Starting /dee2/code/volunteer_pipeline.sh SRR5030900
    current disk space = 160665124864
    free memory = 73918268 
SRR5030900 SRAfilesize
5751e6beb7e2b845f763e2c219d5646e  SRR5030900.sra
SRR5030900.sra file validated
SRR5030900 is single end
SRR5030900 is conventional basespace
SRR5030900 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030900_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	32.317	33.0	31.0	34.0	31.0	34.0
2	32.679	34.0	31.0	34.0	31.0	34.0
3	32.675	34.0	31.0	34.0	31.0	34.0
4	36.2545	37.0	37.0	37.0	35.0	37.0
5	36.2935	37.0	37.0	37.0	35.0	37.0
6	36.08675	37.0	35.0	37.0	35.0	37.0
7	36.12775	37.0	35.0	37.0	35.0	37.0
8	36.187	37.0	36.0	37.0	35.0	37.0
9	37.87625	39.0	38.0	39.0	35.0	39.0
10	37.69375	39.0	38.0	39.0	35.0	39.0
11	37.79975	39.0	38.0	39.0	35.0	39.0
12	37.5335	39.0	38.0	39.0	35.0	39.0
13	37.72925	39.0	37.0	39.0	35.0	39.0
14	39.2125	41.0	39.0	41.0	36.0	41.0
15	39.24	41.0	39.0	41.0	36.0	41.0
16	39.151	40.0	39.0	41.0	36.0	41.0
17	39.23025	40.0	39.0	41.0	36.0	41.0
18	39.32775	41.0	39.0	41.0	36.0	41.0
19	39.1645	40.0	39.0	41.0	36.0	41.0
20	39.06525	40.0	39.0	41.0	35.0	41.0
21	39.14375	40.0	39.0	41.0	36.0	41.0
22	39.30475	41.0	39.0	41.0	36.0	41.0
23	39.19625	40.0	39.0	41.0	36.0	41.0
24	38.51775	40.0	38.0	41.0	34.0	41.0
25	38.6185	40.0	38.0	41.0	34.0	41.0
26	38.81725	40.0	38.0	41.0	34.0	41.0
27	38.9365	40.0	39.0	41.0	35.0	41.0
28	38.791	40.0	38.0	41.0	34.0	41.0
29	38.247	40.0	38.0	41.0	33.0	41.0
30	38.381	40.0	38.0	41.0	33.0	41.0
31	38.85475	40.0	38.0	41.0	35.0	41.0
32	38.735	40.0	38.0	41.0	35.0	41.0
33	37.56325	40.0	37.0	41.0	31.0	41.0
34	37.4865	40.0	37.0	41.0	31.0	41.0
35	37.214	39.0	37.0	40.0	31.0	41.0
36	32.92525	37.0	30.0	40.0	16.0	41.0
37	35.42875	38.0	33.0	40.0	29.0	41.0
38	36.8995	39.0	37.0	40.0	31.0	41.0
39	37.2665	39.0	37.0	40.0	31.0	41.0
40	37.2185	39.0	37.0	41.0	32.0	41.0
41	37.069	39.0	36.0	40.0	32.0	41.0
42	37.014	39.0	36.0	41.0	31.0	41.0
43	37.00225	39.0	36.0	41.0	31.0	41.0
44	37.1855	40.0	37.0	41.0	32.0	41.0
45	36.712	39.0	36.0	41.0	31.0	41.0
46	34.55	38.0	33.0	40.0	24.0	41.0
47	35.6565	39.0	35.0	40.0	28.0	41.0
48	35.77775	39.0	35.0	40.0	29.0	41.0
49	34.967	38.0	35.0	40.0	28.0	41.0
50	30.5125	34.0	28.0	38.0	2.0	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
8	1.0
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	4.0
19	1.0
20	6.0
21	6.0
22	3.0
23	12.0
24	12.0
25	15.0
26	14.0
27	32.0
28	44.0
29	45.0
30	69.0
31	70.0
32	86.0
33	108.0
34	173.0
35	184.0
36	323.0
37	524.0
38	993.0
39	1275.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.535759096612297	22.835633626097867	52.220828105395235	15.407779171894607
2	23.05	27.875	23.05	26.025
3	18.075	18.95	20.974999999999998	42.0
4	26.6	35.025	14.799999999999999	23.575
5	22.45	37.125	27.200000000000003	13.225000000000001
6	34.599999999999994	15.35	38.324999999999996	11.725
7	17.65	23.65	24.975	33.725
8	24.5	40.75	13.200000000000001	21.55
9	18.975	36.925000000000004	30.875000000000004	13.225000000000001
10	20.5	20.4	26.5	32.6
11	32.775	15.4	13.625000000000002	38.2
12	16.775000000000002	19.075	22.625	41.525
13	20.175	21.3	37.175000000000004	21.349999999999998
14	37.625	22.15	26.400000000000002	13.825000000000001
15	37.3	21.425	28.875	12.4
16	13.625000000000002	26.575	23.425	36.375
17	25.1	23.525	37.275000000000006	14.099999999999998
18	27.775	18.725	28.575	24.925
19	35.725	15.125	30.9	18.25
20	47.15	17.625	22.35	12.875
21	21.05	25.825	23.225	29.9
22	32.1	12.7	44.4	10.8
23	24.925	12.85	46.800000000000004	15.425
