	68.05	0.0	0.0	0.0
25	0.0	74.125	0.0	0.0	0.0
26	0.0	75.175	0.0	0.0	0.0
27	0.0	75.75	0.0	0.0	0.0
28	0.0	76.175	0.0	0.0	0.0
29	0.0	76.575	0.0	0.0	0.0
30	0.0	76.925	0.0	0.0	0.0
31	0.0	77.4	0.0	0.0	0.0
32	0.0	78.25	0.0	0.0	0.0
33	0.0	79.375	0.0	0.0	0.0
34	0.0	81.125	0.0	0.0	0.0
35	0.0	82.0	0.0	0.0	0.0
36	0.0	82.4	0.0	0.0	0.0
37	0.0	82.95	0.0	0.0	0.0
38	0.0	83.175	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
TCAAGTA	65	0.0	44.000004	2
CTGAGCT	40	5.315087E-9	44.000004	11
TTCAAGT	65	0.0	44.000004	1
AGTAGAT	20	6.952051E-4	44.000004	7
CGGGGGC	90	0.0	44.000004	32
TCGGTGC	20	6.952051E-4	44.000004	31
GAGCTTG	40	5.315087E-9	44.000004	13
GGATCCG	40	5.315087E-9	44.000004	3
CCGTCTG	40	5.315087E-9	44.000004	7
TCGGATC	40	5.315087E-9	44.000004	1
CATTCAA	40	5.315087E-9	44.000004	3
CGGATCC	40	5.315087E-9	44.000004	2
GATTGTA	20	6.952051E-4	44.000004	11
ACATTCA	40	5.315087E-9	44.000004	2
TCTCGGT	20	6.952051E-4	44.000004	29
CAGGGAC	20	6.952051E-4	44.000004	39
ATTGTAT	20	6.952051E-4	44.000004	12
GATCCGT	40	5.315087E-9	44.000004	4
CGGTGCC	20	6.952051E-4	44.000004	32
>>END_MODULE
Read 484072 spots for SRR5030923.sra
Written 484072 spots for SRR5030923.sra
Read 484072 spots for SRR5030923.sra
Written 484072 spots for SRR5030923.sra
Read 484072 spots for SRR5030923.sra
Written 484072 spots for SRR5030923.sra
Read 484072 spots for SRR5030923.sra
Written 484072 spots for SRR5030923.sra
Read 484072 spots for SRR5030923.sra
Written 484072 spots for SRR5030923.sra
Read 484072 spots for SRR5030923.sra
Written 484072 spots for SRR5030923.sra
Read 484072 spots for SRR5030923.sra
Written 484072 spots for SRR5030923.sra
Read 484072 spots for SRR5030923.sra
Written 484072 spots for SRR5030923.sra
Read 484079 spots for SRR5030923.sra
Written 484079 spots for SRR5030923.sra
Read 484072 spots for SRR5030923.sra
Written 484072 spots for SRR5030923.sra
Read 484072 spots for SRR5030923.sra
Written 484072 spots for SRR5030923.sra
Read 484072 spots for SRR5030923.sra
Written 484072 spots for SRR5030923.sra
SRR ids: ['SRR5030923.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_adkjm89u
SRR5030923.sra spots: 5808871
blocks: [[1, 484072], [484073, 968144], [968145, 1452216], [1452217, 1936288], [1936289, 2420360], [2420361, 2904432], [2904433, 3388504], [3388505, 3872576], [3872577, 4356648], [4356649, 4840720], [4840721, 5324792], [5324793, 5808871]]
SRR5030923 file size 1005735
SRR5030923 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030923 SRR5030923_1.fastq
Input file:	SRR5030923_1.fastq
trimmed:	SRR5030923-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 06:45:49 2020 >> started

