Starting /dee2/code/volunteer_pipeline.sh SRR5031082
    current disk space = 160501088256
    free memory = 73956136 
SRR5031082 SRAfilesize
b62d0262945a24856bac58cf0d15e226  SRR5031082.sra
SRR5031082.sra file validated
SRR5031082 is single end
SRR5031082 is conventional basespace
SRR5031082 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031082_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	31.95	31.0	31.0	34.0	30.0	34.0
2	32.4285	33.0	31.0	34.0	31.0	34.0
3	32.4395	34.0	31.0	34.0	31.0	34.0
4	36.19175	37.0	35.0	37.0	35.0	37.0
5	36.13225	37.0	35.0	37.0	35.0	37.0
6	36.0925	37.0	35.0	37.0	35.0	37.0
7	35.809	37.0	35.0	37.0	35.0	37.0
8	35.6775	37.0	35.0	37.0	33.0	37.0
9	36.917	39.0	37.0	39.0	33.0	39.0
10	36.566	39.0	35.0	39.0	32.0	39.0
11	37.3975	39.0	37.0	39.0	34.0	39.0
12	37.62575	39.0	37.0	39.0	35.0	39.0
13	37.502	39.0	37.0	39.0	35.0	39.0
14	38.43175	40.0	38.0	41.0	34.0	41.0
15	36.9475	40.0	36.0	41.0	30.0	41.0
16	36.853	39.0	36.0	40.0	31.0	41.0
17	37.0015	39.0	36.0	41.0	32.0	41.0
18	38.2985	40.0	37.0	41.0	34.0	41.0
19	38.6085	40.0	38.0	41.0	35.0	41.0
20	38.368	40.0	38.0	41.0	34.0	41.0
21	38.555	40.0	38.0	41.0	35.0	41.0
22	37.42325	39.0	37.0	40.0	32.0	41.0
23	37.88875	39.0	37.0	40.0	34.0	41.0
24	37.2355	39.0	37.0	40.0	31.0	41.0
25	38.15575	40.0	38.0	41.0	34.0	41.0
26	38.00075	40.0	37.0	41.0	33.0	41.0
27	38.16075	40.0	38.0	41.0	34.0	41.0
28	38.33875	40.0	38.0	41.0	34.0	41.0
29	38.3945	40.0	38.0	41.0	34.0	41.0
30	38.6755	40.0	38.0	41.0	35.0	41.0
31	38.7215	40.0	38.0	41.0	35.0	41.0
32	38.844	40.0	38.0	41.0	35.0	41.0
33	38.80075	40.0	39.0	41.0	35.0	41.0
34	38.2205	40.0	38.0	41.0	33.0	41.0
35	37.44575	40.0	37.0	41.0	30.0	41.0
36	33.00125	35.0	30.0	40.0	23.0	41.0
37	35.08625	37.0	33.0	39.0	30.0	40.0
38	36.44025	38.0	35.0	39.0	31.0	40.0
39	36.67275	38.0	36.0	40.0	32.0	40.0
40	36.93125	39.0	37.0	40.0	32.0	41.0
41	37.44675	39.0	37.0	40.0	33.0	41.0
42	37.482	40.0	37.0	41.0	33.0	41.0
43	37.7435	40.0	37.0	41.0	33.0	41.0
44	36.9275	39.0	36.0	40.0	31.0	41.0
45	36.968	39.0	37.0	40.0	31.0	41.0
46	36.783	39.0	36.0	40.0	31.0	41.0
47	35.595	38.0	34.0	40.0	28.0	41.0
48	36.491	39.0	35.0	40.0	31.0	41.0
49	36.88075	39.0	36.0	40.0	32.0	41.0
50	35.03975	38.0	34.0	40.0	28.0	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
12	1.0
13	0.0
14	1.0
15	0.0
16	0.0
17	2.0
18	7.0
19	2.0
20	5.0
21	8.0
22	7.0
23	7.0
24	9.0
25	7.0
26	15.0
27	18.0
28	22.0
29	24.0
30	44.0
31	62.0
32	89.0
33	136.0
34	188.0
35	291.0
36	465.0
37	728.0
38	1107.0
39	755.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.227056764191047	27.131782945736433	50.36259064766192	14.278569642410602
2	21.927409261576972	31.714643304130163	17.09637046307885	29.261576971214016
3	27.575	15.575	18.95	37.9
4	36.75	30.349999999999998	11.875	21.025
5	20.8	37.025000000000006	29.799999999999997	12.375
6	25.95	14.025000000000002	45.525	14.499999999999998
7	14.825	20.974999999999998	17.349999999999998	46.85
8	20.775	31.35	15.6	32.275
9	26.200000000000003	34.175	24.525	15.1
10	19.925	15.975	31.2	32.9
11	36.5	10.725	13.8	38.975
12	13.625000000000002	18.85	34.2	33.324999999999996
13	29.025000000000002	14.124999999999998	36.225	20.625
14	31.900000000000002	30.525000000000002	19.425	18.15
15	38.3	14.774999999999999	26.724999999999998	20.200000000000003
16	18.175	16.375	20.674999999999997	44.775
17	30.15	19.675	36.325	13.850000000000001
18	28.249999999999996	13.5	34.25	24.0
19	36.95	13.4	33.800000000000004	15.85
20	51.7	11.525	24.099999999999998	12.675
21	22.925	23.825	24.2	29.049999999999997
22	32.6	10.825	45.85	10.725
23	24.975	11.3	50.425	13.3
24	51.9	11.799999999999999	27.400000000000002	8.9
25	53.5	24.325	13.875000000000002	8.3
26	27.175	48.225	14.124999999999998	10.475
27	15.55	50.5	23.525	10.424999999999999
28	11.275	24.45	49.4	14.875
29	11.774999999999999	10.025	59.550000000000004	18.65
30	8.525	5.35	36.725	49.4
31	13.3	3.8	48.975	33.925
32	27.575	3.875	23.625	44.925
33	57.099999999999994	7.2749999999999995	11.924999999999999	23.7
34	65.77499999999999	5.949999999999999	14.825	13.450000000000001
35	68.875	7.1499999999999995	16.325	7.6499999999999995
36	44.675	6.7	36.1	12.525
37	47.25	9.45	20.724999999999998	22.575
38	24.45	16.225	11.175	48.15
39	12.625	23.7	9.125	54.55
40	15.2	49.2	9.725	25.874999999999996
41	23.400000000000002	52.125	7.199999999999999	17.275
42	50.2	31.275	8.450000000000001	10.075000000000001
43	55.25	29.625	5.6000000000000005	9.525
44	31.125000000000004	49.975	5.4	13.5
45	17.275	53.175	13.025	16.525000000000002
46	12.725	25.974999999999998	16.0	45.300000000000004
47	7.6499999999999995	13.475000000000001	39.65	39.225
48	8.225	13.425	20.674999999999997	57.675
49	13.175	18.4	10.775	57.65
50	16.8	38.85	11.95	32.4
>>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	0.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	1.0
28	2.0
29	1.5
30	1.0
31	1.5
32	2.0
33	2.5
34	3.0
35	10.5
36	18.0
37	19.0
38	20.0
39	20.5
40	21.0
41	28.0
42	35.0
43	62.0
44	89.0
45	99.0
46	109.0
47	235.0
48	361.0
49	436.0
50	511.0
51	749.0
52	987.0
53	714.5
54	442.0
55	517.5
56	593.0
57	470.5
58	348.0
59	232.0
60	116.0
61	96.0
62	76.0
63	111.5
64	147.0
65	97.5
66	48.0
67	33.0
68	18.0
69	19.5
70	21.0
71	22.5
72	24.0
73	14.0
74	4.0
75	2.5
76	1.0
77	1.0
78	1.0
79	0.5
80	0.0
81	0.5
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	0.025
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	40.0
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.9375	30.775000000000002
2	10.0625	8.05
3	3.5624999999999996	4.275
4	2.25	3.5999999999999996
5	1.375	2.75
6	1.0625	2.55
7	1.0	2.8000000000000003
8	0.3125	1.0
9	0.43750000000000006	1.575
>10	2.4375	17.625
>50	0.25	6.65
>100	0.3125	18.35
