Starting /dee2/code/volunteer_pipeline.sh SRR5031097
    current disk space = 160474644480
    free memory = 73934928 
SRR5031097 SRAfilesize
037ba45a752c245f596c71f306ab759d  SRR5031097.sra
SRR5031097.sra file validated
SRR5031097 is single end
SRR5031097 is conventional basespace
SRR5031097 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031097_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	53
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.922	31.0	31.0	34.0	30.0	34.0
2	32.41425	33.0	31.0	34.0	31.0	34.0
3	32.41075	34.0	31.0	34.0	31.0	34.0
4	36.1785	37.0	35.0	37.0	35.0	37.0
5	36.09675	37.0	35.0	37.0	35.0	37.0
6	35.95775	37.0	35.0	37.0	35.0	37.0
7	35.74725	37.0	35.0	37.0	35.0	37.0
8	35.49575	37.0	35.0	37.0	33.0	37.0
9	36.7205	39.0	37.0	39.0	32.0	39.0
10	36.3365	39.0	35.0	39.0	32.0	39.0
11	37.23225	39.0	37.0	39.0	34.0	39.0
12	37.64225	39.0	37.0	39.0	35.0	39.0
13	37.45025	39.0	37.0	39.0	35.0	39.0
14	38.31475	40.0	38.0	41.0	33.0	41.0
15	36.7375	39.0	36.0	41.0	29.0	41.0
16	36.66125	38.0	35.0	40.0	31.0	41.0
17	36.77425	39.0	36.0	40.0	31.0	41.0
18	38.21175	40.0	37.0	41.0	34.0	41.0
19	38.4675	40.0	38.0	41.0	34.0	41.0
20	38.28825	40.0	38.0	41.0	34.0	41.0
21	38.3135	40.0	38.0	41.0	34.0	41.0
22	37.275	39.0	37.0	40.0	32.0	41.0
23	37.7845	39.0	37.0	40.0	33.0	41.0
24	37.15775	39.0	36.0	40.0	31.0	41.0
25	38.04625	40.0	37.0	41.0	33.0	41.0
26	37.8935	40.0	37.0	41.0	33.0	41.0
27	37.93575	40.0	38.0	41.0	33.0	41.0
28	38.25225	40.0	38.0	41.0	34.0	41.0
29	38.2015	40.0	38.0	41.0	33.0	41.0
30	38.58925	40.0	38.0	41.0	34.0	41.0
31	38.593	40.0	38.0	41.0	34.0	41.0
32	38.57725	40.0	38.0	41.0	35.0	41.0
33	38.479	40.0	38.0	41.0	34.0	41.0
34	37.87975	40.0	38.0	41.0	33.0	41.0
35	37.0055	40.0	35.0	41.0	30.0	41.0
36	32.59925	35.0	30.0	39.0	18.0	41.0
37	34.452	37.0	32.0	39.0	26.0	40.0
38	36.05425	38.0	35.0	39.0	30.0	40.0
39	36.268	38.0	35.0	40.0	30.0	40.0
40	36.6275	39.0	36.0	40.0	30.0	41.0
41	36.88225	39.0	36.0	40.0	30.0	41.0
42	37.08075	39.0	36.0	41.0	31.0	41.0
43	37.34675	40.0	37.0	41.0	32.0	41.0
44	36.64025	39.0	35.0	40.0	30.0	41.0
45	36.51425	39.0	35.0	40.0	30.0	41.0
46	36.405	39.0	35.0	40.0	30.0	41.0
47	35.359	38.0	34.0	40.0	27.0	41.0
48	36.34375	39.0	35.0	40.0	30.0	41.0
49	36.64075	39.0	36.0	41.0	31.0	41.0
50	34.7325	38.0	34.0	40.0	27.0	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
13	1.0
14	1.0
15	0.0
16	1.0
17	2.0
18	0.0
19	3.0
20	4.0
21	4.0
22	9.0
23	10.0
24	10.0
25	13.0
26	15.0
27	30.0
28	22.0
29	34.0
30	73.0
31	86.0
32	104.0
33	154.0
34	184.0
35	285.0
36	464.0
37	729.0
38	1126.0
39	636.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.175	25.174999999999997	51.55	15.1
2	25.707133917396746	28.28535669586984	16.62077596996245	29.386733416770966
3	24.775	19.8	18.625	36.8
4	34.125	29.025000000000002	13.15	23.7
5	24.65	37.425000000000004	28.425	9.5
6	34.4	12.425	38.0	15.174999999999999
7	12.950000000000001	24.3	23.45	39.300000000000004
8	26.400000000000002	28.849999999999998	13.900000000000002	30.85
9	20.8	36.199999999999996	27.200000000000003	15.8
10	18.45	20.025000000000002	28.15	33.375
11	35.125	9.4	14.124999999999998	41.349999999999994
12	15.825	17.95	29.599999999999998	36.625
13	31.424999999999997	15.325	35.9	17.349999999999998
14	32.95	26.974999999999998	23.674999999999997	16.400000000000002
15	36.825	15.35	29.349999999999998	18.475
16	19.425	17.825	20.625	42.125
17	27.1	20.5	37.35	15.049999999999999
18	25.900000000000002	17.075000000000003	29.5	27.525
