Starting /dee2/code/volunteer_pipeline.sh SRR5031009
    current disk space = 160544620544
    free memory = 56712760 
SRR5031009 SRAfilesize
ddc477bcdc56bdadeb1faa06b409d63f  SRR5031009.sra
SRR5031009.sra file validated
SRR5031009 is single end
SRR5031009 is conventional basespace
SRR5031009 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031009_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	52
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.32425	33.0	31.0	34.0	31.0	34.0
2	32.54175	34.0	31.0	34.0	31.0	34.0
3	32.53625	34.0	31.0	34.0	31.0	34.0
4	36.12	37.0	35.0	37.0	35.0	37.0
5	36.1155	37.0	35.0	37.0	35.0	37.0
6	35.8935	37.0	35.0	37.0	35.0	37.0
7	35.988	37.0	35.0	37.0	35.0	37.0
8	36.0595	37.0	35.0	37.0	35.0	37.0
9	37.6465	39.0	37.0	39.0	35.0	39.0
10	37.574	39.0	37.0	39.0	35.0	39.0
11	37.19825	39.0	37.0	39.0	33.0	39.0
12	37.585	39.0	37.0	39.0	35.0	39.0
13	37.5115	39.0	37.0	39.0	34.0	39.0
14	39.0195	40.0	38.0	41.0	35.0	41.0
15	38.897	40.0	38.0	41.0	35.0	41.0
16	38.944	40.0	38.0	41.0	35.0	41.0
17	39.02875	40.0	38.0	41.0	35.0	41.0
18	38.97375	40.0	38.0	41.0	35.0	41.0
19	38.7845	40.0	38.0	41.0	35.0	41.0
20	38.797	40.0	38.0	41.0	35.0	41.0
21	38.8335	40.0	38.0	41.0	34.0	41.0
22	38.721	40.0	38.0	41.0	34.0	41.0
23	38.49025	40.0	38.0	41.0	34.0	41.0
24	38.74275	40.0	38.0	41.0	35.0	41.0
25	38.95125	40.0	38.0	41.0	35.0	41.0
26	38.77475	40.0	38.0	41.0	35.0	41.0
27	38.933	40.0	39.0	41.0	35.0	41.0
28	38.83225	40.0	38.0	41.0	35.0	41.0
29	38.56	40.0	38.0	41.0	34.0	41.0
30	38.67875	40.0	38.0	41.0	34.0	41.0
31	38.7625	40.0	38.0	41.0	34.0	41.0
32	38.7325	40.0	38.0	41.0	34.0	41.0
33	38.43175	40.0	38.0	41.0	34.0	41.0
34	38.413	40.0	38.0	41.0	34.0	41.0
35	38.28575	40.0	38.0	41.0	34.0	41.0
36	38.02525	40.0	37.0	41.0	33.0	41.0
37	37.4785	40.0	37.0	41.0	31.0	41.0
38	37.69875	40.0	37.0	41.0	33.0	41.0
39	37.91525	40.0	38.0	41.0	33.0	41.0
40	37.979	40.0	38.0	41.0	33.0	41.0
41	38.203	40.0	38.0	41.0	34.0	41.0
42	38.0585	40.0	38.0	41.0	33.0	41.0
43	37.7415	40.0	37.0	41.0	33.0	41.0
44	37.793	40.0	38.0	41.0	33.0	41.0
45	37.73325	40.0	37.0	41.0	33.0	41.0
46	37.56575	40.0	37.0	41.0	33.0	41.0
47	37.07925	40.0	37.0	41.0	31.0	41.0
48	36.91875	40.0	36.0	41.0	31.0	41.0
49	36.88075	40.0	36.0	41.0	31.0	41.0
50	36.40325	39.0	35.0	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
12	1.0
13	0.0
14	1.0
15	0.0
16	2.0
17	1.0
18	1.0
19	0.0
20	3.0
21	5.0
22	6.0
23	8.0
24	5.0
25	6.0
26	8.0
27	16.0
28	30.0
29	42.0
30	45.0
31	59.0
32	83.0
33	107.0
34	127.0
35	203.0
36	275.0
37	466.0
38	648.0
39	1852.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.775	23.150000000000002	55.400000000000006	13.675
2	25.420326223337515	27.202007528230865	21.656210790464243	25.72145545796738
3	18.575	18.375	20.674999999999997	42.375
4	28.4	38.2	11.625	21.775
5	21.2	38.75	28.999999999999996	11.05
6	35.325	15.299999999999999	37.45	11.924999999999999
7	12.4	24.775	23.375	39.45
8	24.224999999999998	40.625	13.575000000000001	21.575
9	18.45	37.7	30.349999999999998	13.5
10	18.45	21.325	25.8	34.425
11	32.25	10.825	14.649999999999999	42.275
12	17.2	15.174999999999999	25.174999999999997	42.449999999999996
13	22.0	20.95	38.550000000000004	18.5
14	39.300000000000004	22.075	24.4	14.224999999999998
15	38.925	20.974999999999998	28.875	11.225
16	12.45	24.224999999999998	23.799999999999997	39.525
17	26.275	21.5	38.95	13.275
18	30.65	18.025	26.625	24.7
19	40.25	13.750000000000002	30.049999999999997	15.950000000000001
20	52.925	16.75	20.275000000000002	10.05
21	21.65	27.125	24.175	27.05
22	34.25	12.975	45.4	7.375
23	23.575	12.75	49.45	14.224999999999998
24	52.425	12.475	28.825	6.275
25	56.05	21.975	14.05	7.925
26	30.675	48.05	11.95	9.325
27	13.8	54.1	21.05	11.05
28	9.225	26.974999999999998	50.724999999999994	13.075000000000001
29	10.0	11.225	61.9	16.875
30	9.375	4.3	37.974999999999994	48.35
31	13.225000000000001	3.5749999999999997	48.15	35.05
32	25.025	4.575	23.025000000000002	47.375
33	55.800000000000004	6.65	12.075	25.474999999999998
34	67.45	6.825	12.950000000000001	12.775
35	70.525	6.25	15.725	7.5
36	41.949999999999996	6.75	39.975	11.325000000000001
37	46.0	9.1	22.625	22.275
38	24.25	14.274999999999999	12.15	49.325
39	13.075000000000001	21.9	7.55	57.475
40	12.9	50.05	8.924999999999999	28.125
41	21.775	56.25	7.425	14.549999999999999
42	50.775000000000006	32.574999999999996	7.425	9.225
43	58.775	26.525	6.3	8.4
44	31.525	49.75	6.875000000000001	11.85
45	15.325	56.675	11.475	16.525000000000002
46	9.85	27.725	16.8	45.625
47	6.625	13.925	40.775	38.675
48	7.475	11.450000000000001	22.775000000000002	58.3
49	10.475	17.224999999999998	12.85	59.45
50	15.975	41.15	10.674999999999999	32.2
>>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	0.5
18	1.0
19	0.5
20	0.0
21	0.5
22	1.0
23	1.0
24	1.0
25	0.5
26	0.0
27	0.0
28	0.0
29	1.5
30	3.0
31	5.0
32	7.0
33	8.5
34	10.0
35	11.5
36	13.0
37	14.5
38	16.0
39	20.0
40	24.0
41	32.0
42	40.0
43	78.5
44	117.0
45	166.0
46	215.0
47	421.0
48	627.0
49	619.0
50	611.0
51	830.0
52	1049.0
53	675.5
54	302.0
55	345.5
56	389.0
57	334.0
58	279.0
59	171.0
60	63.0
61	49.0
62	35.0
63	62.5
64	90.0
65	56.0
66	22.0
67	15.0
68	8.0
69	11.5
70	15.0
71	34.5
72	54.0
73	28.0
74	2.0
75	1.0
76	0.0
77	0.0
78	0.0
79	1.5
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	0.0
2	0.375
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	34.925
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.51682176091626	26.025
2	10.379384395132426	7.249999999999999
3	4.08017179670723	4.275
4	3.0064423765211163	4.2
5	1.4316392269148175	2.5