>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	185	4.625	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	170	4.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	159	3.975	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	111	2.775	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	109	2.725	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	70	1.7500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	68	1.7000000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	47	1.175	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGC	33	0.8250000000000001	RNA PCR Primer, Index 5 (97% over 35bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	29	0.7250000000000001	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	19	0.475	RNA PCR Primer, Index 1 (96% over 30bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGC	13	0.325	RNA PCR Primer, Index 6 (100% over 50bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTC	13	0.325	RNA PCR Primer, Index 6 (100% over 44bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	11	0.27499999999999997	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	10	0.25	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	9	0.22499999999999998	RNA PCR Primer, Index 6 (100% over 34bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	8	0.2	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	7	0.17500000000000002	RNA PCR Primer, Index 6 (100% over 34bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
TGTAAACATCCCCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
TGTAAACATCCTACCCTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAACAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTCTAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	6	0.15	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTATTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCCATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AAACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
GCACGGGGTCGGCGGCGATGTCGGTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGGCAGTGTAGTTAGCTGATTGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCCATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTCGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGC	5	0.125	RNA PCR Primer, Index 5 (97% over 35bp)
CGCGACCTCAGATCAGCCGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	5	0.125	No Hit
CGCGACCTCCGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	5	0.125	No Hit
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTGGACTTGGAGTCAGAAGGCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACCATTCGTAGACGCCCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	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	0.45	0.0	0.0	0.0
2	0.0	0.45	0.0	0.0	0.0
3	0.0	0.5	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	0.65	0.0	0.0	0.0
7	0.0	1.175	0.0	0.0	0.0
8	0.0	1.3	0.0	0.0	0.0
9	0.0	1.35	0.0	0.0	0.0
10	0.0	1.45	0.0	0.0	0.0
11	0.0	1.575	0.0	0.0	0.0
12	0.0	1.6	0.0	0.0	0.0
13	0.0	1.775	0.0	0.0	0.0
14	0.0	2.05	0.0	0.0	0.0
15	0.0	2.35	0.0	0.0	0.0
16	0.0	3.575	0.0	0.0	0.0
17	0.0	4.475	0.0	0.0	0.0
18	0.0	5.475	0.0	0.0	0.0
19	0.0	5.9	0.0	0.0	0.0
20	0.0	6.7	0.0	0.0	0.0
21	0.0	12.3	0.0	0.0	0.0
22	0.0	23.275	0.0	0.0	0.0
23	0.0	55.825	0.0	0.0	0.0
24	0.0	70.775	0.0	0.0	0.0
25	0.0	76.15	0.0	0.0	0.0
26	0.0	77.925	0.0	0.0	0.0
27	0.0	78.675	0.0	0.0	0.0
28	0.0	79.325	0.0	0.0	0.0
29	0.0	79.825	0.0	0.0	0.0
30	0.0	80.375	0.0	0.0	0.0
31	0.0	81.225	0.0	0.0	0.0
32	0.0	82.9	0.0	0.0	0.0
33	0.0	83.875	0.0	0.0	0.0
34	0.0	86.825	0.0	0.0	0.0
35	0.0	87.975	0.0	0.0	0.0
36	0.0	88.7	0.0	0.0	0.0
37	0.0	89.4	0.0	0.0	0.0
38	0.0	89.7	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGAGACC	20	6.952051E-4	44.000004	5
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
AATCCAG	20	6.952051E-4	44.000004	8
CTGAGCT	40	5.315087E-9	44.000004	11
CTGAGAC	20	6.952051E-4	44.000004	4
ATCCAGG	20	6.952051E-4	44.000004	9
TTCAAGT	20	6.952051E-4	44.000004	1
AGGATAG	20	6.952051E-4	44.000004	13
TCGGTGA	65	0.0	44.000004	15
ATAGGCT	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
TCCAGGA	20	6.952051E-4	44.000004	10
GTGAGTT	20	6.952051E-4	44.000004	18
GAGTTGG	20	6.952051E-4	44.000004	20
GGATAGG	20	6.952051E-4	44.000004	14
>>END_MODULE
Read 92978 spots for SRR5031082.sra
Written 92978 spots for SRR5031082.sra
Read 92978 spots for SRR5031082.sra
Written 92978 spots for SRR5031082.sra
Read 92978 spots for SRR5031082.sra
Written 92978 spots for SRR5031082.sra
Read 92978 spots for SRR5031082.sra
Written 92978 spots for SRR5031082.sra
Read 92978 spots for SRR5031082.sra
Written 92978 spots for SRR5031082.sra
Read 92978 spots for SRR5031082.sra
Written 92978 spots for SRR5031082.sra
Read 92978 spots for SRR5031082.sra
Written 92978 spots for SRR5031082.sra
Read 92978 spots for SRR5031082.sra
Written 92978 spots for SRR5031082.sra
Read 92983 spots for SRR5031082.sra
Written 92983 spots for SRR5031082.sra
Read 92978 spots for SRR5031082.sra
Written 92978 spots for SRR5031082.sra
Read 92978 spots for SRR5031082.sra
Written 92978 spots for SRR5031082.sra
Read 92978 spots for SRR5031082.sra
Written 92978 spots for SRR5031082.sra
SRR ids: ['SRR5031082.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_2q21d_gx
SRR5031082.sra spots: 1115741
blocks: [[1, 92978], [92979, 185956], [185957, 278934], [278935, 371912], [371913, 464890], [464891, 557868], [557869, 650846], [650847, 743824], [743825, 836802], [836803, 929780], [929781, 1022758], [1022759, 1115741]]
SRR5031082 file size 192307
SRR5031082 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031082 SRR5031082_1.fastq
Input file:	SRR5031082_1.fastq
trimmed:	SRR5031082-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- end quality threshold (-q):		10
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ (auto detected)
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	12
Wed Mar  4 07:19:58 2020 >> started

