Starting /dee2/code/volunteer_pipeline.sh SRR5031077
    current disk space = 160483901440
    free memory = 73933112 
SRR5031077 SRAfilesize
8fd1221085909eb85ae09489f9ed6714  SRR5031077.sra
SRR5031077.sra file validated
SRR5031077 is single end
SRR5031077 is conventional basespace
SRR5031077 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031077_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	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.94175	31.0	31.0	34.0	30.0	34.0
2	32.43025	33.0	31.0	34.0	31.0	34.0
3	32.4235	33.0	31.0	34.0	31.0	34.0
4	36.15025	37.0	35.0	37.0	35.0	37.0
5	36.1535	37.0	35.0	37.0	35.0	37.0
6	36.033	37.0	35.0	37.0	35.0	37.0
7	35.80725	37.0	35.0	37.0	35.0	37.0
8	35.56325	37.0	35.0	37.0	33.0	37.0
9	36.85575	39.0	37.0	39.0	33.0	39.0
10	36.7445	39.0	37.0	39.0	32.0	39.0
11	37.34075	39.0	37.0	39.0	34.0	39.0
12	37.714	39.0	37.0	39.0	35.0	39.0
13	37.3225	39.0	37.0	39.0	35.0	39.0
14	38.59375	40.0	38.0	41.0	34.0	41.0
15	36.986	40.0	37.0	41.0	30.0	41.0
16	36.84375	39.0	36.0	40.0	31.0	41.0
17	36.88425	39.0	37.0	40.0	31.0	41.0
18	38.17075	40.0	37.0	41.0	34.0	41.0
19	38.789	40.0	38.0	41.0	36.0	41.0
20	38.42075	40.0	38.0	41.0	34.0	41.0
21	38.64625	40.0	38.0	41.0	35.0	41.0
22	37.68725	40.0	37.0	41.0	32.0	41.0
23	38.1745	39.0	38.0	40.0	34.0	41.0
24	37.426	39.0	37.0	40.0	32.0	41.0
25	38.3295	40.0	38.0	41.0	34.0	41.0
26	38.0855	40.0	38.0	41.0	34.0	41.0
27	38.17175	40.0	38.0	41.0	34.0	41.0
28	38.3215	40.0	38.0	41.0	34.0	41.0
29	38.423	40.0	38.0	41.0	34.0	41.0
30	38.772	40.0	38.0	41.0	35.0	41.0
31	38.92775	40.0	39.0	41.0	36.0	41.0
32	38.82025	40.0	39.0	41.0	35.0	41.0
33	38.83175	40.0	38.0	41.0	35.0	41.0
34	38.4215	40.0	38.0	41.0	34.0	41.0
35	37.5275	40.0	37.0	41.0	30.0	41.0
36	33.0765	35.0	30.0	39.0	23.0	41.0
37	34.90425	37.0	33.0	38.0	30.0	40.0
38	36.3585	38.0	35.0	39.0	31.0	40.0
39	36.91225	38.0	37.0	40.0	32.0	40.0
40	37.36575	39.0	37.0	40.0	33.0	41.0
41	37.86875	40.0	38.0	40.0	33.0	41.0
42	37.644	40.0	38.0	41.0	32.0	41.0
43	37.678	40.0	37.0	41.0	33.0	41.0
44	36.47775	38.0	35.0	40.0	30.0	41.0
45	36.645	39.0	36.0	40.0	30.0	41.0
46	36.85725	39.0	37.0	40.0	30.0	41.0
47	36.033	39.0	35.0	40.0	29.0	41.0
48	36.9935	40.0	37.0	40.0	31.0	41.0
49	37.28775	40.0	37.0	41.0	32.0	41.0
50	35.34125	38.0	34.0	40.0	28.0	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
6	1.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	1.0
13	3.0
14	0.0
15	0.0
16	2.0
17	0.0
18	1.0
19	4.0
20	2.0
21	4.0
22	8.0
23	7.0
24	7.0
25	15.0
26	15.0
27	16.0
28	21.0
29	37.0
30	43.0
31	65.0
32	86.0
33	94.0
34	182.0
35	259.0
36	464.0
37	722.0
38	1190.0
39	751.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	5.605605605605605	22.12212212212212	62.23723723723724	10.035035035035035
2	23.167375531648737	26.695021265949464	22.66700025018764	27.47060295221416
3	17.549999999999997	17.925	19.5	45.025
4	25.874999999999996	41.225	10.4	22.5
5	19.525000000000002	40.849999999999994	29.9	9.725
6	36.275	16.1	38.1	9.525
7	10.75	25.275	24.175	39.800000000000004
8	23.674999999999997	44.4	11.5	20.424999999999997
9	19.025	41.575	29.575000000000003	9.825000000000001
10	16.75	17.375	28.475	37.4
11	28.975	8.450000000000001	13.05	49.525000000000006
12	13.475000000000001	13.575000000000001	25.525	47.425
13	19.375	21.55	38.85	20.225
14	42.425000000000004	22.525000000000002	25.174999999999997	9.875
15	40.25	18.025	28.999999999999996	12.725
16	11.35	26.974999999999998	19.775000000000002	41.9
17	24.425	19.7	41.85	14.025000000000002
18	30.55	17.775	26.8	24.875
19	39.800000000000004	13.275	30.425	16.5
20	53.625	15.525	20.849999999999998	10.0
21	20.025000000000002	27.025	23.425	29.525000000000002
22	31.125000000000004	10.100000000000001	52.05	6.7250000000000005
23	24.725	10.075000000000001	54.6	10.6
24	57.425000000000004	8.975	27.425	6.175
25	59.775	22.25	12.9	5.075
26	27.975	55.675	10.775	5.575
27	12.475	58.275	23.474999999999998	5.775
28	6.375	25.924999999999997	57.699999999999996	10.0
29	6.45	8.725	65.14999999999999	19.675
30	5.65	3.35	40.65	50.349999999999994
31	10.35	2.725	51.775000000000006	35.15
32	24.55	2.1999999999999997	21.8	51.449999999999996
33	63.14999999999999	3.5249999999999995	11.425	21.9
34	74.875	4.175	9.2	11.75
35	73.475	4.1000000000000005	17.375	5.050000000000001
36	45.225	4.45	41.025	9.3
37	52.15	5.55	19.975	22.325
38	22.25	10.525	10.225	56.99999999999999
39	11.475	23.225	4.95	60.35
40	9.875	57.699999999999996	5.1499999999999995	27.275
41	22.975	59.45	4.9	12.675
42	57.3	31.624999999999996	4.45	6.625
43	60.775	29.599999999999998	4.275	5.35
44	28.925	56.8	3.975	10.299999999999999
45	14.05	58.95	8.5	18.5
46	6.8500000000000005	26.974999999999998	16.825000000000003	49.35
47	5.1499999999999995	11.975	42.8	40.075
48	4.625	9.9	20.325	65.14999999999999
49	8.774999999999999	18.8	10.925	61.5
50	17.724999999999998	43.824999999999996	8.525	29.925
>>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	0.0
26	0.0
27	0.0
28	0.0
29	0.5
30	1.0
31	0.5
32	0.0
33	1.5
34	3.0
35	6.0
36	9.0
37	11.5
38	14.0
39	11.0
40	8.0
41	17.5
42	27.0
43	57.0
44	87.0
45	141.5
46	196.0
47	406.0
48	616.0
49	634.5
50	653.0
51	860.0
52	1067.0
53	770.5
54	474.0
55	429.0
56	384.0
57	328.0
58	272.0
59	167.5
60	63.0
61	50.0
62	37.0
63	38.0
64	39.0
65	28.5
66	18.0
67	13.0
68	8.0
69	6.5
70	5.0
71	9.5
72	14.0
73	7.5
74	1.0
75	0.5
76	0.0
77	1.0
78	2.0
79	1.0
80	0.0
81	0.5
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	0.1
2	0.075
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	37.5
