Starting /dee2/code/volunteer_pipeline.sh SRR5030984
    current disk space = 160572555264
    free memory = 73949332 
SRR5030984 SRAfilesize
619dc6ebc1bca33b3c017357171aa6fe  SRR5030984.sra
SRR5030984.sra file validated
SRR5030984 is single end
SRR5030984 is conventional basespace
SRR5030984 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030984_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	32.232	33.0	31.0	34.0	30.0	34.0
2	32.55275	34.0	31.0	34.0	31.0	34.0
3	32.542	34.0	31.0	34.0	31.0	34.0
4	36.15525	37.0	35.0	37.0	35.0	37.0
5	36.0315	37.0	35.0	37.0	35.0	37.0
6	35.87025	37.0	35.0	37.0	35.0	37.0
7	35.76275	37.0	35.0	37.0	35.0	37.0
8	35.91	37.0	35.0	37.0	35.0	37.0
9	37.512	39.0	37.0	39.0	35.0	39.0
10	37.51	39.0	37.0	39.0	35.0	39.0
11	37.12375	39.0	37.0	39.0	33.0	39.0
12	37.5645	39.0	37.0	39.0	34.0	39.0
13	37.49375	39.0	37.0	39.0	35.0	39.0
14	38.9155	40.0	38.0	41.0	35.0	41.0
15	38.7815	40.0	38.0	41.0	34.0	41.0
16	38.89675	40.0	38.0	41.0	35.0	41.0
17	39.03825	40.0	38.0	41.0	35.0	41.0
18	38.8685	41.0	38.0	41.0	35.0	41.0
19	38.7205	40.0	38.0	41.0	34.0	41.0
20	38.7285	40.0	38.0	41.0	34.0	41.0
21	38.85925	40.0	38.0	41.0	35.0	41.0
22	38.82825	40.0	38.0	41.0	35.0	41.0
23	38.621	40.0	38.0	41.0	34.0	41.0
24	38.74125	40.0	38.0	41.0	34.0	41.0
25	38.906	40.0	38.0	41.0	35.0	41.0
26	38.704	40.0	38.0	41.0	34.0	41.0
27	38.90875	40.0	38.0	41.0	35.0	41.0
28	38.6675	40.0	38.0	41.0	34.0	41.0
29	38.44875	40.0	38.0	41.0	34.0	41.0
30	38.1675	40.0	38.0	41.0	33.0	41.0
31	38.4405	40.0	38.0	41.0	34.0	41.0
32	38.35975	40.0	38.0	41.0	34.0	41.0
33	37.927	40.0	38.0	41.0	33.0	41.0
34	37.90125	40.0	38.0	41.0	33.0	41.0
35	37.65525	40.0	37.0	41.0	33.0	41.0
36	37.64725	40.0	37.0	41.0	32.0	41.0
37	37.2345	40.0	37.0	41.0	31.0	41.0
38	37.06475	39.0	36.0	41.0	31.0	41.0
39	37.5605	40.0	37.0	41.0	32.0	41.0
40	37.706	40.0	37.0	41.0	33.0	41.0
41	37.975	40.0	37.0	41.0	33.0	41.0
42	37.8235	40.0	37.0	41.0	33.0	41.0
43	37.84825	40.0	37.0	41.0	33.0	41.0
44	37.759	40.0	37.0	41.0	33.0	41.0
45	37.7065	40.0	37.0	41.0	33.0	41.0
46	37.44875	40.0	37.0	41.0	32.0	41.0
47	36.886	40.0	36.0	41.0	30.0	41.0
48	36.652	39.0	35.0	41.0	30.0	41.0
49	36.76725	40.0	36.0	41.0	31.0	41.0
50	36.232	39.0	35.0	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
13	1.0
14	0.0
15	0.0
16	2.0
17	2.0
18	2.0
19	1.0
20	1.0
21	7.0
22	8.0
23	3.0
24	11.0
25	9.0
26	13.0
27	14.0
28	33.0
29	36.0
30	58.0
31	65.0
32	85.0
33	115.0
34	165.0
35	216.0
36	261.0
37	460.0
38	683.0
39	1749.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.425	25.5	49.95	16.125
2	24.229516411926834	25.88323728388875	18.115760461037333	31.77148584314708
3	25.025	19.675	22.6	32.7
4	33.2	29.75	14.174999999999999	22.875
5	20.125	42.425000000000004	26.35	11.1
6	34.050000000000004	16.625	34.699999999999996	14.625
7	16.1	19.5	22.55	41.85
8	24.375	29.275000000000002	15.9	30.45
9	22.5	33.324999999999996	27.224999999999998	16.950000000000003
10	20.200000000000003	22.375	29.7	27.725
11	29.975	9.950000000000001	17.125	42.95
12	15.325	17.849999999999998	31.3	35.525
13	32.225	18.15	31.75	17.875
14	33.275	31.3	18.775	16.650000000000002
15	34.975	25.424999999999997	26.8	12.8
16	18.575	18.2	22.225	41.0
17	23.275000000000002	21.45	41.3	13.975000000000001
18	26.6	17.125	28.599999999999998	27.675
19	37.125	13.125	32.75	17.0
20	43.275000000000006	14.95	27.450000000000003	14.325
21	22.375	21.975	27.650000000000002	28.000000000000004
22	30.625000000000004	12.525	46.5	10.35
23	27.450000000000003	12.375	43.175000000000004	17.0
24	52.800000000000004	13.65	25.474999999999998	8.075000000000001
25	49.575	25.724999999999998	15.075	9.625
26	28.000000000000004	47.225	13.3	11.475
27	15.7	46.475	24.075	13.750000000000002
28	11.1	23.825	49.275000000000006	15.8
29	12.075	12.975	55.45	19.5
30	10.174999999999999	5.6000000000000005	36.925000000000004	47.3
31	14.725	5.375	46.775	33.125
32	30.25	5.7250000000000005	19.6	44.425
33	54.800000000000004	8.225	14.35	22.625
34	61.375	7.1	16.35	15.174999999999999
35	64.825	6.875000000000001	18.975	9.325
36	42.475	7.35	35.675000000000004	14.499999999999998
37	45.125	10.625	19.35	24.9
38	22.650000000000002	16.25	13.275	47.825
39	16.375	23.875	10.775	48.975
40	15.375	47.85	11.575000000000001	25.2
41	26.275	47.025	9.375	17.325
42	48.75	29.7	12.125	9.425
43	51.2	29.975	7.95	10.875
44	32.324999999999996	47.625	7.5249999999999995	12.525
45	20.275000000000002	48.225	12.675	18.825
46	13.275	26.224999999999998	18.45	42.05
47	8.825	15.5	39.6	36.075
48	10.299999999999999	12.825000000000001	20.65	56.225
49	12.075	19.375	16.525000000000002	52.025
50	18.575	35.875	14.575	30.975
>>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	0.5
6	1.0
7	0.5
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	1.0
20	2.0
21	1.5
22	1.0
23	0.5
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	1.0
30	2.0
31	5.0
32	8.0
33	9.0
34	10.0
35	21.5
36	33.0
37	33.5
38	34.0
39	31.5
40	29.0
41	33.5
42	38.0
43	65.5
44	93.0
45	140.0
46	187.0
47	303.0
48	419.0
49	549.0
50	679.0
51	787.0
52	895.0
53	669.5
54	444.0
55	471.5
56	499.0
57	360.5
58	222.0
59	140.0
60	58.0
61	53.5
62	49.0
63	96.0
64	143.0
65	89.0
66	35.0
67	25.0
68	15.0
69	21.0
70	27.0
71	47.0
72	67.0
73	36.5
74	6.0
75	3.0
76	0.0
77	0.0
78	0.0
79	1.0
80	2.0
81	2.0
82	2.0
83	1.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.22499999999999998
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	35.699999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.36974789915966	26.55
2	10.994397759103641	7.85
3	4.271708683473389	4.575
4	2.450980392156863	3.5000000000000004
5	0.9803921568627451	1.7500000000000002
6	0.8403361344537815	1.7999999999999998
7	0.9103641456582634	2.275
8	0.5602240896358543	1.6
9	0.42016806722689076	1.35
>10	3.5014005602240896	23.775
>50	0.42016806722689076	12.425
>100	0.2801120448179272	12.55
