Starting /dee2/code/volunteer_pipeline.sh SRR5031062
    current disk space = 160493715456
    free memory = 1054516156 
SRR5031062 SRAfilesize
ee66ba9c603934d829299c4a0ac70223  SRR5031062.sra
SRR5031062.sra file validated
SRR5031062 is single end
SRR5031062 is conventional basespace
SRR5031062 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031062_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	56
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.41275	33.0	31.0	34.0	31.0	34.0
2	32.55725	34.0	31.0	34.0	31.0	34.0
3	32.7025	34.0	31.0	34.0	31.0	34.0
4	36.1935	37.0	35.0	37.0	35.0	37.0
5	36.11125	37.0	35.0	37.0	35.0	37.0
6	35.919	37.0	35.0	37.0	35.0	37.0
7	36.05525	37.0	35.0	37.0	35.0	37.0
8	35.997	37.0	35.0	37.0	35.0	37.0
9	37.67475	39.0	37.0	39.0	35.0	39.0
10	37.673	39.0	37.0	39.0	35.0	39.0
11	37.146	39.0	37.0	39.0	33.0	39.0
12	37.43725	39.0	37.0	39.0	34.0	39.0
13	37.43225	39.0	37.0	39.0	34.0	39.0
14	38.93125	41.0	38.0	41.0	34.0	41.0
15	38.94575	41.0	38.0	41.0	35.0	41.0
16	38.92525	40.0	38.0	41.0	35.0	41.0
17	38.81875	40.0	38.0	41.0	34.0	41.0
18	39.248	41.0	39.0	41.0	36.0	41.0
19	38.64875	40.0	38.0	41.0	34.0	41.0
20	39.08475	41.0	38.0	41.0	36.0	41.0
21	38.43575	40.0	38.0	41.0	33.0	41.0
22	39.01675	40.0	39.0	41.0	36.0	41.0
23	37.968	39.0	37.0	41.0	33.0	41.0
24	38.643	40.0	38.0	41.0	35.0	41.0
25	38.9495	40.0	39.0	41.0	35.0	41.0
26	38.68225	40.0	38.0	41.0	34.0	41.0
27	38.757	40.0	38.0	41.0	35.0	41.0
28	38.81425	40.0	38.0	41.0	35.0	41.0
29	38.42775	40.0	38.0	41.0	34.0	41.0
30	38.47625	40.0	38.0	41.0	34.0	41.0
31	38.60325	40.0	38.0	41.0	34.0	41.0
32	38.46975	40.0	38.0	41.0	34.0	41.0
33	38.54925	40.0	38.0	41.0	34.0	41.0
34	38.74275	40.0	38.0	41.0	35.0	41.0
35	38.1875	40.0	38.0	41.0	33.0	41.0
36	38.04	40.0	38.0	41.0	33.0	41.0
37	37.64725	40.0	37.0	41.0	32.0	41.0
38	36.8475	39.0	37.0	41.0	30.0	41.0
39	37.288	39.0	37.0	41.0	31.0	41.0
40	37.72775	40.0	37.0	41.0	33.0	41.0
41	37.9365	40.0	38.0	41.0	33.0	41.0
42	38.20575	40.0	38.0	41.0	33.0	41.0
43	38.50825	40.0	38.0	41.0	34.0	41.0
44	38.294	40.0	38.0	41.0	34.0	41.0
45	38.05675	40.0	38.0	41.0	33.0	41.0
46	37.96225	40.0	38.0	41.0	33.0	41.0
47	37.55925	40.0	37.0	41.0	32.0	41.0
48	37.119	40.0	37.0	41.0	31.0	41.0
49	37.385	40.0	37.0	41.0	32.0	41.0
50	37.10575	40.0	37.0	41.0	31.0	41.0
>>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
11	1.0
12	0.0
13	0.0
14	0.0
15	0.0
16	3.0
17	0.0
18	0.0
19	1.0
20	5.0
21	5.0
22	2.0
23	4.0
24	10.0
25	14.0
26	7.0
27	18.0
28	37.0
29	40.0
30	51.0
31	60.0
32	65.0
33	103.0
34	162.0
35	172.0
36	256.0
37	450.0
38	625.0
39	1909.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	4.75	8.075000000000001	79.975	7.199999999999999
2	10.370741482965933	12.324649298597194	7.865731462925851	69.43887775551102
3	6.75	6.775	11.825	74.65
4	11.25	11.95	68.425	8.375
5	72.0	11.425	10.8	5.775
6	13.5	4.75	71.325	10.424999999999999
7	7.124999999999999	70.825	8.674999999999999	13.375
8	9.075	12.4	6.875000000000001	71.65
9	7.9	11.325000000000001	72.225	8.55
10	69.1	7.375	11.3	12.225
11	16.400000000000002	63.775000000000006	6.2	13.625000000000002
12	67.45	6.4	11.95	14.2
13	8.725	7.5249999999999995	13.775	69.975
14	14.299999999999999	8.15	67.07499999999999	10.475
15	72.425	8.525	9.85	9.2
16	10.575	7.375	9.725	72.32499999999999
17	14.725	7.575	11.575000000000001	66.125
18	10.575	6.05	9.725	73.65
19	12.45	7.425	11.55	68.575
20	75.725	6.7	11.675	5.8999999999999995
21	12.975	67.15	9.2	10.674999999999999
22	59.375	6.925000000000001	30.0	3.6999999999999997
23	22.6	11.774999999999999	59.199999999999996	6.425
24	51.175000000000004	6.65	38.775	3.4000000000000004
25	62.55	21.075	12.0	4.375
26	39.25	47.725	7.575	5.45
27	11.5	60.875	20.75	6.875000000000001
28	6.800000000000001	36.3	49.625	7.2749999999999995
29	6.8500000000000005	10.25	64.5	18.4
30	5.4	3.5749999999999997	51.87500000000001	39.15
31	6.825	1.925	42.9	48.35
32	23.025000000000002	2.5	33.375	41.099999999999994
33	52.225	3.925	9.775	34.075
34	77.625	3.1	8.3	10.975
35	72.125	3.75	18.65	5.475
36	55.15	4.025	35.6	5.225
37	42.699999999999996	5.0	31.65	20.65
38	34.825	7.025	9.700000000000001	48.449999999999996