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.86666666666667	28.825
2	10.266666666666667	7.7
3	2.533333333333333	2.85
4	2.466666666666667	3.6999999999999997
5	1.6	3.0
6	0.9333333333333335	2.1
7	0.26666666666666666	0.7000000000000001
8	0.5333333333333333	1.6
9	0.6666666666666667	2.25
>10	3.5333333333333337	26.275
>50	0.06666666666666667	1.8499999999999999
>100	0.26666666666666666	19.15
>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	298	7.449999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	189	4.725	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	148	3.6999999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	131	3.2750000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	74	1.8499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	45	1.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	43	1.075	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	40	1.0	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (96% over 30bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATCGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTACCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	12	0.3	RNA PCR Primer, Index 1 (100% over 33bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 44bp)
TTTGAACCATCACTCGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 35bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTCTAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	8	0.2	No Hit
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTACCCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TAGTGGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGAAGCTTGGACTTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (96% over 26bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGCCTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTGACCTATGAATTGACAGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGC	5	0.125	RNA PCR Primer, Index 1 (100% over 50bp)
AACATTCAACGCTGTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	5	0.125	No Hit
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (96% over 30bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGCCTGGAAGCTTGGACTTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (96% over 26bp)
>>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	0.225	0.0	0.0	0.0
2	0.0	0.25	0.0	0.0	0.0
3	0.0	0.275	0.0	0.0	0.0
4	0.0	0.275	0.0	0.0	0.0
5	0.0	0.275	0.0	0.0	0.0
6	0.0	0.3	0.0	0.0	0.0
7	0.0	0.725	0.0	0.0	0.0
8	0.0	0.775	0.0	0.0	0.0
9	0.0	0.9	0.0	0.0	0.0
10	0.0	1.0	0.0	0.0	0.0
11	0.0	1.125	0.0	0.0	0.0
12	0.0	1.2	0.0	0.0	0.0
13	0.0	1.375	0.0	0.0	0.0
14	0.0	1.5	0.0	0.0	0.0
15	0.0	1.9	0.0	0.0	0.0
16	0.0	2.45	0.0	0.0	0.0
17	0.0	2.925	0.0	0.0	0.0
18	0.0	3.6	0.0	0.0	0.0
19	0.0	4.05	0.0	0.0	0.0
20	0.0	4.675	0.0	0.0	0.0
21	0.0	8.825	0.0	0.0	0.0
22	0.0	22.625	0.0	0.0	0.0
23	0.0	61.95	0.0	0.0	0.0
24	0.0	78.35	0.0	0.0	0.0
25	0.0	84.4	0.0	0.0	0.0
26	0.0	85.375	0.0	0.0	0.0
27	0.0	85.825	0.0	0.0	0.0
28	0.0	86.025	0.0	0.0	0.0
29	0.0	86.3	0.0	0.0	0.0
30	0.0	86.7	0.0	0.0	0.0
31	0.0	87.45	0.0	0.0	0.0
32	0.0	88.25	0.0	0.0	0.0
33	0.0	89.05	0.0	0.0	0.0
34	0.0	90.05	0.0	0.0	0.0
35	0.0	91.025	0.0	0.0	0.0
36	0.0	91.725	0.0	0.0	0.0
37	0.0	92.3	0.0	0.0	0.0
38	0.0	92.425	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACAGTGA	20	6.952051E-4	44.000004	3
ACCGGTC	20	6.952051E-4	44.000004	10
AACGCTG	45	2.728484E-10	44.000004	8
GAGGTAG	20	6.952051E-4	44.000004	2
GGTGAGT	45	2.728484E-10	44.000004	17
AAGTAAT	65	0.0	44.000004	4
TCAAGTA	65	0.0	44.000004	2
ACGCTGT	45	2.728484E-10	44.000004	9
AACCGGT	20	6.952051E-4	44.000004	9
TTCAAGT	65	0.0	44.000004	1
TTCAACG	45	2.728484E-10	44.000004	5
TCGGTGA	45	2.728484E-10	44.000004	15
GGTCTCT	20	6.952051E-4	44.000004	13
GCTGGAA	20	6.952051E-4	44.000004	20
CATTCAA	45	2.728484E-10	44.000004	3
TCAACGC	45	2.728484E-10	44.000004	6
GTGAGTT	20	6.952051E-4	44.000004	18
GAGTTGG	20	6.952051E-4	44.000004	20
GGATAGG	65	0.0	44.000004	14
GAACCGG	20	6.952051E-4	44.000004	8
>>END_MODULE
Read 239822 spots for SRR5031077.sra
Written 239822 spots for SRR5031077.sra
Read 239822 spots for SRR5031077.sra
Written 239822 spots for SRR5031077.sra
Read 239822 spots for SRR5031077.sra
Written 239822 spots for SRR5031077.sra
Read 239822 spots for SRR5031077.sra
Written 239822 spots for SRR5031077.sra
Read 239822 spots for SRR5031077.sra
Written 239822 spots for SRR5031077.sra
Read 239828 spots for SRR5031077.sra
Written 239828 spots for SRR5031077.sra
Read 239822 spots for SRR5031077.sra
Written 239822 spots for SRR5031077.sra
Read 239822 spots for SRR5031077.sra
Written 239822 spots for SRR5031077.sra
Read 239822 spots for SRR5031077.sra
Written 239822 spots for SRR5031077.sra
Read 239822 spots for SRR5031077.sra
Written 239822 spots for SRR5031077.sra
Read 239822 spots for SRR5031077.sra
Written 239822 spots for SRR5031077.sra
Read 239822 spots for SRR5031077.sra
Written 239822 spots for SRR5031077.sra
SRR ids: ['SRR5031077.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_5e3m1g3t
SRR5031077.sra spots: 2877870
blocks: [[1, 239822], [239823, 479644], [479645, 719466], [719467, 959288], [959289, 1199110], [1199111, 1438932], [1438933, 1678754], [1678755, 1918576], [1918577, 2158398], [2158399, 2398220], [2398221, 2638042], [2638043, 2877870]]
SRR5031077 file size 497758
SRR5031077 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031077 SRR5031077_1.fastq
Input file:	SRR5031077_1.fastq
trimmed:	SRR5031077-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 07:19:36 2020 >> started