19	34.925	14.85	30.599999999999998	19.625
20	48.65	11.325000000000001	28.875	11.15
21	24.8	20.825	26.650000000000002	27.725
22	29.575000000000003	10.100000000000001	48.225	12.1
23	26.224999999999998	11.899999999999999	47.8	14.075
24	52.175000000000004	11.0	26.275	10.549999999999999
25	52.949999999999996	23.974999999999998	15.0	8.075000000000001
26	28.225	47.075	13.325000000000001	11.375
27	15.65	49.475	22.95	11.924999999999999
28	11.5	25.7	49.225	13.575000000000001
29	11.700000000000001	10.95	57.475	19.875
30	9.6	5.65	38.65	46.1
31	12.8	4.775	46.825	35.6
32	27.725	5.55	22.45	44.275
33	55.05	8.275	12.375	24.3
34	65.85	6.175	14.124999999999998	13.850000000000001
35	66.05	7.049999999999999	18.875	8.025
36	45.625	6.4750000000000005	35.65	12.25
37	45.85	9.3	22.35	22.5
38	24.224999999999998	14.674999999999999	11.924999999999999	49.175000000000004
39	15.299999999999999	23.65	8.774999999999999	52.275000000000006
40	14.35	49.325	10.174999999999999	26.150000000000002
41	23.325000000000003	50.675000000000004	8.75	17.25
42	49.3	30.4	10.525	9.775
43	53.175	28.775000000000002	7.825	10.225
44	31.4	48.15	6.325	14.124999999999998
45	18.8	51.1	12.0	18.099999999999998
46	12.525	26.400000000000002	18.075	43.0
47	7.3999999999999995	15.4	39.074999999999996	38.125
48	9.375	11.525	22.0	57.099999999999994
49	13.450000000000001	18.55	13.350000000000001	54.65
50	17.724999999999998	36.35	13.075000000000001	32.85
>>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	0.0
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	1.0
26	2.0
27	1.0
28	0.0
29	1.0
30	2.0
31	3.5
32	5.0
33	4.0
34	3.0
35	7.5
36	12.0
37	15.0
38	18.0
39	16.5
40	15.0
41	18.5
42	22.0
43	69.0
44	116.0
45	127.0
46	138.0
47	248.0
48	358.0
49	450.5
50	543.0
51	766.5
52	990.0
53	730.0
54	470.0
55	517.0
56	564.0
57	425.0
58	286.0
59	207.0
60	128.0
61	88.5
62	49.0
63	88.0
64	127.0
65	97.0
66	67.0
67	48.5
68	30.0
69	24.0
70	18.0
71	22.5
72	27.0
73	15.5
74	4.0
75	3.5
76	3.0
77	2.0
78	1.0
79	1.0
80	1.0
81	1.0
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	0.125
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	39.7
#Duplication Level	Percentage of deduplicated	Percentage of total
1	77.14105793450882	30.625000000000004
2	8.690176322418136	6.9
3	4.785894206549118	5.7
4	1.7632241813602016	2.8000000000000003
5	1.5113350125944585	3.0
6	1.070528967254408	2.55
7	0.6926952141057935	1.925
8	0.5037783375314862	1.6
9	0.4408060453400504	1.575
>10	2.707808564231738	18.975
>50	0.5037783375314862	14.374999999999998
>100	0.1889168765743073	9.975000000000001
>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	163	4.075	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	132	3.3000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	104	2.6	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	99	2.475	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	81	2.025	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	77	1.925	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	72	1.7999999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	70	1.7500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	70	1.7500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	55	1.375	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	51	1.275	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	43	1.075	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGC	42	1.05	RNA PCR Primer, Index 21 (100% over 50bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	