Starting /dee2/code/volunteer_pipeline.sh SRR5031013
    current disk space = 160522485760
    free memory = 73968608 
SRR5031013 SRAfilesize
8dc6c8cce178594ad696c475c6e95c3c  SRR5031013.sra
SRR5031013.sra file validated
SRR5031013 is single end
SRR5031013 is conventional basespace
SRR5031013 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031013_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	32.2645	33.0	31.0	34.0	31.0	34.0
2	32.519	34.0	31.0	34.0	31.0	34.0
3	32.5295	34.0	31.0	34.0	31.0	34.0
4	36.068	37.0	35.0	37.0	35.0	37.0
5	36.01225	37.0	35.0	37.0	35.0	37.0
6	35.84325	37.0	35.0	37.0	33.0	37.0
7	35.74225	37.0	35.0	37.0	33.0	37.0
8	35.88575	37.0	35.0	37.0	35.0	37.0
9	37.45475	39.0	37.0	39.0	34.0	39.0
10	37.4885	39.0	37.0	39.0	35.0	39.0
11	37.1205	39.0	37.0	39.0	33.0	39.0
12	37.4495	39.0	37.0	39.0	34.0	39.0
13	37.4965	39.0	37.0	39.0	34.0	39.0
14	38.7435	40.0	38.0	41.0	34.0	41.0
15	38.7555	40.0	38.0	41.0	34.0	41.0
16	38.80775	40.0	38.0	41.0	35.0	41.0
17	39.028	40.0	38.0	41.0	35.0	41.0
18	38.825	40.0	38.0	41.0	34.0	41.0
19	38.7745	40.0	38.0	41.0	34.0	41.0
20	38.661	40.0	38.0	41.0	34.0	41.0
21	38.71375	40.0	38.0	41.0	34.0	41.0
22	38.71525	40.0	38.0	41.0	34.0	41.0
23	38.462	40.0	38.0	41.0	34.0	41.0
24	38.699	40.0	38.0	41.0	34.0	41.0
25	38.958	40.0	38.0	41.0	35.0	41.0
26	38.778	40.0	38.0	41.0	35.0	41.0
27	38.84575	40.0	38.0	41.0	35.0	41.0
28	38.602	40.0	38.0	41.0	34.0	41.0
29	38.14475	40.0	38.0	41.0	33.0	41.0
30	38.06375	40.0	38.0	41.0	33.0	41.0
31	38.3035	40.0	38.0	41.0	33.0	41.0
32	38.27075	40.0	38.0	41.0	33.0	41.0
33	37.913	40.0	38.0	41.0	33.0	41.0
34	38.03225	40.0	38.0	41.0	33.0	41.0
35	37.90025	40.0	37.0	41.0	33.0	41.0
36	37.84925	40.0	37.0	41.0	33.0	41.0
37	37.246	40.0	37.0	41.0	31.0	41.0
38	36.982	39.0	36.0	41.0	31.0	41.0
39	37.53975	39.0	37.0	41.0	32.0	41.0
40	37.6875	40.0	37.0	41.0	33.0	41.0
41	37.78675	40.0	37.0	41.0	33.0	41.0
42	37.57775	40.0	37.0	41.0	33.0	41.0
43	37.6735	40.0	37.0	41.0	33.0	41.0
44	37.7065	40.0	37.0	41.0	33.0	41.0
45	37.5655	40.0	37.0	41.0	33.0	41.0
46	37.27825	40.0	37.0	41.0	32.0	41.0
47	36.718	40.0	35.0	41.0	30.0	41.0
48	36.4125	39.0	35.0	41.0	30.0	41.0
49	36.5515	39.0	35.0	41.0	31.0	41.0
50	36.06875	39.0	35.0	41.0	30.0	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
16	1.0
17	1.0
18	1.0
19	2.0
20	6.0
21	2.0
22	3.0
23	3.0
24	12.0
25	10.0
26	21.0
27	16.0
28	27.0
29	38.0
30	46.0
31	81.0
32	97.0
33	116.0
34	192.0
35	202.0
36	279.0
37	476.0
38	715.0
39	1653.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.95	24.75	48.125	18.175
2	25.763645468202302	25.963945918878316	18.5277916875313	29.744616925388083
3	26.450000000000003	18.625	22.35	32.574999999999996
4	35.199999999999996	27.750000000000004	14.099999999999998	22.95
5	21.7	42.05	24.975	11.275
6	32.925	14.725	34.975	17.375
7	15.625	19.7	23.674999999999997	41.0
8	22.900000000000002	26.525	18.05	32.525
9	22.325	30.675	27.800000000000004	19.2
10	20.575	24.075	27.725	27.625
11	33.074999999999996	10.625	16.5	39.800000000000004
12	17.025000000000002	20.125	29.675	33.175
13	33.300000000000004	16.2	32.925	17.575
14	29.95	30.099999999999998	20.424999999999997	19.525000000000002
15	34.375	25.174999999999997	26.6	13.850000000000001
16	19.825	19.2	21.55	39.425
17	24.075	21.75	38.675	15.5
18	25.25	17.675	29.275000000000002	27.800000000000004
19	38.2	13.975000000000001	29.2	18.625
