Starting /dee2/code/volunteer_pipeline.sh SRR5030945
    current disk space = 160605470720
    free memory = 73948096 
SRR5030945 SRAfilesize
ff9953316f7e55328e9368381616df9d  SRR5030945.sra
SRR5030945.sra file validated
SRR5030945 is single end
SRR5030945 is conventional basespace
SRR5030945 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030945_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	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.3835	33.0	31.0	34.0	31.0	34.0
2	32.7505	34.0	31.0	34.0	31.0	34.0
3	32.80975	34.0	31.0	34.0	31.0	34.0
4	36.28875	37.0	37.0	37.0	35.0	37.0
5	36.2475	37.0	37.0	37.0	35.0	37.0
6	36.015	37.0	35.0	37.0	35.0	37.0
7	36.102	37.0	35.0	37.0	35.0	37.0
8	36.136	37.0	35.0	37.0	35.0	37.0
9	37.89125	39.0	38.0	39.0	35.0	39.0
10	37.9045	39.0	38.0	39.0	35.0	39.0
11	37.8285	39.0	38.0	39.0	35.0	39.0
12	37.84925	39.0	38.0	39.0	35.0	39.0
13	37.82	39.0	38.0	39.0	35.0	39.0
14	39.16775	41.0	39.0	41.0	36.0	41.0
15	39.26575	41.0	39.0	41.0	36.0	41.0
16	39.15225	41.0	39.0	41.0	36.0	41.0
17	39.191	41.0	39.0	41.0	36.0	41.0
18	39.1925	41.0	39.0	41.0	36.0	41.0
19	38.978	40.0	39.0	41.0	35.0	41.0
20	39.06425	40.0	39.0	41.0	35.0	41.0
21	39.15975	41.0	39.0	41.0	36.0	41.0
22	39.12875	41.0	39.0	41.0	36.0	41.0
23	39.023	40.0	39.0	41.0	35.0	41.0
24	38.3075	40.0	38.0	41.0	34.0	41.0
25	38.5715	40.0	38.0	41.0	34.0	41.0
26	38.6565	40.0	38.0	41.0	34.0	41.0
27	38.6765	40.0	38.0	41.0	34.0	41.0
28	38.501	40.0	38.0	41.0	34.0	41.0
29	38.36025	40.0	38.0	41.0	34.0	41.0
30	38.11475	40.0	38.0	41.0	33.0	41.0
31	38.5235	40.0	38.0	41.0	34.0	41.0
32	38.69775	40.0	38.0	41.0	35.0	41.0
33	37.00725	40.0	37.0	41.0	30.0	41.0
34	36.4245	40.0	36.0	41.0	29.0	41.0
35	32.54675	38.0	31.0	40.0	9.0	41.0
36	29.77375	37.0	21.0	40.0	8.0	41.0
37	29.86225	36.0	23.0	40.0	6.0	41.0
38	32.2525	37.0	30.0	40.0	12.0	41.0
39	31.6755	37.0	30.0	40.0	8.0	41.0
40	32.505	37.0	31.0	40.0	2.0	41.0
41	30.51275	36.0	27.0	40.0	2.0	41.0
42	32.01425	37.0	31.0	40.0	2.0	41.0
43	30.483	37.0	27.0	40.0	2.0	41.0
44	31.3235	37.0	30.0	40.0	2.0	41.0
45	29.2325	37.0	25.0	40.0	2.0	41.0
46	27.16725	35.0	13.0	39.0	2.0	41.0
47	27.167	34.0	15.0	39.0	2.0	41.0
48	27.6095	35.0	9.0	39.0	2.0	41.0
49	26.2545	34.0	2.0	39.0	2.0	41.0
50	23.0545	30.0	2.0	38.0	2.0	40.0
>>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
10	1.0
11	0.0
12	0.0
13	0.0
14	2.0
15	2.0
16	2.0
17	1.0
18	3.0
19	11.0
20	10.0
21	11.0
22	21.0
23	36.0
24	51.0
25	50.0
26	102.0
27	155.0
28	79.0
29	101.0
30	148.0
31	163.0
32	156.0
33	167.0
34	234.0
35	247.0
36	331.0
37	446.0
38	668.0
39	802.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	13.209907430572928	24.668501376032022	45.884413309982484	16.23717788341256
2	26.625	27.025	21.175	25.174999999999997
3	22.05	18.575	23.0	36.375
4	31.775	30.325000000000003	15.35	22.55
5	23.1	39.0	24.9	13.0
6	26.75	17.825	38.5	16.925
7	19.650000000000002	20.05	23.275000000000002	37.025000000000006
8	22.575	30.725	18.05	28.65
9	20.925	32.65	29.45	16.975
10	23.474999999999998	20.474999999999998	29.825000000000003	26.224999999999998
11	36.8	15.425	14.224999999999998	33.550000000000004
12	17.875	24.725	28.549999999999997	28.849999999999998
13	25.25	19.775000000000002	33.975	21.0
14	28.000000000000004	26.700000000000003	24.75	20.549999999999997
15	33.900000000000006	23.925	24.15	18.025
16	19.625	20.175	23.150000000000002	37.05
17	25.474999999999998	24.05	34.0	16.475
18	23.799999999999997	18.35	31.7	26.150000000000002
19	33.900000000000006	16.025	32.800000000000004	17.275
20	40.275	17.5	26.825	15.4
21	25.074999999999996	22.3	24.625	28.000000000000004
22	30.599999999999998	13.325000000000001	43.45	12.625