>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	144	3.5999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	129	3.225	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	120	3.0	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	109	2.725	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	100	2.5	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	96	2.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	88	2.1999999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	52	1.3	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	46	1.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	39	0.975	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	38	0.95	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	34	0.8500000000000001	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTT	26	0.65	RNA PCR Primer, Index 1 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	21	0.525	No Hit
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	19	0.475	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	18	0.44999999999999996	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 30bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTC	16	0.4	RNA PCR Primer, Index 3 (100% over 44bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGC	14	0.35000000000000003	RNA PCR Primer, Index 3 (100% over 50bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	13	0.325	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	11	0.27499999999999997	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	10	0.25	RNA PCR Primer, Index 1 (100% over 31bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	10	0.25	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	8	0.2	No Hit
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	7	0.17500000000000002	No Hit
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	7	0.17500000000000002	RNA PCR Primer, Index 3 (100% over 34bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	7	0.17500000000000002	No Hit
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
AGCTACATTGTCTGCTGGGTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	6	0.15	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	6	0.15	No Hit
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GCACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGC	6	0.15	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTATTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
CGCACGGGGTCGGCGGCGATGTCGGTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	5	0.125	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>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	0.375	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	0.55	0.0	0.0	0.0
5	0.0	0.6	0.0	0.0	0.0
6	0.0	0.625	0.0	0.0	0.0
7	0.0	1.075	0.0	0.0	0.0
8	0.0	1.225	0.0	0.0	0.0
9	0.0	1.425	0.0	0.0	0.0
10	0.0	1.55	0.0	0.0	0.0
11	0.0	1.675	0.0	0.0	0.0
12	0.0	1.8	0.0	0.0	0.0
13	0.0	2.15	0.0	0.0	0.0
14	0.0	2.5	0.0	0.0	0.0
15	0.0	2.875	0.0	0.0	0.0
16	0.0	3.95	0.0	0.0	0.0
17	0.0	4.725	0.0	0.0	0.0
18	0.0	5.65	0.0	0.0	0.0
19	0.0	6.05	0.0	0.0	0.0
20	0.0	7.075	0.0	0.0	0.0
21	0.0	12.825	0.0	0.0	0.0
22	0.0	24.9	0.0	0.0	0.0
23	0.0	54.05	0.0	0.0	0.0
24	0.0	66.4	0.0	0.0	0.0
25	0.0	73.1	0.0	0.0	0.0
26	0.0	74.3	0.0	0.0	0.0
27	0.0	75.175	0.0	0.0	0.0
28	0.0	75.775	0.0	0.0	0.0
29	0.0	76.375	0.0	0.0	0.0
30	0.0	76.825	0.0	0.0	0.0
31	0.0	77.7	0.0	0.0	0.0
32	0.0	78.675	0.0	0.0	0.0
33	0.0	79.85	0.0	0.0	0.0
34	0.0	83.4	0.0	0.0	0.0
35	0.0	84.375	0.0	0.0	0.0
36	0.0	85.1	0.0	0.0	0.0
37	0.0	85.875	0.0	0.0	0.0
38	0.0	86.175	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACTGTTG	20	6.952051E-4	44.000004	18
ATCCTCG	20	6.952051E-4	44.000004	8
TCCTCGA	20	6.952051E-4	44.000004	9
GTTGAAG	20	6.952051E-4	44.000004	10
CCAGTTG	20	6.952051E-4	44.000004	7
AACTGTT	20	6.952051E-4	44.000004	17
GAGTGGA	20	6.952051E-4	44.000004	20
CATCCTC	20	6.952051E-4	44.000004	7
GAAGAAC	20	6.952051E-4	44.000004	13
AGAACTG	20	6.952051E-4	44.000004	15
GTGAGTG	20	6.952051E-4	44.000004	18
GCCAGTT	20	6.952051E-4	44.000004	6
ACATTCA	40	5.315087E-9	44.000004	2
GCTGCCA	20	6.952051E-4	44.000004	3
GCTGTCG	40	5.315087E-9	44.000004	11
GAACTGT	20	6.952051E-4	44.000004	16
TGCCAGT	20	6.952051E-4	44.000004	5
TGAAGAA	20	6.952051E-4	44.000004	12
GGAAGCT	20	6.952051E-4	44.000004	18
AAGAACT	20	6.952051E-4	44.000004	14
>>END_MODULE
Read 192419 spots for SRR5030984.sra
Written 192419 spots for SRR5030984.sra
Read 192419 spots for SRR5030984.sra
Written 192419 spots for SRR5030984.sra
Read 192419 spots for SRR5030984.sra
Written 192419 spots for SRR5030984.sra
Read 192419 spots for SRR5030984.sra
Written 192419 spots for SRR5030984.sra
Read 192419 spots for SRR5030984.sra
Written 192419 spots for SRR5030984.sra
Read 192419 spots for SRR5030984.sra
Written 192419 spots for SRR5030984.sra
Read 192419 spots for SRR5030984.sra
Written 192419 spots for SRR5030984.sra
Read 192419 spots for SRR5030984.sra
Written 192419 spots for SRR5030984.sra
Read 192419 spots for SRR5030984.sra
Written 192419 spots for SRR5030984.sra
Read 192423 spots for SRR5030984.sra
Written 192423 spots for SRR5030984.sra
Read 192419 spots for SRR5030984.sra
Written 192419 spots for SRR5030984.sra
Read 192419 spots for SRR5030984.sra
Written 192419 spots for SRR5030984.sra
SRR ids: ['SRR5030984.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_rls_8aqn
SRR5030984.sra spots: 2309032
blocks: [[1, 192419], [192420, 384838], [384839, 577257], [577258, 769676], [769677, 962095], [962096, 1154514], [1154515, 1346933], [1346934, 1539352], [1539353, 1731771], [1731772, 1924190], [1924191, 2116609], [2116610, 2309032]]
SRR5030984 file size 399135
SRR5030984 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030984 SRR5030984_1.fastq
Input file:	SRR5030984_1.fastq
trimmed:	SRR5030984-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 06:59:46 2020 >> started

