Starting /dee2/code/volunteer_pipeline.sh SRR5031054
    current disk space = 160514441216
    free memory = 56710644 
SRR5031054 SRAfilesize
483ed86049a953254bafc4ab1365673f  SRR5031054.sra
SRR5031054.sra file validated
SRR5031054 is single end
SRR5031054 is conventional basespace
SRR5031054 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031054_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	32.216	33.0	31.0	34.0	31.0	34.0
2	32.538	34.0	31.0	34.0	31.0	34.0
3	32.51475	34.0	31.0	34.0	31.0	34.0
4	36.13075	37.0	35.0	37.0	35.0	37.0
5	35.9025	37.0	35.0	37.0	35.0	37.0
6	35.673	37.0	35.0	37.0	33.0	37.0
7	35.83675	37.0	35.0	37.0	35.0	37.0
8	35.7075	37.0	35.0	37.0	33.0	37.0
9	37.515	39.0	37.0	39.0	35.0	39.0
10	37.71	39.0	37.0	39.0	35.0	39.0
11	37.535	39.0	37.0	39.0	35.0	39.0
12	37.538	39.0	37.0	39.0	35.0	39.0
13	37.62925	39.0	37.0	39.0	35.0	39.0
14	38.9595	40.0	38.0	41.0	35.0	41.0
15	38.86975	40.0	38.0	41.0	35.0	41.0
16	38.8765	40.0	38.0	41.0	35.0	41.0
17	38.81325	40.0	38.0	41.0	34.0	41.0
18	38.974	40.0	38.0	41.0	35.0	41.0
19	38.62675	40.0	38.0	41.0	34.0	41.0
20	38.79825	40.0	38.0	41.0	35.0	41.0
21	38.72475	40.0	38.0	41.0	34.0	41.0
22	38.9555	40.0	38.0	41.0	35.0	41.0
23	38.6535	40.0	38.0	41.0	34.0	41.0
24	38.6765	40.0	38.0	41.0	34.0	41.0
25	38.889	40.0	38.0	41.0	34.0	41.0
26	38.442	40.0	38.0	41.0	34.0	41.0
27	38.491	40.0	38.0	41.0	34.0	41.0
28	38.59875	40.0	38.0	41.0	34.0	41.0
29	38.27	40.0	38.0	41.0	33.0	41.0
30	38.0915	40.0	38.0	41.0	32.0	41.0
31	38.388	40.0	38.0	41.0	34.0	41.0
32	38.2215	40.0	38.0	41.0	34.0	41.0
33	38.186	40.0	38.0	41.0	33.0	41.0
34	38.21025	40.0	38.0	41.0	34.0	41.0
35	38.124	40.0	38.0	41.0	33.0	41.0
36	37.80675	40.0	37.0	41.0	33.0	41.0
37	37.48325	40.0	37.0	41.0	31.0	41.0
38	36.66125	39.0	36.0	41.0	30.0	41.0
39	37.102	39.0	37.0	41.0	30.0	41.0
40	37.36375	40.0	37.0	41.0	31.0	41.0
41	37.60275	40.0	37.0	41.0	33.0	41.0
42	37.924	40.0	37.0	41.0	33.0	41.0
43	38.23825	40.0	38.0	41.0	34.0	41.0
44	37.94175	40.0	38.0	41.0	33.0	41.0
45	37.975	40.0	38.0	41.0	33.0	41.0
46	37.84325	40.0	37.0	41.0	33.0	41.0
47	37.24525	40.0	37.0	41.0	31.0	41.0
48	36.892	40.0	36.0	41.0	30.0	41.0
49	37.09275	40.0	36.0	41.0	31.0	41.0
50	36.457	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
10	1.0
11	0.0
12	0.0
13	1.0
14	0.0
15	0.0
16	0.0
17	2.0
18	2.0
19	5.0
20	0.0
21	1.0
22	8.0
23	10.0
24	7.0
25	15.0
26	19.0
27	18.0
28	32.0
29	30.0
30	40.0
31	53.0
32	107.0
33	125.0
34	138.0
35	217.0
36	281.0
37	400.0
38	680.0
39	1808.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.525	25.85	50.775000000000006	14.85
2	23.90488110137672	27.934918648310386	19.499374217772214	28.660826032540676
3	22.75	20.849999999999998	22.15	34.25
4	32.800000000000004	29.75	13.25	24.2
5	23.400000000000002	37.15	28.125	11.325000000000001
6	34.949999999999996	15.5	35.949999999999996	13.600000000000001
7	15.525	23.1	22.325	39.050000000000004
8	26.900000000000002	29.65	14.75	28.7
9	20.4	35.575	29.675	14.35
10	19.475	23.5	27.925	29.099999999999998
11	34.325	9.975000000000001	16.75	38.95
12	16.225	17.95	29.375	36.449999999999996
13	28.425	18.125	35.325	18.125
14	32.15	30.099999999999998	22.55	15.2
15	36.425000000000004	23.474999999999998	26.400000000000002	13.700000000000001
16	18.275	19.25	24.099999999999998	38.375
17	25.974999999999998	24.75	35.975	13.3
