Starting /dee2/code/volunteer_pipeline.sh SRR5030887
    current disk space = 160643629056
    free memory = 56712440 
SRR5030887 SRAfilesize
3d352b3abb0987a3875cedf6bbefa2bc  SRR5030887.sra
SRR5030887.sra file validated
SRR5030887 is single end
SRR5030887 is conventional basespace
SRR5030887 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030887_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	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.3435	33.0	31.0	34.0	31.0	34.0
2	32.686	34.0	31.0	34.0	31.0	34.0
3	32.79275	34.0	31.0	34.0	31.0	34.0
4	36.2445	37.0	37.0	37.0	35.0	37.0
5	36.18725	37.0	37.0	37.0	35.0	37.0
6	35.9765	37.0	35.0	37.0	35.0	37.0
7	36.11075	37.0	35.0	37.0	35.0	37.0
8	36.16625	37.0	36.0	37.0	35.0	37.0
9	37.87775	39.0	38.0	39.0	35.0	39.0
10	37.89575	39.0	38.0	39.0	35.0	39.0
11	37.86625	39.0	38.0	39.0	35.0	39.0
12	37.87225	39.0	38.0	39.0	35.0	39.0
13	37.86275	39.0	38.0	39.0	35.0	39.0
14	39.27975	41.0	39.0	41.0	36.0	41.0
15	39.3265	41.0	39.0	41.0	36.0	41.0
16	39.2105	41.0	39.0	41.0	36.0	41.0
17	39.32475	41.0	39.0	41.0	36.0	41.0
18	39.35675	41.0	39.0	41.0	36.0	41.0
19	39.16625	40.0	39.0	41.0	36.0	41.0
20	39.21175	40.0	39.0	41.0	36.0	41.0
21	39.17825	41.0	39.0	41.0	36.0	41.0
22	39.27825	41.0	39.0	41.0	36.0	41.0
23	39.13075	40.0	39.0	41.0	36.0	41.0
24	38.3765	40.0	38.0	41.0	34.0	41.0
25	38.67125	40.0	38.0	41.0	34.0	41.0
26	38.72475	40.0	38.0	41.0	34.0	41.0
27	38.71725	40.0	38.0	41.0	35.0	41.0
28	38.69275	40.0	38.0	41.0	34.0	41.0
29	38.63725	40.0	38.0	41.0	34.0	41.0
30	38.3365	40.0	38.0	41.0	33.0	41.0
31	38.771	40.0	38.0	41.0	35.0	41.0
32	38.924	40.0	39.0	41.0	35.0	41.0
33	37.193	40.0	37.0	41.0	30.0	41.0
34	36.6795	40.0	37.0	41.0	30.0	41.0
35	32.952	38.0	31.0	40.0	15.0	41.0
36	30.08325	37.0	23.0	40.0	8.0	41.0
37	30.21975	37.0	25.0	39.0	7.0	41.0
38	32.506	37.0	30.0	40.0	16.0	41.0
39	31.90425	37.0	30.0	40.0	8.0	41.0
40	32.615	38.0	32.0	40.0	8.0	41.0
41	30.66975	36.0	27.0	40.0	2.0	41.0
42	32.04725	37.0	31.0	40.0	2.0	41.0
43	30.59575	37.0	28.0	40.0	2.0	41.0
44	31.33125	37.0	30.0	40.0	2.0	41.0
45	29.42725	37.0	26.0	40.0	2.0	41.0
46	27.45375	35.0	15.0	39.0	2.0	41.0
47	27.33125	35.0	17.0	39.0	2.0	41.0
48	27.84625	35.0	16.0	39.0	2.0	41.0
49	26.18525	35.0	2.0	39.0	2.0	41.0
50	22.79	30.0	2.0	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
17	3.0
18	2.0
19	6.0
20	11.0
21	20.0
22	22.0
23	33.0
24	34.0
25	66.0
26	85.0
27	151.0
28	69.0
29	114.0
30	130.0
31	178.0
32	168.0
33	139.0
34	234.0
35	254.0
36	332.0
37	470.0
38	668.0
39	811.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.137137137137136	24.974974974974977	45.845845845845844	17.04204204204204
2	26.375	24.425	20.150000000000002	29.049999999999997
3	23.05	21.0	21.4	34.55
4	33.175	25.874999999999996	16.525000000000002	24.425
5	22.3	40.699999999999996	24.65	12.35
6	29.95	15.825	37.6	16.625
7	19.025	20.599999999999998	24.725	35.65
8	27.1	28.499999999999996	16.875	27.525
9	20.575	32.85	30.625000000000004	15.950000000000001
10	22.625	22.875	29.625	24.875
11	35.325	12.9	16.150000000000002	35.625
12	17.775	21.125	28.7	32.4
13	28.999999999999996	18.075	34.35	18.575
14	28.625	29.875	22.575	18.925
15	34.8	24.325	24.875	16.0
16	19.75	19.45	24.125	36.675000000000004
17	24.224999999999998	24.975	35.875	14.924999999999999
18	23.625	17.9	31.025000000000002	27.450000000000003
19	34.849999999999994	15.9	31.474999999999998	17.775
20	41.475	15.950000000000001	28.675	13.900000000000002
21	25.374999999999996	20.8	26.974999999999998	26.85
22	29.275000000000002	13.875000000000002	43.45	13.4
23	24.7	16.375	40.9	18.025
24	47.775	14.95	26.200000000000003	11.075
25	47.325	22.525000000000002	16.650000000000002	13.5
