Starting /dee2/code/volunteer_pipeline.sh SRR5031041
    current disk space = 160508198912
    free memory = 73945592 
SRR5031041 SRAfilesize
5609776f61c5aa66e9337870809e4ed4  SRR5031041.sra
SRR5031041.sra file validated
SRR5031041 is single end
SRR5031041 is conventional basespace
SRR5031041 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031041_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.34725	33.0	31.0	34.0	31.0	34.0
2	32.59425	34.0	31.0	34.0	31.0	34.0
3	32.63075	34.0	31.0	34.0	31.0	34.0
4	36.1985	37.0	35.0	37.0	35.0	37.0
5	36.0975	37.0	35.0	37.0	35.0	37.0
6	35.82175	37.0	35.0	37.0	33.0	37.0
7	35.95825	37.0	35.0	37.0	35.0	37.0
8	35.79375	37.0	35.0	37.0	35.0	37.0
9	37.4955	39.0	37.0	39.0	35.0	39.0
10	37.77075	39.0	37.0	39.0	35.0	39.0
11	37.62325	39.0	37.0	39.0	35.0	39.0
12	37.70475	39.0	37.0	39.0	35.0	39.0
13	37.6335	39.0	37.0	39.0	35.0	39.0
14	39.08225	41.0	38.0	41.0	36.0	41.0
15	39.0765	41.0	39.0	41.0	36.0	41.0
16	39.0615	40.0	38.0	41.0	36.0	41.0
17	38.889	40.0	38.0	41.0	35.0	41.0
18	39.024	40.0	38.0	41.0	35.0	41.0
19	38.605	40.0	38.0	41.0	34.0	41.0
20	38.794	40.0	38.0	41.0	34.0	41.0
21	38.78475	40.0	38.0	41.0	34.0	41.0
22	38.9895	40.0	39.0	41.0	35.0	41.0
23	38.64075	40.0	38.0	41.0	34.0	41.0
24	38.7115	40.0	38.0	41.0	34.0	41.0
25	38.92	40.0	39.0	41.0	35.0	41.0
26	38.4375	40.0	38.0	41.0	34.0	41.0
27	38.60625	40.0	38.0	41.0	34.0	41.0
28	38.646	40.0	38.0	41.0	34.0	41.0
29	38.48875	40.0	38.0	41.0	34.0	41.0
30	38.37275	40.0	38.0	41.0	34.0	41.0
31	38.49875	40.0	38.0	41.0	34.0	41.0
32	38.39875	40.0	38.0	41.0	34.0	41.0
33	38.276	40.0	38.0	41.0	34.0	41.0
34	38.34275	40.0	38.0	41.0	34.0	41.0
35	38.30875	40.0	38.0	41.0	34.0	41.0
36	38.0105	40.0	38.0	41.0	33.0	41.0
37	37.75025	40.0	37.0	41.0	32.0	41.0
38	36.85475	39.0	36.0	41.0	30.0	41.0
39	37.3815	39.0	37.0	41.0	32.0	41.0
40	37.531	40.0	37.0	41.0	32.0	41.0
41	37.87925	40.0	38.0	41.0	33.0	41.0
42	38.165	40.0	38.0	41.0	33.0	41.0
43	38.44725	40.0	38.0	41.0	34.0	41.0
44	38.1885	40.0	38.0	41.0	33.0	41.0
45	38.1135	40.0	38.0	41.0	33.0	41.0
46	37.962	40.0	38.0	41.0	33.0	41.0
47	37.57475	40.0	37.0	41.0	32.0	41.0
48	37.032	40.0	36.0	41.0	31.0	41.0
49	37.50525	40.0	37.0	41.0	32.0	41.0
50	37.142	40.0	36.0	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
15	1.0
16	0.0
17	3.0
18	1.0
19	3.0
20	2.0
21	5.0
22	4.0
23	6.0
24	10.0
25	9.0
26	11.0
27	18.0
28	28.0
29	39.0
30	40.0
31	61.0
32	88.0
33	101.0
34	134.0
35	187.0
36	282.0
37	403.0
38	682.0
39	1882.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.375	22.425	56.25	13.950000000000001
2	23.173173173173172	27.7027027027027	21.146146146146148	27.97797797797798
3	17.9	18.025	20.325	43.75
4	27.35	35.75	12.975	23.925
5	22.875	36.85	28.225	12.049999999999999
6	35.775	14.249999999999998	37.6	12.375
7	11.725	27.250000000000004	24.175	36.85
8	24.224999999999998	39.4	14.124999999999998	22.25
9	19.925	38.224999999999994	28.95	12.9
10	17.849999999999998	21.099999999999998	26.05	35.0
11	31.175000000000004	12.174999999999999	13.175	43.475
12	16.45	15.925	23.925	43.7
13	19.900000000000002	20.825	37.35	21.925
14	37.05	23.849999999999998	25.7	13.4
15	37.625	22.5	28.275	11.600000000000001
16	13.05	26.900000000000002	20.974999999999998	39.074999999999996
17	25.674999999999997	22.875	37.475	13.975000000000001
18	27.450000000000003	17.675	29.525000000000002	25.35
19	39.025	13.65	28.549999999999997	18.775
20	50.8	15.55	22.675	10.975
21	21.9	25.650000000000002	23.05	29.4
22	31.674999999999997	12.925	48.025	7.375
23	22.6	13.075000000000001	51.125	13.200000000000001
24	53.37499999999999	12.25	28.15	6.225
25	57.099999999999994	21.8	13.700000000000001	7.3999999999999995
26	29.575000000000003	49.95	11.3	9.175
27	13.900000000000002	54.6	21.15	10.35
28	9.125	27.525	51.925	11.425
