Starting /dee2/code/volunteer_pipeline.sh SRR5031094
    current disk space = 160485687296
    free memory = 73933592 
SRR5031094 SRAfilesize
0bd5b2999d551910e821359cadf0a62b  SRR5031094.sra
SRR5031094.sra file validated
SRR5031094 is single end
SRR5031094 is conventional basespace
SRR5031094 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031094_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	53
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.87725	31.0	31.0	34.0	30.0	34.0
2	32.3535	33.0	31.0	34.0	31.0	34.0
3	32.40925	33.0	31.0	34.0	31.0	34.0
4	36.141	37.0	35.0	37.0	35.0	37.0
5	36.117	37.0	35.0	37.0	35.0	37.0
6	35.976	37.0	35.0	37.0	35.0	37.0
7	35.70575	37.0	35.0	37.0	35.0	37.0
8	35.536	37.0	35.0	37.0	33.0	37.0
9	36.81425	39.0	37.0	39.0	33.0	39.0
10	36.54625	39.0	35.0	39.0	32.0	39.0
11	37.258	39.0	37.0	39.0	34.0	39.0
12	37.5395	39.0	37.0	39.0	35.0	39.0
13	37.39475	39.0	37.0	39.0	34.0	39.0
14	38.11725	40.0	37.0	41.0	33.0	41.0
15	37.0725	39.0	36.0	41.0	31.0	41.0
16	36.66475	38.0	36.0	40.0	31.0	41.0
17	36.77125	39.0	36.0	40.0	31.0	41.0
18	38.00775	39.0	37.0	41.0	34.0	41.0
19	38.33425	39.0	37.0	41.0	34.0	41.0
20	38.09575	39.0	37.0	40.0	34.0	41.0
21	38.32525	40.0	38.0	41.0	34.0	41.0
22	37.09625	39.0	36.0	40.0	31.0	41.0
23	37.52975	39.0	37.0	40.0	32.0	41.0
24	36.70475	39.0	36.0	40.0	30.0	41.0
25	37.816	40.0	37.0	41.0	32.0	41.0
26	37.85225	40.0	37.0	40.0	33.0	41.0
27	38.00975	40.0	37.0	41.0	33.0	41.0
28	38.16125	40.0	38.0	41.0	33.0	41.0
29	37.96425	40.0	38.0	41.0	33.0	41.0
30	38.4535	40.0	38.0	41.0	34.0	41.0
31	38.42875	40.0	38.0	41.0	34.0	41.0
32	38.426	40.0	38.0	41.0	34.0	41.0
33	38.15625	40.0	38.0	41.0	34.0	41.0
34	37.36975	40.0	37.0	41.0	31.0	41.0
35	36.96375	39.0	35.0	41.0	30.0	41.0
36	32.6605	35.0	30.0	39.0	21.0	41.0
37	34.5835	37.0	33.0	39.0	27.0	40.0
38	36.2465	38.0	35.0	39.0	30.0	40.0
39	36.46775	38.0	35.0	39.0	31.0	40.0
40	36.7055	38.0	36.0	40.0	31.0	41.0
41	37.0895	39.0	36.0	40.0	31.0	41.0
42	36.98925	39.0	36.0	40.0	31.0	41.0
43	37.3365	40.0	37.0	41.0	32.0	41.0
44	36.65425	39.0	36.0	40.0	30.0	41.0
45	36.61625	39.0	36.0	40.0	30.0	41.0
46	36.351	39.0	35.0	40.0	30.0	41.0
47	35.27	38.0	34.0	40.0	28.0	41.0
48	36.28875	39.0	35.0	40.0	30.0	41.0
49	36.5785	39.0	36.0	40.0	31.0	41.0
50	34.4525	37.0	33.0	40.0	27.0	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
9	1.0
10	0.0
11	0.0
12	2.0
13	0.0
14	1.0
15	1.0
16	2.0
17	0.0
18	1.0
19	2.0
20	2.0
21	7.0
22	5.0
23	7.0
24	9.0
25	16.0
26	22.0
27	18.0
28	25.0
29	53.0
30	46.0
31	70.0
32	111.0
33	141.0
34	220.0
35	309.0
36	513.0
37	794.0
38	1054.0
39	568.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.102525631407852	25.63140785196299	49.81245311327832	14.453613403350838
2	23.704630788485606	29.912390488110134	16.871088861076345	29.511889862327912
3	27.05	16.575	20.9	35.475
4	36.75	29.45	13.05	20.75
5	23.65	35.625	28.349999999999998	12.375
6	28.999999999999996	14.975	41.349999999999994	14.674999999999999
7	17.0	20.95	19.5	42.55
8	22.175	30.55	15.0	32.275
9	25.35	32.2	26.525	15.925
10	21.625	16.35	29.825000000000003	32.2
11	34.1	12.525	14.774999999999999	38.6
12	15.575	19.225	32.725	32.475
13	30.375000000000004	14.099999999999998	34.2	21.325
14	32.074999999999996	29.299999999999997	20.825	17.8
15	36.95	17.125	27.075	18.85
16	17.575	16.775000000000002	22.400000000000002	43.25
17	29.849999999999998	17.75	36.525	15.875
18	28.599999999999998	13.450000000000001	33.85	24.099999999999998