26	29.2	40.300000000000004	14.575	15.925
27	17.1	44.324999999999996	21.675	16.900000000000002
28	14.099999999999998	25.825	42.575	17.5
29	13.925	14.625	53.125	18.325
30	12.125	9.25	34.75	43.875
31	15.1	7.175	45.4	32.324999999999996
32	27.525	7.425	23.5	41.55
33	47.525	11.0	16.400000000000002	25.074999999999996
34	55.35	8.4	17.349999999999998	18.9
35	57.275	8.625	20.25	13.850000000000001
36	60.199999999999996	10.05	15.975	13.775
37	37.724999999999994	13.950000000000001	22.15	26.174999999999997
38	26.724999999999998	16.575	14.899999999999999	41.8
39	19.375	24.15	14.799999999999999	41.675000000000004
40	18.025	43.275000000000006	13.825000000000001	24.875
41	25.75	42.575	12.950000000000001	18.725
42	45.5	28.199999999999996	14.424999999999999	11.875
43	43.275000000000006	32.175	11.700000000000001	12.85
44	31.225	44.125	9.425	15.225
45	21.6	43.9	13.225000000000001	21.275
46	15.25	28.799999999999997	24.4	31.55
47	13.225000000000001	17.299999999999997	32.824999999999996	36.65
48	13.175	13.025	23.625	50.175000000000004
49	15.65	23.0	15.55	45.800000000000004
50	29.5	23.5	12.975	34.025
>>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	0.5
14	1.0
15	1.5
16	2.0
17	1.0
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	2.0
30	4.0
31	6.5
32	9.0
33	18.5
34	28.0
35	41.5
36	55.0
37	74.0
38	93.0
39	90.5
40	88.0
41	77.5
42	67.0
43	96.5
44	126.0
45	169.5
46	213.0
47	259.5
48	306.0
49	392.0
50	478.0
51	633.5
52	789.0
53	636.0
54	483.0
55	433.0
56	383.0
57	339.0
58	295.0
59	224.0
60	153.0
61	122.5
62	92.0
63	120.0
64	148.0
65	93.5
66	39.0
67	28.5
68	18.0
69	27.0
70	36.0
71	52.0
72	68.0
73	39.5
74	11.0
75	6.5
76	2.0
77	3.5
78	5.0
79	4.5
80	4.0
81	3.5
82	3.0
83	1.5
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	0.1
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	warn
#Total Deduplicated Percentage	51.449999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.90379008746356	41.625
2	7.968901846452867	8.200000000000001
3	3.158406219630709	4.875
4	1.7006802721088436	3.5000000000000004
5	1.0204081632653061	2.625
6	0.8260447035957239	2.55
7	0.7288629737609329	2.625
8	0.5344995140913509	2.1999999999999997
9	0.2915451895043732	1.35
>10	2.7210884353741496	23.799999999999997
>50	0.1457725947521866	6.65
>100	0.0	0.0
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	99	2.475	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	99	2.475	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	68	1.7000000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 30bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGC	26	0.65	RNA PCR Primer, Index 10 (100% over 50bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	25	0.625	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	22	0.5499999999999999	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	22	0.5499999999999999	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	20	0.5	RNA PCR Primer, Index 7 (97% over 35bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	19	0.475	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (96% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (96% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	17	0.42500000000000004	No Hit
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	16	0.4	RNA PCR Primer, Index 1 (100% over 33bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	16	0.4	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	15	0.375	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	14	0.35000000000000003	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	14	0.35000000000000003	No Hit