24	49.85	15.1	26.1	8.95
25	52.725	20.849999999999998	14.924999999999999	11.5
26	30.875000000000004	44.675	12.5	11.95
27	16.075	49.55	21.4	12.975
28	11.825	26.35	47.8	14.025000000000002
29	10.549999999999999	12.8	57.85	18.8
30	10.5	7.9750000000000005	35.8	45.725
31	15.125	4.9750000000000005	45.550000000000004	34.35
32	24.8	7.375	23.175	44.65
33	51.425	8.95	14.174999999999999	25.45
34	61.525	8.1	15.6	14.774999999999999
35	63.849999999999994	8.1	16.45	11.600000000000001
36	42.95	9.1	34.675	13.275
37	44.675	10.674999999999999	22.225	22.425
38	24.099999999999998	14.475	14.325	47.099999999999994
39	16.875	20.8	10.4	51.925
40	15.35	46.5	12.275	25.874999999999996
41	23.325000000000003	51.025	10.2	15.45
42	48.575	30.375000000000004	10.775	10.274999999999999
43	53.77499999999999	27.675	9.45	9.1
44	32.074999999999996	46.775	8.95	12.2
45	16.925	52.7	12.950000000000001	17.424999999999997
46	12.2	28.925	18.45	40.425
47	9.775	15.45	39.625	35.15
48	11.625	12.174999999999999	22.275	53.925
49	13.975000000000001	17.775	15.1	53.15
50	18.325	37.8	13.350000000000001	30.525000000000002
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.5
10	1.0
11	0.5
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	1.0
26	2.0
27	2.5
28	3.0
29	3.0
30	3.0
31	11.0
32	19.0
33	19.5
34	20.0
35	27.5
36	35.0
37	41.0
38	47.0
39	56.0
40	65.0
41	56.5
42	48.0
43	90.0
44	132.0
45	202.0
46	272.0
47	398.0
48	524.0
49	552.5
50	581.0
51	757.0
52	933.0
53	653.5
54	374.0
55	353.5
56	333.0
57	307.5
58	282.0
59	167.0
60	52.0
61	44.0
62	36.0
63	60.0
64	84.0
65	58.5
66	33.0
67	22.0
68	11.0
69	17.0
70	23.0
71	46.0
72	69.0
73	36.0
74	3.0
75	3.0
76	3.0
77	3.0
78	3.0
79	4.5
80	6.0
81	3.5
82	1.0
83	0.5
84	0.0
85	0.5
86	1.0
87	0.5
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	0.375
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	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	40.2
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.05721393034825	30.575000000000003
2	8.955223880597014	7.199999999999999
3	4.41542288557214	5.325
4	2.674129353233831	4.3
5	1.3681592039800996	2.75
6	0.8706467661691543	2.1
7	0.808457711442786	2.275
8	0.7462686567164178	2.4
9	0.3731343283582089	1.35
>10	3.482587064676617	27.975
>50	0.12437810945273632	4.775
>100	0.12437810945273632	8.975
>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	191	4.775	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	168	4.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	99	2.475	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	92	2.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	49	1.225	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	46	1.15	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	46	1.15	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	35	0.8750000000000001	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	35	0.8750000000000001	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	30	0.75	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	27	0.675	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	26	0.65	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	18	0.44999999999999996	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	17	0.42500000000000004	RNA PCR Primer, Index 7 (97% over 35bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (96% over 28bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	14	0.35000000000000003	No Hit
