Starting /dee2/code/volunteer_pipeline.sh SRR5031049
    current disk space = 160485244928
    free memory = 73954452 
SRR5031049 SRAfilesize
d033f8b335e4d608626a310b034b5244  SRR5031049.sra
SRR5031049.sra file validated
SRR5031049 is single end
SRR5031049 is conventional basespace
SRR5031049 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031049_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	32.2685	33.0	31.0	34.0	30.0	34.0
2	32.4745	34.0	31.0	34.0	31.0	34.0
3	32.59225	34.0	31.0	34.0	31.0	34.0
4	36.17825	37.0	35.0	37.0	35.0	37.0
5	35.82725	37.0	35.0	37.0	35.0	37.0
6	35.801	37.0	35.0	37.0	33.0	37.0
7	35.8475	37.0	35.0	37.0	35.0	37.0
8	35.6295	37.0	35.0	37.0	33.0	37.0
9	37.41475	39.0	37.0	39.0	34.0	39.0
10	37.71325	39.0	37.0	39.0	35.0	39.0
11	37.47975	39.0	37.0	39.0	34.0	39.0
12	37.59375	39.0	37.0	39.0	35.0	39.0
13	37.60475	39.0	37.0	39.0	35.0	39.0
14	38.936	40.0	38.0	41.0	35.0	41.0
15	38.84825	40.0	38.0	41.0	35.0	41.0
16	38.9025	40.0	38.0	41.0	35.0	41.0
17	38.831	40.0	38.0	41.0	35.0	41.0
18	38.9475	40.0	38.0	41.0	35.0	41.0
19	38.4255	40.0	38.0	41.0	34.0	41.0
20	38.6965	40.0	38.0	41.0	34.0	41.0
21	38.67375	40.0	38.0	41.0	34.0	41.0
22	38.896	40.0	38.0	41.0	35.0	41.0
23	38.69675	40.0	38.0	41.0	34.0	41.0
24	38.6675	40.0	38.0	41.0	34.0	41.0
25	38.92175	40.0	38.0	41.0	35.0	41.0
26	38.62525	40.0	38.0	41.0	34.0	41.0
27	38.49575	40.0	38.0	41.0	34.0	41.0
28	38.6415	40.0	38.0	41.0	34.0	41.0
29	38.16725	40.0	38.0	41.0	33.0	41.0
30	38.13525	40.0	38.0	41.0	33.0	41.0
31	38.386	40.0	38.0	41.0	34.0	41.0
32	38.352	40.0	38.0	41.0	34.0	41.0
33	38.27075	40.0	38.0	41.0	34.0	41.0
34	38.275	40.0	38.0	41.0	34.0	41.0
35	38.073	40.0	38.0	41.0	33.0	41.0
36	37.72475	40.0	37.0	41.0	33.0	41.0
37	37.4295	40.0	37.0	41.0	31.0	41.0
38	36.512	39.0	36.0	41.0	30.0	41.0
39	36.892	39.0	36.0	41.0	30.0	41.0
40	37.32975	40.0	37.0	41.0	31.0	41.0
41	37.4485	40.0	37.0	41.0	31.0	41.0
42	37.7055	40.0	37.0	41.0	33.0	41.0
43	37.95375	40.0	38.0	41.0	33.0	41.0
44	37.80175	40.0	37.0	41.0	33.0	41.0
45	37.77	40.0	37.0	41.0	33.0	41.0
46	37.604	40.0	37.0	41.0	33.0	41.0
47	37.1645	40.0	37.0	41.0	31.0	41.0
48	36.72275	40.0	36.0	41.0	30.0	41.0
49	36.986	40.0	36.0	41.0	31.0	41.0
50	36.47375	39.0	35.0	41.0	31.0	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
14	1.0
15	1.0
16	0.0
17	3.0
18	4.0
19	0.0
20	5.0
21	6.0
22	6.0
23	6.0
24	10.0
25	9.0
26	14.0
27	26.0
28	20.0
29	39.0
30	40.0
31	60.0
32	95.0
33	122.0
34	173.0
35	196.0
36	303.0
37	442.0
38	680.0
39	1739.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.575000000000001	24.95	51.65	14.825
2	22.188830453293264	27.02228900576008	18.156774355121463	32.632106185825194
3	26.400000000000002	20.075000000000003	20.849999999999998	32.675
4	31.974999999999998	27.875	14.099999999999998	26.05
5	20.849999999999998	41.325	26.900000000000002	10.925
6	36.775000000000006	13.975000000000001	35.025	14.224999999999998
7	15.325	21.15	23.575	39.95
8	25.0	27.725	15.075	32.2
9	22.35	34.449999999999996	27.775	15.425
10	21.525	22.7	27.800000000000004	27.975
11	29.4	10.2	18.275	42.125
12	14.95	16.875	31.525	36.65
13	32.875	17.275	30.75	19.1
14	30.8	32.9	19.975	16.325
15	36.825	24.7	26.025	12.45
16	17.775	21.45	22.400000000000002	38.375
17	24.099999999999998	22.3	38.324999999999996	15.275