29	9.625	11.600000000000001	61.150000000000006	17.625
30	8.95	5.1	38.800000000000004	47.15
31	11.65	4.3999999999999995	48.825	35.125
32	23.875	4.8	24.099999999999998	47.225
33	56.3	6.65	12.625	24.425
34	68.75	6.325	11.725	13.200000000000001
35	69.175	6.075	16.625	8.125
36	42.175000000000004	6.45	40.175	11.200000000000001
37	48.525	8.05	22.35	21.075
38	25.45	13.8	11.200000000000001	49.55
39	14.249999999999998	21.275	8.15	56.325
40	12.049999999999999	50.925	8.924999999999999	28.1
41	21.75	56.225	7.9750000000000005	14.05
42	51.65	30.975	9.1	8.275
43	58.599999999999994	26.224999999999998	6.275	8.9
44	31.825	51.725	6.0249999999999995	10.424999999999999
45	16.1	57.825	9.575	16.5
46	10.375	28.549999999999997	16.650000000000002	44.425
47	7.375	13.450000000000001	41.949999999999996	37.225
48	8.35	10.525	23.0	58.12500000000001
49	9.675	18.675	12.35	59.3
50	17.025000000000002	40.675	9.725	32.574999999999996
>>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	0.5
8	1.0
9	0.5
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	0.5
22	1.0
23	0.5
24	0.0
25	0.5
26	1.0
27	1.5
28	2.0
29	3.5
30	5.0
31	7.0
32	9.0
33	8.0
34	7.0
35	11.0
36	15.0
37	20.5
38	26.0
39	27.0
40	28.0
41	39.0
42	50.0
43	81.5
44	113.0
45	156.0
46	199.0
47	391.0
48	583.0
49	596.5
50	610.0
51	820.0
52	1030.0
53	700.5
54	371.0
55	377.5
56	384.0
57	351.0
58	318.0
59	180.0
60	42.0
61	42.5
62	43.0
63	66.0
64	89.0
65	54.0
66	19.0
67	14.5
68	10.0
69	9.5
70	9.0
71	19.0
72	29.0
73	17.5
74	6.0
75	3.0
76	0.0
77	0.0
78	0.0
79	0.0
80	0.0
81	0.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
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	36.125
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.64013840830451	27.325
2	9.688581314878892	7.000000000000001
3	3.944636678200692	4.275
4	2.422145328719723	3.5000000000000004
5	1.6608996539792389	3.0
6	0.8996539792387545	1.95
7	1.0380622837370241	2.625
8	0.4152249134948097	1.2
9	0.27681660899653976	0.8999999999999999
>10	3.598615916955018	27.250000000000004
>50	0.13840830449826988	3.15
>100	0.27681660899653976	17.825
>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	243	6.075	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	176	4.3999999999999995	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	160	4.0	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	134	3.35	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	75	1.875	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	51	1.275	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	47	1.175	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	46	1.15	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	45	1.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAG	20	0.5	RNA PCR Primer, Index 2 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	19	0.475	RNA PCR Primer, Index 1 (100% over 30bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGC	16	0.4	RNA PCR Primer, Index 13 (100% over 50bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTC	16	0.4	RNA PCR Primer, Index 13 (100% over 44bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	13	0.325	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	12	0.3	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	12	0.3	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	8	0.2	No Hit
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	8	0.2	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGAATTCTCGGGTGC	8	0.2	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTAGTTCAATGGTAGAATTCTCGCCTCCCTGGAATTCTCGGGTG	7	0.17500000000000002	No Hit
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	7	0.17500000000000002	No Hit