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	13	0.325	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	13	0.325	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTC	12	0.3	RNA PCR Primer, Index 10 (100% over 44bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	11	0.27499999999999997	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 29bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	11	0.27499999999999997	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	10	0.25	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	10	0.25	RNA PCR Primer, Index 1 (95% over 23bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	10	0.25	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	10	0.25	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	10	0.25	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	9	0.22499999999999998	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	9	0.22499999999999998	No Hit
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	9	0.22499999999999998	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	9	0.22499999999999998	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	9	0.22499999999999998	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	8	0.2	No Hit
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCC	8	0.2	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	7	0.17500000000000002	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	7	0.17500000000000002	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	7	0.17500000000000002	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	7	0.17500000000000002	No Hit
CTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCTA	7	0.17500000000000002	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATTGTCTGCTGGGTTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	6	0.15	No Hit
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCCAGGAACTCCAGTCACTA	6	0.15	RNA PCR Primer, Index 10 (97% over 35bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	6	0.15	RNA PCR Primer, Index 1 (100% over 32bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTTATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	6	0.15	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AAACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	5	0.125	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGGAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CCCCTATGATGAGGACCTTTTCACAGACCTGTACTGATATATCTGTGAGG	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGC	5	0.125	RNA PCR Primer, Index 1 (96% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (96% over 30bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTGGAATTCTCGGGT	5	0.125	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	5	0.125	No Hit
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	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	0.7	0.0	0.0	0.0
2	0.0	0.7	0.0	0.0	0.0
3	0.0	0.825	0.0	0.0	0.0
4	0.0	0.85	0.0	0.0	0.0
5	0.0	0.875	0.0	0.0	0.0
6	0.0	0.95	0.0	0.0	0.0
7	0.0	1.4	0.0	0.0	0.0
8	0.0	1.5	0.0	0.0	0.0
9	0.0	1.55	0.0	0.0	0.0
10	0.0	1.7	0.0	0.0	0.0
11	0.0	1.8	0.0	0.0	0.0
12	0.0	2.05	0.0	0.0	0.0
13	0.0	2.25	0.0	0.0	0.0
14	0.0	2.575	0.0	0.0	0.0
15	0.0	2.825	0.0	0.0	0.0
16	0.0	3.8	0.0	0.0	0.0
17	0.0	4.25	0.0	0.0	0.0
18	0.0	5.1	0.0	0.0	0.0
19	0.0	5.65	0.0	0.0	0.0
20	0.0	6.45	0.0	0.0	0.0
21	0.0	10.525	0.0	0.0	0.0
22	0.0	18.85	0.0	0.0	0.0
23	0.0	43.6	0.0	0.0	0.0
24	0.0	55.825	0.0	0.0	0.0
25	0.0	61.35	0.0	0.0	0.0
26	0.0	62.8	0.0	0.0	0.0
27	0.0	63.7	0.0	0.0	0.0
28	0.0	64.275	0.0	0.0	0.0
29	0.0	64.375	0.0	0.0	0.0
30	0.0	64.825	0.0	0.0	0.0
31	0.0	65.625	0.0	0.0	0.0
32	0.0	66.175	0.0	0.0	0.0
33	0.0	67.425	0.0	0.0	0.0
34	0.0	71.2	0.0	0.0	0.0
35	0.0	72.3	0.0	0.0	0.0
36	0.0	72.95	0.0	0.0	0.0
37	0.0	74.45	0.0	0.0	0.0