18	25.224999999999998	18.175	30.0	26.6
19	34.575	14.774999999999999	32.425	18.224999999999998
20	45.800000000000004	13.900000000000002	27.400000000000002	12.9
21	23.575	20.674999999999997	27.575	28.175
22	28.575	11.95	49.525000000000006	9.950000000000001
23	25.2	12.7	47.475	14.625
24	52.55	13.725000000000001	26.55	7.175
25	54.225	23.150000000000002	14.424999999999999	8.200000000000001
26	29.049999999999997	48.025	13.175	9.75
27	14.75	50.1	22.825	12.325
28	10.05	25.4	50.4	14.149999999999999
29	10.725	12.575	58.45	18.25
30	9.175	6.4	37.675	46.75
31	13.8	5.0	47.325	33.875
32	25.8	5.575	23.25	45.375
33	54.474999999999994	8.375	13.425	23.724999999999998
34	64.125	6.9	14.674999999999999	14.299999999999999
35	65.725	6.575	19.175	8.525
36	42.375	7.3999999999999995	38.15	12.075
37	46.975	9.525	21.375	22.125
38	25.025	14.424999999999999	12.025	48.525
39	15.4	22.8	8.924999999999999	52.87500000000001
40	14.075	50.0	10.6	25.324999999999996
41	23.674999999999997	52.1	8.525	15.7
42	49.95	30.675	10.274999999999999	9.1
43	54.35	28.525	7.85	9.275
44	31.075000000000003	49.1	7.324999999999999	12.5
45	16.725	53.574999999999996	10.975	18.725
46	12.625	26.650000000000002	17.675	43.05
47	9.175	14.025000000000002	40.125	36.675000000000004
48	9.975000000000001	11.799999999999999	21.675	56.55
49	12.4	19.6	13.350000000000001	54.65
50	18.275	37.974999999999994	11.975	31.775
>>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	0.5
10	1.0
11	0.5
12	0.0
13	0.0
14	0.0
15	0.5
16	1.0
17	1.0
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	0.5
26	0.0
27	0.5
28	1.0
29	1.5
30	2.0
31	6.5
32	11.0
33	13.5
34	16.0
35	16.5
36	17.0
37	28.0
38	39.0
39	42.5
40	46.0
41	54.0
42	62.0
43	95.0
44	128.0
45	160.5
46	193.0
47	336.0
48	479.0
49	580.0
50	681.0
51	776.0
52	871.0
53	654.0
54	437.0
55	442.5
56	448.0
57	335.5
58	223.0
59	147.5
60	72.0
61	54.0
62	36.0
63	75.0
64	114.0
65	71.0
66	28.0
67	22.0
68	16.0
69	15.0
70	14.0
71	33.0
72	52.0
73	30.5
74	9.0
75	4.5
76	0.0
77	0.5
78	1.0
79	0.5
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	0.125
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	37.525
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.01665556295802	28.15
2	10.459693537641572	7.85
3	4.596935376415723	5.175
4	2.1985343104596935	3.3000000000000003
5	1.6655562958027983	3.125
6	0.7328447701532311	1.6500000000000001
7	0.866089273817455	2.275
8	0.6662225183211192	2.0
9	0.2664890073284477	0.8999999999999999
>10	2.798134576948701	20.1
>50	0.5329780146568954	14.7
>100	0.19986675549633579	10.775
>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	153	3.8249999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	145	3.6249999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	133	3.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	95	2.375	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	95	2.