39	10.95	20.424999999999997	5.825	62.8
40	7.825	49.65	5.025	37.5
41	21.725	61.8	3.775	12.7
42	50.2	38.65	5.625	5.525
43	63.949999999999996	27.175	3.4000000000000004	5.475
44	40.5	49.6	3.7249999999999996	6.175
45	12.45	61.9	5.975	19.675
46	7.95	36.65	18.2	37.2
47	4.45	11.125	35.65	48.775
48	5.675	6.5	31.125000000000004	56.699999999999996
49	5.975	19.25	10.075000000000001	64.7
50	19.025	35.25	6.275	39.45
>>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	0.0
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	0.0
26	0.0
27	0.5
28	1.0
29	1.5
30	2.0
31	1.5
32	1.0
33	1.5
34	2.0
35	3.0
36	4.0
37	9.5
38	15.0
39	11.5
40	8.0
41	9.5
42	11.0
43	22.0
44	33.0
45	44.5
46	56.0
47	112.0
48	168.0
49	171.5
50	175.0
51	260.5
52	346.0
53	323.0
54	300.0
55	366.5
56	433.0
57	1294.0
58	2155.0
59	1116.0
60	77.0
61	59.5
62	42.0
63	51.5
64	61.0
65	35.5
66	10.0
67	8.5
68	7.0
69	13.0
70	19.0
71	39.5
72	60.0
73	33.0
74	6.0
75	5.0
76	4.0
77	2.0
78	0.0
79	0.5
80	1.0
81	0.5
82	0.0
83	1.0
84	2.0
85	1.0
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	0.0
2	0.2
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	22.6
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.10619469026548	17.2
2	10.508849557522124	4.75
3	2.9867256637168142	2.025
4	2.3230088495575223	2.1
5	1.7699115044247788	2.0
6	0.6637168141592921	0.8999999999999999
7	0.6637168141592921	1.05
8	0.5530973451327433	1.0
9	0.6637168141592921	1.35
>10	2.9867256637168142	13.200000000000001
>50	0.33185840707964603	5.75
>100	0.22123893805309736	14.799999999999999
>500	0.22123893805309736	33.875
>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
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	711	17.775	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	644	16.1	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	421	10.525	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	171	4.275	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	87	2.175	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	74	1.8499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	69	1.725	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	33	0.8250000000000001	No Hit
TCCTGTACTGAGCTGCCCCGAGTTTTGGAATTCTCGGGTGCCAAGGAACT	31	0.775	RNA PCR Primer, Index 1 (100% over 25bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	26	0.65	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
TCCTGTACTGAGCTGCCCCGATTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	21	0.525	RNA PCR Primer, Index 7 (100% over 35bp)
TATTGCACTTGTCCCGGCCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	16	0.4	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	15	0.375	No Hit
TATTGCACTTGTCCCGGCCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TCGTTTCCCGGGCGGCGCACCATGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAATGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTATTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	13	0.325	RNA PCR Primer, Index 1 (100% over 33bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGC	11	0.27499999999999997	RNA PCR Primer, Index 34 (100% over 50bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	10	0.25	RNA PCR Primer, Index 1 (100% over 33bp)
TCCTGTACTGAGCTGCCCCGAGTATTGGAATTCTCGGGTGCCAAGGAACT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 25bp)
TATTGCACTTGTCCCGGCCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	9	0.22499999999999998	No Hit
TATTGCACTTGTCCCGGCCTGTTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCCTGTACTGAGCTGCCCCGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTC	8	0.2	RNA PCR Primer, Index 34 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTGGAATTCTCGGGTGC	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TATTGCACTTGTCCCGGCCTGTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAAAAAGCTCGTAGTTGGATCTTGGGATGGAATTCTCGGGTGCCAAGG	5	0.125	Illumina Small RNA Adapter 2 (100% over 21bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGAGGTAGTAGGTTGCATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	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	0.275	0.0	0.0	0.0
