Starting /dee2/code/volunteer_pipeline.sh SRR5031080
    current disk space = 160480772096
    free memory = 73935800 
SRR5031080 SRAfilesize
2de625440404b4bd0f44efa9a89f63d4  SRR5031080.sra
SRR5031080.sra file validated
SRR5031080 is single end
SRR5031080 is conventional basespace
SRR5031080 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031080_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	32.127	33.0	31.0	34.0	30.0	34.0
2	32.5185	34.0	31.0	34.0	31.0	34.0
3	32.4885	34.0	31.0	34.0	31.0	34.0
4	36.20425	37.0	35.0	37.0	35.0	37.0
5	36.1515	37.0	35.0	37.0	35.0	37.0
6	36.09525	37.0	35.0	37.0	35.0	37.0
7	35.91225	37.0	35.0	37.0	35.0	37.0
8	35.7945	37.0	35.0	37.0	35.0	37.0
9	37.0585	39.0	37.0	39.0	33.0	39.0
10	37.0205	39.0	37.0	39.0	33.0	39.0
11	37.54525	39.0	37.0	39.0	35.0	39.0
12	37.732	39.0	37.0	39.0	35.0	39.0
13	37.3135	39.0	37.0	39.0	34.0	39.0
14	38.62425	40.0	38.0	41.0	34.0	41.0
15	37.35525	40.0	37.0	41.0	31.0	41.0
16	36.4885	39.0	36.0	40.0	29.0	41.0
17	36.80775	39.0	36.0	41.0	31.0	41.0
18	38.1855	40.0	37.0	41.0	34.0	41.0
19	38.84975	40.0	38.0	41.0	36.0	41.0
20	38.58	40.0	38.0	41.0	35.0	41.0
21	38.81025	40.0	38.0	41.0	35.0	41.0
22	37.72025	40.0	37.0	41.0	32.0	41.0
23	38.157	39.0	38.0	40.0	34.0	41.0
24	37.8395	40.0	37.0	41.0	33.0	41.0
25	38.45875	40.0	38.0	41.0	34.0	41.0
26	38.1315	40.0	38.0	41.0	34.0	41.0
27	38.36075	40.0	38.0	41.0	34.0	41.0
28	38.571	40.0	38.0	41.0	34.0	41.0
29	38.74575	40.0	39.0	41.0	35.0	41.0
30	38.9725	40.0	39.0	41.0	35.0	41.0
31	39.02475	40.0	39.0	41.0	35.0	41.0
32	38.98625	40.0	39.0	41.0	35.0	41.0
33	38.89625	40.0	39.0	41.0	35.0	41.0
34	38.6365	40.0	39.0	41.0	35.0	41.0
35	37.87625	40.0	37.0	41.0	31.0	41.0
36	33.44525	35.0	30.0	40.0	23.0	41.0
37	35.03825	37.0	33.0	39.0	30.0	40.0
38	36.5225	38.0	35.0	39.0	31.0	40.0
39	36.984	39.0	37.0	40.0	33.0	40.0
40	37.4655	39.0	37.0	40.0	33.0	41.0
41	37.81675	40.0	38.0	40.0	34.0	41.0
42	37.66825	40.0	38.0	41.0	33.0	41.0
43	37.7855	40.0	38.0	41.0	33.0	41.0
44	36.72775	39.0	36.0	40.0	31.0	41.0
45	37.02375	39.0	37.0	40.0	31.0	41.0
46	37.18425	40.0	37.0	40.0	31.0	41.0
47	36.33075	39.0	36.0	40.0	30.0	41.0
48	37.346	40.0	37.0	40.0	33.0	41.0
49	37.52	40.0	38.0	41.0	33.0	41.0
50	35.69775	38.0	35.0	40.0	30.0	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
11	1.0
12	0.0
13	0.0
14	0.0
15	2.0
16	0.0
17	2.0
18	0.0
19	3.0
20	6.0
21	4.0
22	6.0
23	7.0
24	10.0
25	7.0
26	7.0
27	17.0
28	22.0
29	37.0
30	38.0
31	63.0
32	85.0
33	107.0
34	177.0
35	223.0
36	393.0
37	708.0
38	1201.0
39	874.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	5.026256564141035	23.43085771442861	60.86521630407602	10.677669417354338
2	21.827284105131415	27.909887359198997	20.95118898623279	29.311639549436798
3	15.475	17.474999999999998	18.575	48.475
4	24.0	38.875	11.0	26.125
5	20.375	36.725	32.0	10.9
6	38.824999999999996	13.0	37.525	10.65
7	9.625	27.35	24.95	38.074999999999996
8	26.75	42.0	11.475	19.775000000000002
9	17.65	44.45	28.4	9.5
10	16.150000000000002	19.2	26.974999999999998	37.675
11	31.45	9.2	12.525	46.825
12	14.124999999999998	12.425	24.075	49.375
13	19.400000000000002	18.9	40.175	21.525
14	41.449999999999996	21.425	25.55	11.575000000000001
15	38.824999999999996	17.25	30.45	13.475000000000001
16	11.75	26.875	19.475	41.9
17	25.275	21.125	39.375	14.224999999999998
18	28.9	17.474999999999998	27.55	26.075
19	39.050000000000004	12.45	30.375000000000004	18.125
20	54.025	14.75	22.75	8.475000000000001
21	21.525	26.0	24.7	27.775
22	31.424999999999997	9.725	52.2	6.65
23	22.775000000000002	11.075	56.75	9.4
24	57.325	9.0	28.599999999999998	5.075
25	62.025	20.625	11.975	5.375
26	29.849999999999998	54.800000000000004	9.85	5.5
27	11.450000000000001	60.75000000000001	21.45	6.35
28	6.875000000000001	27.3	56.875	8.95
29	6.35	8.924999999999999	66.8	17.925
30	6.550000000000001	3.0	40.975	49.475
31	9.825000000000001	2.6	51.24999999999999	36.325
32	23.525	3.2750000000000004	22.875	50.324999999999996
33	61.0	4.425	10.9	23.674999999999997
34	76.075	4.2	9.15	10.575
35	75.125	4.3	15.8	4.775
36	45.2	4.875	41.475	8.450000000000001
37	51.2	6.175	21.725	20.9
38	24.0	10.7	9.225	56.074999999999996
39	10.75	21.675	5.050000000000001	62.525
40	9.775	56.325	4.875	29.025000000000002
41	21.224999999999998	62.275000000000006	4.5	12.0
42	56.474999999999994	32.85	4.55	6.125
43	62.975	26.8	4.1000000000000005	6.125
44	30.675	55.85	3.9	9.575
45	12.725	62.425	7.75	17.1
46	5.825	28.199999999999996	16.125	49.85
47	4.15	11.475	44.0	40.375
48	5.075	8.975	22.3	63.65
49	8.35	17.45	10.15	64.05
50	16.900000000000002	43.65	7.925	31.525
>>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	0.5
18	1.0
19	0.5
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	0.5
30	1.0
31	2.0
32	3.0
33	3.0
34	3.0
35	5.5
36	8.0
37	10.5
38	13.0
39	17.0
40	21.0
41	17.5
42	14.0
43	50.5
44	87.0
45	136.0
46	185.0
47	377.0
48	569.0
49	598.5
50	628.0
51	887.0
52	1146.0
53	773.0
54	400.0
55	403.5
56	407.0
57	351.0
58	295.0
59	196.5
60	98.0
61	63.5
62	29.0
63	31.5
64	34.0
65	33.5
66	33.0
67	19.0
68	5.0
69	5.5
70	6.0
71	8.5
72	11.0
73	6.5
74	2.0
75	1.0
76	0.0
77	0.5
78	1.0
79	0.5
80	0.0
81	0.0
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	0.025
2	0.125
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	36.199999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.48342541436463	27.325
2	10.151933701657459	7.35
3	3.9364640883977895	4.275
4	2.209944751381215	3.2
