Starting /dee2/code/volunteer_pipeline.sh SRR5031015
    current disk space = 160553680896
    free memory = 73934852 
SRR5031015 SRAfilesize
93f3fd53b129ca74ed184ec261cfdbbf  SRR5031015.sra
SRR5031015.sra file validated
SRR5031015 is single end
SRR5031015 is conventional basespace
SRR5031015 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031015_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	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.33875	33.0	31.0	34.0	30.0	34.0
2	32.44225	34.0	31.0	34.0	31.0	34.0
3	32.4605	34.0	31.0	34.0	30.0	34.0
4	36.166	37.0	35.0	37.0	35.0	37.0
5	36.05925	37.0	35.0	37.0	35.0	37.0
6	35.84675	37.0	35.0	37.0	33.0	37.0
7	35.90925	37.0	35.0	37.0	35.0	37.0
8	36.0035	37.0	35.0	37.0	35.0	37.0
9	37.66725	39.0	37.0	39.0	35.0	39.0
10	37.51225	39.0	37.0	39.0	35.0	39.0
11	37.21325	39.0	37.0	39.0	33.0	39.0
12	37.6485	39.0	37.0	39.0	35.0	39.0
13	37.6325	39.0	37.0	39.0	35.0	39.0
14	39.077	40.0	38.0	41.0	36.0	41.0
15	38.95975	40.0	38.0	41.0	35.0	41.0
16	38.8525	40.0	38.0	41.0	35.0	41.0
17	38.978	40.0	38.0	41.0	35.0	41.0
18	38.886	40.0	38.0	41.0	35.0	41.0
19	38.74	40.0	38.0	41.0	34.0	41.0
20	38.76775	40.0	38.0	41.0	34.0	41.0
21	38.8795	40.0	38.0	41.0	35.0	41.0
22	38.8075	40.0	38.0	41.0	34.0	41.0
23	38.535	40.0	38.0	41.0	34.0	41.0
24	38.807	40.0	38.0	41.0	35.0	41.0
25	38.887	40.0	38.0	41.0	35.0	41.0
26	38.6815	40.0	38.0	41.0	34.0	41.0
27	38.83225	40.0	38.0	41.0	35.0	41.0
28	38.71125	40.0	38.0	41.0	35.0	41.0
29	38.47875	40.0	38.0	41.0	34.0	41.0
30	38.596	40.0	38.0	41.0	34.0	41.0
31	38.61975	40.0	38.0	41.0	34.0	41.0
32	38.54625	40.0	38.0	41.0	35.0	41.0
33	38.40525	40.0	38.0	41.0	34.0	41.0
34	38.139	40.0	38.0	41.0	33.0	41.0
35	38.066	40.0	38.0	41.0	33.0	41.0
36	37.8615	40.0	37.0	41.0	33.0	41.0
37	37.4345	40.0	37.0	41.0	31.0	41.0
38	37.4135	40.0	37.0	41.0	31.0	41.0
39	37.87725	40.0	38.0	41.0	33.0	41.0
40	37.93075	40.0	38.0	41.0	33.0	41.0
41	38.27225	40.0	38.0	41.0	34.0	41.0
42	38.13825	40.0	38.0	41.0	33.0	41.0
43	37.63375	40.0	37.0	41.0	33.0	41.0
44	37.7935	40.0	37.0	41.0	33.0	41.0
45	37.7025	40.0	37.0	41.0	33.0	41.0
46	37.51	40.0	37.0	41.0	33.0	41.0
47	37.09725	40.0	37.0	41.0	31.0	41.0
48	36.9855	40.0	36.0	41.0	31.0	41.0
49	37.04775	40.0	36.0	41.0	31.0	41.0
50	36.5645	39.0	36.0	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
15	3.0
16	0.0
17	0.0
18	0.0
19	3.0
20	3.0
21	5.0
22	4.0
23	12.0
24	8.0
25	14.0
26	7.0
27	17.0
28	32.0
29	37.0
30	55.0
31	69.0
32	75.0
33	119.0
34	128.0
35	168.0
36	292.0
37	411.0
38	687.0
39	1851.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.8	21.375	56.75	14.075
2	24.490309589730682	26.9066196828593	21.79713063176441	26.80594009564561
3	16.875	19.650000000000002	22.1	41.375
4	26.35	36.925000000000004	14.725	22.0
5	22.7	37.824999999999996	27.85	11.625
6	36.1	16.175	35.425000000000004	12.3
7	14.899999999999999	24.4	24.349999999999998	36.35
8	21.95	40.050000000000004	15.525	22.475
9	19.425	36.025	31.65	12.9
10	20.1	20.724999999999998	26.75	32.425
11	29.475	11.825	15.125	43.575
12	16.3	15.725	25.25	42.725
13	20.7	21.349999999999998	37.3	20.65
14	38.975	24.05	23.525	13.450000000000001
15	40.2	22.625	26.075	11.1
16	12.8	26.450000000000003	21.825	38.925
17	24.525	22.375	39.65	13.450000000000001
18	28.999999999999996	19.375	27.925	23.7