2	0.0	0.3	0.0	0.0	0.0
3	0.0	0.325	0.0	0.0	0.0
4	0.0	0.325	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	0.6	0.0	0.0	0.0
8	0.0	0.7	0.0	0.0	0.0
9	0.0	0.7	0.0	0.0	0.0
10	0.0	0.8	0.0	0.0	0.0
11	0.0	0.875	0.0	0.0	0.0
12	0.0	0.975	0.0	0.0	0.0
13	0.0	1.0	0.0	0.0	0.0
14	0.0	1.175	0.0	0.0	0.0
15	0.0	1.4	0.0	0.0	0.0
16	0.0	2.075	0.0	0.0	0.0
17	0.0	2.2	0.0	0.0	0.0
18	0.0	2.975	0.0	0.0	0.0
19	0.0	3.25	0.0	0.0	0.0
20	0.0	3.675	0.0	0.0	0.0
21	0.0	5.775	0.0	0.0	0.0
22	0.0	20.6	0.0	0.0	0.0
23	0.0	50.85	0.0	0.0	0.0
24	0.0	78.75	0.0	0.0	0.0
25	0.0	84.675	0.0	0.0	0.0
26	0.0	86.25	0.0	0.0	0.0
27	0.0	86.575	0.0	0.0	0.0
28	0.0	86.85	0.0	0.0	0.0
29	0.0	87.1	0.0	0.0	0.0
30	0.0	87.45	0.0	0.0	0.0
31	0.0	87.975	0.0	0.0	0.0
32	0.0	88.75	0.0	0.0	0.0
33	0.0	89.175	0.0	0.0	0.0
34	0.0	90.6	0.0	0.0	0.0
35	0.0	90.925	0.0	0.0	0.0
36	0.0	91.575	0.0	0.0	0.0
37	0.0	91.975	0.0	0.0	0.0
38	0.0	92.225	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TAAACAT	20	6.952051E-4	44.000004	3
AAACATC	20	6.952051E-4	44.000004	4
GAGTTGG	80	0.0	44.000004	20
CCCCGAG	160	0.0	44.000004	16
CCCGATG	65	0.0	44.000004	17
AGTTGGA	80	0.0	44.000004	21
CGATGGA	65	0.0	44.000004	19
CCGATGG	65	0.0	44.000004	18
TGTAAAC	20	6.952051E-4	44.000004	1
GTAAACA	20	6.952051E-4	44.000004	2
AACATCC	20	6.952051E-4	44.000004	5
GAGTGGA	50	1.4551915E-11	44.0	20
AGTGGAA	50	1.4551915E-11	44.0	21
CCCCGAT	70	0.0	44.0	16
CCCGAGT	125	0.0	44.0	17
CCCGAGA	35	1.02281774E-7	44.0	17
CGAGTTG	70	0.0	44.0	19
CCGAGTT	75	0.0	44.0	18
CCGAGTG	50	1.4551915E-11	44.0	18
CGAGTGG	50	1.4551915E-11	44.0	19
>>END_MODULE
Read 126331 spots for SRR5031062.sra
Written 126331 spots for SRR5031062.sra
Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
Written 126331 spots for SRR5031062.sra
Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
Written 126331 spots for SRR5031062.sra
Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
Written 126331 spots for SRR5031062.sra
Read 126331 spots for SRR5031062.sra
Written 126331 spots for SRR5031062.sra
Read 126331 spots for SRR5031062.sra
Written 126331 spots for SRR5031062.sra
Read 126331 spots for SRR5031062.sra
Written 126331 spots for SRR5031062.sra
Read 126331 spots for SRR5031062.sra
Written 126331 spots for SRR5031062.sra
Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
Written 126331 spots for SRR5031062.sra
Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
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Read 126331 spots for SRR5031062.sra
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Read 126348 spots for SRR5031062.sra
Written 126348 spots for SRR5031062.sra
SRR ids: ['SRR5031062.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_6ji4ossw
SRR5031062.sra spots: 6063905
blocks: [[1, 126331], [126332, 252662], [252663, 378993], [378994, 505324], [505325, 631655], [631656, 757986], [757987, 884317], [884318, 1010648], [1010649, 1136979], [1136980, 1263310], [1263311, 1389641], [1389642, 1515972], [1515973, 1642303], [1642304, 1768634], [1768635, 1894965], [1894966, 2021296], [2021297, 2147627], [2147628, 2273958], [2273959, 2400289], [2400290, 2526620], [2526621, 2652951], [2652952, 2779282], [2779283, 2905613], [2905614, 3031944], [3031945, 3158275], [3158276, 3284606], [3284607, 3410937], [3410938, 3537268], [3537269, 3663599], [3663600, 3789930], [3789931, 3916261], [3916262, 4042592], [4042593, 4168923], [4168924, 4295254], [4295255, 4421585], [4421586, 4547916], [4547917, 4674247], [4674248, 4800578], [4800579, 4926909], [4926910, 5053240], [5053241, 5179571], [5179572, 5305902], [5305903, 5432233], [5432234, 5558564], [5558565, 5684895], [5684896, 5811226], [5811227, 5937557], [5937558, 6063905]]
SRR5031062 file size 1049960
SRR5031062 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5031062 SRR5031062_1.fastq
Input file:	SRR5031062_1.fastq
trimmed:	SRR5031062-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- end quality threshold (-q):		10
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ (auto detected)
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	32
Wed Mar  4 07:16:21 2020 >> started

