Starting /dee2/code/volunteer_pipeline.sh SRR5031083
    current disk space = 160497844224
    free memory = 73954772 
SRR5031083 SRAfilesize
7b662077957759110dc775a1c140e061  SRR5031083.sra
SRR5031083.sra file validated
SRR5031083 is single end
SRR5031083 is conventional basespace
SRR5031083 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031083_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	32.1745	33.0	31.0	34.0	30.0	34.0
2	32.55775	34.0	31.0	34.0	31.0	34.0
3	32.519	34.0	31.0	34.0	31.0	34.0
4	36.186	37.0	35.0	37.0	35.0	37.0
5	36.20175	37.0	35.0	37.0	35.0	37.0
6	36.05275	37.0	35.0	37.0	35.0	37.0
7	35.884	37.0	35.0	37.0	35.0	37.0
8	35.837	37.0	35.0	37.0	35.0	37.0
9	37.12075	39.0	37.0	39.0	33.0	39.0
10	36.917	39.0	37.0	39.0	33.0	39.0
11	37.443	39.0	37.0	39.0	34.0	39.0
12	37.72875	39.0	37.0	39.0	35.0	39.0
13	37.3195	39.0	37.0	39.0	35.0	39.0
14	38.62275	40.0	38.0	41.0	34.0	41.0
15	37.31275	40.0	37.0	41.0	31.0	41.0
16	36.49625	39.0	36.0	40.0	30.0	41.0
17	36.67625	39.0	36.0	40.0	31.0	41.0
18	38.17625	40.0	37.0	41.0	34.0	41.0
19	38.72775	40.0	38.0	41.0	35.0	41.0
20	38.48325	40.0	38.0	41.0	34.0	41.0
21	38.7185	40.0	38.0	41.0	35.0	41.0
22	37.676	39.0	37.0	40.0	32.0	41.0
23	38.20225	39.0	38.0	40.0	34.0	41.0
24	37.6435	39.0	37.0	40.0	32.0	41.0
25	38.3385	40.0	38.0	41.0	34.0	41.0
26	37.92875	40.0	37.0	41.0	33.0	41.0
27	38.2	40.0	38.0	41.0	34.0	41.0
28	38.445	40.0	38.0	41.0	34.0	41.0
29	38.67325	40.0	38.0	41.0	35.0	41.0
30	38.84825	40.0	38.0	41.0	35.0	41.0
31	38.895	40.0	38.0	41.0	35.0	41.0
32	38.92225	40.0	39.0	41.0	35.0	41.0
33	39.00525	40.0	39.0	41.0	35.0	41.0
34	38.66875	40.0	39.0	41.0	35.0	41.0
35	37.907	40.0	37.0	41.0	31.0	41.0
36	32.99975	35.0	30.0	40.0	23.0	41.0
37	34.6325	37.0	33.0	38.0	29.0	40.0
38	36.444	38.0	35.0	39.0	30.0	40.0
39	37.07	39.0	37.0	40.0	33.0	40.0
40	37.53575	39.0	37.0	40.0	33.0	41.0
41	38.11125	40.0	38.0	40.0	34.0	41.0
42	37.9845	40.0	38.0	41.0	33.0	41.0
43	38.09575	40.0	38.0	41.0	33.0	41.0
44	37.08525	39.0	36.0	40.0	31.0	41.0
45	37.209	39.0	37.0	40.0	32.0	41.0
46	37.1975	40.0	37.0	41.0	32.0	41.0
47	36.2155	39.0	35.0	40.0	29.0	41.0
48	37.36675	40.0	37.0	41.0	32.0	41.0
49	37.55725	40.0	38.0	41.0	33.0	41.0
50	35.6785	38.0	34.0	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	1.0
16	1.0
17	0.0
18	2.0
19	3.0
20	3.0
21	3.0
22	9.0
23	2.0
24	6.0
25	10.0
26	13.0
27	11.0
28	23.0
29	24.0
30	43.0
31	66.0
32	84.0
33	121.0
34	189.0
35	241.0
36	394.0
37	699.0
38	1263.0
39	788.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	5.302651325662831	23.911955977988995	58.40420210105053	12.38119059529765
2	22.942206654991242	29.44708531398549	22.516887665749312	25.093820365273956
3	16.625	17.825	17.424999999999997	48.125
4	26.424999999999997	40.975	10.6	22.0
5	21.2	38.1	29.875	10.825
6	36.325	14.174999999999999	38.675	10.825
7	10.225	25.474999999999998	25.525	38.775
8	23.45	44.625	12.9	19.025
9	17.925	42.5	28.575	11.0
10	16.375	19.475	27.625	36.525
11	32.475	10.45	11.975	45.1
12	14.374999999999998	14.6	23.25	47.775
13	19.05	20.7	40.550000000000004	19.7
14	42.449999999999996	20.7	25.45	11.4
15	40.2	17.05	29.45	13.3
16	11.3	26.424999999999997	19.725	42.55
17	25.825	19.925	39.375	14.875
18	30.45	18.224999999999998	27.275	24.05
19	40.025	12.049999999999999	31.15	16.775000000000002
20	56.05	14.2	20.8	8.95
21	20.4	27.150000000000002	22.475	29.975
22	33.125	9.0	51.5	6.375
23	23.225	10.8	56.025000000000006	9.950000000000001
24	56.725	8.325000000000001	29.15	5.800000000000001
25	62.724999999999994	21.075	11.825	4.375
26	30.25	53.87499999999999	9.675	6.2
27	11.700000000000001	60.775	21.0	6.525
28	6.5	28.025	55.275	10.2
29	7.5	7.9	67.4	17.2
30	5.75	3.5000000000000004	41.15	49.6
31	9.625	2.4	50.875	37.1
32	23.125	3.075	24.775	49.025
33	60.12499999999999	4.7	10.100000000000001	25.074999999999996
34	75.75	4.2250000000000005	9.725	10.299999999999999
35	75.47500000000001	4.275	15.075	5.175
36	46.875	4.625	40.075	8.425
37	50.175000000000004	6.950000000000001	22.925	19.950000000000003
38	25.1	11.1	9.25	54.55
39	10.25	20.9	6.275	62.575
40	9.825000000000001	54.6	6.05	29.525000000000002
41	20.4	62.3	4.725	12.575
42	55.125	33.275	5.25	6.35
43	63.849999999999994	26.275	3.5249999999999995	6.35
44	32.5	54.7	3.9	8.9
45	13.125	62.55	8.075000000000001	16.25
46	6.825	29.299999999999997	16.0	47.875
47	4.6	11.075	43.575	40.75
48	5.3	9.075	23.1	62.525
49	7.775	16.725	9.700000000000001	65.8
50	15.6	43.5	7.8	33.1
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.5
26	1.0
27	0.5
28	0.0
29	0.0
30	0.0
31	0.5
32	1.0
33	3.5
34	6.0
35	7.5
36	9.0
37	11.0
38	13.0
39	15.5
40	18.0
41	20.0
42	22.0
43	58.0
44	94.0
45	148.0
46	202.0
47	402.5
48	603.0
49	601.5
50	600.0
51	858.5
52	1117.0
53	759.5
54	402.0
55	382.5
56	363.0
57	332.5
58	302.0
59	187.5
60	73.0
61	53.5
62	34.0
63	58.5
64	83.0
65	52.5
66	22.0
67	16.0
68	10.0
69	10.0
70	10.0
71	11.0
72	12.0
73	7.0
74	2.0
75	1.0
76	0.0
77	0.0
78	0.0
79	0.5
80	1.0
81	0.5
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	0.05
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	36.125
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.91695501730104	27.425
2	10.103806228373703	7.3
3	3.944636678200692	4.275
4	1.6608996539792389	2.4
5	1.453287197231834	2.625
6	1.453287197231834	3.15
7	0.5536332179930795	1.4000000000000001
8	0.7612456747404844	2.1999999999999997
9	0.4152249134948097	1.35
>10	3.3910034602076125	25.874999999999996
>50	0.06920415224913494	1.875
>100	0.27681660899653976	20.125