19	35.725	15.0	32.05	17.224999999999998
20	48.975	13.55	24.474999999999998	13.0
21	23.724999999999998	24.3	23.95	28.025
22	32.7	12.575	43.675000000000004	11.05
23	24.4	12.475	48.525	14.6
24	48.925000000000004	12.950000000000001	26.974999999999998	11.15
25	52.65	22.45	15.325	9.575
26	28.825	46.075	14.774999999999999	10.325
27	17.325	48.699999999999996	22.775000000000002	11.200000000000001
28	13.425	25.1	46.150000000000006	15.325
29	11.450000000000001	12.25	57.825	18.475
30	10.025	6.675000000000001	35.449999999999996	47.85
31	14.249999999999998	4.8500000000000005	46.85	34.050000000000004
32	26.3	5.75	24.325	43.625
33	54.275	7.8	13.025	24.9
34	62.55	7.025	15.825	14.6
35	66.27499999999999	8.025	16.675	9.025
36	42.8	7.9	35.225	14.075
37	45.824999999999996	9.75	21.45	22.975
38	26.0	15.7	12.025	46.275
39	14.85	22.95	9.625	52.575
40	16.925	46.975	9.950000000000001	26.150000000000002
41	23.325000000000003	49.8	9.125	17.75
42	47.525	30.85	10.225	11.4
43	52.849999999999994	28.799999999999997	7.199999999999999	11.15
44	31.474999999999998	46.175	6.65	15.7
45	18.3	50.525	13.975000000000001	17.2
46	13.225000000000001	26.224999999999998	15.65	44.9
47	8.85	15.425	38.375	37.35
48	10.075000000000001	13.475000000000001	20.625	55.825
49	15.075	17.849999999999998	13.05	54.025
50	16.05	37.45	14.575	31.924999999999997
>>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	1.0
24	2.0
25	1.0
26	0.0
27	0.5
28	1.0
29	0.5
30	0.0
31	3.0
32	6.0
33	7.5
34	9.0
35	14.5
36	20.0
37	18.5
38	17.0
39	20.5
40	24.0
41	28.0
42	32.0
43	65.0
44	98.0
45	123.0
46	148.0
47	238.5
48	329.0
49	405.5
50	482.0
51	702.5
52	923.0
53	687.0
54	451.0
55	531.0
56	611.0
57	497.5
58	384.0
59	268.0
60	152.0
61	104.5
62	57.0
63	87.5
64	118.0
65	80.5
66	43.0
67	30.5
68	18.0
69	17.5
70	17.0
71	32.5
72	48.0
73	27.0
74	6.0
75	3.5
76	1.0
77	1.0
78	1.0
79	0.5
80	0.0
81	1.0
82	2.0
83	1.0
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	42.55
#Duplication Level	Percentage of deduplicated	Percentage of total
1	77.73207990599295	33.074999999999996
2	8.578143360752057	7.3
3	4.6415981198589895	5.925
4	2.1739130434782608	3.6999999999999997
5	1.4688601645123385	3.125
6	0.9400705052878966	2.4
7	0.6462984723854289	1.925
8	0.4700352526439483	1.6
9	0.4112808460634548	1.575
>10	2.4676850763807283	18.9
>50	0.2937720329024677	8.6
>100	0.17626321974148063	11.875
>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
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	178	4.45	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	159	3.975	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	138	3.45	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	96	2.4	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	79	1.975	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	61	1.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	55	1.375	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	53	1.325	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	46	1.15	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	43	1.075	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	38	0.95	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	36	0.8999999999999999	RNA PCR Primer, Index 1 (97% over 35bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGC	23	0.575	RNA PCR Primer, Index 18 (100% over 50bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	18	0.44999999999999996	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	