Starting /dee2/code/volunteer_pipeline.sh SRR5030973
    current disk space = 160578486272
    free memory = 73950452 
SRR5030973 SRAfilesize
6695f5d4d740e83e5a5a398b01f91a06  SRR5030973.sra
SRR5030973.sra file validated
SRR5030973 is single end
SRR5030973 is conventional basespace
SRR5030973 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030973_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	32.466	33.0	31.0	34.0	31.0	34.0
2	32.808	34.0	31.0	34.0	31.0	34.0
3	32.71275	34.0	31.0	34.0	31.0	34.0
4	36.278	37.0	37.0	37.0	35.0	37.0
5	36.17725	37.0	37.0	37.0	35.0	37.0
6	35.84775	37.0	35.0	37.0	33.0	37.0
7	36.0575	37.0	35.0	37.0	35.0	37.0
8	36.1875	37.0	36.0	37.0	35.0	37.0
9	37.836	39.0	38.0	39.0	35.0	39.0
10	37.94575	39.0	38.0	39.0	35.0	39.0
11	37.74975	39.0	38.0	39.0	35.0	39.0
12	37.72675	39.0	38.0	39.0	35.0	39.0
13	37.75075	39.0	38.0	39.0	35.0	39.0
14	39.06925	41.0	38.0	41.0	36.0	41.0
15	39.191	41.0	39.0	41.0	36.0	41.0
16	39.2195	41.0	39.0	41.0	36.0	41.0
17	39.24075	41.0	39.0	41.0	36.0	41.0
18	39.2535	41.0	39.0	41.0	36.0	41.0
19	38.90875	40.0	38.0	41.0	35.0	41.0
20	39.0555	40.0	39.0	41.0	35.0	41.0
21	39.03925	40.0	38.0	41.0	36.0	41.0
22	39.059	40.0	39.0	41.0	36.0	41.0
23	38.82225	40.0	38.0	41.0	35.0	41.0
24	38.9415	40.0	39.0	41.0	35.0	41.0
25	38.93825	40.0	39.0	41.0	35.0	41.0
26	38.6725	40.0	38.0	41.0	34.0	41.0
27	38.7605	40.0	38.0	41.0	35.0	41.0
28	38.6305	40.0	38.0	41.0	34.0	41.0
29	38.2285	40.0	38.0	41.0	33.0	41.0
30	38.5565	40.0	38.0	41.0	34.0	41.0
31	38.662	40.0	38.0	41.0	35.0	41.0
32	38.29725	40.0	38.0	41.0	34.0	41.0
33	38.2425	40.0	38.0	41.0	34.0	41.0
34	38.06425	40.0	38.0	41.0	34.0	41.0
35	37.894	40.0	38.0	41.0	33.0	41.0
36	37.3815	39.0	37.0	41.0	31.0	41.0
37	37.54275	40.0	37.0	41.0	32.0	41.0
38	37.56375	40.0	37.0	41.0	32.0	41.0
39	37.931	40.0	38.0	41.0	33.0	41.0
40	37.98525	40.0	38.0	41.0	33.0	41.0
41	38.16025	40.0	38.0	41.0	33.0	41.0
42	38.12125	40.0	38.0	41.0	33.0	41.0
43	38.10275	40.0	38.0	41.0	33.0	41.0
44	37.93525	40.0	38.0	41.0	33.0	41.0
45	37.55225	40.0	37.0	41.0	33.0	41.0
46	37.3655	40.0	37.0	41.0	31.0	41.0
47	37.102	40.0	37.0	41.0	31.0	41.0
48	36.907	40.0	37.0	41.0	30.0	41.0
49	37.1665	40.0	37.0	41.0	31.0	41.0
50	36.7165	40.0	36.0	41.0	31.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
6	1.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	1.0
15	1.0
16	2.0
17	1.0
18	1.0
19	0.0
20	1.0
21	3.0
22	5.0
23	4.0
24	10.0
25	9.0
26	17.0
27	13.0
28	25.0
29	28.0
30	45.0
31	66.0
32	73.0
33	104.0
34	140.0
35	175.0
36	256.0
37	416.0
38	744.0
39	1859.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	6.433041301627034	22.428035043804755	58.84856070087609	12.290362953692116
2	23.125	27.075	23.775	26.025
3	17.224999999999998	18.575	19.525000000000002	44.675
4	27.800000000000004	38.800000000000004	11.425	21.975
5	22.35	37.675	28.65	11.325000000000001
6	36.35	14.475	37.724999999999994	11.450000000000001
7	10.475	26.1	25.3	38.125
8	24.325	41.925000000000004	12.8	20.95
9	17.849999999999998	41.675000000000004	29.625	10.85
10	17.8	20.674999999999997	27.575	33.95
11	31.45	10.125	13.15	45.275
12	14.85	14.45	24.675	46.025
13	19.1	22.650000000000002	38.875	19.375
14	40.550000000000004	21.625	25.85	11.975
15	40.325	20.025000000000002	28.275	11.375
16	11.65	27.625	20.925	39.800000000000004
17	25.275	22.85	39.574999999999996	12.3
18	29.525000000000002	19.375	26.400000000000002	24.7
19	39.324999999999996	13.200000000000001	29.075	18.4
20	53.400000000000006	15.375	21.25	9.975000000000001
21	19.675	26.875	24.2	29.25
22	31.275	10.299999999999999	52.25	6.175
23	24.75	11.475	52.7	11.075
24	55.375	12.225	28.475	3.925
25	58.650000000000006	22.575	12.8	5.975
26	29.925	52.75	11.525	5.800000000000001
27	12.8	57.175	22.375	7.6499999999999995
28	7.425	26.974999999999998	54.85	10.75
29	7.049999999999999	10.25	64.67500000000001	18.025
30	7.725	3.925	40.575	47.775
31	10.875	2.8000000000000003	49.675000000000004	36.65
32	25.650000000000002	3.25	22.725	48.375
33	59.5	4.5249999999999995	11.75	24.224999999999998
34	72.775	5.175	11.175	10.875
35	72.02499999999999	5.025	16.950000000000003	6.0
36	44.35	4.35	40.8	10.5
37	48.875	6.9	22.0	22.225
38	23.775	12.325	9.700000000000001	54.2
39	11.899999999999999	22.5	6.4	59.199999999999996
40	12.3	53.525	5.45	28.725
41	22.575	58.35	5.425	13.65
42	54.25	32.5	6.25	7.000000000000001
43	59.475	29.049999999999997	4.1000000000000005	7.375
44	31.075000000000003	54.525	4.9	9.5
45	14.099999999999998	58.650000000000006	9.225	18.025
46	7.35	28.075	17.2	47.375
47	4.3	12.950000000000001	42.475	40.275
