Starting /dee2/code/volunteer_pipeline.sh SRR5031074
    current disk space = 160489259008
    free memory = 73949684 
SRR5031074 SRAfilesize
3620cc2739233e6d6175b25f2925644a  SRR5031074.sra
SRR5031074.sra file validated
SRR5031074 is single end
SRR5031074 is conventional basespace
SRR5031074 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031074_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	32.33075	33.0	31.0	34.0	31.0	34.0
2	32.57275	34.0	31.0	34.0	31.0	34.0
3	32.649	34.0	31.0	34.0	31.0	34.0
4	36.23025	37.0	37.0	37.0	35.0	37.0
5	35.905	37.0	35.0	37.0	35.0	37.0
6	35.8865	37.0	35.0	37.0	35.0	37.0
7	35.92275	37.0	35.0	37.0	35.0	37.0
8	35.781	37.0	35.0	37.0	35.0	37.0
9	37.56825	39.0	37.0	39.0	35.0	39.0
10	37.783	39.0	37.0	39.0	35.0	39.0
11	37.6215	39.0	37.0	39.0	35.0	39.0
12	37.682	39.0	37.0	39.0	35.0	39.0
13	37.595	39.0	37.0	39.0	35.0	39.0
14	39.03725	40.0	38.0	41.0	36.0	41.0
15	38.991	40.0	38.0	41.0	35.0	41.0
16	38.9705	40.0	38.0	41.0	36.0	41.0
17	38.84325	40.0	38.0	41.0	35.0	41.0
18	38.97725	40.0	38.0	41.0	35.0	41.0
19	38.6845	40.0	38.0	41.0	34.0	41.0
20	38.84025	40.0	38.0	41.0	34.0	41.0
21	38.78875	40.0	38.0	41.0	35.0	41.0
22	38.90225	40.0	39.0	41.0	35.0	41.0
23	38.631	40.0	38.0	41.0	34.0	41.0
24	38.56175	40.0	38.0	41.0	34.0	41.0
25	38.77775	40.0	38.0	41.0	34.0	41.0
26	38.493	40.0	38.0	41.0	34.0	41.0
27	38.43125	40.0	38.0	41.0	34.0	41.0
28	38.5145	40.0	38.0	41.0	34.0	41.0
29	38.19975	40.0	38.0	41.0	33.0	41.0
30	37.83725	40.0	38.0	41.0	32.0	41.0
31	38.2755	40.0	38.0	41.0	33.0	41.0
32	38.1625	40.0	38.0	41.0	33.0	41.0
33	38.208	40.0	38.0	41.0	33.0	41.0
34	38.33675	40.0	38.0	41.0	33.0	41.0
35	38.25525	40.0	38.0	41.0	34.0	41.0
36	37.87575	40.0	37.0	41.0	33.0	41.0
37	37.34675	40.0	37.0	41.0	31.0	41.0
38	36.62875	39.0	36.0	41.0	30.0	41.0
39	36.926	39.0	36.0	41.0	30.0	41.0
40	37.3005	40.0	37.0	41.0	31.0	41.0
41	37.5105	40.0	37.0	41.0	32.0	41.0
42	37.72175	40.0	37.0	41.0	33.0	41.0
43	38.025	40.0	38.0	41.0	33.0	41.0
44	37.6555	40.0	37.0	41.0	33.0	41.0
45	37.6295	40.0	37.0	41.0	33.0	41.0
46	37.60725	40.0	37.0	41.0	33.0	41.0
47	37.016	40.0	36.0	41.0	31.0	41.0
48	36.63725	39.0	36.0	41.0	30.0	41.0
49	36.9265	40.0	36.0	41.0	31.0	41.0
50	36.32075	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
9	1.0
10	0.0
11	0.0
12	0.0
13	0.0
14	1.0
15	0.0
16	2.0
17	1.0
18	2.0
19	6.0
20	3.0
21	4.0
22	1.0
23	5.0
24	5.0
25	13.0
26	19.0
27	16.0
28	24.0
29	41.0
30	56.0
31	60.0
32	94.0
33	119.0
34	146.0
35	201.0
36	284.0
37	446.0
38	761.0
39	1689.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.5	24.775	45.875	18.85
2	23.61632857500626	27.372902579514154	18.757826195842725	30.252942649636864
3	23.45	19.85	20.424999999999997	36.275
4	33.800000000000004	26.375	15.125	24.7
5	23.400000000000002	38.550000000000004	25.45	12.6
6	33.4	14.6	34.775	17.224999999999998
7	15.2	22.725	23.200000000000003	38.875
8	24.725	27.950000000000003	18.099999999999998	29.225
9	21.975	32.625	27.025	18.375
10	20.525	24.025	27.224999999999998	28.225
11	33.425	11.375	16.900000000000002	38.3
12	17.95	18.4	30.225	33.425
13	29.025000000000002	18.099999999999998	34.150000000000006	18.725
14	29.349999999999998	30.725	20.849999999999998	19.075
15	33.6	26.900000000000002	25.424999999999997	14.075
16	20.674999999999997	20.674999999999997	22.650000000000002	36.0
17	26.125	24.2	34.599999999999994	15.075
18	22.975	18.975	29.675	28.375
19	39.4	13.425	28.449999999999996	18.725
