Starting /dee2/code/volunteer_pipeline.sh SRR5030995
    current disk space = 160554205184
    free memory = 73950196 
SRR5030995 SRAfilesize
d102a0f956797c176f8e20c53fbca5c1  SRR5030995.sra
SRR5030995.sra file validated
SRR5030995 is single end
SRR5030995 is conventional basespace
SRR5030995 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030995_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	32.3095	33.0	31.0	34.0	31.0	34.0
2	32.5785	34.0	31.0	34.0	31.0	34.0
3	32.58325	34.0	31.0	34.0	31.0	34.0
4	36.17225	37.0	35.0	37.0	35.0	37.0
5	36.118	37.0	35.0	37.0	35.0	37.0
6	35.92575	37.0	35.0	37.0	35.0	37.0
7	35.8885	37.0	35.0	37.0	35.0	37.0
8	35.974	37.0	35.0	37.0	35.0	37.0
9	37.61875	39.0	37.0	39.0	35.0	39.0
10	37.5515	39.0	37.0	39.0	35.0	39.0
11	37.34425	39.0	37.0	39.0	34.0	39.0
12	37.59375	39.0	37.0	39.0	35.0	39.0
13	37.64	39.0	37.0	39.0	35.0	39.0
14	39.0265	40.0	38.0	41.0	36.0	41.0
15	38.92125	40.0	38.0	41.0	35.0	41.0
16	39.03725	40.0	38.0	41.0	36.0	41.0
17	39.0895	40.0	38.0	41.0	35.0	41.0
18	38.9805	41.0	38.0	41.0	35.0	41.0
19	38.843	40.0	38.0	41.0	35.0	41.0
20	38.818	40.0	38.0	41.0	35.0	41.0
21	38.939	40.0	38.0	41.0	35.0	41.0
22	38.7765	40.0	38.0	41.0	34.0	41.0
23	38.566	40.0	38.0	41.0	34.0	41.0
24	38.83225	40.0	38.0	41.0	35.0	41.0
25	38.9405	40.0	39.0	41.0	35.0	41.0
26	38.83225	40.0	38.0	41.0	35.0	41.0
27	39.03175	40.0	39.0	41.0	35.0	41.0
28	38.838	40.0	38.0	41.0	35.0	41.0
29	38.37225	40.0	38.0	41.0	34.0	41.0
30	38.331	40.0	38.0	41.0	33.0	41.0
31	38.52025	40.0	38.0	41.0	34.0	41.0
32	38.60575	40.0	38.0	41.0	34.0	41.0
33	38.03375	40.0	38.0	41.0	33.0	41.0
34	37.99075	40.0	38.0	41.0	33.0	41.0
35	37.7645	40.0	37.0	41.0	33.0	41.0
36	37.7225	40.0	37.0	41.0	33.0	41.0
37	37.0095	39.0	36.0	41.0	31.0	41.0
38	37.16675	39.0	36.0	41.0	31.0	41.0
39	37.67425	39.0	37.0	41.0	33.0	41.0
40	37.77725	40.0	37.0	41.0	33.0	41.0
41	37.9435	40.0	37.0	41.0	33.0	41.0
42	37.901	40.0	37.0	41.0	33.0	41.0
43	37.815	40.0	37.0	41.0	33.0	41.0
44	37.815	40.0	37.0	41.0	33.0	41.0
45	37.772	40.0	37.0	41.0	33.0	41.0
46	37.5125	40.0	37.0	41.0	33.0	41.0
47	36.7715	40.0	35.0	41.0	30.0	41.0
48	36.705	39.0	35.0	41.0	30.0	41.0
49	36.728	40.0	35.0	41.0	31.0	41.0
50	36.086	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
11	1.0
12	1.0
13	0.0
14	0.0
15	0.0
16	2.0
17	0.0
18	2.0
19	5.0
20	5.0
21	0.0
22	4.0
23	5.0
24	11.0
25	7.0
26	12.0
27	16.0
28	21.0
29	34.0
30	43.0
31	75.0
32	100.0
33	100.0
34	162.0
35	186.0
36	250.0
37	484.0
38	779.0
39	1695.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.175	25.4	45.875	17.549999999999997
2	24.617698671346204	25.294560040110305	19.754324392078214	30.33341689646528
3	24.099999999999998	20.225	23.425	32.25
4	34.1	26.05	16.425	23.425
5	23.0	37.7	26.6	12.7
6	33.575	14.799999999999999	35.125	16.5
7	17.525	21.175	22.575	38.725
8	25.374999999999996	25.624999999999996	18.625	30.375000000000004
9	23.65	30.175	27.625	18.55
10	23.75	22.8	28.325	25.124999999999996
11	31.674999999999997	10.475	19.3	38.550000000000004
12	16.85	18.875	32.475	31.8
13	31.525	17.2	32.550000000000004	18.725
14	29.45	32.074999999999996	19.675	18.8
15	36.175000000000004	24.275	25.75	13.8
16	19.525000000000002	19.35	25.85	35.275
17	27.250000000000004	22.675	35.8	14.274999999999999
18	24.275	18.675	29.299999999999997	27.750000000000004
19	36.4	15.425	29.9	18.275
20	41.525	16.775000000000002	26.424999999999997	15.275
21	24.975	18.8	27.250000000000004	28.975