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	80	2.0	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	68	1.7000000000000002	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	63	1.575	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	62	1.55	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	61	1.525	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	43	1.075	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	40	1.0	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	33	0.8250000000000001	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	19	0.475	RNA PCR Primer, Index 1 (100% over 33bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAT	19	0.475	RNA PCR Primer, Index 1 (100% over 35bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGC	15	0.375	RNA PCR Primer, Index 26 (100% over 50bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	13	0.325	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	13	0.325	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTC	12	0.3	RNA PCR Primer, Index 26 (100% over 44bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	11	0.27499999999999997	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	10	0.25	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	9	0.22499999999999998	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	8	0.2	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	7	0.17500000000000002	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	7	0.17500000000000002	No Hit
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTAT	6	0.15	RNA PCR Primer, Index 26 (100% over 48bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
AACATTCAACGCTGTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTGGAATTCTCGGGTGC	5	0.125	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	5	0.125	No Hit
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	5	0.125	No Hit
CTAGACTGAGGCTCCTTGAGGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	5	0.125	No Hit
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	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	0.375	0.0	0.0	0.0
2	0.0	0.45	0.0	0.0	0.0
3	0.0	0.675	0.0	0.0	0.0
4	0.0	0.675	0.0	0.0	0.0
5	0.0	0.725	0.0	0.0	0.0
6	0.0	0.85	0.0	0.0	0.0
7	0.0	1.25	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	1.55	0.0	0.0	0.0
12	0.0	1.925	0.0	0.0	0.0
13	0.0	2.125	0.0	0.0	0.0
14	0.0	2.45	0.0	0.0	0.0
15	0.0	2.725	0.0	0.0	0.0
16	0.0	3.65	0.0	0.0	0.0
17	0.0	4.125	0.0	0.0	0.0
18	0.0	5.1	0.0	0.0	0.0
19	0.0	5.65	0.0	0.0	0.0
20	0.0	6.475	0.0	0.0	0.0
21	0.0	11.15	0.0	0.0	0.0
22	0.0	22.35	0.0	0.0	0.0
23	0.0	53.9	0.0	0.0	0.0
24	0.0	68.725	0.0	0.0	0.0
25	0.0	74.825	0.0	0.0	0.0
26	0.0	76.175	0.0	0.0	0.0
27	0.0	76.975	0.0	0.0	0.0
28	0.0	77.4	0.0	0.0	0.0
29	0.0	78.175	0.0	0.0	0.0
30	0.0	78.775	0.0	0.0	0.0
31	0.0	79.525	0.0	0.0	0.0
32	0.0	80.475	0.0	0.0	0.0
33	0.0	81.375	0.0	0.0	0.0
34	0.0	84.2	0.0	0.0	0.0
35	0.0	85.475	0.0	0.0	0.0
36	0.0	86.225	0.0	0.0	0.0
37	0.0	87.25	0.0	0.0	0.0
38	0.0	87.875	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTAGATT	20	6.952051E-4	44.000004	8
AGCTTGG	20	6.952051E-4	44.000004	14
TTGTATA	20	6.952051E-4	44.000004	13
AGTAGAT	20	6.952051E-4	44.000004	7
GAGCTTG	20	6.952051E-4	44.000004	13
GGATCCG	20	6.952051E-4	44.000004	3
CCGTCTG	20	6.952051E-4	44.000004	7
TCGGATC	20	6.952051E-4	44.000004	1
CATTCAA	20	6.952051E-4	44.000004	3
CGGATCC	20	6.952051E-4	44.000004	2
GATTGTA	20	6.952051E-4	44.000004	11
ACATTCA	20	6.952051E-4	44.000004	2
GTATAGT	20	6.952051E-4	44.000004	15
TAGTAGA	20	6.952051E-4	44.000004	6
ATTGTAT	20	6.952051E-4	44.000004	12
GATCCGT	20	6.952051E-4	44.000004	4
TCCGTCT	20	6.952051E-4	44.000004	6
ATCCGTC	20	6.952051E-4	44.000004	5
TGTATAG	20	6.952051E-4	44.000004	14
AGATTGT	20	6.952051E-4	44.000004	10