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACTGGACTTGGAGTCAGAAGGCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTATAAAGCAATGAGACTGATTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	5	0.125	No Hit
TTCAAGTAATCCAGGATAGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	5	0.125	No Hit
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	5	0.125	RNA PCR Primer, Index 1 (100% over 34bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTGTGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	5	0.125	No Hit
>>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	0.45	0.0	0.0	0.0
2	0.0	0.45	0.0	0.0	0.0
3	0.0	0.525	0.0	0.0	0.0
4	0.0	0.575	0.0	0.0	0.0
5	0.0	0.6	0.0	0.0	0.0
6	0.0	0.625	0.0	0.0	0.0
7	0.0	1.125	0.0	0.0	0.0
8	0.0	1.3	0.0	0.0	0.0
9	0.0	1.3	0.0	0.0	0.0
10	0.0	1.475	0.0	0.0	0.0
11	0.0	1.775	0.0	0.0	0.0
12	0.0	1.975	0.0	0.0	0.0
13	0.0	2.1	0.0	0.0	0.0
14	0.0	2.35	0.0	0.0	0.0
15	0.0	2.575	0.0	0.0	0.0
16	0.0	3.425	0.0	0.0	0.0
17	0.0	4.075	0.0	0.0	0.0
18	0.0	4.875	0.0	0.0	0.0
19	0.0	5.275	0.0	0.0	0.0
20	0.0	6.275	0.0	0.0	0.0
21	0.0	10.425	0.0	0.0	0.0
22	0.0	21.35	0.0	0.0	0.0
23	0.0	55.425	0.0	0.0	0.0
24	0.0	72.2	0.0	0.0	0.0
25	0.0	78.15	0.0	0.0	0.0
26	0.0	79.3	0.0	0.0	0.0
27	0.0	80.1	0.0	0.0	0.0
28	0.0	80.65	0.0	0.0	0.0
29	0.0	81.2	0.0	0.0	0.0
30	0.0	81.6	0.0	0.0	0.0
31	0.0	82.55	0.0	0.0	0.0
32	0.0	83.475	0.0	0.0	0.0
33	0.0	84.475	0.0	0.0	0.0
34	0.0	86.6	0.0	0.0	0.0
35	0.0	87.725	0.0	0.0	0.0
36	0.0	88.575	0.0	0.0	0.0
37	0.0	89.15	0.0	0.0	0.0
38	0.0	89.55	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GCCCTAG	20	6.952051E-4	44.000004	11
ATCCTAG	20	6.952051E-4	44.000004	5
ACTAATC	20	6.952051E-4	44.000004	1
GTAGAAC	20	6.952051E-4	44.000004	6
AATCCTA	20	6.952051E-4	44.000004	4
TCCTAGC	20	6.952051E-4	44.000004	6
GAAGCTT	20	6.952051E-4	44.000004	19
ACCCGTA	20	6.952051E-4	44.000004	2
CGTAGAA	20	6.952051E-4	44.000004	5
GAGTTGG	20	6.952051E-4	44.000004	20
CCGTAGA	20	6.952051E-4	44.000004	4
CCCGTAG	20	6.952051E-4	44.000004	3
CACCCGT	20	6.952051E-4	44.000004	1
CTAATCC	20	6.952051E-4	44.000004	2
CTGGAAG	20	6.952051E-4	44.000004	16
TAATCCT	20	6.952051E-4	44.000004	3
GGAAGCT	20	6.952051E-4	44.000004	18
GCTTGGC	20	6.952051E-4	44.000004	15
GACTGGA	20	6.952051E-4	44.000004	14
ACCTTGC	20	6.952051E-4	44.000004	15
>>END_MODULE
Read 390819 spots for SRR5031041.sra
Written 390819 spots for SRR5031041.sra
Read 390819 spots for SRR5031041.sra
Written 390819 spots for SRR5031041.sra
Read 390819 spots for SRR5031041.sra
Written 390819 spots for SRR5031041.sra
Read 390819 spots for SRR5031041.sra
Written 390819 spots for SRR5031041.sra
Read 390819 spots for SRR5031041.sra
Written 390819 spots for SRR5031041.sra
Read 390819 spots for SRR5031041.sra
Written 390819 spots for SRR5031041.sra
Read 390819 spots for SRR5031041.sra
Written 390819 spots for SRR5031041.sra
Read 390819 spots for SRR5031041.sra
Written 390819 spots for SRR5031041.sra
Read 390826 spots for SRR5031041.sra
Written 390826 spots for SRR5031041.sra
Read 390819 spots for SRR5031041.sra
Written 390819 spots for SRR5031041.sra
Read 390819 spots for SRR5031041.sra
Written 390819 spots for SRR5031041.sra
Read 390819 spots for SRR5031041.sra
Written 390819 spots for SRR5031041.sra
SRR ids: ['SRR5031041.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_640bgct0
SRR5031041.sra spots: 4689835
blocks: [[1, 390819], [390820, 781638], [781639, 1172457], [1172458, 1563276], [1563277, 1954095], [1954096, 2344914], [2344915, 2735733], [2735734, 3126552], [3126553, 3517371], [3517372, 3908190], [3908191, 4299009], [4299010, 4689835]]
SRR5031041 file size 811799
SRR5031041 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031041 SRR5031041_1.fastq
Input file:	SRR5031041_1.fastq
trimmed:	SRR5031041-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 07:11:57 2020 >> started