18	23.95	20.225	29.525000000000002	26.3
19	37.574999999999996	15.174999999999999	28.125	19.125
20	44.0	14.85	28.275	12.875
21	24.9	18.75	27.85	28.499999999999996
22	28.749999999999996	13.25	48.65	9.35
23	26.125	13.450000000000001	45.25	15.174999999999999
24	52.949999999999996	14.975	25.025	7.049999999999999
25	50.975	24.625	15.925	8.475000000000001
26	27.175	47.775	13.125	11.924999999999999
27	14.6	48.5	25.275	11.625
28	9.675	24.15	49.725	16.45
29	11.3	12.950000000000001	58.225	17.525
30	9.075	6.075	36.575	48.275
31	13.575000000000001	4.324999999999999	47.675	34.425
32	27.900000000000002	5.575	21.675	44.85
33	56.35	7.9	13.025	22.725
34	64.45	7.074999999999999	15.375	13.100000000000001
35	66.675	5.6000000000000005	19.025	8.7
36	40.699999999999996	7.6	39.35	12.35
37	45.025	10.6	20.45	23.925
38	22.925	15.4	12.125	49.55
39	15.950000000000001	23.25	9.65	51.15
40	15.875	49.575	10.25	24.3
41	24.45	49.9	9.5	16.150000000000002
42	50.4	28.9	10.85	9.85
43	52.275000000000006	29.175	8.924999999999999	9.625
44	31.7	48.775	6.05	13.475000000000001
45	19.075	49.475	13.425	18.025
46	12.049999999999999	24.75	18.95	44.25
47	8.674999999999999	14.924999999999999	40.35	36.05
48	10.375	12.1	20.349999999999998	57.175
49	14.549999999999999	18.2	12.675	54.574999999999996
50	18.325	38.3	13.700000000000001	29.675
>>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	0.5
10	1.0
11	0.5
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.5
20	1.0
21	1.0
22	1.0
23	0.5
24	0.0
25	0.5
26	1.0
27	1.0
28	1.0
29	1.5
30	2.0
31	6.5
32	11.0
33	10.0
34	9.0
35	16.5
36	24.0
37	29.5
38	35.0
39	36.0
40	37.0
41	39.5
42	42.0
43	76.0
44	110.0
45	145.0
46	180.0
47	308.5
48	437.0
49	538.0
50	639.0
51	769.5
52	900.0
53	678.5
54	457.0
55	485.0
56	513.0
57	374.5
58	236.0
59	153.0
60	70.0
61	59.0
62	48.0
63	81.5
64	115.0
65	71.5
66	28.0
67	20.0
68	12.0
69	17.0
70	22.0
71	38.5
72	55.0
73	30.5
74	6.0
75	3.5
76	1.0
77	2.0
78	3.0
79	3.0
80	3.0
81	1.5
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	0.17500000000000002
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	37.125
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.69023569023568	28.1
2	9.62962962962963	7.1499999999999995
3	4.30976430976431	4.8
4	2.6936026936026933	4.0
5	1.2121212121212122	2.25
6	1.2794612794612794	2.85
7	0.6734006734006733	1.7500000000000002
8	0.47138047138047134	1.4000000000000001
9	0.33670033670033667	1.125
>10	3.0303030303030303	21.5
>50	0.40404040404040403	11.05
>100	0.26936026936026936	14.025000000000002
>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	172	4.3	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	172	4.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	112	2.8000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	105	2.625	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	96	2.4	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	81	2.025	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	75	1.875	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	72	1.7999999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	67	1.