Starting /dee2/code/volunteer_pipeline.sh SRR5031032
    current disk space = 160535920640
    free memory = 73949528 
SRR5031032 SRAfilesize
cd8baea71aab13268a0c77e0f89d2a8b  SRR5031032.sra
SRR5031032.sra file validated
SRR5031032 is single end
SRR5031032 is conventional basespace
SRR5031032 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031032_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	32.43225	33.0	31.0	34.0	31.0	34.0
2	32.70425	34.0	31.0	34.0	31.0	34.0
3	32.78475	34.0	31.0	34.0	31.0	34.0
4	36.3365	37.0	37.0	37.0	35.0	37.0
5	36.04225	37.0	35.0	37.0	35.0	37.0
6	35.88575	37.0	35.0	37.0	35.0	37.0
7	35.98425	37.0	35.0	37.0	35.0	37.0
8	35.7895	37.0	35.0	37.0	35.0	37.0
9	37.55275	39.0	37.0	39.0	35.0	39.0
10	37.84925	39.0	38.0	39.0	35.0	39.0
11	37.74575	39.0	38.0	39.0	35.0	39.0
12	37.58175	39.0	37.0	39.0	35.0	39.0
13	37.6155	39.0	37.0	39.0	35.0	39.0
14	39.02775	40.0	38.0	41.0	35.0	41.0
15	39.071	40.0	38.0	41.0	35.0	41.0
16	38.94625	40.0	38.0	41.0	35.0	41.0
17	38.96625	40.0	38.0	41.0	35.0	41.0
18	39.14975	40.0	38.0	41.0	36.0	41.0
19	38.80325	40.0	38.0	41.0	35.0	41.0
20	38.98975	40.0	39.0	41.0	35.0	41.0
21	38.88225	40.0	38.0	41.0	35.0	41.0
22	39.0455	40.0	39.0	41.0	36.0	41.0
23	38.81925	40.0	39.0	41.0	35.0	41.0
24	38.92275	40.0	38.0	41.0	35.0	41.0
25	39.093	41.0	39.0	41.0	35.0	41.0
26	38.70075	40.0	38.0	41.0	34.0	41.0
27	38.759	40.0	38.0	41.0	35.0	41.0
28	38.8395	40.0	38.0	41.0	35.0	41.0
29	38.382	40.0	38.0	41.0	34.0	41.0
30	38.244	40.0	38.0	41.0	33.0	41.0
31	38.52375	40.0	38.0	41.0	34.0	41.0
32	38.46025	40.0	38.0	41.0	34.0	41.0
33	38.4755	40.0	38.0	41.0	34.0	41.0
34	38.51175	40.0	38.0	41.0	34.0	41.0
35	38.267	40.0	38.0	41.0	34.0	41.0
36	38.0335	40.0	37.0	41.0	33.0	41.0
37	37.5785	40.0	37.0	41.0	32.0	41.0
38	36.95675	39.0	36.0	41.0	30.0	41.0
39	37.439	39.0	37.0	41.0	32.0	41.0
40	37.72125	40.0	37.0	41.0	33.0	41.0
41	37.8015	40.0	37.0	41.0	33.0	41.0
42	37.99875	40.0	37.0	41.0	33.0	41.0
43	38.20275	40.0	38.0	41.0	34.0	41.0
44	37.95875	40.0	37.0	41.0	33.0	41.0
45	37.9565	40.0	37.0	41.0	33.0	41.0
46	37.84525	40.0	37.0	41.0	33.0	41.0
47	37.35725	40.0	37.0	41.0	32.0	41.0
48	37.0965	40.0	36.0	41.0	31.0	41.0
49	37.29325	40.0	37.0	41.0	32.0	41.0
50	36.657	39.0	35.0	41.0	31.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
5	1.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	1.0
13	1.0
14	1.0
15	1.0
16	1.0
17	0.0
18	0.0
19	2.0
20	3.0
21	3.0
22	8.0
23	5.0
24	7.0
25	6.0
26	9.0
27	20.0
28	26.0
29	26.0
30	46.0
31	66.0
32	79.0
33	100.0
34	149.0
35	177.0
36	265.0
37	440.0
38	723.0
39	1834.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.0	25.724999999999998	50.3	14.975
2	24.34934934934935	27.25225225225225	18.76876876876877	29.629629629629626
3	24.474999999999998	20.25	23.200000000000003	32.074999999999996
4	32.725	28.275	15.174999999999999	23.825
5	23.875	38.6	26.05	11.475
6	36.425000000000004	15.35	32.1	16.125
7	16.3	21.625	22.825	39.25
8	24.775	28.875	16.475	29.875
9	20.575	34.075	27.700000000000003	17.65
10	20.525	22.8	27.0	29.675
11	31.775	10.625	16.925	40.675
12	15.725	18.05	31.2	35.025
13	32.425	17.65	32.574999999999996	17.349999999999998
14	32.425	31.2	20.05	16.325
15	35.05	24.75	25.825	14.374999999999998
16	18.975	19.2	22.775000000000002	39.050000000000004
17	24.25	22.275	38.95	14.524999999999999
18	25.1	18.2	29.625	27.075
19	35.449999999999996	14.05	31.3	19.2
20	43.3	14.35	28.625	13.725000000000001
21	23.875	20.3	26.525	29.299999999999997