6	0.5726556907659269	1.2
7	0.5010737294201861	1.225
8	0.7158196134574087	2.0
9	0.5726556907659269	1.7999999999999998
>10	3.650680028632784	25.624999999999996
>50	0.28632784538296346	5.8999999999999995
>100	0.28632784538296346	18.0
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	245	6.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	192	4.8	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	156	3.9	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	127	3.175	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	61	1.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	58	1.4500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	53	1.325	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	48	1.2	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	40	1.0	RNA PCR Primer, Index 7 (100% over 35bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	40	1.0	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	38	0.95	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	28	0.7000000000000001	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGC	23	0.575	RNA PCR Primer, Index 29 (100% over 50bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	20	0.5	RNA PCR Primer, Index 1 (100% over 33bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTC	16	0.4	RNA PCR Primer, Index 29 (100% over 44bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	12	0.3	No Hit
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	11	0.27499999999999997	No Hit
TTCAAGTAATCCAGGATAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	10	0.25	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 31bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	9	0.22499999999999998	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TTCAAGTAATCCAGGATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	6	0.15	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTGGACTTGGAGTCAGAAGGCATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	5	0.125	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	5	0.125	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CAGCAGCACACTGTGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGAATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
>>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	0.625	0.0	0.0	0.0
2	0.0	0.625	0.0	0.0	0.0
3	0.0	0.65	0.0	0.0	0.0
4	0.0	0.725	0.0	0.0	0.0
5	0.0	0.725	0.0	0.0	0.0
6	0.0	0.75	0.0	0.0	0.0
7	0.0	1.4	0.0	0.0	0.0
8	0.0	1.5	0.0	0.0	0.0
9	0.0	1.5	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	2.175	0.0	0.0	0.0
13	0.0	2.25	0.0	0.0	0.0
14	0.0	2.4	0.0	0.0	0.0
15	0.0	2.55	0.0	0.0	0.0
16	0.0	4.0	0.0	0.0	0.0
17	0.0	4.6	0.0	0.0	0.0
18	0.0	5.625	0.0	0.0	0.0
19	0.0	6.2	0.0	0.0	0.0
20	0.0	7.325	0.0	0.0	0.0
21	0.0	12.625	0.0	0.0	0.0
22	0.0	23.1	0.0	0.0	0.0
23	0.0	56.875	0.0	0.0	0.0
24	0.0	73.725	0.0	0.0	0.0
25	0.0	79.525	0.0	0.0	0.0
26	0.0	80.45	0.0	0.0	0.0
27	0.0	80.85	0.0	0.0	0.0
28	0.0	81.3	0.0	0.0	0.0
29	0.0	81.8	0.0	0.0	0.0
30	0.0	82.225	0.0	0.0	0.0
31	0.0	83.15	0.0	0.0	0.0
32	0.0	84.15	0.0	0.0	0.0
33	0.0	85.25	0.0	0.0	0.0
34	0.0	87.225	0.0	0.0	0.0
35	0.0	87.9	0.0	0.0	0.0
36	0.0	88.325	0.0	0.0	0.0
37	0.0	88.875	0.0	0.0	0.0
38	0.0	89.3	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ATCCCCG	20	6.952051E-4	44.000004	8
GAGTGGA	20	6.952051E-4	44.000004	20
ACTGAGC	20	6.952051E-4	44.000004	7
GTACTGA	20	6.952051E-4	44.000004	5
CCTGTAC	20	6.952051E-4	44.000004	2
CATCCCC	20	6.952051E-4	44.000004	7
GAGCTTG	20	6.952051E-4	44.000004	13
GGATCCG	20	6.952051E-4	44.000004	3
CCGTCTG	20	6.952051E-4	44.000004	7
GAGCTGC	20	6.952051E-4	44.000004	10
TCGGATC	20	6.952051E-4	44.000004	1
CGGATCC	20	6.952051E-4	44.000004	2
GTGAGTG	20	6.952051E-4	44.000004	18
ACATCCC	20	6.952051E-4	44.000004	6
TGCCCCG	20	6.952051E-4	44.000004	14
CCCCGAC	20	6.952051E-4	44.000004	10
GCTGCCC	20	6.952051E-4	44.000004	12
GATCCGT	20	6.952051E-4	44.000004	4
CTGGAAG	20	6.952051E-4	44.000004	16
CCCGACT	20	6.952051E-4	44.000004	11
>>END_MODULE
Read 509879 spots for SRR5031009.sra
Written 509879 spots for SRR5031009.sra
Read 509879 spots for SRR5031009.sra
Written 509879 spots for SRR5031009.sra
Read 509879 spots for SRR5031009.sra
Written 509879 spots for SRR5031009.sra
Read 509879 spots for SRR5031009.sra
Written 509879 spots for SRR5031009.sra
Read 509879 spots for SRR5031009.sra
Written 509879 spots for SRR5031009.sra
Read 509879 spots for SRR5031009.sra
Written 509879 spots for SRR5031009.sra
Read 509879 spots for SRR5031009.sra
Written 509879 spots for SRR5031009.sra
Read 509889 spots for SRR5031009.sra
Written 509889 spots for SRR5031009.sra
Read 509879 spots for SRR5031009.sra
Written 509879 spots for SRR5031009.sra
Read 509879 spots for SRR5031009.sra
Written 509879 spots for SRR5031009.sra
Read 509879 spots for SRR5031009.sra
Written 509879 spots for SRR5031009.sra
Read 509879 spots for SRR5031009.sra
Written 509879 spots for SRR5031009.sra
SRR ids: ['SRR5031009.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_uc8elqia
SRR5031009.sra spots: 6118558
blocks: [[1, 509879], [509880, 1019758], [1019759, 1529637], [1529638, 2039516], [2039517, 2549395], [2549396, 3059274], [3059275, 3569153], [3569154, 4079032], [4079033, 4588911], [4588912, 5098790], [5098791, 5608669], [5608670, 6118558]]
SRR5031009 file size 1059433
SRR5031009 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031009 SRR5031009_1.fastq
Input file:	SRR5031009_1.fastq
trimmed:	SRR5031009-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 07:05:26 2020 >> started