23	25.025	14.35	42.15	18.475
24	48.975	13.775	25.374999999999996	11.875
25	47.075	23.474999999999998	16.475	12.975
26	27.025	42.375	14.95	15.65
27	17.925	44.074999999999996	21.575	16.425
28	14.875	24.975	43.15	17.0
29	14.75	13.900000000000002	52.225	19.125
30	11.5	8.85	34.75	44.9
31	14.825	7.725	44.5	32.95
32	27.875	7.449999999999999	23.625	41.05
33	48.875	12.1	15.075	23.95
34	56.625	8.55	17.025000000000002	17.8
35	56.425000000000004	9.075	21.0	13.5
36	60.675000000000004	10.25	15.8	13.275
37	37.475	13.750000000000002	21.925	26.85
38	25.424999999999997	17.1	13.975000000000001	43.5
39	18.075	25.05	14.000000000000002	42.875
40	17.875	43.325	14.7	24.099999999999998
41	27.05	40.225	12.85	19.875
42	46.375	28.050000000000004	14.6	10.975
43	43.775	32.725	10.9	12.6
44	31.5	44.025	9.75	14.725
45	20.45	45.050000000000004	12.975	21.525
46	16.45	28.15	25.674999999999997	29.725
47	11.450000000000001	16.375	33.775	38.4
48	13.725000000000001	12.775	21.475	52.025
49	14.774999999999999	25.224999999999998	15.275	44.725
50	28.799999999999997	25.15	13.175	32.875
>>END_MODULE
>>Per sequence GC content	warn
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.5
6	1.0
7	0.5
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	0.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	1.0
24	2.0
25	1.0
26	0.0
27	1.5
28	3.0
29	2.0
30	1.0
31	7.0
32	13.0
33	22.5
34	32.0
35	43.0
36	54.0
37	60.0
38	66.0
39	70.0
40	74.0
41	77.5
42	81.0
43	101.5
44	122.0
45	168.5
46	215.0
47	268.5
48	322.0
49	433.5
50	545.0
51	656.5
52	768.0
53	608.5
54	449.0
55	411.5
56	374.0
57	351.0
58	328.0
59	238.5
60	149.0
61	116.5
62	84.0
63	131.0
64	178.0
65	107.0
66	36.0
67	23.0
68	10.0
69	16.0
70	22.0
71	34.0
72	46.0
73	26.0
74	6.0
75	5.5
76	5.0
77	4.0
78	3.0
79	4.5
80	6.0
81	5.0
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	0.075
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	0.0
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	warn
#Total Deduplicated Percentage	52.225
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.51699377692675	42.05
2	8.664432742939205	9.049999999999999
3	2.824317855433222	4.425
4	2.2498803255146003	4.7
5	1.0052656773575874	2.625
6	0.7180469123982767	2.25
7	0.47869794159885115	1.7500000000000002
8	0.430828147438966	1.7999999999999998
9	0.430828147438966	2.025
>10	2.584968884633796	23.849999999999998
>50	0.0	0.0
>100	0.09573958831977022	5.475
>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
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	117	2.9250000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	102	2.55	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	50	1.25	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	43	1.075	RNA PCR Primer, Index 1 (100% over 26bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	41	1.0250000000000001	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	40	1.0	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	32	0.8	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGC	23	0.575	RNA PCR Primer, Index 27 (100% over 50bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAT	23	0.575	RNA PCR Primer, Index 1 (100% over 35bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 30bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	18	0.44999999999999996	No Hit
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	15	0.375	RNA PCR Primer, Index 1 (100% over 33bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	15	0.375	RNA PCR Primer, Index 1 (96% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTC	15	0.375	RNA PCR Primer, Index 27 (100% over 44bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	15	0.375	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	14	0.35000000000000003	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	13	0.325	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	13	0.325	No Hit