20	43.175000000000004	14.475	28.125	14.224999999999998
21	25.8	19.7	26.900000000000002	27.6
22	30.9	13.175	44.5	11.425
23	27.125	12.925	42.475	17.474999999999998
24	51.475	14.875	24.775	8.875
25	48.15	26.55	14.649999999999999	10.65
26	28.025	43.625	14.075	14.274999999999999
27	15.875	45.525	23.200000000000003	15.4
28	11.025	23.775	46.925	18.275
29	15.024999999999999	13.675	53.5	17.8
30	10.775	7.5249999999999995	34.849999999999994	46.85
31	15.375	5.7	47.575	31.35
32	30.075000000000003	6.45	21.45	42.025
33	52.0	11.75	14.000000000000002	22.25
34	57.99999999999999	7.7	18.7	15.6
35	63.775000000000006	6.525	18.425	11.275
36	41.949999999999996	7.475	36.5	14.075
37	43.575	13.225000000000001	19.375	23.825
38	24.099999999999998	18.125	12.4	45.375
39	16.575	22.85	13.200000000000001	47.375
40	16.925	45.1	13.825000000000001	24.15
41	24.15	45.975	10.125	19.75
42	46.2	27.875	15.375	10.549999999999999
43	49.425000000000004	27.35	9.475	13.750000000000002
44	33.45	45.050000000000004	8.450000000000001	13.05
45	21.5	47.9	12.825000000000001	17.775
46	16.2	26.150000000000002	17.349999999999998	40.300000000000004
47	10.45	15.55	39.95	34.050000000000004
48	13.875000000000002	12.675	20.9	52.55
49	13.125	18.0	15.875	53.0
50	17.349999999999998	34.775	14.325	33.550000000000004
>>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	1.0
18	2.0
19	1.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.5
26	1.0
27	1.0
28	1.0
29	1.5
30	2.0
31	8.0
32	14.0
33	14.0
34	14.0
35	20.0
36	26.0
37	33.5
38	41.0
39	36.5
40	32.0
41	38.5
42	45.0
43	67.0
44	89.0
45	142.5
46	196.0
47	307.0
48	418.0
49	509.5
50	601.0
51	706.0
52	811.0
53	628.5
54	446.0
55	496.0
56	546.0
57	388.5
58	231.0
59	159.0
60	87.0
61	69.5
62	52.0
63	123.5
64	195.0
65	112.0
66	29.0
67	24.5
68	20.0
69	19.0
70	18.0
71	42.5
72	67.0
73	36.0
74	5.0
75	4.5
76	4.0
77	2.5
78	1.0
79	2.5
80	4.0
81	2.5
82	1.0
83	0.5
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	38.800000000000004
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.64432989690721	29.349999999999998
2	9.471649484536082	7.35
3	3.865979381443299	4.5
4	3.0283505154639174	4.7
5	1.4819587628865978	2.875
6	1.1597938144329898	2.7
7	0.7087628865979382	1.925
8	0.902061855670103	2.8000000000000003
9	0.3865979381443299	1.35
>10	2.7061855670103094	18.725
>50	0.3221649484536082	8.25
>100	0.3221649484536082	15.475
>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
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	148	3.6999999999999997	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	126	3.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	119	2.9749999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	113	2.825	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	113	2.825	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	87	2.175	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	75	1.875	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	65	1.625	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	52	1.3	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	51	1.275	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	27	0.675	No Hit