Wed Mar  4 06:59:48 2020 >> done (1.304s)
2309032 reads processed; of these:
    153 ( 0.01%) short reads filtered out after trimming by size control
      4 ( 0.00%) empty reads filtered out after trimming by size control
2308875 (99.99%) reads available; of these:
 137482 ( 5.95%) trimmed reads available after processing
2171393 (94.05%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     45	  0.00%
 19	     61	  0.00%
 20	    134	  0.01%
 21	    148	  0.01%
 22	    299	  0.01%
 23	    341	  0.01%
 24	    335	  0.01%
 25	    503	  0.02%
 26	    432	  0.02%
 27	    524	  0.02%
 28	    665	  0.03%
 29	   1016	  0.04%
 30	    726	  0.03%
 31	    780	  0.03%
 32	    915	  0.04%
 33	   1068	  0.05%
 34	   1223	  0.05%
 35	   2181	  0.09%
 36	   1990	  0.09%
 37	   2128	  0.09%
 38	   2086	  0.09%
 39	   2452	  0.11%
 40	   2538	  0.11%
 41	   2845	  0.12%
 42	   3782	  0.16%
 43	   5843	  0.25%
 44	   8090	  0.35%
 45	   9714	  0.42%
 46	  13504	  0.58%
 47	  16105	  0.70%
 48	  24514	  1.06%
 49	  30495	  1.32%
 50	2171393	 94.05%
2308875 reads passed initial QC