Wed Mar  4 07:19:59 2020 >> done (0.860s)
1115741 reads processed; of these:
    117 ( 0.01%) short reads filtered out after trimming by size control
      2 ( 0.00%) empty reads filtered out after trimming by size control
1115622 (99.99%) reads available; of these:
  94165 ( 8.44%) trimmed reads available after processing
1021457 (91.56%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     39	  0.00%
 19	     50	  0.00%
 20	     84	  0.01%
 21	    127	  0.01%
 22	    199	  0.02%
 23	    228	  0.02%
 24	    249	  0.02%
 25	    334	  0.03%
 26	    235	  0.02%
 27	    289	  0.03%
 28	    340	  0.03%
 29	    577	  0.05%
 30	    352	  0.03%
 31	    351	  0.03%
 32	    476	  0.04%
 33	    877	  0.08%
 34	   1251	  0.11%
 35	   3153	  0.28%
 36	   1805	  0.16%
 37	   1719	  0.15%
 38	   1638	  0.15%
 39	   1817	  0.16%
 40	   2014	  0.18%
 41	   2251	  0.20%
 42	   2682	  0.24%
 43	   4684	  0.42%
 44	   5180	  0.46%
 45	   7511	  0.67%
 46	   9037	  0.81%
 47	   7558	  0.68%
 48	  18880	  1.69%
 49	  18178	  1.63%
 50	1021457	 91.56%
1115622 reads passed initial QC