Wed Mar  4 06:45:52 2020 >> done (2.904s)
5808871 reads processed; of these:
    220 ( 0.00%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
5808642 (100.00%) reads available; of these:
 725963 (12.50%) trimmed reads available after processing
5082679 (87.50%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     54	  0.00%
 19	    103	  0.00%
 20	    171	  0.00%
 21	    253	  0.00%
 22	    475	  0.01%
 23	    565	  0.01%
 24	    555	  0.01%
 25	    761	  0.01%
 26	    669	  0.01%
 27	    898	  0.02%
 28	   1186	  0.02%
 29	   1933	  0.03%
 30	   1423	  0.02%
 31	   1962	  0.03%
 32	   5259	  0.09%
 33	  17826	  0.31%
 34	  58353	  1.00%
 35	  12947	  0.22%
 36	  14853	  0.26%
 37	   6473	  0.11%
 38	  14058	  0.24%
 39	  10724	  0.18%
 40	  24298	  0.42%
 41	  13382	  0.23%
 42	  36466	  0.63%
 43	  14675	  0.25%
 44	  79993	  1.38%
 45	  40807	  0.70%
 46	  33374	  0.57%
 47	  37645	  0.65%
 48	 144201	  2.48%
 49	 149621	  2.58%
 50	5082679	 87.50%
5808642 reads passed initial QC


criterion=sequence-density
sequence-density=81.60
sequence-density-rank=1
fanout-score=18.44
fanout-score-rank=3
prefix-density=84.57
prefix-fanout=17.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCC


criterion=fanout-score
sequence-density=1.93
sequence-density-rank=8
fanout-score=388.00
fanout-score-rank=1
prefix-density=83.87
prefix-fanout=8.9
sequence=GGAATTCTCGGTGCCAAGGA
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -t 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCC -o SRR5030923 -
Input file:	STDIN
trimmed:	SRR5030923-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCC
-- 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 06:46:14 2020 >> started

Wed Mar  4 06:46:23 2020 >> done (9.033s)
5666968 reads processed; of these:
 189100 ( 3.34%) short reads filtered out after trimming by size control
  21172 ( 0.37%) empty reads filtered out after trimming by size control
5456696 (96.29%) reads available; of these:
4844603 (88.78%) trimmed reads available after processing
 612093 (11.22%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  28588	  0.52%
 19	  56313	  1.03%
 20	 230737	  4.23%
 21	 598062	 10.96%
 22	1824746	 33.44%
 23	 928448	 17.01%
 24	 345330	  6.33%
 25	  56423	  1.03%
 26	  27978	  0.51%
 27	  28094	  0.51%
 28	  31258	  0.57%
 29	  24248	  0.44%
 30	  40259	  0.74%
 31	  49040	  0.90%
 32	  53944	  0.99%
 33	 101349	  1.86%
 34	  48803	  0.89%
 35	  33518	  0.61%
 36	  46930	  0.86%
 37	  22504	  0.41%
 38	  28308	  0.52%
 39	  25883	  0.47%
 40	  37735	  0.69%
 41	  45115	  0.83%
 42	  55373	  1.01%
 43	  36587	  0.67%
 44	  39075	  0.72%
 45	  35757	  0.66%
 46	  29516	  0.54%
 47	  22940	  0.42%
 48	  11228	  0.21%
 49	  18995	  0.35%
 50	 493612	  9.05%


criterion=sequence-density
sequence-density=5.82
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=19
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.43
sequence-density-rank=33
fanout-score=9.77
fanout-score-rank=1
prefix-density=0.80
prefix-fanout=5.3
sequence=GGAATTCTCGGGGCCCAGG
                                 Started job on |	Mar 04 06:46:47
                             Started mapping on |	Mar 04 06:46:47
                                    Finished on |	Mar 04 06:47:30
       Mapping speed, Million of reads per hour |	468.70

                          Number of input reads |	5598370
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2806897
                        Uniquely mapped reads % |	50.14%
                          Average mapped length |	27.13
                       Number of splices: Total |	2472
            Number of splices: Annotated (sjdb) |	313
                       Number of splices: GT/AG |	2215
                       Number of splices: GC/AG |	25
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	230
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.25
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	2226941
             % of reads mapped to multiple loci |	39.78%
        Number of reads mapped to too many loci |	110476
             % of reads mapped to too many loci |	1.97%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.54%
                     % of reads unmapped: other |	0.57%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	564532	564532	564532
N_multimapping	2226941	2226941	2226941
N_noFeature	118417	143708	2232416
N_ambiguous	1494717	1010289	20593
UnstrandedReadsAssigned:1193763 PositiveStrandReadsAssigned:1652900 NegativeStrandReadsAssigned:553888
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5030923 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: SRR5030923-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 5,598,370 reads, 1,113,936 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 751 rounds

 109283 SRR5030923.ke.tsv
  52636 SRR5030923.se.tsv
 161919 total
==> SRR5030923.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

==> SRR5030923.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030923 completed mapping pipeline successfully