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	51	1.275	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	50	1.25	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	43	1.075	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGC	37	0.9249999999999999	RNA PCR Primer, Index 21 (100% over 50bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	29	0.7250000000000001	RNA PCR Primer, Index 1 (97% over 35bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	20	0.5	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	17	0.42500000000000004	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTC	16	0.4	RNA PCR Primer, Index 21 (100% over 44bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	13	0.325	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	12	0.3	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	12	0.3	RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	11	0.27499999999999997	No Hit
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	11	0.27499999999999997	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	11	0.27499999999999997	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	8	0.2	No Hit
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTATTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTTGGAATT	6	0.15	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	6	0.15	RNA PCR Primer, Index 6 (100% over 34bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	6	0.15	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
TAACAGTCTACAGCCATGGTCGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	5	0.125	RNA PCR Primer, Index 1 (97% over 35bp)
TCCCTGAGACCCTAACTTGTGAAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	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	1.075	0.0	0.0	0.0
2	0.0	1.075	0.0	0.0	0.0
3	0.0	1.125	0.0	0.0	0.0
4	0.0	1.15	0.0	0.0	0.0
5	0.0	1.25	0.0	0.0	0.0
6	0.0	1.35	0.0	0.0	0.0
7	0.0	1.925	0.0	0.0	0.0
8	0.0	2.025	0.0	0.0	0.0
9	0.0	2.05	0.0	0.0	0.0
10	0.0	2.125	0.0	0.0	0.0
11	0.0	2.275	0.0	0.0	0.0
12	0.0	2.475	0.0	0.0	0.0
13	0.0	2.65	0.0	0.0	0.0
14	0.0	2.775	0.0	0.0	0.0
15	0.0	3.075	0.0	0.0	0.0
16	0.0	4.325	0.0	0.0	0.0
17	0.0	4.725	0.0	0.0	0.0
18	0.0	5.425	0.0	0.0	0.0
19	0.0	5.95	0.0	0.0	0.0
20	0.0	6.825	0.0	0.0	0.0
21	0.0	12.625	0.0	0.0	0.0
22	0.0	24.2	0.0	0.0	0.0
23	0.0	55.45	0.0	0.0	0.0
24	0.0	68.375	0.0	0.0	0.0
25	0.0	74.325	0.0	0.0	0.0
26	0.0	75.925	0.0	0.0	0.0
27	0.0	76.575	0.0	0.0	0.0
28	0.0	77.3	0.0	0.0	0.0
29	0.0	77.675	0.0	0.0	0.0
30	0.0	78.425	0.0	0.0	0.0
31	0.0	79.15	0.0	0.0	0.0
32	0.0	80.5	0.0	0.0	0.0
33	0.0	81.95	0.0	0.0	0.0
34	0.0	85.225	0.0	0.0	0.0
35	0.0	85.975	0.0	0.0	0.0
36	0.0	86.775	0.0	0.0	0.0
37	0.0	87.675	0.0	0.0	0.0
38	0.0	88.125	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TCAAGTA	30	1.7904422E-6	44.531647	2
TTCAAGT	30	1.7904422E-6	44.531647	1
AAGCTGC	25	3.4343255E-5	44.531647	1
AGCTGCC	25	3.4343255E-5	44.531647	2
TCCCTGA	45	2.419256E-10	44.531647	1
GAGGTAG	40	4.7512003E-9	44.531643	2
ACATTCA	20	6.54202E-4	44.531643	2
TGAGGTA	40	4.7512003E-9	44.531643	1
AACATTC	20	6.54202E-4	44.531643	1
TGAGACC	45	2.746674E-10	43.975002	5
ACTGTTG	25	3.7082697E-5	43.975002	18
GGTTGTA	25	3.7082697E-5	43.975002	11
GTTGAAG	25	3.7082697E-5	43.975002	10
AAGTAAT	30	1.9592044E-6	43.975002	4
AATCCAG	25	3.7082697E-5	43.975002	8
CAGTTGA	25	3.7082697E-5	43.975002	8
CTGAGAC	45	2.746674E-10	43.975002	4
ATCCAGG	25	3.7082697E-5	43.975002	9