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	13	0.325	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	13	0.325	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	12	0.3	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	12	0.3	No Hit
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	12	0.3	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	12	0.3	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	10	0.25	No Hit
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	10	0.25	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	10	0.25	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	10	0.25	No Hit
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	10	0.25	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	10	0.25	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	9	0.22499999999999998	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	8	0.2	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	8	0.2	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	8	0.2	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	8	0.2	No Hit
GAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTTGGAATTCTCGGGTGC	8	0.2	No Hit
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	8	0.2	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	8	0.2	No Hit
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	6	0.15	RNA PCR Primer, Index 1 (100% over 32bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAAGCGG	6	0.15	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
CGACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	5	0.125	RNA PCR Primer, Index 1 (100% over 34bp)
TACCATGATGATAACATAGTTCAGCAGACTTAACTCTGATGAACAATCAT	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAATTCCA	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	5	0.125	No Hit
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	5	0.125	RNA PCR Primer, Index 1 (100% over 34bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	5	0.125	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCA	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	5	0.125	No Hit
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	5	0.125	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGAAGAAAGGT	5	0.125	No Hit
GAGCAATGATGACCCCAACATGCCATCTGAGTGGCTTTGCTGAAATCCAG	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	0.625	0.0	0.0	0.0
2	0.0	0.65	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	0.85	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	1.525	0.0	0.0	0.0
9	0.0	1.575	0.0	0.0	0.0
10	0.0	1.625	0.0	0.0	0.0
11	0.0	1.75	0.0	0.0	0.0
12	0.0	1.925	0.0	0.0	0.0
13	0.0	2.05	0.0	0.0	0.0
14	0.0	2.25	0.0	0.0	0.0
15	0.0	2.675	0.0	0.0	0.0
16	0.0	3.675	0.0	0.0	0.0
17	0.0	4.35	0.0	0.0	0.0
18	0.0	5.325	0.0	0.0	0.0
19	0.0	5.9	0.0	0.0	0.0
20	0.0	6.7	0.0	0.0	0.0
21	0.0	10.6	0.0	0.0	0.0
22	0.0	19.925	0.0	0.0	0.0
23	0.0	44.95	0.0	0.0	0.0
24	0.0	56.7	0.0	0.0	0.0
25	0.0	62.05	0.0	0.0	0.0
26	0.0	63.325	0.0	0.0	0.0
27	0.0	63.925	0.0	0.0	0.0
28	0.0	64.5	0.0	0.0	0.0
29	0.0	64.825	0.0	0.0	0.0
30	0.0	65.325	0.0	0.0	0.0
31	0.0	66.0	0.0	0.0	0.0
32	0.0	67.425	0.0	0.0	0.0
33	0.0	68.25	0.0	0.0	0.0
34	0.0	72.3	0.0	0.0	0.0
35	0.0	73.425	0.0	0.0	0.0
36	0.0	73.9	0.0	0.0	0.0
37	0.0	74.775	0.0	0.0	0.0
38	0.0	75.25	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	45	2.728484E-10	44.000004	8
GGTGAGT	40	5.315087E-9	44.000004	17
ACGCTGT	45	2.728484E-10	44.000004	9