38	0.0	74.725	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACAGTGA	20	6.952051E-4	44.000004	3
ACCGGTC	20	6.952051E-4	44.000004	10
AACGCTG	40	5.315087E-9	44.000004	8
ACGCTGT	40	5.315087E-9	44.000004	9
AACCGGT	20	6.952051E-4	44.000004	9
TTCAACG	40	5.315087E-9	44.000004	5
GGTCTCT	20	6.952051E-4	44.000004	13
CATTCAA	40	5.315087E-9	44.000004	3
TCAACGC	40	5.315087E-9	44.000004	6
ACATTCA	40	5.315087E-9	44.000004	2
GGATAGG	20	6.952051E-4	44.000004	14
GCTGTCG	40	5.315087E-9	44.000004	11
GAACCGG	20	6.952051E-4	44.000004	8
GTCTCTT	20	6.952051E-4	44.000004	14
AGTGAAC	20	6.952051E-4	44.000004	5
TCTCTTT	20	6.952051E-4	44.000004	15
GTGAACC	20	6.952051E-4	44.000004	6
CGGTCTC	20	6.952051E-4	44.000004	12
CTGTCGG	40	5.315087E-9	44.000004	12
TGAACCG	20	6.952051E-4	44.000004	7
>>END_MODULE
Read 254691 spots for SRR5030887.sra
Written 254691 spots for SRR5030887.sra
Read 254691 spots for SRR5030887.sra
Written 254691 spots for SRR5030887.sra
Read 254691 spots for SRR5030887.sra
Written 254691 spots for SRR5030887.sra
Read 254691 spots for SRR5030887.sra
Written 254691 spots for SRR5030887.sra
Read 254691 spots for SRR5030887.sra
Written 254691 spots for SRR5030887.sra
Read 254691 spots for SRR5030887.sra
Written 254691 spots for SRR5030887.sra
Read 254691 spots for SRR5030887.sra
Written 254691 spots for SRR5030887.sra
Read 254691 spots for SRR5030887.sra
Written 254691 spots for SRR5030887.sra
Read 254691 spots for SRR5030887.sra
Written 254691 spots for SRR5030887.sra
Read 254691 spots for SRR5030887.sra
Written 254691 spots for SRR5030887.sra
Read 254691 spots for SRR5030887.sra
Written 254691 spots for SRR5030887.sra
Read 254691 spots for SRR5030887.sra
Written 254691 spots for SRR5030887.sra
SRR ids: ['SRR5030887.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_5fn_99jl
SRR5030887.sra spots: 3056292
blocks: [[1, 254691], [254692, 509382], [509383, 764073], [764074, 1018764], [1018765, 1273455], [1273456, 1528146], [1528147, 1782837], [1782838, 2037528], [2037529, 2292219], [2292220, 2546910], [2546911, 2801601], [2801602, 3056292]]
SRR5030887 file size 528646
SRR5030887 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030887 SRR5030887_1.fastq
Input file:	SRR5030887_1.fastq
trimmed:	SRR5030887-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 06:36:55 2020 >> started

Wed Mar  4 06:36:57 2020 >> done (1.878s)
3056292 reads processed; of these:
    179 ( 0.01%) short reads filtered out after trimming by size control
      3 ( 0.00%) empty reads filtered out after trimming by size control
3056110 (99.99%) reads available; of these:
 350016 (11.45%) trimmed reads available after processing
2706094 (88.55%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     43	  0.00%
 19	     62	  0.00%
 20	    142	  0.00%
 21	    183	  0.01%
 22	    309	  0.01%
 23	    394	  0.01%
 24	    424	  0.01%
 25	    611	  0.02%
 26	    464	  0.02%
 27	    626	  0.02%
 28	    865	  0.03%
 29	   1370	  0.04%
 30	   1011	  0.03%
 31	   1385	  0.05%
 32	   3367	  0.11%
 33	  10383	  0.34%
 34	  23678	  0.77%
 35	   5715	  0.19%
 36	   6208	  0.20%
 37	   3416	  0.11%
 38	   7168	  0.23%
 39	   6636	  0.22%
 40	  12361	  0.40%
 41	   6987	  0.23%
 42	  17077	  0.56%
 43	   8007	  0.26%
 44	  32896	  1.08%
 45	  21670	  0.71%
 46	  20581	  0.67%
 47	  22112	  0.72%
 48	  61474	  2.01%
 49	  72391	  2.37%
 50	2706094	 88.55%
3056110 reads passed initial QC


criterion=sequence-density
sequence-density=73.89
sequence-density-rank=1
fanout-score=21.84
fanout-score-rank=2
prefix-density=76.19
prefix-fanout=21.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCC


criterion=fanout-score
sequence-density=3.12