5	1.3812154696132597	2.5
6	0.9668508287292817	2.1
7	0.7596685082872928	1.925
8	0.7596685082872928	2.1999999999999997
9	0.48342541436464087	1.575
>10	3.4530386740331496	24.4
>50	0.13812154696132595	3.225
>100	0.2762430939226519	19.925
>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	255	6.375	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	219	5.475	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	181	4.5249999999999995	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	142	3.55	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	76	1.9	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	53	1.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	38	0.95	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 30bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	32	0.8	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	30	0.75	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTACCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTG	21	0.525	RNA PCR Primer, Index 2 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	15	0.375	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCCGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATCGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 30bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGCCCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTCACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGGGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
TTTGAACCATCACTCGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGCCTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	5	0.125	No Hit
TGAGGTAGGAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGC	5	0.125	RNA PCR Primer, Index 4 (100% over 50bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCCATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTC	5	0.125	RNA PCR Primer, Index 4 (100% over 44bp)
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTACCTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTCTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>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	0.325	0.0	0.0	0.0
2	0.0	0.325	0.0	0.0	0.0
3	0.0	0.375	0.0	0.0	0.0
4	0.0	0.375	0.0	0.0	0.0
5	0.0	0.4	0.0	0.0	0.0
6	0.0	0.475	0.0	0.0	0.0
7	0.0	0.625	0.0	0.0	0.0
8	0.0	0.75	0.0	0.0	0.0
9	0.0	0.85	0.0	0.0	0.0
10	0.0	1.0	0.0	0.0	0.0
11	0.0	1.15	0.0	0.0	0.0
12	0.0	1.275	0.0	0.0	0.0
13	0.0	1.375	0.0	0.0	0.0
14	0.0	1.6	0.0	0.0	0.0
15	0.0	1.95	0.0	0.0	0.0
16	0.0	2.875	0.0	0.0	0.0
17	0.0	3.45	0.0	0.0	0.0
18	0.0	4.325	0.0	0.0	0.0
19	0.0	4.575	0.0	0.0	0.0
20	0.0	5.6	0.0	0.0	0.0
21	0.0	9.55	0.0	0.0	0.0
22	0.0	22.225	0.0	0.0	0.0
23	0.0	61.9	0.0	0.0	0.0
24	0.0	80.5	0.0	0.0	0.0
25	0.0	86.125	0.0	0.0	0.0
26	0.0	86.875	0.0	0.0	0.0
27	0.0	87.25	0.0	0.0	0.0
28	0.0	87.625	0.0	0.0	0.0
29	0.0	87.9	0.0	0.0	0.0
30	0.0	88.4	0.0	0.0	0.0
31	0.0	89.075	0.0	0.0	0.0
32	0.0	89.5	0.0	0.0	0.0
33	0.0	90.325	0.0	0.0	0.0
34	0.0	91.55	0.0	0.0	0.0
35	0.0	92.2	0.0	0.0	0.0
36	0.0	92.55	0.0	0.0	0.0
37	0.0	92.975	0.0	0.0	0.0
38	0.0	93.175	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGAGACC	45	2.728484E-10	44.000004	5
CTCGACT	20	6.952051E-4	44.000004	11
ATCCCCG	20	6.952051E-4	44.000004	8
ATCCTCG	20	6.952051E-4	44.000004	8
GAGGTAG	20	6.952051E-4	44.000004	2
TCCTCGA	20	6.952051E-4	44.000004	9
GGTGAGT	20	6.952051E-4	44.000004	17
ACGCTGT	20	6.952051E-4	44.000004	9
AATCCAG	45	2.728484E-10	44.000004	8
TCGACTG	20	6.952051E-4	44.000004	12
CTGAGAC	45	2.728484E-10	44.000004	4
TAAACAT	45	2.728484E-10	44.000004	3
ATCCAGG	40	5.315087E-9	44.000004	9
AAACATC	45	2.728484E-10	44.000004	4
AGGATAG	45	2.728484E-10	44.000004	13
CATCCTC	20	6.952051E-4	44.000004	7
TCGGTGA	20	6.952051E-4	44.000004	15
CCTCGAC	20	6.952051E-4	44.000004	10
CATCCCC	20	6.952051E-4	44.000004	7
ATAGGCT	40	5.315087E-9	44.000004	16
>>END_MODULE
Read 240844 spots for SRR5031080.sra
Written 240844 spots for SRR5031080.sra
Read 240844 spots for SRR5031080.sra
Written 240844 spots for SRR5031080.sra
Read 240844 spots for SRR5031080.sra
Written 240844 spots for SRR5031080.sra
Read 240844 spots for SRR5031080.sra
Written 240844 spots for SRR5031080.sra
Read 240844 spots for SRR5031080.sra
Written 240844 spots for SRR5031080.sra
Read 240844 spots for SRR5031080.sra
Written 240844 spots for SRR5031080.sra
Read 240844 spots for SRR5031080.sra
Written 240844 spots for SRR5031080.sra
Read 240844 spots for SRR5031080.sra
Written 240844 spots for SRR5031080.sra
Read 240844 spots for SRR5031080.sra
Written 240844 spots for SRR5031080.sra
Read 240845 spots for SRR5031080.sra
Written 240845 spots for SRR5031080.sra
Read 240844 spots for SRR5031080.sra
Written 240844 spots for SRR5031080.sra
Read 240844 spots for SRR5031080.sra
Written 240844 spots for SRR5031080.sra
SRR ids: ['SRR5031080.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_knbk5t2d
SRR5031080.sra spots: 2890129
blocks: [[1, 240844], [240845, 481688], [481689, 722532], [722533, 963376], [963377, 1204220], [1204221, 1445064], [1445065, 1685908], [1685909, 1926752], [1926753, 2167596], [2167597, 2408440], [2408441, 2649284], [2649285, 2890129]]
SRR5031080 file size 499861
SRR5031080 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031080 SRR5031080_1.fastq
Input file:	SRR5031080_1.fastq
trimmed:	SRR5031080-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 07:19:50 2020 >> started

