Starting /dee2/code/volunteer_pipeline.sh SRR5030985
    current disk space = 160574128128
    free memory = 73948904 
SRR5030985 SRAfilesize
d9a3e6074719498e3de1650049cb0501  SRR5030985.sra
SRR5030985.sra file validated
SRR5030985 is single end
SRR5030985 is conventional basespace
SRR5030985 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030985_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	32.34475	33.0	31.0	34.0	31.0	34.0
2	32.52375	34.0	31.0	34.0	31.0	34.0
3	32.52875	34.0	31.0	34.0	31.0	34.0
4	36.10975	37.0	35.0	37.0	35.0	37.0
5	35.98225	37.0	35.0	37.0	35.0	37.0
6	35.84525	37.0	35.0	37.0	33.0	37.0
7	35.82525	37.0	35.0	37.0	35.0	37.0
8	35.93575	37.0	35.0	37.0	35.0	37.0
9	37.50175	39.0	37.0	39.0	34.0	39.0
10	37.556	39.0	37.0	39.0	35.0	39.0
11	37.18825	39.0	37.0	39.0	33.0	39.0
12	37.59	39.0	37.0	39.0	35.0	39.0
13	37.5695	39.0	37.0	39.0	35.0	39.0
14	38.98975	40.0	38.0	41.0	35.0	41.0
15	38.941	40.0	38.0	41.0	35.0	41.0
16	38.987	40.0	38.0	41.0	35.0	41.0
17	39.07375	40.0	38.0	41.0	36.0	41.0
18	38.964	41.0	38.0	41.0	35.0	41.0
19	38.85275	40.0	38.0	41.0	35.0	41.0
20	38.77225	40.0	38.0	41.0	34.0	41.0
21	38.86925	40.0	38.0	41.0	35.0	41.0
22	38.83725	40.0	38.0	41.0	35.0	41.0
23	38.57325	40.0	38.0	41.0	34.0	41.0
24	38.77325	40.0	38.0	41.0	34.0	41.0
25	38.94625	40.0	38.0	41.0	35.0	41.0
26	38.76175	40.0	38.0	41.0	34.0	41.0
27	38.895	40.0	38.0	41.0	35.0	41.0
28	38.672	40.0	38.0	41.0	34.0	41.0
29	38.35375	40.0	38.0	41.0	33.0	41.0
30	38.173	40.0	38.0	41.0	33.0	41.0
31	38.4125	40.0	38.0	41.0	34.0	41.0
32	38.584	40.0	38.0	41.0	34.0	41.0
33	38.35125	40.0	38.0	41.0	34.0	41.0
34	38.33275	40.0	38.0	41.0	33.0	41.0
35	38.08625	40.0	38.0	41.0	33.0	41.0
36	37.804	40.0	37.0	41.0	33.0	41.0
37	37.2885	40.0	37.0	41.0	31.0	41.0
38	37.12675	39.0	36.0	41.0	31.0	41.0
39	37.71375	40.0	37.0	41.0	33.0	41.0
40	37.7455	40.0	37.0	41.0	33.0	41.0
41	38.01775	40.0	38.0	41.0	33.0	41.0
42	37.8635	40.0	37.0	41.0	33.0	41.0
43	37.81225	40.0	37.0	41.0	33.0	41.0
44	37.56125	40.0	37.0	41.0	33.0	41.0
45	37.55675	40.0	37.0	41.0	33.0	41.0
46	37.4845	40.0	37.0	41.0	33.0	41.0
47	37.07425	40.0	36.0	41.0	31.0	41.0
48	36.8175	39.0	36.0	41.0	31.0	41.0
49	36.837	39.0	36.0	41.0	31.0	41.0
50	36.099	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
15	1.0
16	1.0
17	2.0
18	5.0
19	0.0
20	2.0
21	5.0
22	5.0
23	6.0
24	9.0
25	6.0
26	12.0
27	25.0
28	27.0
29	37.0
30	37.0
31	65.0
32	74.0
33	128.0
34	152.0
35	210.0
36	287.0
37	393.0
38	769.0
39	1742.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.525	24.375	48.675000000000004	16.425
2	21.51454363089268	27.30692076228686	20.511534603811434	30.667001003009027
3	26.325	16.675	23.075000000000003	33.925
4	34.150000000000006	27.6	15.525	22.725
5	21.675	36.199999999999996	26.775	15.35
6	28.4	17.0	38.125	16.475
7	19.35	21.0	21.025	38.625
8	23.925	26.650000000000002	18.375	31.05
9	27.05	30.375000000000004	25.95	16.625
10	22.85	19.55	31.125000000000004	26.474999999999998
11	31.574999999999996	12.75	17.925	37.75
12	15.525	19.400000000000002	33.975	31.1
13	28.975	17.775	33.025	20.225
14	27.900000000000002	32.300000000000004	19.15	20.65
15	37.4	22.15	24.925	15.525
16	18.25	19.825	24.175	37.75
17	26.924999999999997	21.55	37.525	14.000000000000002
18	26.55	15.8	33.875	23.775
19	36.575	14.75	32.15	16.525000000000002
20	44.224999999999994	16.625	24.8	14.35
21	23.95	21.9	25.05	29.099999999999998
22	28.95	15.375	45.050000000000004	10.625
23	26.025	14.025000000000002	42.525	17.424999999999997
24	49.35	16.325	24.875	9.45
25	47.25	24.425	16.85	11.475
26	27.675	44.800000000000004	14.674999999999999	12.85
27	17.349999999999998	44.4	24.099999999999998	14.149999999999999
28	13.675	22.925	46.550000000000004	16.85
29	12.475	14.075	54.65	18.8
30	11.600000000000001	7.85	34.575	45.975
31	16.0	5.475	46.7	31.825
32	28.225	6.950000000000001	20.775	44.05
33	52.400000000000006	10.35	14.799999999999999	22.45
34	56.75	9.375	17.375	16.5
35	62.3	8.025	19.0	10.674999999999999
36	40.625	8.85	36.075	14.45