22	28.625	13.700000000000001	45.1	12.575
23	27.325	14.7	40.25	17.724999999999998
24	49.55	14.899999999999999	26.474999999999998	9.075
25	47.825	23.775	16.125	12.275
26	29.875	42.1	14.399999999999999	13.625000000000002
27	17.2	44.1	23.525	15.174999999999999
28	12.65	24.5	45.324999999999996	17.525
29	14.875	13.275	52.900000000000006	18.95
30	12.1	7.6499999999999995	35.35	44.9
31	14.6	6.4750000000000005	43.325	35.6
32	28.375	6.825	22.475	42.325
33	49.525000000000006	11.0	14.75	24.725
34	57.175	9.125	17.625	16.075
35	62.45	7.049999999999999	20.125	10.375
36	43.725	8.325000000000001	34.475	13.475000000000001
37	42.5	13.675	21.075	22.75
38	24.175	18.3	12.775	44.75
39	17.0	23.925	11.725	47.349999999999994
40	15.25	45.2	14.325	25.224999999999998
41	23.875	46.2	11.55	18.375
42	44.975	28.125	14.725	12.174999999999999
43	49.0	27.6	10.174999999999999	13.225000000000001
44	32.824999999999996	43.824999999999996	9.0	14.35
45	20.150000000000002	47.3	13.625000000000002	18.925
46	16.175	26.3	18.65	38.875
47	11.875	15.475	38.025	34.625
48	13.975000000000001	12.0	21.65	52.37500000000001
49	13.350000000000001	20.175	16.45	50.025
50	17.825	34.449999999999996	15.299999999999999	32.425
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.5
4	1.0
5	0.5
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.5
12	1.0
13	0.5
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	2.0
28	4.0
29	5.0
30	6.0
31	10.5
32	15.0
33	15.0
34	15.0
35	23.0
36	31.0
37	36.0
38	41.0
39	47.5
40	54.0
41	52.5
42	51.0
43	82.0
44	113.0
45	145.0
46	177.0
47	299.0
48	421.0
49	537.0
50	653.0
51	701.0
52	749.0
53	612.0
54	475.0
55	485.0
56	495.0
57	362.0
58	229.0
59	146.0
60	63.0
61	56.5
62	50.0
63	97.5
64	145.0
65	91.5
66	38.0
67	31.0
68	24.0
69	33.0
70	42.0
71	66.5
72	91.0
73	48.5
74	6.0
75	3.0
76	0.0
77	1.5
78	3.0
79	3.0
80	3.0
81	3.5
82	4.0
83	2.0
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	0.27499999999999997
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	38.775
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.08123791102514	28.725
2	11.02514506769826	8.55
3	4.25531914893617	4.95
4	2.7724049000644744	4.3
5	1.4184397163120568	2.75
6	1.3539651837524178	3.15
7	0.7736943907156674	2.1
8	0.6447453255963894	2.0
9	0.3868471953578337	1.35
>10	2.643455834945197	19.3
>50	0.3868471953578337	10.65
>100	0.2578981302385558	12.174999999999999
>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
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	146	3.65	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	119	2.9749999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	119	2.9749999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	103	2.5749999999999997	No Hit
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	95	2.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	83	2.075	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	82	2.0500000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAT	56	1.4000000000000001	RNA PCR Primer, Index 1 (100% over 35bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	56	1.4000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	54	1.35	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	42	1.05	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	40	1.0	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	27	0.675	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	24	0.6	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	