>>END_MODULE
Read 285598 spots for SRR5031054.sra
Written 285598 spots for SRR5031054.sra
Read 285598 spots for SRR5031054.sra
Written 285598 spots for SRR5031054.sra
Read 285598 spots for SRR5031054.sra
Written 285598 spots for SRR5031054.sra
Read 285598 spots for SRR5031054.sra
Written 285598 spots for SRR5031054.sra
Read 285598 spots for SRR5031054.sra
Written 285598 spots for SRR5031054.sra
Read 285598 spots for SRR5031054.sra
Written 285598 spots for SRR5031054.sra
Read 285598 spots for SRR5031054.sra
Written 285598 spots for SRR5031054.sra
Read 285598 spots for SRR5031054.sra
Written 285598 spots for SRR5031054.sra
Read 285598 spots for SRR5031054.sra
Written 285598 spots for SRR5031054.sra
Read 285598 spots for SRR5031054.sra
Written 285598 spots for SRR5031054.sra
Read 285600 spots for SRR5031054.sra
Written 285600 spots for SRR5031054.sra
Read 285598 spots for SRR5031054.sra
Written 285598 spots for SRR5031054.sra
SRR ids: ['SRR5031054.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_47yt0_n8
SRR5031054.sra spots: 3427178
blocks: [[1, 285598], [285599, 571196], [571197, 856794], [856795, 1142392], [1142393, 1427990], [1427991, 1713588], [1713589, 1999186], [1999187, 2284784], [2284785, 2570382], [2570383, 2855980], [2855981, 3141578], [3141579, 3427178]]
SRR5031054 file size 592943
SRR5031054 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031054 SRR5031054_1.fastq
Input file:	SRR5031054_1.fastq
trimmed:	SRR5031054-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 07:14:51 2020 >> started

Wed Mar  4 07:14:53 2020 >> done (2.054s)
3427178 reads processed; of these:
    335 ( 0.01%) short reads filtered out after trimming by size control
     13 ( 0.00%) empty reads filtered out after trimming by size control
3426830 (99.99%) reads available; of these:
 163298 ( 4.77%) trimmed reads available after processing
3263532 (95.23%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     91	  0.00%
 19	    100	  0.00%
 20	    237	  0.01%
 21	    280	  0.01%
 22	    462	  0.01%
 23	    557	  0.02%
 24	    574	  0.02%
 25	    757	  0.02%
 26	    581	  0.02%
 27	    751	  0.02%
 28	    875	  0.03%
 29	   1451	  0.04%
 30	    926	  0.03%
 31	    971	  0.03%
 32	   1022	  0.03%
 33	   1293	  0.04%
 34	   1638	  0.05%
 35	   3110	  0.09%
 36	   2698	  0.08%
 37	   3094	  0.09%
 38	   2839	  0.08%
 39	   3089	  0.09%
 40	   3368	  0.10%
 41	   3443	  0.10%
 42	   4553	  0.13%
 43	   6786	  0.20%
 44	   9293	  0.27%
 45	  11441	  0.33%
 46	  15669	  0.46%
 47	  19665	  0.57%
 48	  30184	  0.88%
 49	  31500	  0.92%
 50	3263532	 95.23%
3426830 reads passed initial QC


criterion=sequence-density
sequence-density=87.40
sequence-density-rank=1
fanout-score=20.96
fanout-score-rank=1
prefix-density=89.32
prefix-fanout=20.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCC


criterion=fanout-score
sequence-density=87.40
sequence-density-rank=1
fanout-score=20.96
fanout-score-rank=1
prefix-density=89.32
prefix-fanout=20.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCC -o SRR5031054 -
Input file:	STDIN
trimmed:	SRR5031054-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCC
-- 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 07:15:11 2020 >> started

Wed Mar  4 07:15:17 2020 >> done (5.340s)