Wed Mar  4 07:12:00 2020 >> done (2.966s)
4689835 reads processed; of these:
    365 ( 0.01%) short reads filtered out after trimming by size control
     19 ( 0.00%) empty reads filtered out after trimming by size control
4689451 (99.99%) reads available; of these:
 206715 ( 4.41%) trimmed reads available after processing
4482736 (95.59%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     74	  0.00%
 19	    133	  0.00%
 20	    263	  0.01%
 21	    333	  0.01%
 22	    630	  0.01%
 23	    725	  0.02%
 24	    706	  0.02%
 25	    890	  0.02%
 26	    705	  0.02%
 27	    947	  0.02%
 28	   1072	  0.02%
 29	   1926	  0.04%
 30	   1073	  0.02%
 31	   1215	  0.03%
 32	   1318	  0.03%
 33	   1511	  0.03%
 34	   1903	  0.04%
 35	   3997	  0.09%
 36	   3290	  0.07%
 37	   3664	  0.08%
 38	   3309	  0.07%
 39	   3608	  0.08%
 40	   4098	  0.09%
 41	   4291	  0.09%
 42	   5648	  0.12%
 43	   8286	  0.18%
 44	  11609	  0.25%
 45	  15365	  0.33%
 46	  19956	  0.43%
 47	  25802	  0.55%
 48	  39630	  0.85%
 49	  38738	  0.83%
 50	4482736	 95.59%
4689451 reads passed initial QC