20	43.125	15.5	28.375	13.0
21	26.474999999999998	19.875	25.324999999999996	28.325
22	31.674999999999997	15.1	42.475	10.75
23	26.650000000000002	14.325	40.400000000000006	18.625
24	48.975	15.575	24.5	10.95
25	47.075	27.1	15.775	10.05
26	27.3	42.575	14.975	15.15
27	16.775000000000002	42.699999999999996	24.325	16.2
28	13.25	23.974999999999998	44.125	18.65
29	15.275	13.025	52.7	19.0
30	10.174999999999999	7.375	36.65	45.800000000000004
31	15.675	5.175	44.85	34.300000000000004
32	30.5	6.675000000000001	22.375	40.45
33	50.975	10.65	13.125	25.25
34	56.3	7.575	19.075	17.05
35	61.975	8.425	18.9	10.7
36	44.925	8.525	32.275	14.274999999999999
37	42.9	12.15	19.775000000000002	25.174999999999997
38	23.849999999999998	19.375	12.125	44.65
39	17.575	24.025	12.325	46.075
40	17.4	44.775	13.275	24.55
41	24.8	45.050000000000004	9.9	20.25
42	45.025	28.95	14.499999999999998	11.525
43	48.55	28.449999999999996	10.25	12.75
44	33.4	43.775	7.225	15.6
45	22.275	45.574999999999996	14.2	17.95
46	17.575	25.474999999999998	18.35	38.6
47	9.925	16.475	37.724999999999994	35.875
48	12.775	13.375	21.349999999999998	52.5
49	14.674999999999999	18.775	15.35	51.2
50	17.625	33.025	14.899999999999999	34.449999999999996
>>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	0.0
22	0.0
23	1.0
24	2.0
25	1.0
26	0.0
27	0.0
28	0.0
29	2.5
30	5.0
31	11.5
32	18.0
33	14.0
34	10.0
35	20.0
36	30.0
37	28.0
38	26.0
39	36.0
40	46.0
41	47.5
42	49.0
43	66.5
44	84.0
45	126.0
46	168.0
47	269.5
48	371.0
49	470.5
50	570.0
51	692.0
52	814.0
53	632.0
54	450.0
55	509.0
56	568.0
57	419.0
58	270.0
59	173.5
60	77.0
61	66.5
62	56.0
63	125.0
64	194.0
65	120.0
66	46.0
67	31.5
68	17.0
69	28.0
70	39.0
71	58.0
72	77.0
73	41.0
74	5.0
75	3.0
76	1.0
77	1.5
78	2.0
79	2.5
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	0.15
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	36.225
#Duplication Level	Percentage of deduplicated	Percentage of total
1	73.29192546583852	26.55
2	11.939268461007591	8.649999999999999
3	3.7267080745341614	4.05
4	2.9675638371290542	4.3
5	1.6563146997929608	3.0
6	0.759144237405107	1.6500000000000001
7	0.6211180124223602	1.575
8	0.759144237405107	2.1999999999999997
9	0.06901311249137336	0.22499999999999998
>10	3.657694962042788	26.674999999999997
>50	0.13802622498274672	3.4750000000000005
>100	0.4140786749482402	17.65
>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
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	138	3.45	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	131	3.2750000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	115	2.875	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	111	2.775	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	107	2.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	104	2.6	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	81	2.025	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	58	1.4500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGC	49	1.225	RNA PCR Primer, Index 33 (100% over 50bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	47	1.175	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	36	0.8999999999999999	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	30	0.75	RNA PCR Primer, Index 7 (100% over 35bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	25	0.625	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTC	22	0.5499999999999999	RNA PCR Primer, Index 33 (100% over 44bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	22	0.5499999999999999	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	19	0.475	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	15	0.375	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	13	0.325	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	13	0.325	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	13	0.325	RNA PCR Primer, Index 1 (100% over 25bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	12	0.3	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	12	0.3	RNA PCR Primer, Index 1 (100% over 31bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	12	0.3	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	12	0.3	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	11	0.27499999999999997	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	11	0.27499999999999997	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	10	0.25	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ACGAACGAGACTCTGGCATGCTAACTAGTTACGCGACCCCTGGAATTCTC	6	0.15	No Hit
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTCTCGGGTGCC	6	0.15	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTAT	5	0.125	RNA PCR Primer, Index 33 (100% over 48bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGCATTCTCGGGTGCC	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	5	0.125	RNA PCR Primer, Index 2 (100% over 34bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	5	0.125	No Hit
CTGCGTTCGCGCTCTCCCCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	5	0.125	No Hit
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	5	0.125	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	5	0.125	No Hit
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
>>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	1.375	0.0	0.0	0.0
2	0.0	1.375	0.0	0.0	0.0
3	0.0	1.55	0.0	0.0	0.0
4	0.0	1.55	0.0	0.0	0.0
5	0.0	1.625	0.0	0.0	0.0
6	0.0	1.75	0.0	0.0	0.0
7	0.0	2.475	0.0	0.0	0.0
8	0.0	2.725	0.0	0.0	0.0
9	0.0	2.775	0.0	0.0	0.0
10	0.0	2.875	0.0	0.0	0.0
11	0.0	2.95	0.0	0.0	0.0
12	0.0	3.175	0.0	0.0	0.0
13	0.0	3.3	0.0	0.0	0.0
14	0.0	3.625	0.0	0.0	0.0
15	0.0	3.875	0.0	0.0	0.0
16	0.0	5.05	0.0	0.0	0.0
17	0.0	5.7	0.0	0.0	0.0
18	0.0	6.925	0.0	0.0	0.0
19	0.0	7.375	0.0	0.0	0.0
20	0.0	8.275	0.0	0.0	0.0
21	0.0	14.175	0.0	0.0	0.0
22	0.0	25.1	0.0	0.0	0.0
23	0.0	50.625	0.0	0.0	0.0
24	0.0	63.125	0.0	0.0	0.0
25	0.0	68.95	0.0	0.0	0.0
26	0.0	70.725	0.0	0.0	0.0
27	0.0	71.55	0.0	0.0	0.0
28	0.0	72.1	0.0	0.0	0.0
29	0.0	72.675	0.0	0.0	0.0
30	0.0	73.125	0.0	0.0	0.0
31	0.0	73.575	0.0	0.0	0.0
32	0.0	75.025	0.0	0.0	0.0
33	0.0	75.725	0.0	0.0	0.0
34	0.0	80.8	0.0	0.0	0.0
35	0.0	81.925	0.0	0.0	0.0
36	0.0	82.5	0.0	0.0	0.0
37	0.0	83.65	0.0	0.0	0.0
38	0.0	84.15	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACAGTGA	20	6.952051E-4	44.000004	3
ACCGGTC	20	6.952051E-4	44.000004	10
GGTGAGT	20	6.952051E-4	44.000004	17
AACCGGT	20	6.952051E-4	44.000004	9
GGTCTCT	20	6.952051E-4	44.000004	13
ATAGGCT	20	6.952051E-4	44.000004	16
CTTGGCT	20	6.952051E-4	44.000004	16
GAACCGG	20	6.952051E-4	44.000004	8
GTCTCTT	20	6.952051E-4	44.000004	14
AGGCTTG	20	6.952051E-4	44.000004	18
CGGTGAG	20	6.952051E-4	44.000004	16
AGTGAAC	20	6.952051E-4	44.000004	5
TCTCTTT	20	6.952051E-4	44.000004	15
CGGTCTC	20	6.952051E-4	44.000004	12