25	0.625	RNA PCR Primer, Index 1 (97% over 35bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	25	0.625	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	23	0.575	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	21	0.525	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	19	0.475	RNA PCR Primer, Index 1 (96% over 30bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTC	15	0.375	RNA PCR Primer, Index 21 (100% over 44bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	13	0.325	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	12	0.3	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	12	0.3	RNA PCR Primer, Index 1 (100% over 31bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	9	0.22499999999999998	RNA PCR Primer, Index 6 (100% over 34bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAACAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGACCCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGCACTCCAGTCACGTTTCGATCTCGTATGC	8	0.2	RNA PCR Primer, Index 21 (98% over 50bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	8	0.2	RNA PCR Primer, Index 1 (100% over 24bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTCTAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (97% over 35bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGGGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
TTTGAACCATCACTCGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	6	0.15	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTACCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGGCCCAAGTCCTTCTGCTCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TGTAAACATCCTCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	5	0.125	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
AAGCTGCCAGTTGACGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGGCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (96% over 30bp)
AGCTACATCTGGCTCCTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	5	0.125	No Hit
TCCCTGAGACCCTACCTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
>>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	1.475	0.0	0.0	0.0
2	0.0	1.475	0.0	0.0	0.0
3	0.0	1.6	0.0	0.0	0.0
4	0.0	1.65	0.0	0.0	0.0
5	0.0	1.7	0.0	0.0	0.0
6	0.0	1.775	0.0	0.0	0.0
7	0.0	2.425	0.0	0.0	0.0
8	0.0	2.625	0.0	0.0	0.0
9	0.0	2.775	0.0	0.0	0.0
10	0.0	3.025	0.0	0.0	0.0
11	0.0	3.1	0.0	0.0	0.0
12	0.0	3.4	0.0	0.0	0.0
13	0.0	3.65	0.0	0.0	0.0
14	0.0	4.025	0.0	0.0	0.0
15	0.0	4.375	0.0	0.0	0.0
16	0.0	5.65	0.0	0.0	0.0
17	0.0	6.375	0.0	0.0	0.0
18	0.0	7.475	0.0	0.0	0.0
19	0.0	7.825	0.0	0.0	0.0
20	0.0	9.05	0.0	0.0	0.0
21	0.0	13.5	0.0	0.0	0.0
22	0.0	25.425	0.0	0.0	0.0
23	0.0	56.225	0.0	0.0	0.0
24	0.0	71.125	0.0	0.0	0.0
25	0.0	76.975	0.0	0.0	0.0
26	0.0	78.35	0.0	0.0	0.0
27	0.0	79.075	0.0	0.0	0.0
28	0.0	79.575	0.0	0.0	0.0
29	0.0	80.325	0.0	0.0	0.0
30	0.0	80.8	0.0	0.0	0.0
31	0.0	81.5	0.0	0.0	0.0
32	0.0	82.975	0.0	0.0	0.0
33	0.0	83.7	0.0	0.0	0.0
34	0.0	86.65	0.0	0.0	0.0
35	0.0	87.575	0.0	0.0	0.0
36	0.0	88.25	0.0	0.0	0.0
37	0.0	89.025	0.0	0.0	0.0
38	0.0	89.3	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACAGTGA	20	6.952051E-4	44.000004	3
TTGTATA	20	6.952051E-4	44.000004	13
AGGATAG	20	6.952051E-4	44.000004	13
GGTCTCT	20	6.952051E-4	44.000004	13
CCGCTGA	20	6.952051E-4	44.000004	27
ATAGGCT	20	6.952051E-4	44.000004	16
GTATAGT	20	6.952051E-4	44.000004	15
GGATAGG	20	6.952051E-4	44.000004	14
ATCAGAC	20	6.952051E-4	44.000004	12
ATAGTTT	20	6.952051E-4	44.000004	17