22	28.475	12.7	47.3	11.525
23	27.775	12.575	44.525	15.125
24	53.15	13.350000000000001	25.624999999999996	7.875
25	52.349999999999994	24.3	15.299999999999999	8.05
26	28.4	47.275	13.025	11.3
27	15.975	47.85	24.224999999999998	11.95
28	11.55	24.625	48.675000000000004	15.15
29	11.525	13.0	55.35	20.125
30	9.125	6.7	37.974999999999994	46.2
31	13.375	5.025	45.675	35.925000000000004
32	29.025000000000002	5.1	21.925	43.95
33	54.87499999999999	8.05	13.625000000000002	23.45
34	63.24999999999999	6.45	16.225	14.075
35	64.67500000000001	7.000000000000001	19.825	8.5
36	43.75	7.5249999999999995	35.875	12.85
37	44.675	9.55	21.4	24.375
38	23.599999999999998	15.425	12.225	48.75
39	15.375	24.4	10.475	49.75
40	15.125	48.5	11.175	25.2
41	26.35	49.05	7.95	16.650000000000002
42	49.425000000000004	29.599999999999998	10.4	10.575
43	51.775000000000006	29.549999999999997	7.675	11.0
44	31.4	48.8	6.800000000000001	13.0
45	18.55	49.325	12.725	19.400000000000002
46	13.700000000000001	25.724999999999998	18.825	41.75
47	8.85	14.7	38.15	38.3
48	10.2	12.225	20.9	56.675
49	12.65	20.075000000000003	14.099999999999998	53.175
50	19.75	37.025000000000006	12.4	30.825000000000003
>>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	0.5
16	1.0
17	0.5
18	0.0
19	0.5
20	1.0
21	1.0
22	1.0
23	1.0
24	1.0
25	1.0
26	1.0
27	1.0
28	1.0
29	3.0
30	5.0
31	8.0
32	11.0
33	10.5
34	10.0
35	12.5
36	15.0
37	17.0
38	19.0
39	24.5
40	30.0
41	37.5
42	45.0
43	80.0
44	115.0
45	149.5
46	184.0
47	324.5
48	465.0
49	557.5
50	650.0
51	759.5
52	869.0
53	664.5
54	460.0
55	459.0
56	458.0
57	346.5
58	235.0
59	146.0
60	57.0
61	48.5
62	40.0
63	96.0
64	152.0
65	86.5
66	21.0
67	21.0
68	21.0
69	25.0
70	29.0
71	61.5
72	94.0
73	47.0
74	0.0
75	0.5
76	1.0
77	1.5
78	2.0
79	3.5
80	5.0
81	3.0
82	1.0
83	0.5
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.1
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	36.375
#Duplication Level	Percentage of deduplicated	Percentage of total
1	73.67697594501719	26.8
2	10.652920962199312	7.75
3	3.9862542955326457	4.35
4	3.230240549828179	4.7
5	1.6494845360824744	3.0
6	1.3058419243986255	2.85
7	0.6872852233676976	1.7500000000000002
8	0.4123711340206186	1.2
9	0.4123711340206186	1.35
>10	3.3676975945017182	24.425
>50	0.4123711340206186	11.85
>100	0.2061855670103093	9.975000000000001
>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
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	146	3.65	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	127	3.175	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	126	3.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	99	2.475	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	96	2.4	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	86	2.15	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	76	1.9	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	64	1.6	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	53	1.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	50	1.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	45	1.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	42	1.05	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	40	1.0	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	39	0.975	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTG	27	0.675	RNA PCR Primer, Index 2 (97% over 35bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	26	0.65	RNA PCR Primer, Index 1 (100% over 26bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	25	0.625	No Hit