15	0.375	RNA PCR Primer, Index 1 (100% over 31bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	13	0.325	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTC	13	0.325	RNA PCR Primer, Index 18 (100% over 44bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (96% over 30bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	10	0.25	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	10	0.25	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAACAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CGCACGGGGTCGGCGGCGATGTCGGTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTATTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GCACGGGGTCGGCGGCGATGTCGGTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	6	0.15	RNA PCR Primer, Index 6 (100% over 34bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTAT	6	0.15	RNA PCR Primer, Index 18 (100% over 48bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	6	0.15	No Hit
TATGCAAGGGCAAGCTCTCTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	6	0.15	No Hit
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	6	0.15	No Hit
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	5	0.125	RNA PCR Primer, Index 1 (97% over 35bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	5	0.125	No Hit
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGCCCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTGCC	5	0.125	No Hit
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
TATTGCACTCGTCCCGGCCTCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGGCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (96% over 30bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	5	0.125	No Hit
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGC	5	0.125	RNA PCR Primer, Index 18 (100% over 39bp)
>>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	0.8	0.0	0.0	0.0
2	0.0	0.85	0.0	0.0	0.0
3	0.0	1.05	0.0	0.0	0.0
4	0.0	1.1	0.0	0.0	0.0
5	0.0	1.25	0.0	0.0	0.0
6	0.0	1.325	0.0	0.0	0.0
7	0.0	1.925	0.0	0.0	0.0
8	0.0	2.325	0.0	0.0	0.0
9	0.0	2.4	0.0	0.0	0.0
10	0.0	2.725	0.0	0.0	0.0
11	0.0	2.825	0.0	0.0	0.0
12	0.0	3.275	0.0	0.0	0.0
13	0.0	3.45	0.0	0.0	0.0
14	0.0	3.75	0.0	0.0	0.0
15	0.0	4.2	0.0	0.0	0.0
16	0.0	5.7	0.0	0.0	0.0
17	0.0	6.375	0.0	0.0	0.0
18	0.0	7.625	0.0	0.0	0.0
19	0.0	8.225	0.0	0.0	0.0
20	0.0	9.025	0.0	0.0	0.0
21	0.0	14.675	0.0	0.0	0.0
22	0.0	24.2	0.0	0.0	0.0
23	0.0	54.475	0.0	0.0	0.0
24	0.0	68.875	0.0	0.0	0.0
25	0.0	74.475	0.0	0.0	0.0
26	0.0	76.275	0.0	0.0	0.0
27	0.0	77.175	0.0	0.0	0.0
28	0.0	77.85	0.0	0.0	0.0
29	0.0	78.65	0.0	0.0	0.0
30	0.0	79.25	0.0	0.0	0.0
31	0.0	80.175	0.0	0.0	0.0
32	0.0	81.95	0.0	0.0	0.0
33	0.0	82.825	0.0	0.0	0.0
34	0.0	85.375	0.0	0.0	0.0
35	0.0	86.275	0.0	0.0	0.0
36	0.0	87.25	0.0	0.0	0.0
37	0.0	88.325	0.0	0.0	0.0
38	0.0	88.65	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GGTGAGT	20	6.952051E-4	44.000004	17
ACGCTGT	20	6.952051E-4	44.000004	9
CTGAGAC	20	6.952051E-4	44.000004	4
TCGGTGA	20	6.952051E-4	44.000004	15
CCTGAGA	20	6.952051E-4	44.000004	3
GGCTTGG	45	2.728484E-10	44.000004	19
CGGTGAG	20	6.952051E-4	44.000004	16
CCCTGAG	20	6.952051E-4	44.000004	2
TTGGCTT	40	5.315087E-9	44.000004	17
TTTGGAA	40	5.315087E-9	44.000004	21
CGACTGG	20	6.952051E-4	44.000004	13
TGGCTTG	40	5.315087E-9	44.000004	18
TCCCTGA	20	6.952051E-4	44.000004	1
CGCTGTC	20	6.952051E-4	44.000004	10
AACGCTG	25	3.6958358E-5	44.0	8
GAGGTAG	30	1.9515464E-6	44.0	2
GTTTGGA	30	1.9515464E-6	44.0	20
