Starting /dee2/code/volunteer_pipeline.sh SRR5031051
    current disk space = 160529432576
    free memory = 1047214672 
SRR5031051 SRAfilesize
7f744aaff245219aac7ae271db7aaf10  SRR5031051.sra
SRR5031051.sra file validated
SRR5031051 is single end
SRR5031051 is conventional basespace
SRR5031051 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031051_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	32.3765	33.0	31.0	34.0	31.0	34.0
2	32.6445	34.0	31.0	34.0	31.0	34.0
3	32.699	34.0	31.0	34.0	31.0	34.0
4	36.23875	37.0	37.0	37.0	35.0	37.0
5	35.88325	37.0	35.0	37.0	35.0	37.0
6	35.9135	37.0	35.0	37.0	35.0	37.0
7	35.98575	37.0	35.0	37.0	35.0	37.0
8	36.00025	37.0	35.0	37.0	35.0	37.0
9	37.674	39.0	37.0	39.0	35.0	39.0
10	37.7535	39.0	37.0	39.0	35.0	39.0
11	37.63325	39.0	37.0	39.0	35.0	39.0
12	37.71575	39.0	37.0	39.0	35.0	39.0
13	37.6485	39.0	37.0	39.0	35.0	39.0
14	39.0485	40.0	38.0	41.0	35.0	41.0
15	38.96625	40.0	38.0	41.0	35.0	41.0
16	38.999	40.0	38.0	41.0	35.0	41.0
17	38.97925	40.0	38.0	41.0	35.0	41.0
18	38.9855	40.0	38.0	41.0	35.0	41.0
19	38.519	40.0	38.0	41.0	34.0	41.0
20	38.8295	40.0	38.0	41.0	35.0	41.0
21	38.78325	40.0	38.0	41.0	35.0	41.0
22	39.01575	40.0	38.0	41.0	36.0	41.0
23	38.762	40.0	38.0	41.0	35.0	41.0
24	38.87425	40.0	38.0	41.0	35.0	41.0
25	39.074	40.0	39.0	41.0	35.0	41.0
26	38.8975	40.0	38.0	41.0	35.0	41.0
27	38.7925	40.0	38.0	41.0	35.0	41.0
28	38.7605	40.0	38.0	41.0	34.0	41.0
29	38.26725	40.0	38.0	41.0	33.0	41.0
30	38.15975	40.0	38.0	41.0	33.0	41.0
31	38.47875	40.0	38.0	41.0	34.0	41.0
32	38.42225	40.0	38.0	41.0	34.0	41.0
33	38.388	40.0	38.0	41.0	34.0	41.0
34	38.4045	40.0	38.0	41.0	34.0	41.0
35	38.235	40.0	38.0	41.0	34.0	41.0
36	37.9025	40.0	37.0	41.0	33.0	41.0
37	37.29075	40.0	37.0	41.0	31.0	41.0
38	36.83425	39.0	36.0	41.0	30.0	41.0
39	37.35475	39.0	37.0	41.0	32.0	41.0
40	37.50175	40.0	37.0	41.0	32.0	41.0
41	37.62975	40.0	37.0	41.0	33.0	41.0
42	37.81125	40.0	37.0	41.0	33.0	41.0
43	38.0035	40.0	37.0	41.0	34.0	41.0
44	37.7525	40.0	37.0	41.0	33.0	41.0
45	37.64825	40.0	37.0	41.0	33.0	41.0
46	37.5735	40.0	37.0	41.0	33.0	41.0
47	37.08	40.0	36.0	41.0	31.0	41.0
48	36.79975	39.0	35.0	41.0	31.0	41.0
49	36.8925	40.0	36.0	41.0	31.0	41.0
50	36.1555	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
3	1.0
4	0.0
5	0.0
6	0.0
7	0.0
8	1.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	1.0
15	1.0
16	1.0
17	0.0
18	0.0
19	3.0
20	5.0
21	2.0
22	3.0
23	5.0
24	7.0
25	9.0
26	8.0
27	15.0
28	25.0
29	47.0
30	39.0
31	62.0
32	89.0
33	109.0
34	186.0
35	168.0
36	264.0
37	406.0
38	824.0
39	1719.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.375	25.124999999999996	46.650000000000006	16.85
2	22.47247247247247	27.927927927927925	20.145145145145147	29.454454454454453
3	24.3	15.55	23.1	37.05
4	34.1	27.925	15.725	22.25
5	22.95	34.75	27.875	14.424999999999999
6	29.549999999999997	15.299999999999999	38.0	17.150000000000002
7	19.900000000000002	20.775	19.575	39.75
8	21.75	27.224999999999998	18.9	32.125
9	25.374999999999996	31.775	24.975	17.875
10	23.525	18.75	28.799999999999997	28.925
11	33.675	13.3	16.175	36.85
12	16.950000000000003	20.175	31.125000000000004	31.75
13	28.775000000000002	16.975	34.25	20.0
14	29.5	29.325000000000003	19.475	21.7
15	35.8	22.175	26.25	15.775
16	20.175	18.575	23.0	38.25
17	28.175	22.525000000000002	35.55	13.750000000000002
18	26.450000000000003	15.325	31.1	27.125
19	34.375	15.15	32.15	18.325
20	43.675000000000004	15.0	27.250000000000004	14.075
21	26.075	22.95	21.75	29.225
22	30.7	15.325	42.575	11.4
23	25.825	13.475000000000001	42.75	17.95
24	47.775	16.325	26.6	9.3
25	48.1	23.674999999999997	16.8	11.425
26	28.625	41.425	15.875	14.075
27	17.05	43.925	23.925	15.1
28	14.649999999999999	23.974999999999998	43.55	17.825
29	13.975000000000001	13.725000000000001	52.97500000000001	19.325
30	11.5	8.125	34.025	46.35
31	15.35	6.075	44.85	33.725
32	27.875	6.35	24.25	41.525
33	50.875	9.55	15.475	24.099999999999998
34	56.974999999999994	7.85	18.625	16.55
35	62.5	8.5	17.5	11.5
36	42.225	9.425	34.025	14.325
37	42.6	12.975	22.275	22.15
38	26.625	18.175	13.725000000000001	41.475
39	17.7	21.725	13.125	47.449999999999996
40	17.65	43.625	14.099999999999998	24.625
41	23.7	46.050000000000004	9.825000000000001	20.424999999999997
42	45.25	29.049999999999997	14.725	10.975
43	50.125	27.3	9.950000000000001	12.625
44	35.25	42.525	7.9	14.325
45	21.8	46.5	15.299999999999999	16.400000000000002
46	18.125	25.374999999999996	16.2	40.300000000000004
47	12.65	15.0	37.425000000000004	34.925
48	14.499999999999998	13.25	20.549999999999997	51.7