37	45.475	11.425	19.175	23.925
38	23.875	17.9	12.6	45.625
39	17.175	24.224999999999998	11.200000000000001	47.4
40	16.85	46.775	12.6	23.775
41	24.05	45.225	11.200000000000001	19.525000000000002
42	46.675	28.299999999999997	13.900000000000002	11.125
43	49.025	29.5	9.950000000000001	11.525
44	30.2	46.475	8.450000000000001	14.875
45	21.3	47.025	14.725	16.950000000000003
46	15.375	25.174999999999997	17.675	41.775
47	11.225	17.025000000000002	38.224999999999994	33.525
48	12.725	14.6	18.575	54.1
49	14.099999999999998	20.549999999999997	15.35	50.0
50	18.224999999999998	35.875	14.2	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	0.0
22	0.0
23	0.0
24	0.0
25	1.5
26	3.0
27	3.5
28	4.0
29	4.0
30	4.0
31	8.5
32	13.0
33	17.5
34	22.0
35	24.5
36	27.0
37	34.5
38	42.0
39	45.0
40	48.0
41	54.5
42	61.0
43	89.5
44	118.0
45	140.5
46	163.0
47	288.5
48	414.0
49	511.0
50	608.0
51	708.5
52	809.0
53	608.0
54	407.0
55	493.5
56	580.0
57	439.0
58	298.0
59	187.5
60	77.0
61	63.5
62	50.0
63	83.0
64	116.0
65	82.5
66	49.0
67	34.0
68	19.0
69	19.5
70	20.0
71	27.5
72	35.0
73	20.0
74	5.0
75	3.0
76	1.0
77	1.0
78	1.0
79	2.0
80	3.0
81	2.5
82	2.0
83	1.0
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	0.3
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	39.95
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.53066332916146	29.775000000000002
2	10.075093867334168	8.05
3	4.943679599499374	5.925
4	2.690863579474343	4.3
5	1.376720901126408	2.75
6	1.376720901126408	3.3000000000000003
7	0.688360450563204	1.925
8	0.688360450563204	2.1999999999999997
9	0.18773466833541927	0.675
>10	2.8785982478097623	20.424999999999997
>50	0.37546933667083854	11.475
>100	0.18773466833541927	9.2
>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	156	3.9	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	106	2.65	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	106	2.65	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	93	2.325	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	90	2.25	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	87	2.175	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	73	1.825	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	61	1.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	55	1.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	45	1.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAC	34	0.8500000000000001	RNA PCR Primer, Index 5 (100% over 35bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTC	26	0.65	RNA PCR Primer, Index 5 (100% over 44bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	25	0.625	RNA PCR Primer, Index 1 (100% over 33bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	25	0.625	RNA PCR Primer, Index 1 (100% over 30bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	21	0.525	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	16	0.4	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	15	0.375	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	15	0.375	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	14	0.35000000000000003	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	14	0.35000000000000003	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGC	12	0.3	RNA PCR Primer, Index 5 (100% over 50bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	12	0.3	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	10	0.25	RNA PCR Primer, Index 1 (100% over 25bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	9	0.22499999999999998	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	8	0.2	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
ACGCCCTTCCCCCCCTTCTTCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	7	0.17500000000000002	No Hit
TTTGGCAATGGTAGAACTCACACCGTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCCAGGAACTCCAGTCACAC	6	0.15	RNA PCR Primer, Index 5 (97% over 35bp)
