Starting /dee2/code/volunteer_pipeline.sh SRR5031031
    current disk space = 160536313856
    free memory = 73931592 
SRR5031031 SRAfilesize
a793e7c9d9cf243a0028e7e8a8f0fe8e  SRR5031031.sra
SRR5031031.sra file validated
SRR5031031 is single end
SRR5031031 is conventional basespace
SRR5031031 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031031_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	32.22275	33.0	31.0	34.0	30.0	34.0
2	32.52325	34.0	31.0	34.0	31.0	34.0
3	32.519	34.0	31.0	34.0	31.0	34.0
4	36.118	37.0	35.0	37.0	35.0	37.0
5	36.0375	37.0	35.0	37.0	35.0	37.0
6	35.76575	37.0	35.0	37.0	35.0	37.0
7	35.89625	37.0	35.0	37.0	35.0	37.0
8	35.809	37.0	35.0	37.0	33.0	37.0
9	37.519	39.0	37.0	39.0	35.0	39.0
10	37.6735	39.0	37.0	39.0	35.0	39.0
11	37.584	39.0	37.0	39.0	34.0	39.0
12	37.54825	39.0	37.0	39.0	35.0	39.0
13	37.567	39.0	37.0	39.0	35.0	39.0
14	38.911	40.0	38.0	41.0	35.0	41.0
15	39.01	40.0	38.0	41.0	36.0	41.0
16	38.921	40.0	38.0	41.0	35.0	41.0
17	38.781	40.0	38.0	41.0	34.0	41.0
18	38.94475	40.0	38.0	41.0	35.0	41.0
19	38.4975	40.0	38.0	41.0	34.0	41.0
20	38.747	40.0	38.0	41.0	34.0	41.0
21	38.6775	40.0	38.0	41.0	34.0	41.0
22	38.86225	40.0	38.0	41.0	35.0	41.0
23	38.56575	40.0	38.0	41.0	34.0	41.0
24	38.67975	40.0	38.0	41.0	34.0	41.0
25	38.922	41.0	39.0	41.0	35.0	41.0
26	38.5465	40.0	38.0	41.0	34.0	41.0
27	38.663	40.0	38.0	41.0	34.0	41.0
28	38.5625	40.0	38.0	41.0	34.0	41.0
29	38.28575	40.0	38.0	41.0	33.0	41.0
30	38.15275	40.0	38.0	41.0	33.0	41.0
31	38.359	40.0	38.0	41.0	34.0	41.0
32	38.3305	40.0	38.0	41.0	34.0	41.0
33	38.2025	40.0	38.0	41.0	34.0	41.0
34	38.155	40.0	38.0	41.0	34.0	41.0
35	38.04125	40.0	38.0	41.0	34.0	41.0
36	37.721	40.0	37.0	41.0	32.0	41.0
37	37.46375	40.0	37.0	41.0	31.0	41.0
38	36.743	39.0	36.0	41.0	30.0	41.0
39	37.2675	39.0	37.0	41.0	31.0	41.0
40	37.52575	40.0	37.0	41.0	32.0	41.0
41	37.72025	40.0	38.0	41.0	32.0	41.0
42	37.91825	40.0	38.0	41.0	33.0	41.0
43	38.1875	40.0	38.0	41.0	34.0	41.0
44	37.8525	40.0	38.0	41.0	33.0	41.0
45	37.79	40.0	37.0	41.0	33.0	41.0
46	37.659	40.0	37.0	41.0	33.0	41.0
47	37.07525	40.0	37.0	41.0	31.0	41.0
48	36.708	40.0	36.0	41.0	30.0	41.0
49	37.02375	40.0	36.0	41.0	31.0	41.0
50	36.50125	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
12	1.0
13	1.0
14	0.0
15	0.0
16	1.0
17	0.0
18	2.0
19	1.0
20	4.0
21	4.0
22	7.0
23	10.0
24	10.0
25	16.0
26	18.0
27	22.0
28	36.0
29	25.0
30	55.0
31	81.0
32	77.0
33	116.0
34	137.0
35	191.0
36	268.0
37	418.0
38	673.0
39	1826.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.225	24.925	52.1	14.75
2	22.728410513141426	28.685857321652065	21.32665832290363	27.25907384230288
3	17.849999999999998	17.775	19.6	44.775
4	27.35	34.625	14.149999999999999	23.875
5	21.575	34.55	31.65	12.225
6	34.925	14.325	37.625	13.125
7	14.524999999999999	24.8	22.775000000000002	37.9
8	23.65	39.5	15.275	21.575
9	19.875	38.275	27.900000000000002	13.950000000000001
10	20.349999999999998	19.8	25.124999999999996	34.725
11	32.925	11.975	15.15	39.95
12	16.85	15.575	24.55	43.025000000000006
13	20.724999999999998	19.125	40.150000000000006	20.0
14	38.85	23.875	24.025	13.25
15	36.475	21.65	29.675	12.2
16	14.149999999999999	24.05	22.675	39.125
17	27.875	23.1	34.849999999999994	14.174999999999999
18	30.25	17.5	28.475	23.775