49	16.05	18.3	15.049999999999999	50.6
50	18.175	35.699999999999996	14.424999999999999	31.7
>>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	0.5
14	1.0
15	0.5
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.5
22	1.0
23	1.0
24	1.0
25	0.5
26	0.0
27	0.5
28	1.0
29	2.0
30	3.0
31	6.5
32	10.0
33	10.5
34	11.0
35	22.0
36	33.0
37	31.0
38	29.0
39	40.0
40	51.0
41	48.5
42	46.0
43	77.0
44	108.0
45	122.0
46	136.0
47	266.0
48	396.0
49	466.5
50	537.0
51	683.5
52	830.0
53	615.0
54	400.0
55	494.0
56	588.0
57	442.0
58	296.0
59	199.5
60	103.0
61	80.5
62	58.0
63	120.5
64	183.0
65	118.0
66	53.0
67	34.0
68	15.0
69	21.0
70	27.0
71	49.0
72	71.0
73	37.5
74	4.0
75	2.5
76	1.0
77	2.0
78	3.0
79	3.0
80	3.0
81	2.0
82	1.0
83	0.5
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.1
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	39.074999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.43186180422265	29.475
2	10.044785668586051	7.85
3	4.286628278950736	5.025
4	2.7511196417146513	4.3
5	0.8317338451695457	1.625
6	1.0236724248240563	2.4
7	0.5118362124120281	1.4000000000000001
8	1.0236724248240563	3.2
9	0.5758157389635317	2.025
>10	3.0070377479206654	21.925
>50	0.2559181062060141	8.025
>100	0.2559181062060141	12.75
>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
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	146	3.65	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	131	3.2750000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	130	3.25	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	103	2.5749999999999997	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	99	2.475	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	87	2.175	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	83	2.075	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	52	1.3	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	43	1.075	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	35	0.8750000000000001	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	31	0.775	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGA	29	0.7250000000000001	RNA PCR Primer, Index 7 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	21	0.525	RNA PCR Primer, Index 1 (100% over 33bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	19	0.475	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	18	0.44999999999999996	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	18	0.44999999999999996	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 30bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTC	15	0.375	RNA PCR Primer, Index 23 (100% over 44bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	15	0.375	RNA PCR Primer, Index 1 (100% over 31bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	12	0.3	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	12	0.3	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	11	0.27499999999999997	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	11	0.27499999999999997	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	10	0.25	RNA PCR Primer, Index 1 (100% over 25bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	10	0.25	No Hit
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGC	9	0.22499999999999998	RNA PCR Primer, Index 23 (100% over 50bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	8	0.2	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	8	0.2	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	8	0.2	No Hit
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	8	0.2	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
TCCCTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAAT	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ACCCTGTAGATCCGAATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTCAGGATGGCCGAGCGGTCTAAGGCTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
GCATTGGTAGTTCAATGGTAGAATTCTCGCCTCCCTGGAATTCTCGGGTG	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	6	0.15	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	6	0.15	No Hit
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGTG	6	0.15	No Hit
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
CTAGACTGAGGCTCCTTGAGGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
TATTGCACTTGTCCCGGCCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTGGAATTCTCGGGT	5	0.125	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>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	0.25	0.0	0.0	0.0
2	0.0	0.25	0.0	0.0	0.0
3	0.0	0.375	0.0	0.0	0.0
4	0.0	0.4	0.0	0.0	0.0
5	0.0	0.425	0.0	0.0	0.0
6	0.0	0.55	0.0	0.0	0.0