TATTGCACTTGTCCCGGCCTGTATTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	6	0.15	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGAAATGCGGATATGGGACTGAGATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	6	0.15	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	6	0.15	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTTGGAATTCTC	5	0.125	No Hit
AGCTCGGTCTGAGGCCCCTCAGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CTAGACTGAGGCTCCTTGAGGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATCATGATGGGCTCCTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTG	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CTGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTC	5	0.125	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	5	0.125	No Hit
AAGGGATTCTGATGTTGGTCACACTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	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	0.325	0.0	0.0	0.0
2	0.0	0.325	0.0	0.0	0.0
3	0.0	0.4	0.0	0.0	0.0
4	0.0	0.425	0.0	0.0	0.0
5	0.0	0.5	0.0	0.0	0.0
6	0.0	0.65	0.0	0.0	0.0
7	0.0	1.45	0.0	0.0	0.0
8	0.0	1.6	0.0	0.0	0.0
9	0.0	1.675	0.0	0.0	0.0
10	0.0	1.8	0.0	0.0	0.0
11	0.0	2.05	0.0	0.0	0.0
12	0.0	2.55	0.0	0.0	0.0
13	0.0	2.75	0.0	0.0	0.0
14	0.0	3.0	0.0	0.0	0.0
15	0.0	3.375	0.0	0.0	0.0
16	0.0	5.0	0.0	0.0	0.0
17	0.0	5.8	0.0	0.0	0.0
18	0.0	7.025	0.0	0.0	0.0
19	0.0	7.375	0.0	0.0	0.0
20	0.0	8.05	0.0	0.0	0.0
21	0.0	13.65	0.0	0.0	0.0
22	0.0	24.0	0.0	0.0	0.0
23	0.0	51.825	0.0	0.0	0.0
24	0.0	62.85	0.0	0.0	0.0
25	0.0	69.15	0.0	0.0	0.0
26	0.0	70.875	0.0	0.0	0.0
27	0.0	71.75	0.0	0.0	0.0
28	0.0	72.475	0.0	0.0	0.0
29	0.0	73.125	0.0	0.0	0.0
30	0.0	73.675	0.0	0.0	0.0
31	0.0	74.7	0.0	0.0	0.0
32	0.0	75.65	0.0	0.0	0.0
33	0.0	76.7	0.0	0.0	0.0
34	0.0	80.175	0.0	0.0	0.0
35	0.0	81.475	0.0	0.0	0.0
36	0.0	82.775	0.0	0.0	0.0
37	0.0	84.375	0.0	0.0	0.0
38	0.0	84.875	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	20	6.952051E-4	44.000004	8
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
ACGCTGT	20	6.952051E-4	44.000004	9
AATCCAG	20	6.952051E-4	44.000004	8
ATCCAGG	20	6.952051E-4	44.000004	9
TTCAAGT	20	6.952051E-4	44.000004	1
TTCAACG	20	6.952051E-4	44.000004	5
AGGATAG	20	6.952051E-4	44.000004	13
ATAGGCT	20	6.952051E-4	44.000004	16
TCAACGC	20	6.952051E-4	44.000004	6
GGATAGG	20	6.952051E-4	44.000004	14
CTTGGCT	20	6.952051E-4	44.000004	16
AGTAATC	20	6.952051E-4	44.000004	5
AGGCTTG	20	6.952051E-4	44.000004	18
TAATCCA	20	6.952051E-4	44.000004	7
GCTTGGC	20	6.952051E-4	44.000004	15
CAGGATA	20	6.952051E-4	44.000004	12
GTAATCC	20	6.952051E-4	44.000004	6
GATAGGC	20	6.952051E-4	44.000004	15
>>END_MODULE
Read 205583 spots for SRR5030985.sra
Written 205583 spots for SRR5030985.sra
Read 205583 spots for SRR5030985.sra
Written 205583 spots for SRR5030985.sra
Read 205583 spots for SRR5030985.sra
Written 205583 spots for SRR5030985.sra
Read 205583 spots for SRR5030985.sra
Written 205583 spots for SRR5030985.sra
Read 205583 spots for SRR5030985.sra
Written 205583 spots for SRR5030985.sra
Read 205583 spots for SRR5030985.sra
Written 205583 spots for SRR5030985.sra
Read 205583 spots for SRR5030985.sra
Written 205583 spots for SRR5030985.sra
Read 205583 spots for SRR5030985.sra
Written 205583 spots for SRR5030985.sra
Read 205583 spots for SRR5030985.sra
Written 205583 spots for SRR5030985.sra
Read 205583 spots for SRR5030985.sra
Written 205583 spots for SRR5030985.sra
Read 205590 spots for SRR5030985.sra
Written 205590 spots for SRR5030985.sra
Read 205583 spots for SRR5030985.sra
Written 205583 spots for SRR5030985.sra
SRR ids: ['SRR5030985.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_trbgw1hd
SRR5030985.sra spots: 2467003
blocks: [[1, 205583], [205584, 411166], [411167, 616749], [616750, 822332], [822333, 1027915], [1027916, 1233498], [1233499, 1439081], [1439082, 1644664], [1644665, 1850247], [1850248, 2055830], [2055831, 2261413], [2261414, 2467003]]
SRR5030985 file size 426517
SRR5030985 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030985 SRR5030985_1.fastq
Input file:	SRR5030985_1.fastq
trimmed:	SRR5030985-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 07:00:03 2020 >> started