sequence-density-rank=2
fanout-score=74.56
fanout-score-rank=1
prefix-density=75.89
prefix-fanout=3.1
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCC -o SRR5030887 -
Input file:	STDIN
trimmed:	SRR5030887-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCC
-- 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 06:37:12 2020 >> started

Wed Mar  4 06:37:16 2020 >> done (4.873s)
2973513 reads processed; of these:
 139960 ( 4.71%) short reads filtered out after trimming by size control
  23797 ( 0.80%) empty reads filtered out after trimming by size control
2809756 (94.49%) reads available; of these:
2305093 (82.04%) trimmed reads available after processing
 504663 (17.96%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  16057	  0.57%
 19	  24961	  0.89%
 20	 125550	  4.47%
 21	 276179	  9.83%
 22	 722768	 25.72%
 23	 354695	 12.62%
 24	 159392	  5.67%
 25	  43793	  1.56%
 26	  22663	  0.81%
 27	  19167	  0.68%
 28	  20847	  0.74%
 29	  17513	  0.62%
 30	  22245	  0.79%
 31	  25680	  0.91%
 32	  28624	  1.02%
 33	 117081	  4.17%
 34	  33755	  1.20%
 35	  25710	  0.92%
 36	  36259	  1.29%
 37	  15235	  0.54%
 38	  18897	  0.67%
 39	  17094	  0.61%
 40	  26023	  0.93%
 41	  31239	  1.11%
 42	  39428	  1.40%
 43	  26146	  0.93%
 44	  24130	  0.86%
 45	  29377	  1.05%
 46	  23771	  0.85%
 47	  18862	  0.67%
 48	   7474	  0.27%
 49	  14139	  0.50%
 50	 425002	 15.13%


criterion=sequence-density
sequence-density=6.07
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.59
sequence-density-rank=19
fanout-score=11.16
fanout-score-rank=1
prefix-density=6.61
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 06:37:38
                             Started mapping on |	Mar 04 06:37:39
                                    Finished on |	Mar 04 06:38:03
       Mapping speed, Million of reads per hour |	433.85

                          Number of input reads |	2892353
                      Average input read length |	30
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1515607
                        Uniquely mapped reads % |	52.40%
                          Average mapped length |	28.97
                       Number of splices: Total |	1849
            Number of splices: Annotated (sjdb) |	266
                       Number of splices: GT/AG |	1722
                       Number of splices: GC/AG |	27
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	100
                      Mismatch rate per base, % |	0.22%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.35
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	882588
             % of reads mapped to multiple loci |	30.51%
        Number of reads mapped to too many loci |	67121
             % of reads mapped to too many loci |	2.32%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	14.21%
                     % of reads unmapped: other |	0.55%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	494158	494158	494158
N_multimapping	882588	882588	882588
N_noFeature	72578	91013	1095166
N_ambiguous	849086	483059	16509
UnstrandedReadsAssigned:593943 PositiveStrandReadsAssigned:941535 NegativeStrandReadsAssigned:403932
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030887 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: SRR5030887-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,892,353 reads, 687,962 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,114 rounds

 109283 SRR5030887.ke.tsv
  52636 SRR5030887.se.tsv
 161919 total
==> SRR5030887.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

==> SRR5030887.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030887 completed mapping pipeline successfully