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTC	13	0.325	RNA PCR Primer, Index 43 (100% over 44bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	12	0.3	No Hit
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	12	0.3	No Hit
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	12	0.3	No Hit
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGC	11	0.27499999999999997	RNA PCR Primer, Index 43 (100% over 50bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	9	0.22499999999999998	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	9	0.22499999999999998	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	9	0.22499999999999998	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	8	0.2	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	8	0.2	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	8	0.2	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	7	0.17500000000000002	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	7	0.17500000000000002	RNA PCR Primer, Index 3 (100% over 34bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	7	0.17500000000000002	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	7	0.17500000000000002	No Hit
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGAAGAAAGGT	7	0.17500000000000002	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	6	0.15	RNA PCR Primer, Index 1 (100% over 33bp)
TTCAAGTAATCCAGGATAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	6	0.15	RNA PCR Primer, Index 1 (100% over 32bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	6	0.15	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	6	0.15	No Hit
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
TAAGGCACGCGGTGAATGAATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	5	0.125	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATAATTTGTGGTAGTGGGGGACTGCGTTCGCGCTCTCCCCTGTGGAAT	5	0.125	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTTTGGAAT	5	0.125	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTAAGGCACGCGGTGAATGCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAC	5	0.125	RNA PCR Primer, Index 30 (97% over 36bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.325	0.0	0.0	0.0
2	0.0	0.375	0.0	0.0	0.0
3	0.0	0.475	0.0	0.0	0.0
4	0.0	0.475	0.0	0.0	0.0
5	0.0	0.5	0.0	0.0	0.0
6	0.0	0.525	0.0	0.0	0.0
7	0.0	0.975	0.0	0.0	0.0
8	0.0	1.05	0.0	0.0	0.0
9	0.0	1.15	0.0	0.0	0.0
10	0.0	1.175	0.0	0.0	0.0
11	0.0	1.4	0.0	0.0	0.0
12	0.0	1.7	0.0	0.0	0.0
13	0.0	1.9	0.0	0.0	0.0
14	0.0	2.1	0.0	0.0	0.0
15	0.0	2.5	0.0	0.0	0.0
16	0.0	3.225	0.0	0.0	0.0
17	0.0	3.9	0.0	0.0	0.0
18	0.0	4.6	0.0	0.0	0.0
19	0.0	5.1	0.0	0.0	0.0
20	0.0	6.125	0.0	0.0	0.0
21	0.0	10.45	0.0	0.0	0.0
22	0.0	19.7	0.0	0.0	0.0
23	0.0	49.525	0.0	0.0	0.0
24	0.0	63.5	0.0	0.0	0.0
25	0.0	69.025	0.0	0.0	0.0
26	0.0	70.15	0.0	0.0	0.0
27	0.0	70.6	0.0	0.0	0.0
28	0.0	71.0	0.0	0.0	0.0
29	0.0	71.7	0.0	0.0	0.0
30	0.0	72.05	0.0	0.0	0.0
31	0.0	72.625	0.0	0.0	0.0
32	0.0	73.525	0.0	0.0	0.0
33	0.0	74.675	0.0	0.0	0.0
34	0.0	76.75	0.0	0.0	0.0
35	0.0	77.525	0.0	0.0	0.0
36	0.0	78.1	0.0	0.0	0.0
37	0.0	78.8	0.0	0.0	0.0
38	0.0	79.35	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGTTGGA	20	6.952051E-4	44.000004	20
TAAACAT	20	6.952051E-4	44.000004	3
TTGTATA	20	6.952051E-4	44.000004	13
CTTTAAC	20	6.952051E-4	44.000004	12
AAACATC	20	6.952051E-4	44.000004	4
GAGCTTG	20	6.952051E-4	44.000004	13
GGATCCG	20	6.952051E-4	44.000004	3
CCGTCTG	20	6.952051E-4	44.000004	7
TCGGATC	20	6.952051E-4	44.000004	1
CATTCAA	45	2.728484E-10	44.000004	3
CGGATCC	20	6.952051E-4	44.000004	2