Wed Mar  4 07:00:05 2020 >> done (2.329s)
2467003 reads processed; of these:
    195 ( 0.01%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
2466799 (99.99%) reads available; of these:
 157276 ( 6.38%) trimmed reads available after processing
2309523 (93.62%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     62	  0.00%
 19	     80	  0.00%
 20	    122	  0.00%
 21	    148	  0.01%
 22	    263	  0.01%
 23	    302	  0.01%
 24	    330	  0.01%
 25	    475	  0.02%
 26	    412	  0.02%
 27	    522	  0.02%
 28	    613	  0.02%
 29	    825	  0.03%
 30	    658	  0.03%
 31	    768	  0.03%
 32	    809	  0.03%
 33	   1116	  0.05%
 34	   1314	  0.05%
 35	   2548	  0.10%
 36	   2171	  0.09%
 37	   2579	  0.10%
 38	   2377	  0.10%
 39	   2533	  0.10%
 40	   2782	  0.11%
 41	   3124	  0.13%
 42	   4143	  0.17%
 43	   5942	  0.24%
 44	   7731	  0.31%
 45	   9909	  0.40%
 46	  15464	  0.63%
 47	  18311	  0.74%
 48	  29875	  1.21%
 49	  38968	  1.58%
 50	2309523	 93.62%
2466799 reads passed initial QC