22	0.5499999999999999	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTC	19	0.475	RNA PCR Primer, Index 15 (100% over 44bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	14	0.35000000000000003	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGC	14	0.35000000000000003	RNA PCR Primer, Index 15 (100% over 50bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	13	0.325	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	11	0.27499999999999997	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	11	0.27499999999999997	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	10	0.25	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 31bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	9	0.22499999999999998	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	8	0.2	No Hit
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATG	8	0.2	RNA PCR Primer, Index 15 (100% over 36bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	8	0.2	No Hit
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	8	0.2	No Hit
GAAGGATCATTATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTC	8	0.2	RNA PCR Primer, Index 15 (100% over 38bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	7	0.17500000000000002	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	7	0.17500000000000002	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	7	0.17500000000000002	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GCTGTACTGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTG	7	0.17500000000000002	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	7	0.17500000000000002	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	6	0.15	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTG	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GAATGTTGCTCGGTGAACCCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
AACATTCATTGCTGTCGGTGGGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	5	0.125	RNA PCR Primer, Index 1 (100% over 34bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGAATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGAATTCTCGGGTGC	5	0.125	No Hit
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	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	0.425	0.0	0.0	0.0
2	0.0	0.425	0.0	0.0	0.0
3	0.0	0.575	0.0	0.0	0.0
4	0.0	0.6	0.0	0.0	0.0
5	0.0	0.625	0.0	0.0	0.0
6	0.0	0.775	0.0	0.0	0.0
7	0.0	1.375	0.0	0.0	0.0
8	0.0	1.475	0.0	0.0	0.0
9	0.0	1.55	0.0	0.0	0.0
10	0.0	1.775	0.0	0.0	0.0
11	0.0	2.05	0.0	0.0	0.0
12	0.0	2.4	0.0	0.0	0.0
13	0.0	2.825	0.0	0.0	0.0
14	0.0	2.975	0.0	0.0	0.0
15	0.0	3.625	0.0	0.0	0.0
16	0.0	5.6	0.0	0.0	0.0
17	0.0	6.15	0.0	0.0	0.0
18	0.0	7.25	0.0	0.0	0.0
19	0.0	7.675	0.0	0.0	0.0
20	0.0	8.625	0.0	0.0	0.0
21	0.0	13.25	0.0	0.0	0.0
22	0.0	23.85	0.0	0.0	0.0
23	0.0	49.9	0.0	0.0	0.0
24	0.0	62.55	0.0	0.0	0.0
25	0.0	68.225	0.0	0.0	0.0
26	0.0	69.525	0.0	0.0	0.0
27	0.0	70.3	0.0	0.0	0.0
28	0.0	70.9	0.0	0.0	0.0
29	0.0	71.675	0.0	0.0	0.0
30	0.0	72.025	0.0	0.0	0.0
31	0.0	72.6	0.0	0.0	0.0
32	0.0	73.45	0.0	0.0	0.0
33	0.0	74.725	0.0	0.0	0.0
34	0.0	78.9	0.0	0.0	0.0
35	0.0	80.675	0.0	0.0	0.0
36	0.0	81.9	0.0	0.0	0.0
37	0.0	83.35	0.0	0.0	0.0
38	0.0	83.975	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CTTGGCT	20	6.952051E-4	44.000004	16
GGCTTGG	20	6.952051E-4	44.000004	19
GCTTGGC	20	6.952051E-4	44.000004	15
GAGCTTG	30	1.9515464E-6	44.0	13
GGATCCG	30	1.9515464E-6	44.0	3
CCGTCTG	30	1.9515464E-6	44.0	7