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	23	0.575	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTC	19	0.475	RNA PCR Primer, Index 4 (100% over 44bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGC	18	0.44999999999999996	RNA PCR Primer, Index 4 (100% over 50bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	18	0.44999999999999996	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	17	0.42500000000000004	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	13	0.325	RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	11	0.27499999999999997	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	10	0.25	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	10	0.25	RNA PCR Primer, Index 1 (100% over 25bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	10	0.25	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	9	0.22499999999999998	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 31bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	9	0.22499999999999998	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGAATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTGTGCTTGATCTAACCATGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	6	0.15	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	6	0.15	RNA PCR Primer, Index 3 (100% over 34bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGTACCGTGAGTAATAATGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	5	0.125	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TATGCAAGGGCAAGCTCTCTTCTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	5	0.125	No Hit
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGGCAATGGTAGAACTCACATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CAAAGAATTCTCCTTTTGGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGA	5	0.125	RNA PCR Primer, Index 2 (97% over 36bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAACAGTCTACAGCCATGGTCGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>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	0.575	0.0	0.0	0.0
2	0.0	0.6	0.0	0.0	0.0
3	0.0	0.65	0.0	0.0	0.0
4	0.0	0.725	0.0	0.0	0.0
5	0.0	0.775	0.0	0.0	0.0
6	0.0	0.95	0.0	0.0	0.0
7	0.0	1.45	0.0	0.0	0.0
8	0.0	1.5	0.0	0.0	0.0
9	0.0	1.55	0.0	0.0	0.0
10	0.0	1.775	0.0	0.0	0.0
11	0.0	1.9	0.0	0.0	0.0
12	0.0	2.225	0.0	0.0	0.0
13	0.0	2.575	0.0	0.0	0.0
14	0.0	2.825	0.0	0.0	0.0
15	0.0	3.175	0.0	0.0	0.0
16	0.0	4.1	0.0	0.0	0.0
17	0.0	4.775	0.0	0.0	0.0
18	0.0	5.575	0.0	0.0	0.0
19	0.0	5.975	0.0	0.0	0.0
20	0.0	6.825	0.0	0.0	0.0
21	0.0	11.775	0.0	0.0	0.0
22	0.0	24.35	0.0	0.0	0.0
23	0.0	53.8	0.0	0.0	0.0
24	0.0	67.475	0.0	0.0	0.0
25	0.0	73.55	0.0	0.0	0.0
26	0.0	75.25	0.0	0.0	0.0
27	0.0	76.15	0.0	0.0	0.0
28	0.0	76.625	0.0	0.0	0.0
29	0.0	77.375	0.0	0.0	0.0
30	0.0	77.8	0.0	0.0	0.0
31	0.0	78.675	0.0	0.0	0.0
32	0.0	80.175	0.0	0.0	0.0
33	0.0	81.125	0.0	0.0	0.0
34	0.0	84.225	0.0	0.0	0.0
35	0.0	85.45	0.0	0.0	0.0
36	0.0	86.05	0.0	0.0	0.0
37	0.0	86.925	0.0	0.0	0.0
38	0.0	87.425	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CGCGACC	20	6.952051E-4	44.000004	1
ACAGTGA	20	6.952051E-4	44.000004	3
ACCGGTC	20	6.952051E-4	44.000004	10
GAGGTAG	20	6.952051E-4	44.000004	2
AACCGGT	20	6.952051E-4	44.000004	9
CAGTTGA	20	6.952051E-4	44.000004	8
CTGAGCT	40	5.315087E-9	44.000004	11
CCAGTTG	20	6.952051E-4	44.000004	7
GCGACCT	20	6.952051E-4	44.000004	2
GGTCTCT	20	6.952051E-4	44.000004	13