criterion=sequence-density
sequence-density=85.20
sequence-density-rank=1
fanout-score=21.29
fanout-score-rank=1
prefix-density=87.80
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCC


criterion=fanout-score
sequence-density=85.20
sequence-density-rank=1
fanout-score=21.29
fanout-score-rank=1
prefix-density=87.80
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCC -o SRR5030985 -
Input file:	STDIN
trimmed:	SRR5030985-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCC
-- 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 07:00:23 2020 >> started

Wed Mar  4 07:00:29 2020 >> done (6.231s)
2409432 reads processed; of these:
 151421 ( 6.28%) short reads filtered out after trimming by size control
  11023 ( 0.46%) empty reads filtered out after trimming by size control
2246988 (93.26%) reads available; of these:
2140609 (95.27%) trimmed reads available after processing
 106379 ( 4.73%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  12930	  0.58%
 19	  21919	  0.98%
 20	 131927	  5.87%
 21	 252911	 11.26%
 22	 673540	 29.98%
 23	 292956	 13.04%
 24	 144991	  6.45%
 25	  42752	  1.90%
 26	  21618	  0.96%
 27	  16603	  0.74%
 28	  18111	  0.81%
 29	  14642	  0.65%
 30	  20596	  0.92%
 31	  28764	  1.28%
 32	  28680	  1.28%
 33	  90853	  4.04%
 34	  36780	  1.64%
 35	  32088	  1.43%
 36	  38045	  1.69%
 37	  16323	  0.73%
 38	  18255	  0.81%
 39	  16370	  0.73%
 40	  25969	  1.16%
 41	  29441	  1.31%
 42	  33902	  1.51%
 43	  24303	  1.08%
 44	  18336	  0.82%
 45	  23302	  1.04%
 46	  16025	  0.71%
 47	  12028	  0.54%
 48	   1208	  0.05%
 49	   2590	  0.12%
 50	  88230	  3.93%


criterion=sequence-density
sequence-density=3.29
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=13
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCT


criterion=fanout-score
sequence-density=0.55
sequence-density-rank=29
fanout-score=17.79
fanout-score-rank=1
prefix-density=9.69
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:00:58
                             Started mapping on |	Mar 04 07:00:59
                                    Finished on |	Mar 04 07:01:22
       Mapping speed, Million of reads per hour |	360.68

                          Number of input reads |	2304355
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1277513
                        Uniquely mapped reads % |	55.44%
                          Average mapped length |	24.98
                       Number of splices: Total |	1307
            Number of splices: Annotated (sjdb) |	258
                       Number of splices: GT/AG |	1199
                       Number of splices: GC/AG |	17
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	91
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.66
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	710202
             % of reads mapped to multiple loci |	30.82%
        Number of reads mapped to too many loci |	56356
             % of reads mapped to too many loci |	2.45%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.27%
                     % of reads unmapped: other |	1.02%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	316640	316640	316640
N_multimapping	710202	710202	710202
N_noFeature	59260	77857	828473
N_ambiguous	706959	311476	11895
UnstrandedReadsAssigned:511294 PositiveStrandReadsAssigned:888180 NegativeStrandReadsAssigned:437145
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030985 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: SRR5030985-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,304,355 reads, 614,414 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,164 rounds

 109283 SRR5030985.ke.tsv
  52636 SRR5030985.se.tsv
 161919 total
==> SRR5030985.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

==> SRR5030985.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030985 completed mapping pipeline successfully