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	24	0.6	RNA PCR Primer, Index 5 (97% over 35bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	23	0.575	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTC	20	0.5	RNA PCR Primer, Index 46 (100% over 44bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	20	0.5	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	13	0.325	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	12	0.3	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	11	0.27499999999999997	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	11	0.27499999999999997	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCGTATGC	10	0.25	RNA PCR Primer, Index 46 (100% over 50bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	10	0.25	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	9	0.22499999999999998	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	9	0.22499999999999998	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 31bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	9	0.22499999999999998	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	8	0.2	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	8	0.2	No Hit
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	7	0.17500000000000002	RNA PCR Primer, Index 3 (100% over 34bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	7	0.17500000000000002	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GAGAGTGATGATTTCACAGACTAGAGTCTCTGACGTGGAATTCTCGGGTG	6	0.15	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	6	0.15	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	6	0.15	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	6	0.15	No Hit
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCC	5	0.125	RNA PCR Primer, Index 6 (97% over 36bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGTGGAATTCTCGGGTGC	5	0.125	No Hit
CAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTGGAATTC	5	0.125	No Hit
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	5	0.125	No Hit
CTAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTGTGCTTGATCTAACCATGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AACCCGTAGATCCGATCTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>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	0.25	0.0	0.0	0.0
2	0.0	0.275	0.0	0.0	0.0
3	0.0	0.325	0.0	0.0	0.0
4	0.0	0.325	0.0	0.0	0.0
5	0.0	0.325	0.0	0.0	0.0
6	0.0	0.45	0.0	0.0	0.0
7	0.0	1.15	0.0	0.0	0.0
8	0.0	1.325	0.0	0.0	0.0
9	0.0	1.35	0.0	0.0	0.0
10	0.0	1.5	0.0	0.0	0.0
11	0.0	1.65	0.0	0.0	0.0
12	0.0	1.875	0.0	0.0	0.0
13	0.0	2.075	0.0	0.0	0.0
14	0.0	2.35	0.0	0.0	0.0
15	0.0	2.9	0.0	0.0	0.0
16	0.0	3.75	0.0	0.0	0.0
17	0.0	4.25	0.0	0.0	0.0
18	0.0	5.275	0.0	0.0	0.0
19	0.0	5.75	0.0	0.0	0.0
20	0.0	6.75	0.0	0.0	0.0
21	0.0	11.8	0.0	0.0	0.0
22	0.0	21.95	0.0	0.0	0.0
23	0.0	49.65	0.0	0.0	0.0
24	0.0	61.775	0.0	0.0	0.0
25	0.0	67.5	0.0	0.0	0.0
26	0.0	69.05	0.0	0.0	0.0
27	0.0	69.8	0.0	0.0	0.0
28	0.0	70.375	0.0	0.0	0.0
29	0.0	71.025	0.0	0.0	0.0
30	0.0	71.7	0.0	0.0	0.0
31	0.0	72.375	0.0	0.0	0.0
32	0.0	73.175	0.0	0.0	0.0
33	0.0	74.325	0.0	0.0	0.0
34	0.0	79.525	0.0	0.0	0.0
35	0.0	80.575	0.0	0.0	0.0
36	0.0	81.725	0.0	0.0	0.0
37	0.0	82.95	0.0	0.0	0.0
38	0.0	83.4	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGCACTC	20	6.952051E-4	44.000004	4
ACTCGTC	20	6.952051E-4	44.000004	7
TTGCACT	20	6.952051E-4	44.000004	3
CAGTTGA	20	6.952051E-4	44.000004	8
CCAGTTG	20	6.952051E-4	44.000004	7
CCCGGCC	20	6.952051E-4	44.000004	13
GAGCTTG	45	2.728484E-10	44.000004	13
GGATCCG	45	2.728484E-10	44.000004	3
CCGTCTG	45	2.728484E-10	44.000004	7
TCGGATC	45	2.728484E-10	44.000004	1
GTCTGAG	45	2.728484E-10	44.000004	9
TAGTTTG	20	6.952051E-4	44.000004	18
CGGATCC	45	2.728484E-10	44.000004	2
TATTGCA	20	6.952051E-4	44.000004	1