7	0.0	1.0	0.0	0.0	0.0
8	0.0	1.025	0.0	0.0	0.0
9	0.0	1.175	0.0	0.0	0.0
10	0.0	1.3	0.0	0.0	0.0
11	0.0	1.5	0.0	0.0	0.0
12	0.0	1.625	0.0	0.0	0.0
13	0.0	1.725	0.0	0.0	0.0
14	0.0	1.95	0.0	0.0	0.0
15	0.0	2.125	0.0	0.0	0.0
16	0.0	3.475	0.0	0.0	0.0
17	0.0	4.025	0.0	0.0	0.0
18	0.0	5.0	0.0	0.0	0.0
19	0.0	5.65	0.0	0.0	0.0
20	0.0	6.575	0.0	0.0	0.0
21	0.0	12.0	0.0	0.0	0.0
22	0.0	21.25	0.0	0.0	0.0
23	0.0	47.3	0.0	0.0	0.0
24	0.0	60.075	0.0	0.0	0.0
25	0.0	65.9	0.0	0.0	0.0
26	0.0	67.925	0.0	0.0	0.0
27	0.0	68.975	0.0	0.0	0.0
28	0.0	69.65	0.0	0.0	0.0
29	0.0	70.3	0.0	0.0	0.0
30	0.0	70.9	0.0	0.0	0.0
31	0.0	71.95	0.0	0.0	0.0
32	0.0	74.2	0.0	0.0	0.0
33	0.0	75.475	0.0	0.0	0.0
34	0.0	80.275	0.0	0.0	0.0
35	0.0	81.55	0.0	0.0	0.0
36	0.0	82.8	0.0	0.0	0.0
37	0.0	84.6	0.0	0.0	0.0
38	0.0	85.125	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	45	2.728484E-10	44.000004	8
CGCTGAT	20	6.952051E-4	44.000004	28
ACGCTGT	45	2.728484E-10	44.000004	9
TAAACAT	20	6.952051E-4	44.000004	3
AAACATC	20	6.952051E-4	44.000004	4
TTCAACG	45	2.728484E-10	44.000004	5
CCGCTGA	20	6.952051E-4	44.000004	27
ACCCGCT	20	6.952051E-4	44.000004	25
CTGATGG	20	6.952051E-4	44.000004	30
TCAACGC	45	2.728484E-10	44.000004	6
GAGTTGG	20	6.952051E-4	44.000004	20
CCCGCTG	20	6.952051E-4	44.000004	26
GCTGATG	20	6.952051E-4	44.000004	29
GCTTGGC	40	5.315087E-9	44.000004	15
AGTTGGA	20	6.952051E-4	44.000004	21
TTGGCTT	20	6.952051E-4	44.000004	17
GACCCGC	20	6.952051E-4	44.000004	24
TGAGTTG	20	6.952051E-4	44.000004	19
TGTAAAC	20	6.952051E-4	44.000004	1
GTAAACA	20	6.952051E-4	44.000004	2
>>END_MODULE
Read 45840 spots for SRR5031051.sra
Written 45840 spots for SRR5031051.sra
Read 45840 spots for SRR5031051.sra
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Read 45840 spots for SRR5031051.sra
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Read 45840 spots for SRR5031051.sra
Written 45840 spots for SRR5031051.sra
Read 45840 spots for SRR5031051.sra
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Read 45840 spots for SRR5031051.sra
Written 45840 spots for SRR5031051.sra
Read 45840 spots for SRR5031051.sra
Written 45840 spots for SRR5031051.sra
Read 45840 spots for SRR5031051.sra
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Read 45840 spots for SRR5031051.sra
Written 45840 spots for SRR5031051.sra
Read 45840 spots for SRR5031051.sra
Written 45840 spots for SRR5031051.sra
Read 45840 spots for SRR5031051.sra
Written 45840 spots for SRR5031051.sra
Read 45840 spots for SRR5031051.sra
Written 45840 spots for SRR5031051.sra
Read 45840 spots for SRR5031051.sra
Written 45840 spots for SRR5031051.sra
Read 45840 spots for SRR5031051.sra
Written 45840 spots for SRR5031051.sra
Read 45840 spots for SRR5031051.sra
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Written 45840 spots for SRR5031051.sra
Read 45840 spots for SRR5031051.sra
Written 45840 spots for SRR5031051.sra
Read 45840 spots for SRR5031051.sra
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Read 45840 spots for SRR5031051.sra
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Read 45840 spots for SRR5031051.sra
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Read 45880 spots for SRR5031051.sra
Written 45880 spots for SRR5031051.sra
SRR ids: ['SRR5031051.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_bvyg6jv0
SRR5031051.sra spots: 2200360
blocks: [[1, 45840], [45841, 91680], [91681, 137520], [137521, 183360], [183361, 229200], [229201, 275040], [275041, 320880], [320881, 366720], [366721, 412560], [412561, 458400], [458401, 504240], [504241, 550080], [550081, 595920], [595921, 641760], [641761, 687600], [687601, 733440], [733441, 779280], [779281, 825120], [825121, 870960], [870961, 916800], [916801, 962640], [962641, 1008480], [1008481, 1054320], [1054321, 1100160], [1100161, 1146000], [1146001, 1191840], [1191841, 1237680], [1237681, 1283520], [1283521, 1329360], [1329361, 1375200], [1375201, 1421040], [1421041, 1466880], [1466881, 1512720], [1512721, 1558560], [1558561, 1604400], [1604401, 1650240], [1650241, 1696080], [1696081, 1741920], [1741921, 1787760], [1787761, 1833600], [1833601, 1879440], [1879441, 1925280], [1925281, 1971120], [1971121, 2016960], [2016961, 2062800], [2062801, 2108640], [2108641, 2154480], [2154481, 2200360]]
SRR5031051 file size 380302
SRR5031051 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5031051 SRR5031051_1.fastq
Input file:	SRR5031051_1.fastq
trimmed:	SRR5031051-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):	32
Wed Mar  4 07:13:52 2020 >> started

