Starting /dee2/code/volunteer_pipeline.sh SRR5030999
    current disk space = 160564690944
    free memory = 56714952 
SRR5030999 SRAfilesize
efb4d87658f4dfed27c3f97be2f76f68  SRR5030999.sra
SRR5030999.sra file validated
SRR5030999 is single end
SRR5030999 is conventional basespace
SRR5030999 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030999_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	32.36375	33.0	31.0	34.0	31.0	34.0
2	32.5585	34.0	31.0	34.0	31.0	34.0
3	32.5135	34.0	31.0	34.0	31.0	34.0
4	36.17825	37.0	35.0	37.0	35.0	37.0
5	36.08025	37.0	35.0	37.0	35.0	37.0
6	35.90975	37.0	35.0	37.0	35.0	37.0
7	35.97275	37.0	35.0	37.0	35.0	37.0
8	36.02425	37.0	35.0	37.0	35.0	37.0
9	37.70875	39.0	37.0	39.0	35.0	39.0
10	37.5795	39.0	37.0	39.0	35.0	39.0
11	37.317	39.0	37.0	39.0	33.0	39.0
12	37.58225	39.0	37.0	39.0	35.0	39.0
13	37.60425	39.0	37.0	39.0	35.0	39.0
14	39.0385	40.0	38.0	41.0	36.0	41.0
15	39.07425	40.0	38.0	41.0	36.0	41.0
16	39.01325	40.0	38.0	41.0	36.0	41.0
17	39.06825	40.0	38.0	41.0	36.0	41.0
18	38.9565	40.0	38.0	41.0	35.0	41.0
19	38.61825	40.0	38.0	41.0	34.0	41.0
20	38.669	40.0	38.0	41.0	34.0	41.0
21	38.79425	40.0	38.0	41.0	35.0	41.0
22	38.80675	40.0	38.0	41.0	35.0	41.0
23	38.437	40.0	38.0	41.0	34.0	41.0
24	38.7905	40.0	38.0	41.0	35.0	41.0
25	38.912	40.0	38.0	41.0	35.0	41.0
26	38.8005	40.0	38.0	41.0	34.0	41.0
27	38.98225	40.0	38.0	41.0	35.0	41.0
28	38.85	40.0	38.0	41.0	35.0	41.0
29	38.63475	40.0	38.0	41.0	34.0	41.0
30	38.6585	40.0	38.0	41.0	34.0	41.0
31	38.79975	40.0	38.0	41.0	35.0	41.0
32	38.81425	40.0	38.0	41.0	35.0	41.0
33	38.487	40.0	38.0	41.0	34.0	41.0
34	38.38825	40.0	38.0	41.0	34.0	41.0
35	38.1535	40.0	38.0	41.0	33.0	41.0
36	37.94375	40.0	37.0	41.0	33.0	41.0
37	37.319	40.0	37.0	41.0	31.0	41.0
38	37.282	39.0	37.0	41.0	31.0	41.0
39	37.87725	40.0	37.0	41.0	33.0	41.0
40	37.98775	40.0	37.0	41.0	33.0	41.0
41	38.12025	40.0	38.0	41.0	33.0	41.0
42	37.97975	40.0	38.0	41.0	33.0	41.0
43	37.74675	40.0	37.0	41.0	33.0	41.0
44	37.80125	40.0	37.0	41.0	33.0	41.0
45	37.81075	40.0	37.0	41.0	33.0	41.0
46	37.71	40.0	37.0	41.0	33.0	41.0
47	37.3555	40.0	37.0	41.0	32.0	41.0
48	37.19775	40.0	37.0	41.0	32.0	41.0
49	37.30325	40.0	37.0	41.0	32.0	41.0
50	36.5335	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
17	1.0
18	2.0
19	2.0
20	2.0
21	7.0
22	4.0
23	5.0
24	5.0
25	8.0
26	14.0
27	16.0
28	24.0
29	33.0
30	45.0
31	59.0
32	77.0
33	112.0
34	154.0
35	181.0
36	281.0
37	446.0
38	698.0
39	1824.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.5249999999999995	23.474999999999998	54.75	14.249999999999998
2	23.181133968891118	25.89061716006021	22.528850978424487	28.399397892624183
3	18.65	17.675	19.85	43.824999999999996
4	27.474999999999998	36.25	13.15	23.125
5	20.925	38.0	28.775000000000002	12.3
6	34.9	14.575	38.15	12.375
7	14.124999999999998	24.45	23.5	37.925
8	23.25	39.625	14.499999999999998	22.625
9	19.975	38.175	28.9	12.950000000000001
10	19.6	20.375	26.125	33.900000000000006
11	31.825	11.200000000000001	15.375	41.6
12	17.150000000000002	15.299999999999999	23.575	43.974999999999994
13	21.8	20.175	38.0	20.025000000000002
14	37.925	24.625	25.025	12.425
15	39.175	20.875	28.849999999999998	11.1
16	12.15	25.324999999999996	22.325	40.2
17	26.05	22.45	37.375	14.124999999999998
18	29.775000000000002	18.25	27.150000000000002	24.825