criterion=sequence-density
sequence-density=89.78
sequence-density-rank=1
fanout-score=18.42
fanout-score-rank=1
prefix-density=91.50
prefix-fanout=18.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCC


criterion=fanout-score
sequence-density=89.78
sequence-density-rank=1
fanout-score=18.42
fanout-score-rank=1
prefix-density=91.50
prefix-fanout=18.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCC -o SRR5031041 -
Input file:	STDIN
trimmed:	SRR5031041-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCC
-- 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 07:12:24 2020 >> started

Wed Mar  4 07:12:30 2020 >> done (6.174s)
4585241 reads processed; of these:
 200818 ( 4.38%) short reads filtered out after trimming by size control
  18119 ( 0.40%) empty reads filtered out after trimming by size control
4366304 (95.23%) reads available; of these:
4228093 (96.83%) trimmed reads available after processing
 138211 ( 3.17%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  24364	  0.56%
 19	  47435	  1.09%
 20	 202941	  4.65%
 21	 501314	 11.48%
 22	1631830	 37.37%
 23	 775975	 17.77%
 24	 281185	  6.44%
 25	  52405	  1.20%
 26	  26197	  0.60%
 27	  24028	  0.55%
 28	  27048	  0.62%
 29	  21925	  0.50%
 30	  37718	  0.86%
 31	  51829	  1.19%
 32	  48910	  1.12%
 33	 104219	  2.39%
 34	  43354	  0.99%
 35	  30473	  0.70%
 36	  32400	  0.74%
 37	  19195	  0.44%
 38	  21824	  0.50%
 39	  20313	  0.47%
 40	  28362	  0.65%
 41	  37907	  0.87%
 42	  39509	  0.90%
 43	  29450	  0.67%
 44	  23138	  0.53%
 45	  27345	  0.63%
 46	  21806	  0.50%
 47	  14628	  0.34%
 48	   1585	  0.04%
 49	   2126	  0.05%
 50	 113566	  2.60%


criterion=sequence-density
sequence-density=3.43
sequence-density-rank=1
fanout-score=2.84
fanout-score-rank=4
prefix-density=0.02
prefix-fanout=2.8
sequence=TGAGGTAGTAGGTTGTAT


criterion=fanout-score
sequence-density=0.46
sequence-density-rank=29
fanout-score=15.45
fanout-score-rank=1
prefix-density=7.15
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 07:12:55
                             Started mapping on |	Mar 04 07:12:56
                                    Finished on |	Mar 04 07:13:45
       Mapping speed, Million of reads per hour |	328.45

                          Number of input reads |	4470514
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2202626
                        Uniquely mapped reads % |	49.27%
                          Average mapped length |	24.11
                       Number of splices: Total |	2703
            Number of splices: Annotated (sjdb) |	320
                       Number of splices: GT/AG |	2535
                       Number of splices: GC/AG |	26
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	140
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.62
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.04
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1824718
             % of reads mapped to multiple loci |	40.82%
        Number of reads mapped to too many loci |	83105
             % of reads mapped to too many loci |	1.86%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.36%
                     % of reads unmapped: other |	0.69%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	443170	443170	443170
N_multimapping	1824718	1824718	1824718
N_noFeature	105280	126032	1663991
N_ambiguous	1226888	772984	15233
UnstrandedReadsAssigned:870458 PositiveStrandReadsAssigned:1303610 NegativeStrandReadsAssigned:523402
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031041 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: SRR5031041-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,470,514 reads, 946,997 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,163 rounds

 109283 SRR5031041.ke.tsv
  52636 SRR5031041.se.tsv
 161919 total
==> SRR5031041.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

==> SRR5031041.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031041 completed mapping pipeline successfully