CTGAGCT	60	0.0	44.0	11
TTCAACG	25	3.6958358E-5	44.0	5
GAGCTTG	60	0.0	44.0	13
>>END_MODULE
Read 152695 spots for SRR5031094.sra
Written 152695 spots for SRR5031094.sra
Read 152695 spots for SRR5031094.sra
Written 152695 spots for SRR5031094.sra
Read 152695 spots for SRR5031094.sra
Written 152695 spots for SRR5031094.sra
Read 152695 spots for SRR5031094.sra
Written 152695 spots for SRR5031094.sra
Read 152695 spots for SRR5031094.sra
Written 152695 spots for SRR5031094.sra
Read 152695 spots for SRR5031094.sra
Written 152695 spots for SRR5031094.sra
Read 152695 spots for SRR5031094.sra
Written 152695 spots for SRR5031094.sra
Read 152695 spots for SRR5031094.sra
Written 152695 spots for SRR5031094.sra
Read 152695 spots for SRR5031094.sra
Written 152695 spots for SRR5031094.sra
Read 152695 spots for SRR5031094.sra
Written 152695 spots for SRR5031094.sra
Read 152695 spots for SRR5031094.sra
Written 152695 spots for SRR5031094.sra
Read 152697 spots for SRR5031094.sra
Written 152697 spots for SRR5031094.sra
SRR ids: ['SRR5031094.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_cutv__wc
SRR5031094.sra spots: 1832342
blocks: [[1, 152695], [152696, 305390], [305391, 458085], [458086, 610780], [610781, 763475], [763476, 916170], [916171, 1068865], [1068866, 1221560], [1221561, 1374255], [1374256, 1526950], [1526951, 1679645], [1679646, 1832342]]
SRR5031094 file size 316515
SRR5031094 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031094 SRR5031094_1.fastq
Input file:	SRR5031094_1.fastq
trimmed:	SRR5031094-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 07:22:22 2020 >> started

Wed Mar  4 07:22:23 2020 >> done (1.175s)
1832342 reads processed; of these:
    233 ( 0.01%) short reads filtered out after trimming by size control
      7 ( 0.00%) empty reads filtered out after trimming by size control
1832102 (99.99%) reads available; of these:
 169556 ( 9.25%) trimmed reads available after processing
1662546 (90.75%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     75	  0.00%
 19	    120	  0.01%
 20	    173	  0.01%
 21	    226	  0.01%
 22	    325	  0.02%
 23	    426	  0.02%
 24	    432	  0.02%
 25	    615	  0.03%
 26	    451	  0.02%
 27	    575	  0.03%
 28	    607	  0.03%
 29	   1172	  0.06%
 30	    719	  0.04%
 31	    843	  0.05%
 32	    976	  0.05%
 33	   1645	  0.09%
 34	   2220	  0.12%
 35	   4916	  0.27%
 36	   2964	  0.16%
 37	   2984	  0.16%
 38	   3169	  0.17%
 39	   3638	  0.20%
 40	   4500	  0.25%
 41	   4122	  0.22%
 42	   5231	  0.29%
 43	   8279	  0.45%
 44	   9880	  0.54%
 45	  13422	  0.73%
 46	  14857	  0.81%
 47	  13077	  0.71%
 48	  31144	  1.70%
 49	  35773	  1.95%
 50	1662546	 90.75%
1832102 reads passed initial QC


criterion=sequence-density
sequence-density=89.04
sequence-density-rank=1
fanout-score=20.37
fanout-score-rank=2
prefix-density=90.27
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCC


criterion=fanout-score
sequence-density=4.53
sequence-density-rank=3
fanout-score=63.49
fanout-score-rank=1
prefix-density=90.52
prefix-fanout=3.2
sequence=GAATTCTCGGGGGCCAAGGAACT
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -t 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCC -o SRR5031094 -
Input file:	STDIN
trimmed:	SRR5031094-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCC
-- 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 07:22:36 2020 >> started

Wed Mar  4 07:22:39 2020 >> done (2.808s)