Wed Mar  4 07:13:53 2020 >> done (1.371s)
2200360 reads processed; of these:
    267 ( 0.01%) short reads filtered out after trimming by size control
     15 ( 0.00%) empty reads filtered out after trimming by size control
2200078 (99.99%) reads available; of these:
 113138 ( 5.14%) trimmed reads available after processing
2086940 (94.86%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     59	  0.00%
 19	     63	  0.00%
 20	     83	  0.00%
 21	    125	  0.01%
 22	    248	  0.01%
 23	    296	  0.01%
 24	    314	  0.01%
 25	    417	  0.02%
 26	    406	  0.02%
 27	    372	  0.02%
 28	    484	  0.02%
 29	    659	  0.03%
 30	    490	  0.02%
 31	    597	  0.03%
 32	    613	  0.03%
 33	    811	  0.04%
 34	   1043	  0.05%
 35	   2052	  0.09%
 36	   1828	  0.08%
 37	   2010	  0.09%
 38	   2089	  0.09%
 39	   2173	  0.10%
 40	   2400	  0.11%
 41	   2448	  0.11%
 42	   3348	  0.15%
 43	   4572	  0.21%
 44	   6172	  0.28%
 45	   8058	  0.37%
 46	  12196	  0.55%
 47	  14377	  0.65%
 48	  20215	  0.92%
 49	  22120	  1.01%
 50	2086940	 94.86%
2200078 reads passed initial QC