ACCTGTT	20	6.952051E-4	44.000004	17
GTATAGT	20	6.952051E-4	44.000004	15
TAACCTG	20	6.952051E-4	44.000004	15
GCTGTCG	40	5.315087E-9	44.000004	11
GATCCGT	20	6.952051E-4	44.000004	4
AGGCTTG	20	6.952051E-4	44.000004	18
ACCCTTT	20	6.952051E-4	44.000004	9
CCTTTAA	20	6.952051E-4	44.000004	11
TCCGTCT	20	6.952051E-4	44.000004	6
>>END_MODULE
Read 485384 spots for SRR5030900.sra
Written 485384 spots for SRR5030900.sra
Read 485384 spots for SRR5030900.sra
Written 485384 spots for SRR5030900.sra
Read 485384 spots for SRR5030900.sra
Written 485384 spots for SRR5030900.sra
Read 485384 spots for SRR5030900.sra
Written 485384 spots for SRR5030900.sra
Read 485384 spots for SRR5030900.sra
Written 485384 spots for SRR5030900.sra
Read 485384 spots for SRR5030900.sra
Written 485384 spots for SRR5030900.sra
Read 485384 spots for SRR5030900.sra
Written 485384 spots for SRR5030900.sra
Read 485384 spots for SRR5030900.sra
Written 485384 spots for SRR5030900.sra
Read 485384 spots for SRR5030900.sra
Written 485384 spots for SRR5030900.sra
Read 485384 spots for SRR5030900.sra
Written 485384 spots for SRR5030900.sra
Read 485384 spots for SRR5030900.sra
Written 485384 spots for SRR5030900.sra
Read 485392 spots for SRR5030900.sra
Written 485392 spots for SRR5030900.sra
SRR ids: ['SRR5030900.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_3jrc3xng
SRR5030900.sra spots: 5824616
blocks: [[1, 485384], [485385, 970768], [970769, 1456152], [1456153, 1941536], [1941537, 2426920], [2426921, 2912304], [2912305, 3397688], [3397689, 3883072], [3883073, 4368456], [4368457, 4853840], [4853841, 5339224], [5339225, 5824616]]
SRR5030900 file size 1008462
SRR5030900 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030900 SRR5030900_1.fastq
Input file:	SRR5030900_1.fastq
trimmed:	SRR5030900-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 06:40:28 2020 >> started

Wed Mar  4 06:40:32 2020 >> done (4.108s)
5824616 reads processed; of these:
    308 ( 0.01%) short reads filtered out after trimming by size control
     19 ( 0.00%) empty reads filtered out after trimming by size control
5824289 (99.99%) reads available; of these:
 429469 ( 7.37%) trimmed reads available after processing
5394820 (92.63%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     74	  0.00%
 19	    104	  0.00%
 20	    322	  0.01%
 21	    323	  0.01%
 22	    628	  0.01%
 23	    690	  0.01%
 24	    717	  0.01%
 25	    843	  0.01%
 26	    657	  0.01%
 27	    985	  0.02%
 28	   1161	  0.02%
 29	   2094	  0.04%
 30	   1445	  0.02%
 31	   1924	  0.03%
 32	   2601	  0.04%
 33	   3824	  0.07%
 34	  15465	  0.27%
 35	   6092	  0.10%
 36	   4560	  0.08%
 37	   4391	  0.08%
 38	   6513	  0.11%
 39	   6485	  0.11%
 40	  10763	  0.18%
 41	   8369	  0.14%
 42	  16367	  0.28%
 43	  11049	  0.19%
 44	  32474	  0.56%
 45	  30567	  0.52%
 46	  26392	  0.45%
 47	  32996	  0.57%
 48	  82409	  1.41%
 49	 116185	  1.99%
 50	5394820	 92.63%
5824289 reads passed initial QC


criterion=sequence-density
sequence-density=80.16
sequence-density-rank=1
fanout-score=19.24
fanout-score-rank=2
prefix-density=82.53
prefix-fanout=18.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC


criterion=fanout-score
sequence-density=2.28
sequence-density-rank=4
fanout-score=108.76
fanout-score-rank=1
prefix-density=82.49
prefix-fanout=3.0
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC -o SRR5030900 -
Input file:	STDIN
trimmed:	SRR5030900-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC
-- 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 06:41:01 2020 >> started

Wed Mar  4 06:41:17 2020 >> done (15.703s)
5680480 reads processed; of these:
 223337 ( 3.93%) short reads filtered out after trimming by size control
  17631 ( 0.31%) empty reads filtered out after trimming by size control
5439512 (95.76%) reads available; of these:
4838551 (88.95%) trimmed reads available after processing
 600961 (11.05%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  31282	  0.58%
 19	  55073	  1.01%
 20	 225185	  4.14%
 21	 558186	 10.26%
 22	1737823	 31.95%
 23	 898184	 16.51%
 24	 297494	  5.47%
 25	  54317	  1.00%
 26	  27731	  0.51%
 27	  26596	  0.49%
 28	  29933	  0.55%
 29	  24824	  0.46%
 30	  44462	  0.82%
 31	  60600	  1.11%
 32	  61008	  1.12%
 33	 117945	  2.17%
 34	  60097	  1.10%
 35	  45588	  0.84%
 36	  51285	  0.94%
 37	  27810	  0.51%
 38	  32158	  0.59%
 39	  30505	  0.56%
 40	  40283	  0.74%
 41	  56597	  1.04%
 42	  63978	  1.18%
 43	  49071	  0.90%
 44	  44140	  0.81%
 45	  53123	  0.98%
 46	  43225	  0.79%
 47	  34722	  0.64%
 48	   6886	  0.13%
 49	  19625	  0.36%
 50	 529776	  9.74%


criterion=sequence-density
sequence-density=10.74
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=21
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=1.67
sequence-density-rank=8
fanout-score=2.69
fanout-score-rank=1
prefix-density=0.03
prefix-fanout=2.7
sequence=TGAGGTAGTAGATTGTATAGTT
                                 Started job on |	Mar 04 06:42:49
                             Started mapping on |	Mar 04 06:42:50
                                    Finished on |	Mar 04 06:43:33
       Mapping speed, Million of reads per hour |	467.44

                          Number of input reads |	5583321
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2726870
                        Uniquely mapped reads % |	48.84%
                          Average mapped length |	27.51
                       Number of splices: Total |	2790
            Number of splices: Annotated (sjdb) |	364
                       Number of splices: GT/AG |	2491
                       Number of splices: GC/AG |	39
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	260
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.56
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.07
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	2192521
             % of reads mapped to multiple loci |	39.27%
        Number of reads mapped to too many loci |	149443
             % of reads mapped to too many loci |	2.68%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.49%
                     % of reads unmapped: other |	0.72%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	663930	663930	663930
N_multimapping	2192521	2192521	2192521
N_noFeature	142948	174123	2125576
N_ambiguous	1443112	941841	29760
UnstrandedReadsAssigned:1140810 PositiveStrandReadsAssigned:1610906 NegativeStrandReadsAssigned:571534
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030900 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: SRR5030900-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 5,583,321 reads, 1,087,027 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,199 rounds

 109283 SRR5030900.ke.tsv
  52636 SRR5030900.se.tsv
 161919 total
==> SRR5030900.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

==> SRR5030900.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030900 completed mapping pipeline successfully