CTCTTTT	20	6.952051E-4	44.000004	16
GAGCTTG	40	5.315087E-9	44.000004	13
GGATCCG	40	5.315087E-9	44.000004	3
CCGTCTG	40	5.315087E-9	44.000004	7
TCGGATC	40	5.315087E-9	44.000004	1
CGGATCC	40	5.315087E-9	44.000004	2
GCCAGTT	20	6.952051E-4	44.000004	6
GCTGCCA	20	6.952051E-4	44.000004	3
GAACCGG	20	6.952051E-4	44.000004	8
TCAGATC	20	6.952051E-4	44.000004	8
>>END_MODULE
Read 306236 spots for SRR5031032.sra
Written 306236 spots for SRR5031032.sra
Read 306236 spots for SRR5031032.sra
Written 306236 spots for SRR5031032.sra
Read 306236 spots for SRR5031032.sra
Written 306236 spots for SRR5031032.sra
Read 306236 spots for SRR5031032.sra
Written 306236 spots for SRR5031032.sra
Read 306240 spots for SRR5031032.sra
Written 306240 spots for SRR5031032.sra
Read 306236 spots for SRR5031032.sra
Written 306236 spots for SRR5031032.sra
Read 306236 spots for SRR5031032.sra
Written 306236 spots for SRR5031032.sra
Read 306236 spots for SRR5031032.sra
Written 306236 spots for SRR5031032.sra
Read 306236 spots for SRR5031032.sra
Written 306236 spots for SRR5031032.sra
Read 306236 spots for SRR5031032.sra
Written 306236 spots for SRR5031032.sra
Read 306236 spots for SRR5031032.sra
Written 306236 spots for SRR5031032.sra
Read 306236 spots for SRR5031032.sra
Written 306236 spots for SRR5031032.sra
SRR ids: ['SRR5031032.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_d7b8a38e
SRR5031032.sra spots: 3674836
blocks: [[1, 306236], [306237, 612472], [612473, 918708], [918709, 1224944], [1224945, 1531180], [1531181, 1837416], [1837417, 2143652], [2143653, 2449888], [2449889, 2756124], [2756125, 3062360], [3062361, 3368596], [3368597, 3674836]]
SRR5031032 file size 635870
SRR5031032 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031032 SRR5031032_1.fastq
Input file:	SRR5031032_1.fastq
trimmed:	SRR5031032-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 07:10:22 2020 >> started

Wed Mar  4 07:10:25 2020 >> done (3.104s)
3674836 reads processed; of these:
    380 ( 0.01%) short reads filtered out after trimming by size control
     11 ( 0.00%) empty reads filtered out after trimming by size control
3674445 (99.99%) reads available; of these:
 183047 ( 4.98%) trimmed reads available after processing
3491398 (95.02%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    111	  0.00%
 19	    105	  0.00%
 20	    230	  0.01%
 21	    312	  0.01%
 22	    460	  0.01%
 23	    551	  0.01%
 24	    655	  0.02%
 25	    812	  0.02%
 26	    679	  0.02%
 27	    835	  0.02%
 28	    931	  0.03%
 29	   1440	  0.04%
 30	    979	  0.03%
 31	   1085	  0.03%
 32	   1143	  0.03%
 33	   1489	  0.04%
 34	   1821	  0.05%
 35	   3477	  0.09%
 36	   3096	  0.08%
 37	   3584	  0.10%
 38	   3183	  0.09%
 39	   3577	  0.10%
 40	   4261	  0.12%
 41	   4143	  0.11%
 42	   5226	  0.14%
 43	   7413	  0.20%
 44	  10118	  0.28%
 45	  12232	  0.33%
 46	  17722	  0.48%
 47	  22730	  0.62%
 48	  34024	  0.93%
 49	  34623	  0.94%
 50	3491398	 95.02%
3674445 reads passed initial QC


criterion=sequence-density
sequence-density=87.04
sequence-density-rank=1
fanout-score=20.99
fanout-score-rank=1
prefix-density=88.86
prefix-fanout=20.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCC


criterion=fanout-score
sequence-density=87.04
sequence-density-rank=1
fanout-score=20.99
fanout-score-rank=1
prefix-density=88.86
prefix-fanout=20.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCC
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 SRR5031032 -