19	36.95	13.475000000000001	31.724999999999998	17.849999999999998
20	50.175000000000004	16.85	22.6	10.375
21	22.2	28.475	22.325	27.0
22	33.775	12.375	45.25	8.6
23	23.275000000000002	14.249999999999998	48.475	14.000000000000002
24	50.275000000000006	14.000000000000002	29.25	6.4750000000000005
25	55.025	21.725	14.725	8.525
26	30.775000000000002	47.0	12.625	9.6
27	14.2	53.1	21.875	10.825
28	9.65	27.05	48.875	14.424999999999999
29	10.775	11.5	60.550000000000004	17.175
30	10.05	5.325	38.0	46.625
31	13.825000000000001	4.95	46.2	35.025
32	24.8	4.9	24.825	45.475
33	53.349999999999994	8.025	13.475000000000001	25.15
34	64.97500000000001	6.550000000000001	15.2	13.275
35	67.875	6.75	17.150000000000002	8.225
36	42.449999999999996	7.2749999999999995	38.125	12.15
37	45.800000000000004	10.125	23.75	20.325
38	25.575	15.075	11.825	47.525
39	14.025000000000002	21.2	10.325	54.449999999999996
40	14.174999999999999	47.275	10.7	27.85
41	21.7	53.6	9.25	15.45
42	48.65	31.874999999999996	10.475	9.0
43	57.49999999999999	25.624999999999996	7.249999999999999	9.625
44	33.775	47.05	7.575	11.600000000000001
45	17.4	53.574999999999996	12.025	17.0
46	12.85	27.900000000000002	16.425	42.825
47	8.875	13.775	40.300000000000004	37.05
48	10.475	11.125	23.325000000000003	55.074999999999996
49	12.3	16.5	14.000000000000002	57.199999999999996
50	16.275000000000002	38.975	12.475	32.275
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.5
2	1.0
3	1.0
4	1.0
5	0.5
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.5
12	1.0
13	1.0
14	1.0
15	0.5
16	0.0
17	0.5
18	1.0
19	1.0
20	1.0
21	0.5
22	0.0
23	0.5
24	1.0
25	0.5
26	0.0
27	0.0
28	0.0
29	1.5
30	3.0
31	5.5
32	8.0
33	8.0
34	8.0
35	15.5
36	23.0
37	25.5
38	28.0
39	35.0
40	42.0
41	49.0
42	56.0
43	83.5
44	111.0
45	152.5
46	194.0
47	356.0
48	518.0
49	558.5
50	599.0
51	843.0
52	1087.0
53	733.0
54	379.0
55	377.0
56	375.0
57	318.0
58	261.0
59	163.0
60	65.0
61	50.5
62	36.0
63	61.5
64	87.0
65	54.5
66	22.0
67	13.5
68	5.0
69	13.0
70	21.0
71	41.0
72	61.0
73	32.0
74	3.0
75	1.5
76	0.0
77	0.0
78	0.0
79	0.0
80	0.0
81	0.5
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	0.125
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	36.8
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.66032608695652	27.474999999999998
2	10.597826086956522	7.8
3	4.483695652173913	4.95
4	2.1059782608695654	3.1
5	1.8342391304347827	3.375
6	1.0869565217391304	2.4
7	0.33967391304347827	0.8750000000000001
8	0.4755434782608696	1.4000000000000001
9	0.6793478260869565	2.25
>10	3.260869565217391	23.925
>50	0.20380434782608695	4.825
>100	0.2717391304347826	17.625
>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	219	5.475	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	213	5.325	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	138	3.45	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	135	3.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	73	1.825	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	67	1.675	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	53	1.325	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	47	1.175	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	26	0.65	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTT	24	0.6	RNA PCR Primer, Index 1 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 30bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	18	0.44999999999999996	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	15	0.375	No Hit