Wed Mar  4 07:19:38 2020 >> done (2.069s)
2877870 reads processed; of these:
    225 ( 0.01%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
2877636 (99.99%) reads available; of these:
 239903 ( 8.34%) trimmed reads available after processing
2637733 (91.66%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     77	  0.00%
 19	    125	  0.00%
 20	    166	  0.01%
 21	    268	  0.01%
 22	    435	  0.02%
 23	    525	  0.02%
 24	    523	  0.02%
 25	    728	  0.03%
 26	    457	  0.02%
 27	    709	  0.02%
 28	    717	  0.02%
 29	   1785	  0.06%
 30	    723	  0.03%
 31	    768	  0.03%
 32	    944	  0.03%
 33	   2094	  0.07%
 34	   3057	  0.11%
 35	   9407	  0.33%
 36	   4798	  0.17%
 37	   4059	  0.14%
 38	   3436	  0.12%
 39	   3975	  0.14%
 40	   5116	  0.18%
 41	   6016	  0.21%
 42	   7300	  0.25%
 43	  12348	  0.43%
 44	  12350	  0.43%
 45	  16270	  0.57%
 46	  17627	  0.61%
 47	  17559	  0.61%
 48	  52656	  1.83%
 49	  52885	  1.84%
 50	2637733	 91.66%
2877636 reads passed initial QC