>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	280	7.000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	238	5.949999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	165	4.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	122	3.05	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	75	1.875	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	49	1.225	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	44	1.0999999999999999	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	32	0.8	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	32	0.8	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	17	0.42500000000000004	RNA PCR Primer, Index 7 (100% over 35bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 33bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTACCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGC	9	0.22499999999999998	RNA PCR Primer, Index 7 (100% over 50bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCCGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGCTAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTCTAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	8	0.2	RNA PCR Primer, Index 1 (100% over 31bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATCGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTCACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	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)
AAGCTGCCAGTTGAAGACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	7	0.17500000000000002	No Hit
CTGACCTATGAATTGACAGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TACAGTACTGTGATAACTGACTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	6	0.15	No Hit
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTC	6	0.15	RNA PCR Primer, Index 7 (100% over 44bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGCCCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (96% over 30bp)
TGAGGTAGTAGTTTGTCCAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTGGACTTGGAGTCAGAAGGCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGAAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGACTTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (96% over 26bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	5	0.125	No Hit
TGAGGTAGGAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTCTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CAGCAGCACACTGTGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAACAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.25	0.0	0.0	0.0
2	0.0	0.25	0.0	0.0	0.0
3	0.0	0.35	0.0	0.0	0.0
4	0.0	0.375	0.0	0.0	0.0
5	0.0	0.425	0.0	0.0	0.0
6	0.0	0.45	0.0	0.0	0.0
7	0.0	0.7	0.0	0.0	0.0
8	0.0	0.725	0.0	0.0	0.0
9	0.0	0.8	0.0	0.0	0.0
10	0.0	0.875	0.0	0.0	0.0
11	0.0	1.025	0.0	0.0	0.0
12	0.0	1.2	0.0	0.0	0.0
13	0.0	1.25	0.0	0.0	0.0
14	0.0	1.35	0.0	0.0	0.0
15	0.0	1.625	0.0	0.0	0.0
16	0.0	2.4	0.0	0.0	0.0
17	0.0	3.125	0.0	0.0	0.0
18	0.0	3.8	0.0	0.0	0.0
19	0.0	4.175	0.0	0.0	0.0
20	0.0	5.0	0.0	0.0	0.0
21	0.0	8.7	0.0	0.0	0.0
22	0.0	20.8	0.0	0.0	0.0
23	0.0	59.525	0.0	0.0	0.0
24	0.0	79.175	0.0	0.0	0.0
25	0.0	84.425	0.0	0.0	0.0
26	0.0	85.175	0.0	0.0	0.0
27	0.0	85.625	0.0	0.0	0.0
28	0.0	85.95	0.0	0.0	0.0
29	0.0	86.225	0.0	0.0	0.0
30	0.0	86.475	0.0	0.0	0.0
31	0.0	87.125	0.0	0.0	0.0
32	0.0	87.85	0.0	0.0	0.0
33	0.0	88.625	0.0	0.0	0.0
34	0.0	90.55	0.0	0.0	0.0
35	0.0	91.1	0.0	0.0	0.0
36	0.0	91.4	0.0	0.0	0.0
37	0.0	91.8	0.0	0.0	0.0
38	0.0	92.05	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGGTAG	45	2.728484E-10	44.000004	2
GGTGAGT	45	2.728484E-10	44.000004	17
AATCCAG	45	2.728484E-10	44.000004	8
ATCCAGG	45	2.728484E-10	44.000004	9
TTGTATA	20	6.952051E-4	44.000004	13
CTTTAAC	20	6.952051E-4	44.000004	12
AGGATAG	40	5.315087E-9	44.000004	13
TCGGTGA	65	0.0	44.000004	15
ATAGGCT	40	5.315087E-9	44.000004	16
AACCTGT	20	6.952051E-4	44.000004	16
CATTCAA	65	0.0	44.000004	3
TCCAGGA	45	2.728484E-10	44.000004	10
GTATAGT	20	6.952051E-4	44.000004	15
GGATAGG	40	5.315087E-9	44.000004	14
CGTGGAA	20	6.952051E-4	44.000004	21
TAACCTG	20	6.952051E-4	44.000004	15
ACCCTTT	20	6.952051E-4	44.000004	9
GGCTTGG	40	5.315087E-9	44.000004	19
CGGTGAG	45	2.728484E-10	44.000004	16
CCTTTAA	20	6.952051E-4	44.000004	11
>>END_MODULE
Read 238124 spots for SRR5031083.sra
Written 238124 spots for SRR5031083.sra
Read 238124 spots for SRR5031083.sra
Written 238124 spots for SRR5031083.sra
Read 238124 spots for SRR5031083.sra
Written 238124 spots for SRR5031083.sra
Read 238124 spots for SRR5031083.sra
Written 238124 spots for SRR5031083.sra
Read 238124 spots for SRR5031083.sra
Written 238124 spots for SRR5031083.sra
Read 238124 spots for SRR5031083.sra
Written 238124 spots for SRR5031083.sra
Read 238124 spots for SRR5031083.sra
Written 238124 spots for SRR5031083.sra
Read 238124 spots for SRR5031083.sra
Written 238124 spots for SRR5031083.sra
Read 238124 spots for SRR5031083.sra
Written 238124 spots for SRR5031083.sra
Read 238124 spots for SRR5031083.sra
Written 238124 spots for SRR5031083.sra
Read 238124 spots for SRR5031083.sra
Written 238124 spots for SRR5031083.sra
Read 238131 spots for SRR5031083.sra
Written 238131 spots for SRR5031083.sra
SRR ids: ['SRR5031083.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_va29wsos
SRR5031083.sra spots: 2857495
blocks: [[1, 238124], [238125, 476248], [476249, 714372], [714373, 952496], [952497, 1190620], [1190621, 1428744], [1428745, 1666868], [1666869, 1904992], [1904993, 2143116], [2143117, 2381240], [2381241, 2619364], [2619365, 2857495]]
SRR5031083 file size 494207
SRR5031083 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031083 SRR5031083_1.fastq
Input file:	SRR5031083_1.fastq
trimmed:	SRR5031083-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 07:20:18 2020 >> started