TGAACCG	20	6.952051E-4	44.000004	7
CACAGTG	20	6.952051E-4	44.000004	2
CAGTGAA	20	6.952051E-4	44.000004	4
GATAGGC	20	6.952051E-4	44.000004	15
TAGGCTT	20	6.952051E-4	44.000004	17
CCGGTCT	20	6.952051E-4	44.000004	11
>>END_MODULE
Read 157708 spots for SRR5031013.sra
Written 157708 spots for SRR5031013.sra
Read 157708 spots for SRR5031013.sra
Written 157708 spots for SRR5031013.sra
Read 157708 spots for SRR5031013.sra
Written 157708 spots for SRR5031013.sra
Read 157708 spots for SRR5031013.sra
Written 157708 spots for SRR5031013.sra
Read 157708 spots for SRR5031013.sra
Written 157708 spots for SRR5031013.sra
Read 157708 spots for SRR5031013.sra
Written 157708 spots for SRR5031013.sra
Read 157708 spots for SRR5031013.sra
Written 157708 spots for SRR5031013.sra
Read 157708 spots for SRR5031013.sra
Written 157708 spots for SRR5031013.sra
Read 157708 spots for SRR5031013.sra
Written 157708 spots for SRR5031013.sra
Read 157708 spots for SRR5031013.sra
Written 157708 spots for SRR5031013.sra
Read 157711 spots for SRR5031013.sra
Written 157711 spots for SRR5031013.sra
Read 157708 spots for SRR5031013.sra
Written 157708 spots for SRR5031013.sra
SRR ids: ['SRR5031013.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_buueqmcy
SRR5031013.sra spots: 1892499
blocks: [[1, 157708], [157709, 315416], [315417, 473124], [473125, 630832], [630833, 788540], [788541, 946248], [946249, 1103956], [1103957, 1261664], [1261665, 1419372], [1419373, 1577080], [1577081, 1734788], [1734789, 1892499]]
SRR5031013 file size 326938
SRR5031013 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031013 SRR5031013_1.fastq
Input file:	SRR5031013_1.fastq
trimmed:	SRR5031013-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 07:06:17 2020 >> started

Wed Mar  4 07:06:19 2020 >> done (1.441s)
1892499 reads processed; of these:
    205 ( 0.01%) short reads filtered out after trimming by size control
      2 ( 0.00%) empty reads filtered out after trimming by size control
1892292 (99.99%) reads available; of these:
 119629 ( 6.32%) trimmed reads available after processing
1772663 (93.68%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     63	  0.00%
 19	     60	  0.00%
 20	    120	  0.01%
 21	    161	  0.01%
 22	    256	  0.01%
 23	    289	  0.02%
 24	    349	  0.02%
 25	    488	  0.03%
 26	    388	  0.02%
 27	    528	  0.03%
 28	    554	  0.03%
 29	    883	  0.05%
 30	    636	  0.03%
 31	    660	  0.03%
 32	    834	  0.04%
 33	    910	  0.05%
 34	    990	  0.05%
 35	   1733	  0.09%
 36	   1790	  0.09%
 37	   1960	  0.10%
 38	   2145	  0.11%
 39	   2493	  0.13%
 40	   2886	  0.15%
 41	   2709	  0.14%
 42	   3424	  0.18%
 43	   4803	  0.25%
 44	   7022	  0.37%
 45	   9075	  0.48%
 46	  12674	  0.67%
 47	  14024	  0.74%
 48	  20323	  1.07%
 49	  24399	  1.29%
 50	1772663	 93.68%
1892292 reads passed initial QC


criterion=sequence-density
sequence-density=84.55
sequence-density-rank=1
fanout-score=21.02
fanout-score-rank=1
prefix-density=85.97
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCC


criterion=fanout-score
sequence-density=84.55
sequence-density-rank=1
fanout-score=21.02
fanout-score-rank=1
prefix-density=85.97
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCC -o SRR5031013 -
Input file:	STDIN
trimmed:	SRR5031013-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCC
-- 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 07:06:31 2020 >> started

Wed Mar  4 07:06:33 2020 >> done (2.407s)
1847768 reads processed; of these:
 112071 ( 6.07%) short reads filtered out after trimming by size control
  22571 ( 1.22%) empty reads filtered out after trimming by size control
1713126 (92.71%) reads available; of these:
1616967 (94.39%) trimmed reads available after processing
  96159 ( 5.61%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   8592	  0.50%
 19	  19391	  1.13%
 20	  92153	  5.38%
 21	 202053	 11.79%
 22	 496781	 29.00%
 23	 235084	 13.72%
 24	 114566	  6.69%
 25	  32188	  1.88%
 26	  16264	  0.95%
 27	  12183	  0.71%
 28	  12821	  0.75%
 29	   9741	  0.57%
 30	  15393	  0.90%
 31	  25428	  1.48%
 32	  19348	  1.13%
 33	  88971	  5.19%
 34	  21754	  1.27%
 35	  17215	  1.00%
 36	  20726	  1.21%
 37	  10032	  0.59%
 38	  11335	  0.66%
 39	  10397	  0.61%
 40	  15629	  0.91%
 41	  21111	  1.23%
 42	  25888	  1.51%
 43	  18161	  1.06%
 44	  13741	  0.80%
 45	  18876	  1.10%
 46	  13803	  0.81%
 47	  10326	  0.60%
 48	   1110	  0.06%
 49	   2071	  0.12%
 50	  79994	  4.67%


criterion=sequence-density
sequence-density=6.33
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=39
fanout-score=360.82
fanout-score-rank=1
prefix-density=1.97
prefix-fanout=1.8
sequence=TTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:06:53
                             Started mapping on |	Mar 04 07:06:54
                                    Finished on |	Mar 04 07:07:18
       Mapping speed, Million of reads per hour |	263.65

                          Number of input reads |	1757650
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	908131
                        Uniquely mapped reads % |	51.67%
                          Average mapped length |	24.88
                       Number of splices: Total |	902
            Number of splices: Annotated (sjdb) |	169
                       Number of splices: GT/AG |	839
                       Number of splices: GC/AG |	10
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	51
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.80
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.01
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	564051
             % of reads mapped to multiple loci |	32.09%
        Number of reads mapped to too many loci |	45322
             % of reads mapped to too many loci |	2.58%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.98%
                     % of reads unmapped: other |	0.69%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	285468	285468	285468
N_multimapping	564051	564051	564051
N_noFeature	53206	64684	624075
N_ambiguous	494749	250093	9841
UnstrandedReadsAssigned:360176 PositiveStrandReadsAssigned:593354 NegativeStrandReadsAssigned:274215
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031013 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: SRR5031013-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,757,650 reads, 426,285 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 760 rounds

 109283 SRR5031013.ke.tsv
  52636 SRR5031013.se.tsv
 161919 total
==> SRR5031013.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

==> SRR5031013.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031013 completed mapping pipeline successfully