19	39.550000000000004	13.125	30.099999999999998	17.224999999999998
20	49.975	17.175	21.875	10.975
21	22.275	26.450000000000003	23.400000000000002	27.875
22	33.25	12.5	47.275	6.9750000000000005
23	24.5	12.950000000000001	49.5	13.05
24	52.349999999999994	14.124999999999998	27.200000000000003	6.325
25	55.400000000000006	22.225	14.224999999999998	8.15
26	29.5	48.275	12.049999999999999	10.174999999999999
27	12.875	53.05	23.025000000000002	11.05
28	9.25	26.525	51.175000000000004	13.05
29	10.75	10.674999999999999	60.875	17.7
30	10.025	5.050000000000001	38.275	46.650000000000006
31	13.5	4.2	46.725	35.575
32	24.925	5.625	23.150000000000002	46.300000000000004
33	55.2	6.6000000000000005	12.85	25.35
34	68.475	6.65	12.525	12.35
35	67.975	5.75	18.3	7.9750000000000005
36	42.375	6.550000000000001	39.525	11.55
37	46.825	9.8	22.0	21.375
38	24.75	14.6	11.625	49.025
39	13.125	22.775000000000002	8.0	56.10000000000001
40	13.875000000000002	49.875	9.325	26.924999999999997
41	21.775	55.225	9.4	13.600000000000001
42	51.55	30.725	8.475000000000001	9.25
43	57.599999999999994	26.575	7.7	8.125
44	31.874999999999996	50.5	6.25	11.375
45	15.975	55.574999999999996	11.0	17.45
46	10.174999999999999	27.55	17.775	44.5
47	8.275	13.950000000000001	40.5	37.275000000000006
48	9.15	10.75	23.0	57.099999999999994
49	12.675	17.474999999999998	12.35	57.49999999999999
50	17.675	39.875	11.1	31.35
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	1.0
26	1.0
27	0.5
28	0.0
29	1.0
30	2.0
31	6.0
32	10.0
33	13.0
34	16.0
35	15.0
36	14.0
37	22.0
38	30.0
39	27.0
40	24.0
41	30.5
42	37.0
43	71.0
44	105.0
45	158.0
46	211.0
47	399.0
48	587.0
49	592.0
50	597.0
51	813.5
52	1030.0
53	691.0
54	352.0
55	379.5
56	407.0
57	351.5
58	296.0
59	186.5
60	77.0
61	54.5
62	32.0
63	54.5
64	77.0
65	49.0
66	21.0
67	14.5
68	8.0
69	12.0
70	16.0
71	29.0
72	42.0
73	22.5
74	3.0
75	2.0
76	1.0
77	1.0
78	1.0
79	1.5
80	2.0
81	1.0
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	0.35000000000000003
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	36.325
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.4301445285616	27.400000000000002
2	9.772883688919478	7.1
3	4.748795595320027	5.175
4	1.9958706125258088	2.9000000000000004
5	0.8947006194081212	1.625
6	1.032346868547832	2.25
7	0.8947006194081212	2.275
8	0.6882312456985548	2.0
9	0.4817618719889883	1.575
>10	3.64762560220234	26.5
>50	0.13764624913971094	3.5000000000000004
>100	0.27529249827942187	17.7
>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	251	6.275	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	186	4.65	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	147	3.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	124	3.1	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	78	1.95	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	62	1.55	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	50	1.25	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	43	1.075	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	37	0.9249999999999999	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	27	0.675	RNA PCR Primer, Index 1 (97% over 35bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGC	25	0.625	RNA PCR Primer, Index 19 (100% over 50bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTC	19	0.475	RNA PCR Primer, Index 19 (100% over 44bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	17	0.42500000000000004	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	15	0.375	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	15	0.375	No Hit