TCGGATC	30	1.9515464E-6	44.0	1
CGGATCC	30	1.9515464E-6	44.0	2
GATCCGT	30	1.9515464E-6	44.0	4
TCCGTCT	30	1.9515464E-6	44.0	6
ATCCGTC	30	1.9515464E-6	44.0	5
TGAGCTT	30	1.9515464E-6	44.0	12
CGTCTGA	30	1.9515464E-6	44.0	8
CTGAGCT	35	5.6380304E-6	37.714287	11
AGCTTGG	40	1.4099138E-5	33.0	14
GTTGGAA	50	6.483462E-5	26.4	21
GTCTGAG	60	2.2403775E-4	22.0	9
TCTGAGC	60	2.2403775E-4	22.0	10
TTGGAAT	160	0.0	20.625002	22
AACTCCA	180	0.0	19.555557	44
>>END_MODULE
Read 290106 spots for SRR5030995.sra
Written 290106 spots for SRR5030995.sra
Read 290106 spots for SRR5030995.sra
Written 290106 spots for SRR5030995.sra
Read 290106 spots for SRR5030995.sra
Written 290106 spots for SRR5030995.sra
Read 290106 spots for SRR5030995.sra
Written 290106 spots for SRR5030995.sra
Read 290106 spots for SRR5030995.sra
Written 290106 spots for SRR5030995.sra
Read 290106 spots for SRR5030995.sra
Written 290106 spots for SRR5030995.sra
Read 290106 spots for SRR5030995.sra
Written 290106 spots for SRR5030995.sra
Read 290106 spots for SRR5030995.sra
Written 290106 spots for SRR5030995.sra
Read 290106 spots for SRR5030995.sra
Written 290106 spots for SRR5030995.sra
Read 290106 spots for SRR5030995.sra
Written 290106 spots for SRR5030995.sra
Read 290106 spots for SRR5030995.sra
Written 290106 spots for SRR5030995.sra
Read 290110 spots for SRR5030995.sra
Written 290110 spots for SRR5030995.sra
SRR ids: ['SRR5030995.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_neblptuj
SRR5030995.sra spots: 3481276
blocks: [[1, 290106], [290107, 580212], [580213, 870318], [870319, 1160424], [1160425, 1450530], [1450531, 1740636], [1740637, 2030742], [2030743, 2320848], [2320849, 2610954], [2610955, 2901060], [2901061, 3191166], [3191167, 3481276]]
SRR5030995 file size 602319
SRR5030995 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030995 SRR5030995_1.fastq
Input file:	SRR5030995_1.fastq
trimmed:	SRR5030995-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 07:02:10 2020 >> started

Wed Mar  4 07:02:12 2020 >> done (2.151s)
3481276 reads processed; of these:
    247 ( 0.01%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
3481024 (99.99%) reads available; of these:
 209094 ( 6.01%) trimmed reads available after processing
3271930 (93.99%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     78	  0.00%
 19	     73	  0.00%
 20	    200	  0.01%
 21	    216	  0.01%
 22	    364	  0.01%
 23	    475	  0.01%
 24	    500	  0.01%
 25	    708	  0.02%
 26	    539	  0.02%
 27	    741	  0.02%
 28	    910	  0.03%
 29	   1412	  0.04%
 30	   1014	  0.03%
 31	   1069	  0.03%
 32	   1288	  0.04%
 33	   1603	  0.05%
 34	   1689	  0.05%
 35	   3250	  0.09%
 36	   2904	  0.08%
 37	   3234	  0.09%
 38	   3403	  0.10%
 39	   3725	  0.11%
 40	   3996	  0.11%
 41	   4481	  0.13%
 42	   5812	  0.17%
 43	   8193	  0.24%
 44	  11119	  0.32%
 45	  14362	  0.41%
 46	  21246	  0.61%
 47	  24130	  0.69%
 48	  36724	  1.05%
 49	  49636	  1.43%
 50	3271930	 93.99%
3481024 reads passed initial QC


criterion=sequence-density
sequence-density=83.36
sequence-density-rank=1
fanout-score=20.88
fanout-score-rank=1
prefix-density=85.81
prefix-fanout=20.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC


criterion=fanout-score
sequence-density=83.36
sequence-density-rank=1
fanout-score=20.88
fanout-score-rank=1
prefix-density=85.81
prefix-fanout=20.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC -o SRR5030995 -