Wed Mar  4 07:19:52 2020 >> done (1.695s)
2890129 reads processed; of these:
    162 ( 0.01%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
2889958 (99.99%) reads available; of these:
 222867 ( 7.71%) trimmed reads available after processing
2667091 (92.29%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     39	  0.00%
 19	     79	  0.00%
 20	    134	  0.00%
 21	    268	  0.01%
 22	    419	  0.01%
 23	    493	  0.02%
 24	    488	  0.02%
 25	    713	  0.02%
 26	    457	  0.02%
 27	    650	  0.02%
 28	    832	  0.03%
 29	   1808	  0.06%
 30	    709	  0.02%
 31	    729	  0.03%
 32	    993	  0.03%
 33	   2059	  0.07%
 34	   3045	  0.11%
 35	   9573	  0.33%
 36	   4897	  0.17%
 37	   4174	  0.14%
 38	   3398	  0.12%
 39	   3742	  0.13%
 40	   4727	  0.16%
 41	   5740	  0.20%
 42	   6764	  0.23%
 43	  11230	  0.39%
 44	  11357	  0.39%
 45	  16159	  0.56%
 46	  15821	  0.55%
 47	  16232	  0.56%
 48	  49450	  1.71%
 49	  45688	  1.58%
 50	2667091	 92.29%
2889958 reads passed initial QC