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	12	0.3	No Hit
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 31bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	11	0.27499999999999997	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTGGAATTCTCGGGTGCCA	8	0.2	No Hit
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	8	0.2	RNA PCR Primer, Index 6 (100% over 34bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	8	0.2	No Hit
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	7	0.17500000000000002	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	7	0.17500000000000002	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	7	0.17500000000000002	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGA	6	0.15	RNA PCR Primer, Index 19 (100% over 37bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ATAGTGGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AGAGGTAGTAGGTTGCATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGAATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCTC	5	0.125	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	5	0.125	No Hit
CACCCGTAGAACCGACCTTGCGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TAGCACCATCTGAAATCGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TAAGGCACGCGGTGAATGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGGAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTGGAATTCTCGGGTGC	5	0.125	No Hit
TGTAAACATCCTCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	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	0.675	0.0	0.0	0.0
2	0.0	0.7	0.0	0.0	0.0
3	0.0	0.775	0.0	0.0	0.0
4	0.0	0.825	0.0	0.0	0.0
5	0.0	0.875	0.0	0.0	0.0
6	0.0	0.875	0.0	0.0	0.0
7	0.0	1.35	0.0	0.0	0.0
8	0.0	1.425	0.0	0.0	0.0
9	0.0	1.475	0.0	0.0	0.0
10	0.0	1.725	0.0	0.0	0.0
11	0.0	1.825	0.0	0.0	0.0
12	0.0	2.0	0.0	0.0	0.0
13	0.0	2.125	0.0	0.0	0.0
14	0.0	2.425	0.0	0.0	0.0
15	0.0	2.675	0.0	0.0	0.0
16	0.0	3.85	0.0	0.0	0.0
17	0.0	4.6	0.0	0.0	0.0
18	0.0	5.325	0.0	0.0	0.0
19	0.0	5.675	0.0	0.0	0.0
20	0.0	6.95	0.0	0.0	0.0
21	0.0	11.5	0.0	0.0	0.0
22	0.0	22.6	0.0	0.0	0.0
23	0.0	55.6	0.0	0.0	0.0
24	0.0	71.85	0.0	0.0	0.0
25	0.0	77.3	0.0	0.0	0.0
26	0.0	78.45	0.0	0.0	0.0
27	0.0	79.0	0.0	0.0	0.0
28	0.0	79.55	0.0	0.0	0.0
29	0.0	80.25	0.0	0.0	0.0
30	0.0	80.875	0.0	0.0	0.0
31	0.0	81.35	0.0	0.0	0.0
32	0.0	82.425	0.0	0.0	0.0
33	0.0	83.7	0.0	0.0	0.0
34	0.0	85.55	0.0	0.0	0.0
35	0.0	86.725	0.0	0.0	0.0
36	0.0	87.6	0.0	0.0	0.0
37	0.0	88.275	0.0	0.0	0.0
38	0.0	88.85	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGAGACC	20	6.952051E-4	44.000004	5
CTCGACT	20	6.952051E-4	44.000004	11
ATCCTCG	20	6.952051E-4	44.000004	8
TCCTCGA	20	6.952051E-4	44.000004	9
TCGACTG	20	6.952051E-4	44.000004	12
CTGAGAC	20	6.952051E-4	44.000004	4
TAAACAT	40	5.315087E-9	44.000004	3
CTTTAAC	20	6.952051E-4	44.000004	12
AAACATC	40	5.315087E-9	44.000004	4
CATCCTC	20	6.952051E-4	44.000004	7
CCTGAGA	20	6.952051E-4	44.000004	3
TCGGATC	20	6.952051E-4	44.000004	1
CATTCAA	40	5.315087E-9	44.000004	3
ACATTCA	40	5.315087E-9	44.000004	2
TAACCTG	20	6.952051E-4	44.000004	15
AGGCTTG	45	2.728484E-10	44.000004	18
ACCCTTT	20	6.952051E-4	44.000004	9