Wed Mar  4 07:05:29 2020 >> done (3.736s)
6118558 reads processed; of these:
    315 ( 0.01%) short reads filtered out after trimming by size control
      7 ( 0.00%) empty reads filtered out after trimming by size control
6118236 (99.99%) reads available; of these:
 331127 ( 5.41%) trimmed reads available after processing
5787109 (94.59%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    112	  0.00%
 19	    138	  0.00%
 20	    258	  0.00%
 21	    429	  0.01%
 22	    735	  0.01%
 23	    752	  0.01%
 24	    773	  0.01%
 25	   1046	  0.02%
 26	    805	  0.01%
 27	   1160	  0.02%
 28	   1358	  0.02%
 29	   2831	  0.05%
 30	   1471	  0.02%
 31	   1491	  0.02%
 32	   1641	  0.03%
 33	   2170	  0.04%
 34	   2779	  0.05%
 35	   5719	  0.09%
 36	   4862	  0.08%
 37	   5435	  0.09%
 38	   5024	  0.08%
 39	   5471	  0.09%
 40	   6290	  0.10%
 41	   7003	  0.11%
 42	   9590	  0.16%
 43	  13827	  0.23%
 44	  17556	  0.29%
 45	  22250	  0.36%
 46	  30094	  0.49%
 47	  38590	  0.63%
 48	  66101	  1.08%
 49	  73366	  1.20%
 50	5787109	 94.59%
6118236 reads passed initial QC