Wed Mar  4 07:16:24 2020 >> done (3.471s)
6063905 reads processed; of these:
    405 ( 0.01%) short reads filtered out after trimming by size control
     17 ( 0.00%) empty reads filtered out after trimming by size control
6063483 (99.99%) reads available; of these:
 284095 ( 4.69%) trimmed reads available after processing
5779388 (95.31%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    100	  0.00%
 19	    146	  0.00%
 20	    246	  0.00%
 21	    541	  0.01%
 22	    857	  0.01%
 23	   1021	  0.02%
 24	    888	  0.01%
 25	    987	  0.02%
 26	    759	  0.01%
 27	   1030	  0.02%
 28	   1433	  0.02%
 29	   3557	  0.06%
 30	   1465	  0.02%
 31	   1382	  0.02%
 32	   1357	  0.02%
 33	   1597	  0.03%
 34	   2838	  0.05%
 35	   5124	  0.08%
 36	   5284	  0.09%
 37	   4619	  0.08%
 38	   4303	  0.07%
 39	   4428	  0.07%
 40	   5236	  0.09%
 41	   6125	  0.10%
 42	   8005	  0.13%
 43	  13014	  0.21%
 44	  18589	  0.31%
 45	  22364	  0.37%
 46	  26715	  0.44%
 47	  37405	  0.62%
 48	  55449	  0.91%
 49	  47231	  0.78%
 50	5779388	 95.31%
6063483 reads passed initial QC