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTC	13	0.325	RNA PCR Primer, Index 3 (100% over 44bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	13	0.325	No Hit
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	10	0.25	No Hit
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 31bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	8	0.2	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGC	8	0.2	RNA PCR Primer, Index 3 (100% over 50bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTGTGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	6	0.15	No Hit
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTTGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGAATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	5	0.125	No Hit
CACCCGTAGAACCGACCTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	5	0.125	RNA PCR Primer, Index 3 (100% over 34bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTAGTTCAATGGTAGAATTCTCGCCTCCCTGGAATTCTCGGGTG	5	0.125	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGTGGAATTCTCGGGTGC	5	0.125	No Hit
CAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTTGGAATT	5	0.125	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGAATTCTCGGGTGC	5	0.125	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGATTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	5	0.125	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
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	0.225	0.0	0.0	0.0
2	0.0	0.225	0.0	0.0	0.0
3	0.0	0.275	0.0	0.0	0.0
4	0.0	0.275	0.0	0.0	0.0
5	0.0	0.35	0.0	0.0	0.0
6	0.0	0.425	0.0	0.0	0.0
7	0.0	0.85	0.0	0.0	0.0
8	0.0	0.875	0.0	0.0	0.0
9	0.0	0.9	0.0	0.0	0.0
10	0.0	1.075	0.0	0.0	0.0
11	0.0	1.125	0.0	0.0	0.0
12	0.0	1.35	0.0	0.0	0.0
13	0.0	1.525	0.0	0.0	0.0
14	0.0	1.725	0.0	0.0	0.0
15	0.0	1.95	0.0	0.0	0.0
16	0.0	2.9	0.0	0.0	0.0
17	0.0	3.5	0.0	0.0	0.0
18	0.0	4.225	0.0	0.0	0.0
19	0.0	4.7	0.0	0.0	0.0
20	0.0	5.55	0.0	0.0	0.0
21	0.0	10.275	0.0	0.0	0.0
22	0.0	20.05	0.0	0.0	0.0
23	0.0	51.525	0.0	0.0	0.0
24	0.0	68.0	0.0	0.0	0.0
25	0.0	73.625	0.0	0.0	0.0
26	0.0	74.9	0.0	0.0	0.0
27	0.0	75.375	0.0	0.0	0.0
28	0.0	75.775	0.0	0.0	0.0
29	0.0	76.525	0.0	0.0	0.0
30	0.0	76.95	0.0	0.0	0.0
31	0.0	77.9	0.0	0.0	0.0
32	0.0	79.25	0.0	0.0	0.0
33	0.0	80.475	0.0	0.0	0.0
34	0.0	83.325	0.0	0.0	0.0
35	0.0	84.625	0.0	0.0	0.0
36	0.0	85.75	0.0	0.0	0.0
37	0.0	86.525	0.0	0.0	0.0
38	0.0	87.05	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
ATCCAGG	20	6.952051E-4	44.000004	9
TTCAAGT	20	6.952051E-4	44.000004	1
AGGATAG	20	6.952051E-4	44.000004	13
ATAGGCT	20	6.952051E-4	44.000004	16
TCCAGGA	20	6.952051E-4	44.000004	10
GGATAGG	20	6.952051E-4	44.000004	14
AGTAATC	20	6.952051E-4	44.000004	5
TAATCCA	20	6.952051E-4	44.000004	7
CAGGATA	20	6.952051E-4	44.000004	12
GTAATCC	20	6.952051E-4	44.000004	6
GATAGGC	20	6.952051E-4	44.000004	15
CCAGGAT	20	6.952051E-4	44.000004	11
CAAGTAA	20	6.952051E-4	44.000004	3
CTGAGCT	25	3.6958358E-5	44.0	11
TAAACAT	25	3.6958358E-5	44.0	3
AAACATC	25	3.6958358E-5	44.0	4
GAGCTTG	30	1.9515464E-6	44.0	13
GGATCCG	30	1.9515464E-6	44.0	3