criterion=sequence-density
sequence-density=93.97
sequence-density-rank=1
fanout-score=16.68
fanout-score-rank=2
prefix-density=94.82
prefix-fanout=16.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC


criterion=fanout-score
sequence-density=4.11
sequence-density-rank=3
fanout-score=64.91
fanout-score-rank=1
prefix-density=95.39
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC -o SRR5031077 -
Input file:	STDIN
trimmed:	SRR5031077-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC
-- 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 07:19:53 2020 >> started

Wed Mar  4 07:19:57 2020 >> done (3.710s)
2816410 reads processed; of these:
 109496 ( 3.89%) short reads filtered out after trimming by size control
   9429 ( 0.33%) empty reads filtered out after trimming by size control
2697485 (95.78%) reads available; of these:
2654509 (98.41%) trimmed reads available after processing
  42976 ( 1.59%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  15597	  0.58%
 19	  32414	  1.20%
 20	 152873	  5.67%
 21	 357403	 13.25%
 22	1106359	 41.01%
 23	 514968	 19.09%
 24	 180778	  6.70%
 25	  29800	  1.10%
 26	  14117	  0.52%
 27	  13415	  0.50%
 28	  13915	  0.52%
 29	  11014	  0.41%
 30	  18639	  0.69%
 31	  23899	  0.89%
 32	  23103	  0.86%
 33	  35288	  1.31%
 34	  20663	  0.77%
 35	  14183	  0.53%
 36	  15964	  0.59%
 37	   7160	  0.27%
 38	   7356	  0.27%
 39	   6155	  0.23%
 40	   7158	  0.27%
 41	   8977	  0.33%
 42	   9258	  0.34%
 43	   6388	  0.24%
 44	   4942	  0.18%
 45	   5662	  0.21%
 46	   3899	  0.14%
 47	   2784	  0.10%
 48	    576	  0.02%
 49	   1014	  0.04%
 50	  31764	  1.18%


criterion=sequence-density
sequence-density=6.21
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.43
sequence-density-rank=31
fanout-score=18.26
fanout-score-rank=1
prefix-density=7.87
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 07:20:31
                             Started mapping on |	Mar 04 07:20:31
                                    Finished on |	Mar 04 07:20:58
       Mapping speed, Million of reads per hour |	367.83

                          Number of input reads |	2758711
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1317469
                        Uniquely mapped reads % |	47.76%
                          Average mapped length |	22.89
                       Number of splices: Total |	5617
            Number of splices: Annotated (sjdb) |	2403
                       Number of splices: GT/AG |	5530
                       Number of splices: GC/AG |	37
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	48
                      Mismatch rate per base, % |	0.27%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.77
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.07
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1266539
             % of reads mapped to multiple loci |	45.91%
        Number of reads mapped to too many loci |	38847
             % of reads mapped to too many loci |	1.41%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	4.50%
                     % of reads unmapped: other |	0.42%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	174703	174703	174703
N_multimapping	1266539	1266539	1266539
N_noFeature	67435	76857	967327
N_ambiguous	722708	417409	5927
UnstrandedReadsAssigned:527326 PositiveStrandReadsAssigned:823203 NegativeStrandReadsAssigned:344215
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031077 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: SRR5031077-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,758,711 reads, 562,224 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 692 rounds

 109283 SRR5031077.ke.tsv
  52636 SRR5031077.se.tsv
 161919 total
==> SRR5031077.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

==> SRR5031077.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031077 completed mapping pipeline successfully