GCCAGTT	20	6.952051E-4	44.000004	6
ATAGTTT	20	6.952051E-4	44.000004	17
GTCCCGG	20	6.952051E-4	44.000004	11
GCTGCCA	20	6.952051E-4	44.000004	3
ATTGCAC	20	6.952051E-4	44.000004	2
GATCCGT	45	2.728484E-10	44.000004	4
>>END_MODULE
Read 271471 spots for SRR5031074.sra
Written 271471 spots for SRR5031074.sra
Read 271471 spots for SRR5031074.sra
Written 271471 spots for SRR5031074.sra
Read 271471 spots for SRR5031074.sra
Written 271471 spots for SRR5031074.sra
Read 271471 spots for SRR5031074.sra
Written 271471 spots for SRR5031074.sra
Read 271475 spots for SRR5031074.sra
Written 271475 spots for SRR5031074.sra
Read 271471 spots for SRR5031074.sra
Written 271471 spots for SRR5031074.sra
Read 271471 spots for SRR5031074.sra
Written 271471 spots for SRR5031074.sra
Read 271471 spots for SRR5031074.sra
Written 271471 spots for SRR5031074.sra
Read 271471 spots for SRR5031074.sra
Written 271471 spots for SRR5031074.sra
Read 271471 spots for SRR5031074.sra
Written 271471 spots for SRR5031074.sra
Read 271471 spots for SRR5031074.sra
Written 271471 spots for SRR5031074.sra
Read 271471 spots for SRR5031074.sra
Written 271471 spots for SRR5031074.sra
SRR ids: ['SRR5031074.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ltg7mlc9
SRR5031074.sra spots: 3257656
blocks: [[1, 271471], [271472, 542942], [542943, 814413], [814414, 1085884], [1085885, 1357355], [1357356, 1628826], [1628827, 1900297], [1900298, 2171768], [2171769, 2443239], [2443240, 2714710], [2714711, 2986181], [2986182, 3257656]]
SRR5031074 file size 563561
SRR5031074 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031074 SRR5031074_1.fastq
Input file:	SRR5031074_1.fastq
trimmed:	SRR5031074-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 07:19:03 2020 >> started

Wed Mar  4 07:19:06 2020 >> done (3.338s)
3257656 reads processed; of these:
    269 ( 0.01%) short reads filtered out after trimming by size control
      7 ( 0.00%) empty reads filtered out after trimming by size control
3257380 (99.99%) reads available; of these:
 172209 ( 5.29%) trimmed reads available after processing
3085171 (94.71%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     98	  0.00%
 19	    112	  0.00%
 20	    225	  0.01%
 21	    274	  0.01%
 22	    488	  0.01%
 23	    569	  0.02%
 24	    640	  0.02%
 25	    838	  0.03%
 26	    629	  0.02%
 27	    807	  0.02%
 28	    923	  0.03%
 29	   1413	  0.04%
 30	    880	  0.03%
 31	   1113	  0.03%
 32	   1401	  0.04%
 33	   1442	  0.04%
 34	   1664	  0.05%
 35	   3258	  0.10%
 36	   3095	  0.10%
 37	   3490	  0.11%
 38	   3581	  0.11%
 39	   3733	  0.11%
 40	   4103	  0.13%
 41	   3995	  0.12%
 42	   5037	  0.15%
 43	   6867	  0.21%
 44	   9419	  0.29%
 45	  12094	  0.37%
 46	  18098	  0.56%
 47	  20889	  0.64%
 48	  29716	  0.91%
 49	  31318	  0.96%
 50	3085171	 94.71%
3257380 reads passed initial QC


criterion=sequence-density
sequence-density=83.62
sequence-density-rank=1
fanout-score=20.75
fanout-score-rank=1
prefix-density=86.13
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCGTATGCC


criterion=fanout-score
sequence-density=83.62
sequence-density-rank=1
fanout-score=20.75
fanout-score-rank=1
prefix-density=86.13
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCGTATGCC -o SRR5031074 -
Input file:	STDIN
trimmed:	SRR5031074-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCCCGAATCTCGTATGCC
-- 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 07:19:32 2020 >> started