19	39.300000000000004	14.000000000000002	29.475	17.224999999999998
20	49.0	18.7	20.875	11.425
21	20.925	25.95	24.075	29.049999999999997
22	32.525	12.575	47.325	7.575
23	25.674999999999997	13.675	46.75	13.900000000000002
24	50.24999999999999	14.075	29.875	5.800000000000001
25	54.6	22.7	14.75	7.95
26	31.95	46.1	12.8	9.15
27	13.100000000000001	52.275000000000006	24.075	10.549999999999999
28	8.475000000000001	28.425	49.15	13.950000000000001
29	10.325	11.450000000000001	60.275	17.95
30	9.15	5.55	40.225	45.074999999999996
31	13.0	4.35	45.875	36.775000000000006
32	25.724999999999998	5.2749999999999995	25.3	43.7
33	54.7	5.625	13.950000000000001	25.724999999999998
34	66.75	5.3	13.475000000000001	14.475
35	68.525	6.325	16.6	8.55
36	43.85	7.175	36.775000000000006	12.2
37	44.824999999999996	9.25	23.95	21.975
38	25.974999999999998	13.975000000000001	12.725	47.325
39	14.7	22.675	8.875	53.75
40	13.325000000000001	47.449999999999996	9.25	29.975
41	23.400000000000002	54.074999999999996	7.425	15.1
42	48.25	34.050000000000004	9.85	7.85
43	56.375	27.500000000000004	7.625	8.5
44	33.875	47.099999999999994	7.074999999999999	11.95
45	16.7	54.125	11.95	17.224999999999998
46	10.65	29.599999999999998	16.975	42.775
47	7.6	13.65	38.775	39.975
48	8.25	11.3	24.474999999999998	55.974999999999994
49	11.375	17.849999999999998	13.475000000000001	57.3
50	16.475	37.3	12.425	33.800000000000004
>>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	0.5
24	1.0
25	1.0
26	1.0
27	1.0
28	1.0
29	1.0
30	1.0
31	7.0
32	13.0
33	12.5
34	12.0
35	16.5
36	21.0
37	24.5
38	28.0
39	33.0
40	38.0
41	38.0
42	38.0
43	79.5
44	121.0
45	187.0
46	253.0
47	442.0
48	631.0
49	630.5
50	630.0
51	785.5
52	941.0
53	663.0
54	385.0
55	365.0
56	345.0
57	310.0
58	275.0
59	164.5
60	54.0
61	43.5
62	33.0
63	53.0
64	73.0
65	49.5
66	26.0
67	18.5
68	11.0
69	13.5
70	16.0
71	32.0
72	48.0
73	25.5
74	3.0
75	2.0
76	1.0
77	0.5
78	0.0
79	0.0
80	0.0
81	0.0
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	0.675
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	36.9
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.60975609756098	27.900000000000002
2	9.620596205962059	7.1
3	4.607046070460704	5.1
4	1.9647696476964769	2.9000000000000004
5	1.2872628726287263	2.375
6	0.6097560975609756	1.35
7	1.0162601626016259	2.625
8	0.33875338753387535	1.0
9	0.5420054200542005	1.7999999999999998
>10	3.997289972899729	28.825
>50	0.13550135501355012	3.375
>100	0.27100271002710025	15.65
>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	248	6.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	152	3.8	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	120	3.0	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	106	2.65	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	72	1.7999999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	63	1.575	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	49	1.225	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	48	1.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	45	1.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	43	1.075	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	38	0.95	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	26	0.65	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	21	0.525	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	20	0.5	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 30bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	15	0.375	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	15	0.375	RNA PCR Primer, Index 7 (100% over 35bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	12	0.3	No Hit