3348948 reads processed; of these:
 165662 ( 4.95%) short reads filtered out after trimming by size control
  15536 ( 0.46%) empty reads filtered out after trimming by size control
3167750 (94.59%) reads available; of these:
3016340 (95.22%) trimmed reads available after processing
 151410 ( 4.78%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  17449	  0.55%
 19	  32503	  1.03%
 20	 166401	  5.25%
 21	 394914	 12.47%
 22	1046871	 33.05%
 23	 478635	 15.11%
 24	 207212	  6.54%
 25	  52209	  1.65%
 26	  26475	  0.84%
 27	  22818	  0.72%
 28	  25074	  0.79%
 29	  20178	  0.64%
 30	  27973	  0.88%
 31	  43085	  1.36%
 32	  36181	  1.14%
 33	  96616	  3.05%
 34	  36589	  1.16%
 35	  28497	  0.90%
 36	  35921	  1.13%
 37	  16716	  0.53%
 38	  17878	  0.56%
 39	  16499	  0.52%
 40	  25366	  0.80%
 41	  30856	  0.97%
 42	  34196	  1.08%
 43	  23877	  0.75%
 44	  17444	  0.55%
 45	  24188	  0.76%
 46	  17653	  0.56%
 47	  13904	  0.44%
 48	   1454	  0.05%
 49	   1918	  0.06%
 50	 130200	  4.11%


criterion=sequence-density
sequence-density=7.58
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=48
fanout-score=14.18
fanout-score-rank=1
prefix-density=0.06
prefix-fanout=1.2
sequence=TGGTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTTT
                                 Started job on |	Mar 04 07:15:38
                             Started mapping on |	Mar 04 07:15:39
                                    Finished on |	Mar 04 07:16:06
       Mapping speed, Million of reads per hour |	432.75

                          Number of input reads |	3245632
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1680414
                        Uniquely mapped reads % |	51.77%
                          Average mapped length |	24.59
                       Number of splices: Total |	1935
            Number of splices: Annotated (sjdb) |	255
                       Number of splices: GT/AG |	1809
                       Number of splices: GC/AG |	21
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	104
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.68
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.06
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1177800
             % of reads mapped to multiple loci |	36.29%
        Number of reads mapped to too many loci |	59756
             % of reads mapped to too many loci |	1.84%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.57%
                     % of reads unmapped: other |	0.52%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	387418	387418	387418
N_multimapping	1177800	1177800	1177800
N_noFeature	88252	106480	1175724
N_ambiguous	939036	501784	13874
UnstrandedReadsAssigned:653126 PositiveStrandReadsAssigned:1072150 NegativeStrandReadsAssigned:490816
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031054 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: SRR5031054-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,245,632 reads, 812,796 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,142 rounds

 109283 SRR5031054.ke.tsv
  52636 SRR5031054.se.tsv
 161919 total
==> SRR5031054.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

==> SRR5031054.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031054 completed mapping pipeline successfully