Wed Mar  4 07:20:20 2020 >> done (1.873s)
2857495 reads processed; of these:
    210 ( 0.01%) short reads filtered out after trimming by size control
      7 ( 0.00%) empty reads filtered out after trimming by size control
2857278 (99.99%) reads available; of these:
 212659 ( 7.44%) trimmed reads available after processing
2644619 (92.56%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     54	  0.00%
 19	    103	  0.00%
 20	    189	  0.01%
 21	    280	  0.01%
 22	    526	  0.02%
 23	    599	  0.02%
 24	    571	  0.02%
 25	    763	  0.03%
 26	    436	  0.02%
 27	    627	  0.02%
 28	    698	  0.02%
 29	   1713	  0.06%
 30	    656	  0.02%
 31	    670	  0.02%
 32	   1016	  0.04%
 33	   1710	  0.06%
 34	   2576	  0.09%
 35	   8422	  0.29%
 36	   4780	  0.17%
 37	   3813	  0.13%
 38	   3167	  0.11%
 39	   3358	  0.12%
 40	   4053	  0.14%
 41	   5010	  0.18%
 42	   6192	  0.22%
 43	  10321	  0.36%
 44	  10799	  0.38%
 45	  15911	  0.56%
 46	  17072	  0.60%
 47	  14565	  0.51%
 48	  46658	  1.63%
 49	  45351	  1.59%
 50	2644619	 92.56%
2857278 reads passed initial QC