>>END_MODULE
Read 343565 spots for SRR5031031.sra
Written 343565 spots for SRR5031031.sra
Read 343565 spots for SRR5031031.sra
Written 343565 spots for SRR5031031.sra
Read 343565 spots for SRR5031031.sra
Written 343565 spots for SRR5031031.sra
Read 343565 spots for SRR5031031.sra
Written 343565 spots for SRR5031031.sra
Read 343565 spots for SRR5031031.sra
Written 343565 spots for SRR5031031.sra
Read 343565 spots for SRR5031031.sra
Written 343565 spots for SRR5031031.sra
Read 343565 spots for SRR5031031.sra
Written 343565 spots for SRR5031031.sra
Read 343565 spots for SRR5031031.sra
Written 343565 spots for SRR5031031.sra
Read 343565 spots for SRR5031031.sra
Written 343565 spots for SRR5031031.sra
Read 343565 spots for SRR5031031.sra
Written 343565 spots for SRR5031031.sra
Read 343565 spots for SRR5031031.sra
Written 343565 spots for SRR5031031.sra
Read 343567 spots for SRR5031031.sra
Written 343567 spots for SRR5031031.sra
SRR ids: ['SRR5031031.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_kai98cn5
SRR5031031.sra spots: 4122782
blocks: [[1, 343565], [343566, 687130], [687131, 1030695], [1030696, 1374260], [1374261, 1717825], [1717826, 2061390], [2061391, 2404955], [2404956, 2748520], [2748521, 3092085], [3092086, 3435650], [3435651, 3779215], [3779216, 4122782]]
SRR5031031 file size 713511
SRR5031031 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031031 SRR5031031_1.fastq
Input file:	SRR5031031_1.fastq
trimmed:	SRR5031031-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 07:10:07 2020 >> started

Wed Mar  4 07:10:11 2020 >> done (3.559s)
4122782 reads processed; of these:
    288 ( 0.01%) short reads filtered out after trimming by size control
     13 ( 0.00%) empty reads filtered out after trimming by size control
4122481 (99.99%) reads available; of these:
 203314 ( 4.93%) trimmed reads available after processing
3919167 (95.07%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    105	  0.00%
 19	    103	  0.00%
 20	    188	  0.00%
 21	    285	  0.01%
 22	    450	  0.01%
 23	    580	  0.01%
 24	    601	  0.01%
 25	    776	  0.02%
 26	    631	  0.02%
 27	    891	  0.02%
 28	    974	  0.02%
 29	   1867	  0.05%
 30	   1134	  0.03%
 31	   1179	  0.03%
 32	   1268	  0.03%
 33	   1613	  0.04%
 34	   1818	  0.04%
 35	   3721	  0.09%
 36	   3291	  0.08%
 37	   3484	  0.08%
 38	   3364	  0.08%
 39	   3715	  0.09%
 40	   4041	  0.10%
 41	   4379	  0.11%
 42	   5700	  0.14%
 43	   8571	  0.21%
 44	  12166	  0.30%
 45	  15193	  0.37%
 46	  19911	  0.48%
 47	  24935	  0.60%
 48	  37421	  0.91%
 49	  38959	  0.95%
 50	3919167	 95.07%
4122481 reads passed initial QC


criterion=sequence-density
sequence-density=86.87
sequence-density-rank=1
fanout-score=20.61
fanout-score-rank=1
prefix-density=89.21
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCC


criterion=fanout-score
sequence-density=86.87
sequence-density-rank=1
fanout-score=20.61
fanout-score-rank=1
prefix-density=89.21
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCC -o SRR5031031 -
Input file:	STDIN
trimmed:	SRR5031031-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCC
-- 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 07:10:37 2020 >> started

Wed Mar  4 07:10:46 2020 >> done (8.987s)