AGACGTG	20	6.952051E-4	44.000004	15
GTCTCTT	20	6.952051E-4	44.000004	14
TCAGACG	20	6.952051E-4	44.000004	13
GCTTGGC	40	5.315087E-9	44.000004	15
CAGACGT	20	6.952051E-4	44.000004	14
GATCAGA	20	6.952051E-4	44.000004	11
CAGATCA	20	6.952051E-4	44.000004	9
TTGGCTT	20	6.952051E-4	44.000004	17
TCTCTTT	20	6.952051E-4	44.000004	15
CGGTCTC	20	6.952051E-4	44.000004	12
>>END_MODULE
Read 78561 spots for SRR5031097.sra
Written 78561 spots for SRR5031097.sra
Read 78561 spots for SRR5031097.sra
Written 78561 spots for SRR5031097.sra
Read 78561 spots for SRR5031097.sra
Written 78561 spots for SRR5031097.sra
Read 78561 spots for SRR5031097.sra
Written 78561 spots for SRR5031097.sra
Read 78561 spots for SRR5031097.sra
Written 78561 spots for SRR5031097.sra
Read 78561 spots for SRR5031097.sra
Written 78561 spots for SRR5031097.sra
Read 78561 spots for SRR5031097.sra
Written 78561 spots for SRR5031097.sra
Read 78561 spots for SRR5031097.sra
Written 78561 spots for SRR5031097.sra
Read 78571 spots for SRR5031097.sra
Written 78571 spots for SRR5031097.sra
Read 78561 spots for SRR5031097.sra
Written 78561 spots for SRR5031097.sra
Read 78561 spots for SRR5031097.sra
Written 78561 spots for SRR5031097.sra
Read 78561 spots for SRR5031097.sra
Written 78561 spots for SRR5031097.sra
SRR ids: ['SRR5031097.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_75yco_2h
SRR5031097.sra spots: 942742
blocks: [[1, 78561], [78562, 157122], [157123, 235683], [235684, 314244], [314245, 392805], [392806, 471366], [471367, 549927], [549928, 628488], [628489, 707049], [707050, 785610], [785611, 864171], [864172, 942742]]
SRR5031097 file size 162376
SRR5031097 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031097 SRR5031097_1.fastq
Input file:	SRR5031097_1.fastq
trimmed:	SRR5031097-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 07:23:34 2020 >> started

Wed Mar  4 07:23:35 2020 >> done (0.787s)
942742 reads processed; of these:
   121 ( 0.01%) short reads filtered out after trimming by size control
     9 ( 0.00%) empty reads filtered out after trimming by size control
942612 (99.99%) reads available; of these:
 79568 ( 8.44%) trimmed reads available after processing
863044 (91.56%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    26	  0.00%
 19	    61	  0.01%
 20	    76	  0.01%
 21	   111	  0.01%
 22	   159	  0.02%
 23	   221	  0.02%
 24	   211	  0.02%
 25	   280	  0.03%
 26	   181	  0.02%
 27	   279	  0.03%
 28	   293	  0.03%
 29	   486	  0.05%
 30	   275	  0.03%
 31	   344	  0.04%
 32	   486	  0.05%
 33	   822	  0.09%
 34	  1036	  0.11%
 35	  2559	  0.27%
 36	  1575	  0.17%
 37	  1564	  0.17%
 38	  1529	  0.16%
 39	  1706	  0.18%
 40	  2121	  0.23%
 41	  1917	  0.20%
 42	  2234	  0.24%
 43	  3766	  0.40%
 44	  4243	  0.45%
 45	  6145	  0.65%
 46	  8167	  0.87%
 47	  5831	  0.62%
 48	 15197	  1.61%
 49	 15667	  1.66%
 50	863044	 91.56%
942612 reads passed initial QC


criterion=sequence-density
sequence-density=89.66
sequence-density-rank=1
fanout-score=20.22
fanout-score-rank=2
prefix-density=90.14
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCC


criterion=fanout-score
sequence-density=4.06
sequence-density-rank=2
fanout-score=64.15
fanout-score-rank=1
prefix-density=89.79
prefix-fanout=2.9
sequence=GAATTCTCGGGGGCCAAGGAACT
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 SRR5031097 -
Input file:	STDIN
trimmed:	SRR5031097-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 07:23:43 2020 >> started