CCTTTAA	20	6.952051E-4	44.000004	11
CCCTGAG	20	6.952051E-4	44.000004	2
GGAAGCT	20	6.952051E-4	44.000004	18
>>END_MODULE
Read 331666 spots for SRR5030999.sra
Written 331666 spots for SRR5030999.sra
Read 331666 spots for SRR5030999.sra
Written 331666 spots for SRR5030999.sra
Read 331666 spots for SRR5030999.sra
Written 331666 spots for SRR5030999.sra
Read 331666 spots for SRR5030999.sra
Written 331666 spots for SRR5030999.sra
Read 331666 spots for SRR5030999.sra
Written 331666 spots for SRR5030999.sra
Read 331666 spots for SRR5030999.sra
Written 331666 spots for SRR5030999.sra
Read 331666 spots for SRR5030999.sra
Written 331666 spots for SRR5030999.sra
Read 331669 spots for SRR5030999.sra
Written 331669 spots for SRR5030999.sra
Read 331666 spots for SRR5030999.sra
Written 331666 spots for SRR5030999.sra
Read 331666 spots for SRR5030999.sra
Written 331666 spots for SRR5030999.sra
Read 331666 spots for SRR5030999.sra
Written 331666 spots for SRR5030999.sra
Read 331666 spots for SRR5030999.sra
Written 331666 spots for SRR5030999.sra
SRR ids: ['SRR5030999.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_da130_3w
SRR5030999.sra spots: 3979995
blocks: [[1, 331666], [331667, 663332], [663333, 994998], [994999, 1326664], [1326665, 1658330], [1658331, 1989996], [1989997, 2321662], [2321663, 2653328], [2653329, 2984994], [2984995, 3316660], [3316661, 3648326], [3648327, 3979995]]
SRR5030999 file size 688762
SRR5030999 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030999 SRR5030999_1.fastq
Input file:	SRR5030999_1.fastq
trimmed:	SRR5030999-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 07:03:05 2020 >> started

Wed Mar  4 07:03:07 2020 >> done (2.349s)
3979995 reads processed; of these:
    200 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
3979789 (99.99%) reads available; of these:
 223690 ( 5.62%) trimmed reads available after processing
3756099 (94.38%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     66	  0.00%
 19	     83	  0.00%
 20	    183	  0.00%
 21	    243	  0.01%
 22	    453	  0.01%
 23	    517	  0.01%
 24	    526	  0.01%
 25	    649	  0.02%
 26	    530	  0.01%
 27	    697	  0.02%
 28	    845	  0.02%
 29	   1492	  0.04%
 30	    968	  0.02%
 31	    983	  0.02%
 32	   1134	  0.03%
 33	   1572	  0.04%
 34	   2140	  0.05%
 35	   4382	  0.11%
 36	   3583	  0.09%
 37	   4015	  0.10%
 38	   3532	  0.09%
 39	   3919	  0.10%
 40	   4420	  0.11%
 41	   4659	  0.12%
 42	   6202	  0.16%
 43	   9162	  0.23%
 44	  11554	  0.29%
 45	  14987	  0.38%
 46	  20285	  0.51%
 47	  26123	  0.66%
 48	  42705	  1.07%
 49	  51081	  1.28%
 50	3756099	 94.38%
3979789 reads passed initial QC


criterion=sequence-density
sequence-density=88.76
sequence-density-rank=1
fanout-score=18.87
fanout-score-rank=1
prefix-density=90.02
prefix-fanout=18.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCC


criterion=fanout-score
sequence-density=88.76
sequence-density-rank=1
fanout-score=18.87
fanout-score-rank=1
prefix-density=90.02
prefix-fanout=18.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCC -o SRR5030999 -
Input file:	STDIN
trimmed:	SRR5030999-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCC
-- 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 07:03:25 2020 >> started

Wed Mar  4 07:03:32 2020 >> done (6.552s)
3890356 reads processed; of these:
 180387 ( 4.64%) short reads filtered out after trimming by size control
  35035 ( 0.90%) empty reads filtered out after trimming by size control
3674934 (94.46%) reads available; of these:
3536043 (96.22%) trimmed reads available after processing
 138891 ( 3.78%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  19121	  0.52%
 19	  43613	  1.19%
 20	 178895	  4.87%
 21	 432019	 11.76%
 22	1292949	 35.18%
 23	 653288	 17.78%
 24	 228785	  6.23%
 25	  42123	  1.15%
 26	  21464	  0.58%
 27	  20575	  0.56%
 28	  23828	  0.65%
 29	  19881	  0.54%
 30	  34065	  0.93%
 31	  42954	  1.17%
 32	  50082	  1.36%
 33	  83700	  2.28%
 34	  40680	  1.11%
 35	  24677	  0.67%
 36	  27013	  0.74%
 37	  18699	  0.51%
 38	  20882	  0.57%
 39	  19498	  0.53%
 40	  26522	  0.72%
 41	  35995	  0.98%
 42	  38121	  1.04%
 43	  29018	  0.79%
 44	  23858	  0.65%
 45	  26759	  0.73%
 46	  20591	  0.56%
 47	  14512	  0.39%
 48	   1618	  0.04%
 49	   3105	  0.08%
 50	 116044	  3.16%


criterion=sequence-density
sequence-density=6.05
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=24
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.42
sequence-density-rank=31
fanout-score=16.14
fanout-score-rank=1
prefix-density=6.77
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 07:03:52
                             Started mapping on |	Mar 04 07:03:52
                                    Finished on |	Mar 04 07:04:18
       Mapping speed, Million of reads per hour |	521.22

                          Number of input reads |	3764367
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1812594
                        Uniquely mapped reads % |	48.15%
                          Average mapped length |	24.48
                       Number of splices: Total |	1880
            Number of splices: Annotated (sjdb) |	245
                       Number of splices: GT/AG |	1749
                       Number of splices: GC/AG |	25
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	104
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.69
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.14
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1551423
             % of reads mapped to multiple loci |	41.21%
        Number of reads mapped to too many loci |	87433
             % of reads mapped to too many loci |	2.32%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.49%
                     % of reads unmapped: other |	0.82%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	400350	400350	400350
N_multimapping	1551423	1551423	1551423
N_noFeature	80730	100785	1371675
N_ambiguous	982139	608190	13518
UnstrandedReadsAssigned:749725 PositiveStrandReadsAssigned:1103619 NegativeStrandReadsAssigned:427401
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5030999 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: SRR5030999-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,764,367 reads, 750,668 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,145 rounds

 109283 SRR5030999.ke.tsv
  52636 SRR5030999.se.tsv
 161919 total
==> SRR5030999.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

==> SRR5030999.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	2
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030999 completed mapping pipeline successfully