criterion=sequence-density
sequence-density=92.37
sequence-density-rank=1
fanout-score=8.93
fanout-score-rank=3
prefix-density=93.46
prefix-fanout=8.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGCC


criterion=fanout-score
sequence-density=0.67
sequence-density-rank=16
fanout-score=451.84
fanout-score-rank=1
prefix-density=93.74
prefix-fanout=3.2
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 48 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGCC -o SRR5031062 -
Input file:	STDIN
trimmed:	SRR5031062-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGCC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Unknown format (auto detected)
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	32
Wed Mar  4 07:16:52 2020 >> started

Wed Mar  4 07:17:01 2020 >> done (9.003s)
5933086 reads processed; of these:
 180995 ( 3.05%) short reads filtered out after trimming by size control
  20710 ( 0.35%) empty reads filtered out after trimming by size control
5731381 (96.60%) reads available; of these:
5564731 (97.09%) trimmed reads available after processing
 166650 ( 2.91%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  19557	  0.34%
 19	  31087	  0.54%
 20	 121856	  2.13%
 21	 869999	 15.18%
 22	1863114	 32.51%
 23	1675144	 29.23%
 24	 344725	  6.01%
 25	 104920	  1.83%
 26	  26908	  0.47%
 27	  16123	  0.28%
 28	  17415	  0.30%
 29	  22828	  0.40%
 30	  35299	  0.62%
 31	  37413	  0.65%
 32	  33409	  0.58%
 33	  68913	  1.20%
 34	  34551	  0.60%
 35	  33826	  0.59%
 36	  24809	  0.43%
 37	  14472	  0.25%
 38	  15071	  0.26%
 39	  13616	  0.24%
 40	  18732	  0.33%
 41	  21451	  0.37%
 42	  22076	  0.39%
 43	  19939	  0.35%
 44	  13571	  0.24%
 45	  27114	  0.47%
 46	  21862	  0.38%
 47	  15475	  0.27%
 48	   1616	  0.03%
 49	   1703	  0.03%
 50	 142787	  2.49%


criterion=sequence-density
sequence-density=4.01
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=TATTGCACTTGTCCCGGCCTGTA


criterion=fanout-score
sequence-density=0.20
sequence-density-rank=32
fanout-score=302.00
fanout-score-rank=1
prefix-density=60.61
prefix-fanout=1.0
sequence=AGCTGCCCCGATTT
                                 Started job on |	Mar 04 07:17:42
                             Started mapping on |	Mar 04 07:17:42
                                    Finished on |	Mar 04 07:18:18
       Mapping speed, Million of reads per hour |	586.18

                          Number of input reads |	5861778
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1125405
                        Uniquely mapped reads % |	19.20%
                          Average mapped length |	24.62
                       Number of splices: Total |	16489
            Number of splices: Annotated (sjdb) |	258
                       Number of splices: GT/AG |	16404
                       Number of splices: GC/AG |	36
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	47
                      Mismatch rate per base, % |	0.36%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.71
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.13
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	4289657
             % of reads mapped to multiple loci |	73.18%
        Number of reads mapped to too many loci |	76102
             % of reads mapped to too many loci |	1.30%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.97%
                     % of reads unmapped: other |	0.35%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	446716	446716	446716
N_multimapping	4289657	4289657	4289657
N_noFeature	91268	116930	892642
N_ambiguous	638107	476911	9820
UnstrandedReadsAssigned:396030 PositiveStrandReadsAssigned:531564 NegativeStrandReadsAssigned:222943
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031062 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: SRR5031062-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 5,861,778 reads, 358,619 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,125 rounds

 109283 SRR5031062.ke.tsv
  52636 SRR5031062.se.tsv
 161919 total
==> SRR5031062.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

==> SRR5031062.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031062 completed mapping pipeline successfully