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	10	0.25	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGC	10	0.25	RNA PCR Primer, Index 35 (100% over 50bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	10	0.25	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	10	0.25	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	9	0.22499999999999998	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	8	0.2	No Hit
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTC	8	0.2	RNA PCR Primer, Index 35 (100% over 44bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
TGAGGTAGGAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	7	0.17500000000000002	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTTTGGAAT	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTTGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	6	0.15	No Hit
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	5	0.125	No Hit
CACCCGTAGAACCGACCTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	5	0.125	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAAGGCACGCGGTGAATGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTACAGTACTGTGATAACTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAT	5	0.125	RNA PCR Primer, Index 9 (97% over 36bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.25	0.0	0.0	0.0
2	0.0	0.25	0.0	0.0	0.0
3	0.0	0.35	0.0	0.0	0.0
4	0.0	0.375	0.0	0.0	0.0
5	0.0	0.45	0.0	0.0	0.0
6	0.0	0.45	0.0	0.0	0.0
7	0.0	0.725	0.0	0.0	0.0
8	0.0	0.85	0.0	0.0	0.0
9	0.0	0.925	0.0	0.0	0.0
10	0.0	1.125	0.0	0.0	0.0
11	0.0	1.225	0.0	0.0	0.0
12	0.0	1.35	0.0	0.0	0.0
13	0.0	1.45	0.0	0.0	0.0
14	0.0	1.725	0.0	0.0	0.0
15	0.0	2.075	0.0	0.0	0.0
16	0.0	2.825	0.0	0.0	0.0
17	0.0	3.375	0.0	0.0	0.0
18	0.0	4.45	0.0	0.0	0.0
19	0.0	4.925	0.0	0.0	0.0
20	0.0	6.225	0.0	0.0	0.0
21	0.0	11.675	0.0	0.0	0.0
22	0.0	22.85	0.0	0.0	0.0
23	0.0	53.6	0.0	0.0	0.0
24	0.0	71.125	0.0	0.0	0.0
25	0.0	77.625	0.0	0.0	0.0
26	0.0	78.6	0.0	0.0	0.0
27	0.0	79.2	0.0	0.0	0.0
28	0.0	79.575	0.0	0.0	0.0
29	0.0	80.125	0.0	0.0	0.0
30	0.0	80.375	0.0	0.0	0.0
31	0.0	81.15	0.0	0.0	0.0
32	0.0	82.225	0.0	0.0	0.0
33	0.0	83.4	0.0	0.0	0.0
34	0.0	85.575	0.0	0.0	0.0
35	0.0	86.6	0.0	0.0	0.0
36	0.0	87.2	0.0	0.0	0.0
37	0.0	88.05	0.0	0.0	0.0
38	0.0	88.425	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGAGACC	20	6.952051E-4	44.000004	5
GGTGAGT	45	2.728484E-10	44.000004	17
CTGAGAC	20	6.952051E-4	44.000004	4
TAAACAT	20	6.952051E-4	44.000004	3
CTTTAAC	20	6.952051E-4	44.000004	12
AAACATC	20	6.952051E-4	44.000004	4
GAGTGGA	20	6.952051E-4	44.000004	20
AGTGGAA	20	6.952051E-4	44.000004	21
CCTGAGA	20	6.952051E-4	44.000004	3
AACCTGT	20	6.952051E-4	44.000004	16
TAACCTG	20	6.952051E-4	44.000004	15
GGCTTGG	45	2.728484E-10	44.000004	19
CCTTTAA	20	6.952051E-4	44.000004	11
CCCTGAG	20	6.952051E-4	44.000004	2
GACCCTT	20	6.952051E-4	44.000004	8
AGACCCT	20	6.952051E-4	44.000004	7
TTAACCT	20	6.952051E-4	44.000004	14
TTTAACC	20	6.952051E-4	44.000004	13
GAGACCC	20	6.952051E-4	44.000004	6
TGTAAAC	20	6.952051E-4	44.000004	1
>>END_MODULE