TTCAACG	45	2.728484E-10	44.000004	5
TCGGTGA	45	2.728484E-10	44.000004	15
GAGCTTG	40	5.315087E-9	44.000004	13
GGATCCG	40	5.315087E-9	44.000004	3
CCGTCTG	40	5.315087E-9	44.000004	7
TCGGATC	40	5.315087E-9	44.000004	1
CATTCAA	45	2.728484E-10	44.000004	3
TCAACGC	45	2.728484E-10	44.000004	6
CGGATCC	40	5.315087E-9	44.000004	2
GATTGTA	20	6.952051E-4	44.000004	11
GTGAGTT	20	6.952051E-4	44.000004	18
GTGAGTG	20	6.952051E-4	44.000004	18
ACATTCA	45	2.728484E-10	44.000004	2
GCTGTCG	45	2.728484E-10	44.000004	11
ATTGTAT	20	6.952051E-4	44.000004	12
GATCCGT	40	5.315087E-9	44.000004	4
CGGTGAG	40	5.315087E-9	44.000004	16
>>END_MODULE
Read 220400 spots for SRR5030945.sra
Written 220400 spots for SRR5030945.sra
Read 220400 spots for SRR5030945.sra
Written 220400 spots for SRR5030945.sra
Read 220400 spots for SRR5030945.sra
Written 220400 spots for SRR5030945.sra
Read 220400 spots for SRR5030945.sra
Written 220400 spots for SRR5030945.sra
Read 220400 spots for SRR5030945.sra
Written 220400 spots for SRR5030945.sra
Read 220400 spots for SRR5030945.sra
Written 220400 spots for SRR5030945.sra
Read 220400 spots for SRR5030945.sra
Written 220400 spots for SRR5030945.sra
Read 220400 spots for SRR5030945.sra
Written 220400 spots for SRR5030945.sra
Read 220400 spots for SRR5030945.sra
Written 220400 spots for SRR5030945.sra
Read 220400 spots for SRR5030945.sra
Written 220400 spots for SRR5030945.sra
Read 220400 spots for SRR5030945.sra
Written 220400 spots for SRR5030945.sra
Read 220409 spots for SRR5030945.sra
Written 220409 spots for SRR5030945.sra
SRR ids: ['SRR5030945.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_za48jg8j
SRR5030945.sra spots: 2644809
blocks: [[1, 220400], [220401, 440800], [440801, 661200], [661201, 881600], [881601, 1102000], [1102001, 1322400], [1322401, 1542800], [1542801, 1763200], [1763201, 1983600], [1983601, 2204000], [2204001, 2424400], [2424401, 2644809]]
SRR5030945 file size 457327
SRR5030945 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030945 SRR5030945_1.fastq
Input file:	SRR5030945_1.fastq
trimmed:	SRR5030945-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 06:50:51 2020 >> started

Wed Mar  4 06:50:52 2020 >> done (1.582s)
2644809 reads processed; of these:
    179 ( 0.01%) short reads filtered out after trimming by size control
     10 ( 0.00%) empty reads filtered out after trimming by size control
2644620 (99.99%) reads available; of these:
 299328 (11.32%) trimmed reads available after processing
2345292 (88.68%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     46	  0.00%
 19	     55	  0.00%
 20	    112	  0.00%
 21	    149	  0.01%
 22	    256	  0.01%
 23	    343	  0.01%
 24	    353	  0.01%
 25	    490	  0.02%
 26	    423	  0.02%
 27	    539	  0.02%
 28	    721	  0.03%
 29	   1145	  0.04%
 30	    840	  0.03%
 31	   1130	  0.04%
 32	   3116	  0.12%
 33	   8716	  0.33%
 34	  20425	  0.77%
 35	   4913	  0.19%
 36	   5125	  0.19%
 37	   3094	  0.12%
 38	   6264	  0.24%
 39	   5469	  0.21%
 40	  10080	  0.38%
 41	   5926	  0.22%
 42	  15753	  0.60%
 43	   7365	  0.28%
 44	  30105	  1.14%
 45	  19166	  0.72%
 46	  17707	  0.67%
 47	  18414	  0.70%
 48	  53112	  2.01%
 49	  57976	  2.19%
 50	2345292	 88.68%
2644620 reads passed initial QC


criterion=sequence-density
sequence-density=74.71
sequence-density-rank=1
fanout-score=21.21
fanout-score-rank=3
prefix-density=77.52
prefix-fanout=20.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCC


criterion=fanout-score
sequence-density=1.60
sequence-density-rank=4
fanout-score=455.19
fanout-score-rank=1
prefix-density=76.59
prefix-fanout=9.5
sequence=GGAATTCTCGGTGCCAAGGA