Input file:	STDIN
trimmed:	SRR5031032-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 07:10:51 2020 >> started

Wed Mar  4 07:10:59 2020 >> done (8.054s)
3590935 reads processed; of these:
 181193 ( 5.05%) short reads filtered out after trimming by size control
  14682 ( 0.41%) empty reads filtered out after trimming by size control
3395060 (94.55%) reads available; of these:
3237347 (95.35%) trimmed reads available after processing
 157713 ( 4.65%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  17243	  0.51%
 19	  35766	  1.05%
 20	 188611	  5.56%
 21	 432639	 12.74%
 22	1086535	 32.00%
 23	 501970	 14.79%
 24	 234299	  6.90%
 25	  60473	  1.78%
 26	  29661	  0.87%
 27	  23525	  0.69%
 28	  25164	  0.74%
 29	  20200	  0.59%
 30	  31651	  0.93%
 31	  51454	  1.52%
 32	  38774	  1.14%
 33	 113660	  3.35%
 34	  35245	  1.04%
 35	  26127	  0.77%
 36	  30532	  0.90%
 37	  16425	  0.48%
 38	  18303	  0.54%
 39	  16873	  0.50%
 40	  26303	  0.77%
 41	  34633	  1.02%
 42	  41803	  1.23%
 43	  28112	  0.83%
 44	  20059	  0.59%
 45	  30962	  0.91%
 46	  22607	  0.67%
 47	  17146	  0.51%
 48	   1482	  0.04%
 49	   1820	  0.05%
 50	 135003	  3.98%


criterion=sequence-density
sequence-density=7.19
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=0.02
sequence-density-rank=39
fanout-score=82.50
fanout-score-rank=1
prefix-density=1.92
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:11:28
                             Started mapping on |	Mar 04 07:11:29
                                    Finished on |	Mar 04 07:11:55
       Mapping speed, Million of reads per hour |	481.65

                          Number of input reads |	3478570
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1836885
                        Uniquely mapped reads % |	52.81%
                          Average mapped length |	24.36
                       Number of splices: Total |	2348
            Number of splices: Annotated (sjdb) |	397
                       Number of splices: GT/AG |	2211
                       Number of splices: GC/AG |	20
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	114
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.74
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1184104
             % of reads mapped to multiple loci |	34.04%
        Number of reads mapped to too many loci |	64354
             % of reads mapped to too many loci |	1.85%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.71%
                     % of reads unmapped: other |	0.59%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	457581	457581	457581
N_multimapping	1184104	1184104	1184104
N_noFeature	104027	124512	1286603
N_ambiguous	995658	518868	17290
UnstrandedReadsAssigned:737200 PositiveStrandReadsAssigned:1193505 NegativeStrandReadsAssigned:532992
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031032 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: SRR5031032-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,478,570 reads, 849,333 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,141 rounds

 109283 SRR5031032.ke.tsv
  52636 SRR5031032.se.tsv
 161919 total
==> SRR5031032.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

==> SRR5031032.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	1
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031032 completed mapping pipeline successfully