criterion=sequence-density
sequence-density=93.13
sequence-density-rank=1
fanout-score=16.42
fanout-score-rank=3
prefix-density=93.90
prefix-fanout=16.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC


criterion=fanout-score
sequence-density=3.79
sequence-density-rank=2
fanout-score=68.18
fanout-score-rank=1
prefix-density=93.99
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC -o SRR5031083 -
Input file:	STDIN
trimmed:	SRR5031083-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC
-- 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 07:20:38 2020 >> started

Wed Mar  4 07:20:42 2020 >> done (3.744s)
2796485 reads processed; of these:
 107563 ( 3.85%) short reads filtered out after trimming by size control
  11251 ( 0.40%) empty reads filtered out after trimming by size control
2677671 (95.75%) reads available; of these:
2626509 (98.09%) trimmed reads available after processing
  51162 ( 1.91%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  14186	  0.53%
 19	  29972	  1.12%
 20	 128396	  4.80%
 21	 342561	 12.79%
 22	1099267	 41.05%
 23	 548039	 20.47%
 24	 173639	  6.48%
 25	  29281	  1.09%
 26	  13732	  0.51%
 27	  12678	  0.47%
 28	  13570	  0.51%
 29	  10207	  0.38%
 30	  16588	  0.62%
 31	  22363	  0.84%
 32	  18519	  0.69%
 33	  53590	  2.00%
 34	  16516	  0.62%
 35	  10604	  0.40%
 36	  11752	  0.44%
 37	   6557	  0.24%
 38	   7079	  0.26%
 39	   6253	  0.23%
 40	   7855	  0.29%
 41	   9725	  0.36%
 42	   9839	  0.37%
 43	   7103	  0.27%
 44	   5380	  0.20%
 45	   5996	  0.22%
 46	   4182	  0.16%
 47	   3433	  0.13%
 48	    617	  0.02%
 49	   1020	  0.04%
 50	  37172	  1.39%


criterion=sequence-density
sequence-density=6.84
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=30
fanout-score=16.02
fanout-score-rank=1
prefix-density=6.79
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 07:21:33
                             Started mapping on |	Mar 04 07:21:34
                                    Finished on |	Mar 04 07:22:03
       Mapping speed, Million of reads per hour |	339.95

                          Number of input reads |	2738464
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1248451
                        Uniquely mapped reads % |	45.59%
                          Average mapped length |	23.00
                       Number of splices: Total |	6144
            Number of splices: Annotated (sjdb) |	2427
                       Number of splices: GT/AG |	6063
                       Number of splices: GC/AG |	31
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	49
                      Mismatch rate per base, % |	0.30%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.73
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.02
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1287894
             % of reads mapped to multiple loci |	47.03%
        Number of reads mapped to too many loci |	34154
             % of reads mapped to too many loci |	1.25%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.70%
                     % of reads unmapped: other |	0.43%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	202119	202119	202119
N_multimapping	1287894	1287894	1287894
N_noFeature	71565	81248	937189
N_ambiguous	682949	415437	6274
UnstrandedReadsAssigned:493937 PositiveStrandReadsAssigned:751766 NegativeStrandReadsAssigned:304988
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031083 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: SRR5031083-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,738,464 reads, 527,185 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,077 rounds

 109283 SRR5031083.ke.tsv
  52636 SRR5031083.se.tsv
 161919 total
==> SRR5031083.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

==> SRR5031083.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031083 completed mapping pipeline successfully