1791389 reads processed; of these:
 117999 ( 6.59%) short reads filtered out after trimming by size control
  18100 ( 1.01%) empty reads filtered out after trimming by size control
1655290 (92.40%) reads available; of these:
1596573 (96.45%) trimmed reads available after processing
  58717 ( 3.55%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  10412	  0.63%
 19	  19306	  1.17%
 20	 100313	  6.06%
 21	 194171	 11.73%
 22	 552391	 33.37%
 23	 268708	 16.23%
 24	 116476	  7.04%
 25	  33362	  2.02%
 26	  16786	  1.01%
 27	  12650	  0.76%
 28	  13735	  0.83%
 29	  10570	  0.64%
 30	  16185	  0.98%
 31	  32285	  1.95%
 32	  18541	  1.12%
 33	  49497	  2.99%
 34	  19392	  1.17%
 35	  16425	  0.99%
 36	  17650	  1.07%
 37	   7602	  0.46%
 38	   8779	  0.53%
 39	   6793	  0.41%
 40	   9885	  0.60%
 41	  10833	  0.65%
 42	  11909	  0.72%
 43	   8080	  0.49%
 44	   5444	  0.33%
 45	   8378	  0.51%
 46	   5893	  0.36%
 47	   4048	  0.24%
 48	    584	  0.04%
 49	   1092	  0.07%
 50	  47115	  2.85%


criterion=sequence-density
sequence-density=11.97
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=13
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=2.22
sequence-density-rank=4
fanout-score=20.00
fanout-score-rank=1
prefix-density=2.26
prefix-fanout=19.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGC
                                 Started job on |	Mar 04 07:22:59
                             Started mapping on |	Mar 04 07:23:00
                                    Finished on |	Mar 04 07:23:25
       Mapping speed, Million of reads per hour |	244.22

                          Number of input reads |	1696003
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	904898
                        Uniquely mapped reads % |	53.35%
                          Average mapped length |	23.92
                       Number of splices: Total |	3161
            Number of splices: Annotated (sjdb) |	782
                       Number of splices: GT/AG |	3092
                       Number of splices: GC/AG |	38
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	28
                      Mismatch rate per base, % |	0.35%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.87
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.02
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	606863
             % of reads mapped to multiple loci |	35.78%
        Number of reads mapped to too many loci |	29520
             % of reads mapped to too many loci |	1.74%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.31%
                     % of reads unmapped: other |	0.81%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	184242	184242	184242
N_multimapping	606863	606863	606863
N_noFeature	66749	75886	585325
N_ambiguous	504612	216191	5528
UnstrandedReadsAssigned:333537 PositiveStrandReadsAssigned:612821 NegativeStrandReadsAssigned:314045
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031094 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: SRR5031094-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,696,003 reads, 421,866 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,092 rounds

 109283 SRR5031094.ke.tsv
  52636 SRR5031094.se.tsv
 161919 total
==> SRR5031094.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

==> SRR5031094.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031094 completed mapping pipeline successfully