criterion=sequence-density
sequence-density=88.64
sequence-density-rank=1
fanout-score=18.69
fanout-score-rank=1
prefix-density=90.15
prefix-fanout=18.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCC


criterion=fanout-score
sequence-density=88.64
sequence-density-rank=1
fanout-score=18.69
fanout-score-rank=1
prefix-density=90.15
prefix-fanout=18.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCC -o SRR5031009 -
Input file:	STDIN
trimmed:	SRR5031009-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCC
-- 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 07:05:51 2020 >> started

Wed Mar  4 07:06:01 2020 >> done (9.479s)
5980748 reads processed; of these:
 298767 ( 5.00%) short reads filtered out after trimming by size control
  33018 ( 0.55%) empty reads filtered out after trimming by size control
5648963 (94.45%) reads available; of these:
5425125 (96.04%) trimmed reads available after processing
 223838 ( 3.96%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  30979	  0.55%
 19	  70958	  1.26%
 20	 290867	  5.15%
 21	 682139	 12.08%
 22	1975438	 34.97%
 23	1001054	 17.72%
 24	 350573	  6.21%
 25	  60697	  1.07%
 26	  31653	  0.56%
 27	  31351	  0.55%
 28	  35135	  0.62%
 29	  28589	  0.51%
 30	  48292	  0.85%
 31	  61159	  1.08%
 32	  67682	  1.20%
 33	 156996	  2.78%
 34	  55283	  0.98%
 35	  33481	  0.59%
 36	  36018	  0.64%
 37	  27000	  0.48%
 38	  29150	  0.52%
 39	  28067	  0.50%
 40	  38639	  0.68%
 41	  50630	  0.90%
 42	  53991	  0.96%
 43	  43115	  0.76%
 44	  36763	  0.65%
 45	  41439	  0.73%
 46	  31820	  0.56%
 47	  23123	  0.41%
 48	   2379	  0.04%
 49	   4403	  0.08%
 50	 190100	  3.37%


criterion=sequence-density
sequence-density=10.88
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=19
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.44
sequence-density-rank=30
fanout-score=15.99
fanout-score-rank=1
prefix-density=6.98
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 07:06:23
                             Started mapping on |	Mar 04 07:06:24
                                    Finished on |	Mar 04 07:07:11
       Mapping speed, Million of reads per hour |	443.22

                          Number of input reads |	5786451
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2751942
                        Uniquely mapped reads % |	47.56%
                          Average mapped length |	24.25
                       Number of splices: Total |	3000
            Number of splices: Annotated (sjdb) |	380
                       Number of splices: GT/AG |	2770
                       Number of splices: GC/AG |	23
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	207
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.75
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.12
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	2366495
             % of reads mapped to multiple loci |	40.90%
        Number of reads mapped to too many loci |	141033
             % of reads mapped to too many loci |	2.44%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.35%
                     % of reads unmapped: other |	0.76%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	668014	668014	668014
N_multimapping	2366495	2366495	2366495
N_noFeature	124140	150450	2059495
N_ambiguous	1465985	872442	23120
UnstrandedReadsAssigned:1161817 PositiveStrandReadsAssigned:1729050 NegativeStrandReadsAssigned:669327
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031009 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: SRR5031009-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 5,786,451 reads, 1,118,858 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,166 rounds

 109283 SRR5031009.ke.tsv
  52636 SRR5031009.se.tsv
 161919 total
==> SRR5031009.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

==> SRR5031009.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031009 completed mapping pipeline successfully