criterion=sequence-density
sequence-density=93.59
sequence-density-rank=1
fanout-score=16.73
fanout-score-rank=2
prefix-density=94.45
prefix-fanout=16.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCC


criterion=fanout-score
sequence-density=3.93
sequence-density-rank=2
fanout-score=67.27
fanout-score-rank=1
prefix-density=94.79
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCC -o SRR5031080 -
Input file:	STDIN
trimmed:	SRR5031080-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCC
-- 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 07:20:08 2020 >> started

Wed Mar  4 07:20:12 2020 >> done (4.561s)
2828470 reads processed; of these:
 113037 ( 4.00%) short reads filtered out after trimming by size control
   9389 ( 0.33%) empty reads filtered out after trimming by size control
2706044 (95.67%) reads available; of these:
2658897 (98.26%) trimmed reads available after processing
  47147 ( 1.74%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  15227	  0.56%
 19	  32347	  1.20%
 20	 145167	  5.36%
 21	 350382	 12.95%
 22	1117122	 41.28%
 23	 532078	 19.66%
 24	 179286	  6.63%
 25	  29368	  1.09%
 26	  13850	  0.51%
 27	  13018	  0.48%
 28	  14578	  0.54%
 29	  10912	  0.40%
 30	  17659	  0.65%
 31	  22179	  0.82%
 32	  23980	  0.89%
 33	  34932	  1.29%
 34	  18912	  0.70%
 35	  11741	  0.43%
 36	  12878	  0.48%
 37	   6599	  0.24%
 38	   6748	  0.25%
 39	   6061	  0.22%
 40	   8419	  0.31%
 41	  10153	  0.38%
 42	  10060	  0.37%
 43	   7014	  0.26%
 44	   5150	  0.19%
 45	   5927	  0.22%
 46	   4155	  0.15%
 47	   3025	  0.11%
 48	    617	  0.02%
 49	   1062	  0.04%
 50	  35438	  1.31%


criterion=sequence-density
sequence-density=12.46
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.36
sequence-density-rank=39
fanout-score=33.49
fanout-score-rank=1
prefix-density=11.96
prefix-fanout=1.0
sequence=AGTAATCCAGGCTAGGCTT
                                 Started job on |	Mar 04 07:20:33
                             Started mapping on |	Mar 04 07:20:33
                                    Finished on |	Mar 04 07:21:00
       Mapping speed, Million of reads per hour |	369.00

                          Number of input reads |	2767532
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1312099
                        Uniquely mapped reads % |	47.41%
                          Average mapped length |	23.01
                       Number of splices: Total |	7086
            Number of splices: Annotated (sjdb) |	2709
                       Number of splices: GT/AG |	6989
                       Number of splices: GC/AG |	34
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	61
                      Mismatch rate per base, % |	0.29%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.73
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.04
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1275001
             % of reads mapped to multiple loci |	46.07%
        Number of reads mapped to too many loci |	36512
             % of reads mapped to too many loci |	1.32%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	4.80%
                     % of reads unmapped: other |	0.40%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	180432	180432	180432
N_multimapping	1275001	1275001	1275001
N_noFeature	66443	77031	992583
N_ambiguous	728579	454465	5900
UnstrandedReadsAssigned:517077 PositiveStrandReadsAssigned:780603 NegativeStrandReadsAssigned:313616
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031080 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: SRR5031080-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,767,532 reads, 564,744 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,103 rounds

 109283 SRR5031080.ke.tsv
  52636 SRR5031080.se.tsv
 161919 total
==> SRR5031080.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

==> SRR5031080.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031080 completed mapping pipeline successfully