CTTTAAC	30	1.9592044E-6	43.975002	12
AACTGTT	25	3.7082697E-5	43.975002	17
>>END_MODULE
Read 274283 spots for SRR5031049.sra
Written 274283 spots for SRR5031049.sra
Read 274283 spots for SRR5031049.sra
Written 274283 spots for SRR5031049.sra
Read 274283 spots for SRR5031049.sra
Written 274283 spots for SRR5031049.sra
Read 274283 spots for SRR5031049.sra
Written 274283 spots for SRR5031049.sra
Read 274283 spots for SRR5031049.sra
Written 274283 spots for SRR5031049.sra
Read 274283 spots for SRR5031049.sra
Written 274283 spots for SRR5031049.sra
Read 274283 spots for SRR5031049.sra
Written 274283 spots for SRR5031049.sra
Read 274283 spots for SRR5031049.sra
Written 274283 spots for SRR5031049.sra
Read 274283 spots for SRR5031049.sra
Written 274283 spots for SRR5031049.sra
Read 274283 spots for SRR5031049.sra
Written 274283 spots for SRR5031049.sra
Read 274283 spots for SRR5031049.sra
Written 274283 spots for SRR5031049.sra
Read 274294 spots for SRR5031049.sra
Written 274294 spots for SRR5031049.sra
SRR ids: ['SRR5031049.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_sum0h_zx
SRR5031049.sra spots: 3291407
blocks: [[1, 274283], [274284, 548566], [548567, 822849], [822850, 1097132], [1097133, 1371415], [1371416, 1645698], [1645699, 1919981], [1919982, 2194264], [2194265, 2468547], [2468548, 2742830], [2742831, 3017113], [3017114, 3291407]]
SRR5031049 file size 569414
SRR5031049 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031049 SRR5031049_1.fastq
Input file:	SRR5031049_1.fastq
trimmed:	SRR5031049-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 07:13:10 2020 >> started

Wed Mar  4 07:13:11 2020 >> done (1.769s)
3291407 reads processed; of these:
    278 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
3291123 (99.99%) reads available; of these:
 167283 ( 5.08%) trimmed reads available after processing
3123840 (94.92%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     89	  0.00%
 19	    108	  0.00%
 20	    212	  0.01%
 21	    255	  0.01%
 22	    457	  0.01%
 23	    523	  0.02%
 24	    551	  0.02%
 25	    727	  0.02%
 26	    604	  0.02%
 27	    777	  0.02%
 28	    883	  0.03%
 29	   1328	  0.04%
 30	    899	  0.03%
 31	   1010	  0.03%
 32	   1079	  0.03%
 33	   1552	  0.05%
 34	   1663	  0.05%
 35	   3207	  0.10%
 36	   2854	  0.09%
 37	   3259	  0.10%
 38	   3065	  0.09%
 39	   3391	  0.10%
 40	   3865	  0.12%
 41	   3641	  0.11%
 42	   4509	  0.14%
 43	   6665	  0.20%
 44	   9252	  0.28%
 45	  12075	  0.37%
 46	  17136	  0.52%
 47	  21743	  0.66%
 48	  29964	  0.91%
 49	  29940	  0.91%
 50	3123840	 94.92%
3291123 reads passed initial QC


criterion=sequence-density
sequence-density=87.34
sequence-density-rank=1
fanout-score=20.82
fanout-score-rank=1
prefix-density=88.64
prefix-fanout=20.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCC


criterion=fanout-score
sequence-density=87.34
sequence-density-rank=1
fanout-score=20.82
fanout-score-rank=1
prefix-density=88.64
prefix-fanout=20.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCC -o SRR5031049 -
Input file:	STDIN
trimmed:	SRR5031049-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCC
-- 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 07:13:26 2020 >> started