Wed Mar  4 07:19:40 2020 >> done (7.429s)
3179823 reads processed; of these:
 175424 ( 5.52%) short reads filtered out after trimming by size control
  12672 ( 0.40%) empty reads filtered out after trimming by size control
2991727 (94.08%) reads available; of these:
2809233 (93.90%) trimmed reads available after processing
 182494 ( 6.10%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  16696	  0.56%
 19	  29982	  1.00%
 20	 147117	  4.92%
 21	 323080	 10.80%
 22	 906792	 30.31%
 23	 400308	 13.38%
 24	 180160	  6.02%
 25	  52734	  1.76%
 26	  28127	  0.94%
 27	  23842	  0.80%
 28	  27028	  0.90%
 29	  20674	  0.69%
 30	  29682	  0.99%
 31	  33171	  1.11%
 32	  40733	  1.36%
 33	 152340	  5.09%
 34	  41509	  1.39%
 35	  31265	  1.05%
 36	  34520	  1.15%
 37	  20478	  0.68%
 38	  22189	  0.74%
 39	  21615	  0.72%
 40	  33662	  1.13%
 41	  42745	  1.43%
 42	  46406	  1.55%
 43	  32102	  1.07%
 44	  24143	  0.81%
 45	  30357	  1.01%
 46	  23607	  0.79%
 47	  18521	  0.62%
 48	   2105	  0.07%
 49	   2937	  0.10%
 50	 151100	  5.05%


criterion=sequence-density
sequence-density=5.90
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.40
sequence-density-rank=30
fanout-score=26.05
fanout-score-rank=1
prefix-density=10.26
prefix-fanout=1.0
sequence=CTGAGCTTGGCA
                                 Started job on |	Mar 04 07:20:11
                             Started mapping on |	Mar 04 07:20:12
                                    Finished on |	Mar 04 07:20:37
       Mapping speed, Million of reads per hour |	441.98

                          Number of input reads |	3069284
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1603091
                        Uniquely mapped reads % |	52.23%
                          Average mapped length |	25.43
                       Number of splices: Total |	2127
            Number of splices: Annotated (sjdb) |	352
                       Number of splices: GT/AG |	2006
                       Number of splices: GC/AG |	31
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	90
                      Mismatch rate per base, % |	0.23%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.68
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	972213
             % of reads mapped to multiple loci |	31.68%
        Number of reads mapped to too many loci |	74470
             % of reads mapped to too many loci |	2.43%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	13.02%
                     % of reads unmapped: other |	0.65%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	493980	493980	493980
N_multimapping	972213	972213	972213
N_noFeature	83824	106582	1099925
N_ambiguous	910656	485924	19075
UnstrandedReadsAssigned:608611 PositiveStrandReadsAssigned:1010585 NegativeStrandReadsAssigned:484091
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031074 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: SRR5031074-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,069,284 reads, 785,137 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,153 rounds

 109283 SRR5031074.ke.tsv
  52636 SRR5031074.se.tsv
 161919 total
==> SRR5031074.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

==> SRR5031074.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	2
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	1
SRR5031074 completed mapping pipeline successfully