Input file:	STDIN
trimmed:	SRR5030995-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC
-- 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 07:02:32 2020 >> started

Wed Mar  4 07:02:37 2020 >> done (4.515s)
3398143 reads processed; of these:
 231382 ( 6.81%) short reads filtered out after trimming by size control
  13672 ( 0.40%) empty reads filtered out after trimming by size control
3153089 (92.79%) reads available; of these:
2947900 (93.49%) trimmed reads available after processing
 205189 ( 6.51%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  18967	  0.60%
 19	  37521	  1.19%
 20	 168802	  5.35%
 21	 346694	 11.00%
 22	 912423	 28.94%
 23	 417976	 13.26%
 24	 187825	  5.96%
 25	  51245	  1.63%
 26	  28027	  0.89%
 27	  23761	  0.75%
 28	  27065	  0.86%
 29	  20116	  0.64%
 30	  28514	  0.90%
 31	  35095	  1.11%
 32	  43568	  1.38%
 33	 135945	  4.31%
 34	  51480	  1.63%
 35	  41507	  1.32%
 36	  52947	  1.68%
 37	  21742	  0.69%
 38	  23466	  0.74%
 39	  22065	  0.70%
 40	  33676	  1.07%
 41	  43273	  1.37%
 42	  49896	  1.58%
 43	  36363	  1.15%
 44	  25936	  0.82%
 45	  35707	  1.13%
 46	  27942	  0.89%
 47	  20803	  0.66%
 48	   2305	  0.07%
 49	   3920	  0.12%
 50	 176517	  5.60%


criterion=sequence-density
sequence-density=5.97
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.50
sequence-density-rank=25
fanout-score=14.40
fanout-score-rank=1
prefix-density=7.24
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:03:02
                             Started mapping on |	Mar 04 07:03:02
                                    Finished on |	Mar 04 07:03:31
       Mapping speed, Million of reads per hour |	401.71

                          Number of input reads |	3235970
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1638865
                        Uniquely mapped reads % |	50.65%
                          Average mapped length |	25.37
                       Number of splices: Total |	1929
            Number of splices: Annotated (sjdb) |	505
                       Number of splices: GT/AG |	1805
                       Number of splices: GC/AG |	23
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	101
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.69
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1076892
             % of reads mapped to multiple loci |	33.28%
        Number of reads mapped to too many loci |	92717
             % of reads mapped to too many loci |	2.87%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.48%
                     % of reads unmapped: other |	0.73%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	520213	520213	520213
N_multimapping	1076892	1076892	1076892
N_noFeature	83319	104988	1127198
N_ambiguous	920770	481870	17878
UnstrandedReadsAssigned:634776 PositiveStrandReadsAssigned:1052007 NegativeStrandReadsAssigned:493789
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030995 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: SRR5030995-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,235,970 reads, 806,956 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 867 rounds

 109283 SRR5030995.ke.tsv
  52636 SRR5030995.se.tsv
 161919 total
==> SRR5030995.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

==> SRR5030995.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030995 completed mapping pipeline successfully