Read 446744 spots for SRR5031015.sra
Written 446744 spots for SRR5031015.sra
Read 446744 spots for SRR5031015.sra
Written 446744 spots for SRR5031015.sra
Read 446744 spots for SRR5031015.sra
Written 446744 spots for SRR5031015.sra
Read 446744 spots for SRR5031015.sra
Written 446744 spots for SRR5031015.sra
Read 446744 spots for SRR5031015.sra
Written 446744 spots for SRR5031015.sra
Read 446744 spots for SRR5031015.sra
Written 446744 spots for SRR5031015.sra
Read 446744 spots for SRR5031015.sra
Written 446744 spots for SRR5031015.sra
Read 446744 spots for SRR5031015.sra
Written 446744 spots for SRR5031015.sra
Read 446744 spots for SRR5031015.sra
Written 446744 spots for SRR5031015.sra
Read 446744 spots for SRR5031015.sra
Written 446744 spots for SRR5031015.sra
Read 446749 spots for SRR5031015.sra
Written 446749 spots for SRR5031015.sra
Read 446744 spots for SRR5031015.sra
Written 446744 spots for SRR5031015.sra
SRR ids: ['SRR5031015.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_oig4f4lj
SRR5031015.sra spots: 5360933
blocks: [[1, 446744], [446745, 893488], [893489, 1340232], [1340233, 1786976], [1786977, 2233720], [2233721, 2680464], [2680465, 3127208], [3127209, 3573952], [3573953, 4020696], [4020697, 4467440], [4467441, 4914184], [4914185, 5360933]]
SRR5031015 file size 928117
SRR5031015 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031015 SRR5031015_1.fastq
Input file:	SRR5031015_1.fastq
trimmed:	SRR5031015-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 07:06:56 2020 >> started

Wed Mar  4 07:06:59 2020 >> done (2.668s)
5360933 reads processed; of these:
    285 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
5360642 (99.99%) reads available; of these:
 286339 ( 5.34%) trimmed reads available after processing
5074303 (94.66%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     97	  0.00%
 19	    142	  0.00%
 20	    295	  0.01%
 21	    414	  0.01%
 22	    795	  0.01%
 23	    797	  0.01%
 24	    812	  0.02%
 25	   1066	  0.02%
 26	    792	  0.01%
 27	   1108	  0.02%
 28	   1384	  0.03%
 29	   2862	  0.05%
 30	   1379	  0.03%
 31	   1424	  0.03%
 32	   1540	  0.03%
 33	   1984	  0.04%
 34	   2540	  0.05%
 35	   5055	  0.09%
 36	   4210	  0.08%
 37	   4798	  0.09%
 38	   4341	  0.08%
 39	   4703	  0.09%
 40	   5210	  0.10%
 41	   6305	  0.12%
 42	   8433	  0.16%
 43	  11982	  0.22%
 44	  15067	  0.28%
 45	  18346	  0.34%
 46	  24024	  0.45%
 47	  31553	  0.59%
 48	  55340	  1.03%
 49	  67541	  1.26%
 50	5074303	 94.66%
5360642 reads passed initial QC


criterion=sequence-density
sequence-density=88.93
sequence-density-rank=1
fanout-score=18.95
fanout-score-rank=1
prefix-density=90.73
prefix-fanout=18.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCC


criterion=fanout-score
sequence-density=88.93
sequence-density-rank=1
fanout-score=18.95
fanout-score-rank=1
prefix-density=90.73
prefix-fanout=18.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCC -o SRR5031015 -
Input file:	STDIN
trimmed:	SRR5031015-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCC
-- 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 07:07:21 2020 >> started

Wed Mar  4 07:07:29 2020 >> done (8.343s)
5240178 reads processed; of these:
 228216 ( 4.36%) short reads filtered out after trimming by size control