criterion=sequence-density
sequence-density=84.20
sequence-density-rank=1
fanout-score=22.71
fanout-score-rank=1
prefix-density=86.87
prefix-fanout=22.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC


criterion=fanout-score
sequence-density=84.20
sequence-density-rank=1
fanout-score=22.71
fanout-score-rank=1
prefix-density=86.87
prefix-fanout=22.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC
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 48 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC -o SRR5031051 -
Input file:	STDIN
trimmed:	SRR5031051-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC
-- 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):	32
Wed Mar  4 07:14:08 2020 >> started

Wed Mar  4 07:14:12 2020 >> done (3.215s)
2148312 reads processed; of these:
 116589 ( 5.43%) short reads filtered out after trimming by size control
   9951 ( 0.46%) empty reads filtered out after trimming by size control
2021772 (94.11%) reads available; of these:
1913272 (94.63%) trimmed reads available after processing
 108500 ( 5.37%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  11743	  0.58%
 19	  19256	  0.95%
 20	 100357	  4.96%
 21	 207509	 10.26%
 22	 575205	 28.45%
 23	 281921	 13.94%
 24	 125229	  6.19%
 25	  38274	  1.89%
 26	  20094	  0.99%
 27	  16128	  0.80%
 28	  17875	  0.88%
 29	  15148	  0.75%
 30	  22858	  1.13%
 31	  43612	  2.16%
 32	  29147	  1.44%
 33	 103552	  5.12%
 34	  34156	  1.69%
 35	  29503	  1.46%
 36	  34197	  1.69%
 37	  14004	  0.69%
 38	  17987	  0.89%
 39	  13551	  0.67%
 40	  21031	  1.04%
 41	  24493	  1.21%
 42	  27788	  1.37%
 43	  19263	  0.95%
 44	  13873	  0.69%
 45	  20458	  1.01%
 46	  14819	  0.73%
 47	  11581	  0.57%
 48	    898	  0.04%
 49	   1278	  0.06%
 50	  94984	  4.70%


criterion=sequence-density
sequence-density=3.00
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCT


criterion=fanout-score
sequence-density=0.53
sequence-density-rank=30
fanout-score=16.50
fanout-score-rank=1
prefix-density=8.71
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:14:50
                             Started mapping on |	Mar 04 07:14:50
                                    Finished on |	Mar 04 07:15:17
       Mapping speed, Million of reads per hour |	276.47

                          Number of input reads |	2073538
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1070185
                        Uniquely mapped reads % |	51.61%
                          Average mapped length |	25.00
                       Number of splices: Total |	1605
            Number of splices: Annotated (sjdb) |	291
                       Number of splices: GT/AG |	1537
                       Number of splices: GC/AG |	21
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	47
                      Mismatch rate per base, % |	0.23%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.79
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.04
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	669828
             % of reads mapped to multiple loci |	32.30%
        Number of reads mapped to too many loci |	54534
             % of reads mapped to too many loci |	2.63%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.51%
                     % of reads unmapped: other |	0.95%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	333525	333525	333525
N_multimapping	669828	669828	669828
N_noFeature	75051	90443	707950
N_ambiguous	575412	254294	9699
UnstrandedReadsAssigned:419722 PositiveStrandReadsAssigned:725448 NegativeStrandReadsAssigned:352536
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031051 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: SRR5031051-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,073,538 reads, 502,680 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,138 rounds

 109283 SRR5031051.ke.tsv
  52636 SRR5031051.se.tsv
 161919 total
==> SRR5031051.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

==> SRR5031051.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031051 completed mapping pipeline successfully