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCC -o SRR5030945 -
Input file:	STDIN
trimmed:	SRR5030945-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATTCCTATCTCGTATGCC
-- 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 06:51:06 2020 >> started

Wed Mar  4 06:51:09 2020 >> done (3.155s)
2574097 reads processed; of these:
 124365 ( 4.83%) short reads filtered out after trimming by size control
  17009 ( 0.66%) empty reads filtered out after trimming by size control
2432723 (94.51%) reads available; of these:
2024913 (83.24%) trimmed reads available after processing
 407810 (16.76%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  15597	  0.64%
 19	  20646	  0.85%
 20	 106644	  4.38%
 21	 241667	  9.93%
 22	 637029	 26.19%
 23	 305809	 12.57%
 24	 149402	  6.14%
 25	  40204	  1.65%
 26	  21138	  0.87%
 27	  17830	  0.73%
 28	  17441	  0.72%
 29	  14848	  0.61%
 30	  20065	  0.82%
 31	  35325	  1.45%
 32	  24513	  1.01%
 33	 105157	  4.32%
 34	  26647	  1.10%
 35	  18215	  0.75%
 36	  22627	  0.93%
 37	  13810	  0.57%
 38	  15738	  0.65%
 39	  15352	  0.63%
 40	  22912	  0.94%
 41	  24898	  1.02%
 42	  32347	  1.33%
 43	  22563	  0.93%
 44	  22352	  0.92%
 45	  25166	  1.03%
 46	  20963	  0.86%
 47	  17999	  0.74%
 48	   6351	  0.26%
 49	  11829	  0.49%
 50	 339639	 13.96%


criterion=sequence-density
sequence-density=7.19
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.47
sequence-density-rank=30
fanout-score=14.08
fanout-score-rank=1
prefix-density=6.58
prefix-fanout=1.0
sequence=TGAGCTTGGCTT
                                 Started job on |	Mar 04 06:51:29
                             Started mapping on |	Mar 04 06:51:30
                                    Finished on |	Mar 04 06:51:53
       Mapping speed, Million of reads per hour |	391.81

                          Number of input reads |	2503246
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1342605
                        Uniquely mapped reads % |	53.63%
                          Average mapped length |	28.26
                       Number of splices: Total |	1676
            Number of splices: Annotated (sjdb) |	226
                       Number of splices: GT/AG |	1555
                       Number of splices: GC/AG |	27
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	93
                      Mismatch rate per base, % |	0.22%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.26
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.04
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	712684
             % of reads mapped to multiple loci |	28.47%
        Number of reads mapped to too many loci |	77336
             % of reads mapped to too many loci |	3.09%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	13.86%
                     % of reads unmapped: other |	0.95%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	447957	447957	447957
N_multimapping	712684	712684	712684
N_noFeature	75702	92149	972332
N_ambiguous	714699	388481	12808
UnstrandedReadsAssigned:552204 PositiveStrandReadsAssigned:861975 NegativeStrandReadsAssigned:357465
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030945 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: SRR5030945-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,503,246 reads, 592,469 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,068 rounds

 109283 SRR5030945.ke.tsv
  52636 SRR5030945.se.tsv
 161919 total
==> SRR5030945.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

==> SRR5030945.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030945 completed mapping pipeline successfully