4027711 reads processed; of these:
 170919 ( 4.24%) short reads filtered out after trimming by size control
  13550 ( 0.34%) empty reads filtered out after trimming by size control
3843242 (95.42%) reads available; of these:
3665250 (95.37%) trimmed reads available after processing
 177992 ( 4.63%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  20894	  0.54%
 19	  43490	  1.13%
 20	 177024	  4.61%
 21	 409154	 10.65%
 22	1234282	 32.12%
 23	 686178	 17.85%
 24	 230259	  5.99%
 25	  44034	  1.15%
 26	  23588	  0.61%
 27	  23876	  0.62%
 28	  29386	  0.76%
 29	  25834	  0.67%
 30	  40935	  1.07%
 31	  58053	  1.51%
 32	  61337	  1.60%
 33	 131765	  3.43%
 34	  56521	  1.47%
 35	  37167	  0.97%
 36	  41995	  1.09%
 37	  22508	  0.59%
 38	  27431	  0.71%
 39	  22334	  0.58%
 40	  29694	  0.77%
 41	  39835	  1.04%
 42	  41570	  1.08%
 43	  30321	  0.79%
 44	  23472	  0.61%
 45	  31661	  0.82%
 46	  23638	  0.62%
 47	  17838	  0.46%
 48	   1802	  0.05%
 49	   2506	  0.07%
 50	 152860	  3.98%


criterion=sequence-density
sequence-density=5.72
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.40
sequence-density-rank=30
fanout-score=16.04
fanout-score-rank=1
prefix-density=6.42
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 07:11:16
                             Started mapping on |	Mar 04 07:11:17
                                    Finished on |	Mar 04 07:11:42
       Mapping speed, Million of reads per hour |	567.07

                          Number of input reads |	3938012
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1812467
                        Uniquely mapped reads % |	46.02%
                          Average mapped length |	24.85
                       Number of splices: Total |	2666
            Number of splices: Annotated (sjdb) |	461
                       Number of splices: GT/AG |	2487
                       Number of splices: GC/AG |	25
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	152
                      Mismatch rate per base, % |	0.18%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.78
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1624106
             % of reads mapped to multiple loci |	41.24%
        Number of reads mapped to too many loci |	110033
             % of reads mapped to too many loci |	2.79%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.17%
                     % of reads unmapped: other |	0.77%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	501439	501439	501439
N_multimapping	1624106	1624106	1624106
N_noFeature	91365	115571	1378597
N_ambiguous	960607	596737	15143
UnstrandedReadsAssigned:760495 PositiveStrandReadsAssigned:1100159 NegativeStrandReadsAssigned:418727
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031031 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: SRR5031031-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,938,012 reads, 760,029 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 630 rounds

 109283 SRR5031031.ke.tsv
  52636 SRR5031031.se.tsv
 161919 total
==> SRR5031031.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

==> SRR5031031.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031031 completed mapping pipeline successfully