criterion=sequence-density
sequence-density=89.52
sequence-density-rank=1
fanout-score=20.50
fanout-score-rank=2
prefix-density=91.08
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC


criterion=fanout-score
sequence-density=3.50
sequence-density-rank=3
fanout-score=81.95
fanout-score-rank=1
prefix-density=91.24
prefix-fanout=3.1
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC -o SRR5031082 -
Input file:	STDIN
trimmed:	SRR5031082-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Unknown format (auto detected)
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	12
Wed Mar  4 07:20:07 2020 >> started

Wed Mar  4 07:20:09 2020 >> done (1.526s)
1090831 reads processed; of these:
  58191 ( 5.33%) short reads filtered out after trimming by size control
   5689 ( 0.52%) empty reads filtered out after trimming by size control
1026951 (94.14%) reads available; of these:
 992863 (96.68%) trimmed reads available after processing
  34088 ( 3.32%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   6195	  0.60%
 19	  10886	  1.06%
 20	  63932	  6.23%
 21	 122811	 11.96%
 22	 352698	 34.34%
 23	 169227	 16.48%
 24	  69731	  6.79%
 25	  20479	  1.99%
 26	   9890	  0.96%
 27	   7178	  0.70%
 28	   7800	  0.76%
 29	   6377	  0.62%
 30	   9591	  0.93%
 31	  17694	  1.72%
 32	  10600	  1.03%
 33	  35097	  3.42%
 34	  11322	  1.10%
 35	   9214	  0.90%
 36	   9615	  0.94%
 37	   4013	  0.39%
 38	   4931	  0.48%
 39	   3724	  0.36%
 40	   6036	  0.59%
 41	   6155	  0.60%
 42	   6705	  0.65%
 43	   4377	  0.43%
 44	   2944	  0.29%
 45	   4206	  0.41%
 46	   2972	  0.29%
 47	   2220	  0.22%
 48	    383	  0.04%
 49	    644	  0.06%
 50	  27304	  2.66%


criterion=sequence-density
sequence-density=11.99
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=11
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTGGAATTCT


criterion=fanout-score
sequence-density=2.21
sequence-density-rank=5
fanout-score=18.82
fanout-score-rank=1
prefix-density=2.21
prefix-fanout=18.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGC
                                 Started job on |	Mar 04 07:20:40
                             Started mapping on |	Mar 04 07:20:41
                                    Finished on |	Mar 04 07:21:07
       Mapping speed, Million of reads per hour |	145.63

                          Number of input reads |	1051742
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	565229
                        Uniquely mapped reads % |	53.74%
                          Average mapped length |	23.71
                       Number of splices: Total |	2097
            Number of splices: Annotated (sjdb) |	645
                       Number of splices: GT/AG |	2050
                       Number of splices: GC/AG |	20
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	26
                      Mismatch rate per base, % |	0.33%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.65
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	372042
             % of reads mapped to multiple loci |	35.37%
        Number of reads mapped to too many loci |	16571
             % of reads mapped to too many loci |	1.58%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.64%
                     % of reads unmapped: other |	0.67%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	114471	114471	114471
N_multimapping	372042	372042	372042
N_noFeature	37456	42967	354349
N_ambiguous	321936	130549	3454
UnstrandedReadsAssigned:205837 PositiveStrandReadsAssigned:391713 NegativeStrandReadsAssigned:207426
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031082 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: SRR5031082-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,051,742 reads, 275,056 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,039 rounds

 109283 SRR5031082.ke.tsv
  52636 SRR5031082.se.tsv
 161919 total
==> SRR5031082.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

==> SRR5031082.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031082 completed mapping pipeline successfully