  13574 ( 0.26%) empty reads filtered out after trimming by size control
4998388 (95.39%) reads available; of these:
4818506 (96.40%) trimmed reads available after processing
 179882 ( 3.60%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  24647	  0.49%
 19	  59457	  1.19%
 20	 252130	  5.04%
 21	 594307	 11.89%
 22	1751247	 35.04%
 23	 907908	 18.16%
 24	 324576	  6.49%
 25	  55600	  1.11%
 26	  28713	  0.57%
 27	  28396	  0.57%
 28	  32746	  0.66%
 29	  24362	  0.49%
 30	  42822	  0.86%
 31	  60847	  1.22%
 32	  62462	  1.25%
 33	 104437	  2.09%
 34	  54381	  1.09%
 35	  38169	  0.76%
 36	  40792	  0.82%
 37	  24025	  0.48%
 38	  26437	  0.53%
 39	  23924	  0.48%
 40	  33593	  0.67%
 41	  48281	  0.97%
 42	  51606	  1.03%
 43	  38821	  0.78%
 44	  29916	  0.60%
 45	  34901	  0.70%
 46	  25709	  0.51%
 47	  18420	  0.37%
 48	   1997	  0.04%
 49	   3672	  0.07%
 50	 149087	  2.98%


criterion=sequence-density
sequence-density=10.47
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=19
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.41
sequence-density-rank=30
fanout-score=15.84
fanout-score-rank=1
prefix-density=6.47
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 07:07:52
                             Started mapping on |	Mar 04 07:07:52
                                    Finished on |	Mar 04 07:08:38
       Mapping speed, Million of reads per hour |	400.61

                          Number of input reads |	5118852
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2444099
                        Uniquely mapped reads % |	47.75%
                          Average mapped length |	24.36
                       Number of splices: Total |	2704
            Number of splices: Annotated (sjdb) |	357
                       Number of splices: GT/AG |	2440
                       Number of splices: GC/AG |	35
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	227
                      Mismatch rate per base, % |	0.15%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.68
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.14
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	2152280
             % of reads mapped to multiple loci |	42.05%
        Number of reads mapped to too many loci |	117030
             % of reads mapped to too many loci |	2.29%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.18%
                     % of reads unmapped: other |	0.74%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	522473	522473	522473
N_multimapping	2152280	2152280	2152280
N_noFeature	106044	132509	1853798
N_ambiguous	1297475	802739	17060
UnstrandedReadsAssigned:1040580 PositiveStrandReadsAssigned:1508851 NegativeStrandReadsAssigned:573241
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031015 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: SRR5031015-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 5,118,852 reads, 984,542 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 823 rounds

 109283 SRR5031015.ke.tsv
  52636 SRR5031015.se.tsv
 161919 total
==> SRR5031015.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

==> SRR5031015.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	2
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031015 completed mapping pipeline successfully