Wed Mar  4 07:13:30 2020 >> done (3.492s)
3216325 reads processed; of these:
 172551 ( 5.36%) short reads filtered out after trimming by size control
  32091 ( 1.00%) empty reads filtered out after trimming by size control
3011683 (93.64%) reads available; of these:
2874591 (95.45%) trimmed reads available after processing
 137092 ( 4.55%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  16297	  0.54%
 19	  33181	  1.10%
 20	 188332	  6.25%
 21	 388379	 12.90%
 22	 968130	 32.15%
 23	 423432	 14.06%
 24	 201700	  6.70%
 25	  51652	  1.72%
 26	  26708	  0.89%
 27	  21368	  0.71%
 28	  24440	  0.81%
 29	  17614	  0.58%
 30	  27395	  0.91%
 31	  31749	  1.05%
 32	  44717	  1.48%
 33	  93186	  3.09%
 34	  35405	  1.18%
 35	  25782	  0.86%
 36	  29706	  0.99%
 37	  15406	  0.51%
 38	  16350	  0.54%
 39	  15431	  0.51%
 40	  24802	  0.82%
 41	  32804	  1.09%
 42	  36676	  1.22%
 43	  24360	  0.81%
 44	  18397	  0.61%
 45	  26899	  0.89%
 46	  19315	  0.64%
 47	  13733	  0.46%
 48	   1389	  0.05%
 49	   2026	  0.07%
 50	 114922	  3.82%


criterion=sequence-density
sequence-density=6.19
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=38
fanout-score=100.42
fanout-score-rank=1
prefix-density=1.74
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:13:51
                             Started mapping on |	Mar 04 07:13:51
                                    Finished on |	Mar 04 07:14:17
       Mapping speed, Million of reads per hour |	427.36

                          Number of input reads |	3086481
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1676359
                        Uniquely mapped reads % |	54.31%
                          Average mapped length |	24.46
                       Number of splices: Total |	2251
            Number of splices: Annotated (sjdb) |	698
                       Number of splices: GT/AG |	2142
                       Number of splices: GC/AG |	28
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	80
                      Mismatch rate per base, % |	0.18%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.77
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1029929
             % of reads mapped to multiple loci |	33.37%
        Number of reads mapped to too many loci |	63536
             % of reads mapped to too many loci |	2.06%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.71%
                     % of reads unmapped: other |	0.55%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	380193	380193	380193
N_multimapping	1029929	1029929	1029929
N_noFeature	68567	87294	1138789
N_ambiguous	957877	494391	13982
UnstrandedReadsAssigned:649915 PositiveStrandReadsAssigned:1094674 NegativeStrandReadsAssigned:523588
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031049 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: SRR5031049-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,086,481 reads, 813,729 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,157 rounds

 109283 SRR5031049.ke.tsv
  52636 SRR5031049.se.tsv
 161919 total
==> SRR5031049.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

==> SRR5031049.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031049 completed mapping pipeline successfully