criterion=sequence-density
sequence-density=86.43
sequence-density-rank=1
fanout-score=20.63
fanout-score-rank=1
prefix-density=88.59
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCC


criterion=fanout-score
sequence-density=86.43
sequence-density-rank=1
fanout-score=20.63
fanout-score-rank=1
prefix-density=88.59
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 SRR5030984 -
Input file:	STDIN
trimmed:	SRR5030984-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 07:00:00 2020 >> started

Wed Mar  4 07:00:02 2020 >> done (2.446s)
2255798 reads processed; of these:
 120772 ( 5.35%) short reads filtered out after trimming by size control
   7899 ( 0.35%) empty reads filtered out after trimming by size control
2127127 (94.30%) reads available; of these:
2028095 (95.34%) trimmed reads available after processing
  99032 ( 4.66%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  10620	  0.50%
 19	  23932	  1.13%
 20	 134885	  6.34%
 21	 282006	 13.26%
 22	 668394	 31.42%
 23	 305904	 14.38%
 24	 144735	  6.80%
 25	  36117	  1.70%
 26	  18001	  0.85%
 27	  13758	  0.65%
 28	  14765	  0.69%
 29	  11544	  0.54%
 30	  17073	  0.80%
 31	  20386	  0.96%
 32	  22014	  1.03%
 33	  76798	  3.61%
 34	  21529	  1.01%
 35	  16433	  0.77%
 36	  20258	  0.95%
 37	  10774	  0.51%
 38	  11744	  0.55%
 39	  11339	  0.53%
 40	  18387	  0.86%
 41	  23465	  1.10%
 42	  27754	  1.30%
 43	  19516	  0.92%
 44	  14392	  0.68%
 45	  20153	  0.95%
 46	  14832	  0.70%
 47	  10606	  0.50%
 48	   1112	  0.05%
 49	   1953	  0.09%
 50	  81948	  3.85%


criterion=sequence-density
sequence-density=6.81
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=38
fanout-score=108.34
fanout-score-rank=1
prefix-density=1.82
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:00:22
                             Started mapping on |	Mar 04 07:00:23
                                    Finished on |	Mar 04 07:00:47
       Mapping speed, Million of reads per hour |	327.03

                          Number of input reads |	2180204
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1157626
                        Uniquely mapped reads % |	53.10%
                          Average mapped length |	24.36
                       Number of splices: Total |	1152
            Number of splices: Annotated (sjdb) |	200
                       Number of splices: GT/AG |	1081
                       Number of splices: GC/AG |	14
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	56
                      Mismatch rate per base, % |	0.18%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.84
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	735477
             % of reads mapped to multiple loci |	33.73%
        Number of reads mapped to too many loci |	39761
             % of reads mapped to too many loci |	1.82%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.79%
                     % of reads unmapped: other |	0.55%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	287101	287101	287101
N_multimapping	735477	735477	735477
N_noFeature	50637	63976	781297
N_ambiguous	649130	320205	12564
UnstrandedReadsAssigned:457859 PositiveStrandReadsAssigned:773445 NegativeStrandReadsAssigned:363765
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030984 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: SRR5030984-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,180,204 reads, 564,804 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,099 rounds

 109283 SRR5030984.ke.tsv
  52636 SRR5030984.se.tsv
 161919 total
==> SRR5030984.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

==> SRR5030984.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030984 completed mapping pipeline successfully