Wed Mar  4 07:23:44 2020 >> done (1.540s)
921665 reads processed; of these:
 54070 ( 5.87%) short reads filtered out after trimming by size control
 13496 ( 1.46%) empty reads filtered out after trimming by size control
854099 (92.67%) reads available; of these:
824833 (96.57%) trimmed reads available after processing
 29266 ( 3.43%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  5264	  0.62%
 19	  9585	  1.12%
 20	 45690	  5.35%
 21	107684	 12.61%
 22	298488	 34.95%
 23	143007	 16.74%
 24	 58074	  6.80%
 25	 15623	  1.83%
 26	  7622	  0.89%
 27	  5818	  0.68%
 28	  6110	  0.72%
 29	  5344	  0.63%
 30	  7638	  0.89%
 31	 13926	  1.63%
 32	  8300	  0.97%
 33	 32593	  3.82%
 34	  7408	  0.87%
 35	  5649	  0.66%
 36	  6647	  0.78%
 37	  3092	  0.36%
 38	  3295	  0.39%
 39	  2935	  0.34%
 40	  4515	  0.53%
 41	  5335	  0.62%
 42	  6133	  0.72%
 43	  4065	  0.48%
 44	  2616	  0.31%
 45	  3210	  0.38%
 46	  2305	  0.27%
 47	  1898	  0.22%
 48	   371	  0.04%
 49	   462	  0.05%
 50	 23397	  2.74%


criterion=sequence-density
sequence-density=10.21
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=8
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=2.25
sequence-density-rank=8
fanout-score=17.30
fanout-score-rank=1
prefix-density=2.12
prefix-fanout=17.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGC
                                 Started job on |	Mar 04 07:24:03
                             Started mapping on |	Mar 04 07:24:04
                                    Finished on |	Mar 04 07:24:29
       Mapping speed, Million of reads per hour |	126.01

                          Number of input reads |	875046
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	443462
                        Uniquely mapped reads % |	50.68%
                          Average mapped length |	23.81
                       Number of splices: Total |	1920
            Number of splices: Annotated (sjdb) |	521
                       Number of splices: GT/AG |	1891
                       Number of splices: GC/AG |	20
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	9
                      Mismatch rate per base, % |	0.38%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.64
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.11
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	332392
             % of reads mapped to multiple loci |	37.99%
        Number of reads mapped to too many loci |	13046
             % of reads mapped to too many loci |	1.49%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.34%
                     % of reads unmapped: other |	0.51%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	99192	99192	99192
N_multimapping	332392	332392	332392
N_noFeature	34586	38786	305862
N_ambiguous	246287	125895	3088
UnstrandedReadsAssigned:162589 PositiveStrandReadsAssigned:278781 NegativeStrandReadsAssigned:134512
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031097 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: SRR5031097-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 875,046 reads, 209,401 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 983 rounds

 109283 SRR5031097.ke.tsv
  52636 SRR5031097.se.tsv
 161919 total
==> SRR5031097.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

==> SRR5031097.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031097 completed mapping pipeline successfully