48	6.05	10.299999999999999	21.25	62.4
49	8.725	18.375	11.275	61.625
50	16.925	40.849999999999994	10.025	32.2
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	0.5
26	0.0
27	0.5
28	1.0
29	2.5
30	4.0
31	3.5
32	3.0
33	3.5
34	4.0
35	6.5
36	9.0
37	12.5
38	16.0
39	17.0
40	18.0
41	23.0
42	28.0
43	74.0
44	120.0
45	165.0
46	210.0
47	448.0
48	686.0
49	666.0
50	646.0
51	831.0
52	1016.0
53	707.5
54	399.0
55	359.5
56	320.0
57	311.0
58	302.0
59	185.0
60	68.0
61	48.5
62	29.0
63	43.5
64	58.0
65	37.0
66	16.0
67	11.0
68	6.0
69	11.0
70	16.0
71	19.5
72	23.0
73	11.5
74	0.0
75	0.0
76	0.0
77	0.0
78	0.0
79	0.0
80	0.0
81	0.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.125
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	32.275
#Duplication Level	Percentage of deduplicated	Percentage of total
1	72.50193648334624	23.400000000000002
2	10.689388071262588	6.9
3	4.95739736638265	4.8
4	2.478698683191325	3.2
5	2.2463206816421377	3.6249999999999996
6	0.9295120061967467	1.7999999999999998
7	0.6196746707978312	1.4000000000000001
8	0.3098373353989156	0.8
9	0.6196746707978312	1.7999999999999998
>10	4.105344694035631	27.55
>50	0.23237800154918667	4.75
>100	0.3098373353989156	19.975
>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	309	7.725	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	197	4.925	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	156	3.9	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	137	3.4250000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	68	1.7000000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	66	1.6500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	56	1.4000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	45	1.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	40	1.0	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	38	0.95	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	30	0.75	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	27	0.675	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	27	0.675	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	21	0.525	RNA PCR Primer, Index 1 (100% over 33bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCT	20	0.5	RNA PCR Primer, Index 1 (97% over 35bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTC	16	0.4	RNA PCR Primer, Index 40 (100% over 44bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	10	0.25	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 31bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGAATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	6	0.15	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	6	0.15	No Hit
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	6	0.15	RNA PCR Primer, Index 2 (100% over 34bp)
TTCAAGTAATCCAGGATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	5	0.125	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ATAAAGCTAGATAACCGAAAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
ATAGTGGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
GTACAGTACTGTGATAACTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	5	0.125	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	5	0.125	No Hit
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
CAACGGAATCCCAAAAGCAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CAGCAGCACACTGTGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTGTGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	5	0.125	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTCGTATGC	5	0.125	RNA PCR Primer, Index 40 (100% over 50bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	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	0.125	0.0	0.0	0.0
2	0.0	0.125	0.0	0.0	0.0
3	0.0	0.2	0.0	0.0	0.0
4	0.0	0.25	0.0	0.0	0.0
5	0.0	0.3	0.0	0.0	0.0
6	0.0	0.35	0.0	0.0	0.0
7	0.0	0.85	0.0	0.0	0.0
8	0.0	1.0	0.0	0.0	0.0
9	0.0	1.05	0.0	0.0	0.0
10	0.0	1.15	0.0	0.0	0.0
11	0.0	1.225	0.0	0.0	0.0
12	0.0	1.425	0.0	0.0	0.0
13	0.0	1.65	0.0	0.0	0.0
14	0.0	1.8	0.0	0.0	0.0
15	0.0	2.1	0.0	0.0	0.0
16	0.0	3.15	0.0	0.0	0.0
17	0.0	3.925	0.0	0.0	0.0
18	0.0	4.975	0.0	0.0	0.0
19	0.0	5.225	0.0	0.0	0.0
20	0.0	6.6	0.0	0.0	0.0
21	0.0	11.525	0.0	0.0	0.0
22	0.0	24.325	0.0	0.0	0.0
23	0.0	61.175	0.0	0.0	0.0
24	0.0	78.825	0.0	0.0	0.0
25	0.0	85.0	0.0	0.0	0.0
26	0.0	86.275	0.0	0.0	0.0
27	0.0	86.725	0.0	0.0	0.0
28	0.0	87.125	0.0	0.0	0.0
29	0.0	87.625	0.0	0.0	0.0
30	0.0	87.925	0.0	0.0	0.0
31	0.0	88.725	0.0	0.0	0.0
32	0.0	89.225	0.0	0.0	0.0
33	0.0	89.85	0.0	0.0	0.0
34	0.0	91.325	0.0	0.0	0.0
35	0.0	91.775	0.0	0.0	0.0
36	0.0	92.075	0.0	0.0	0.0
37	0.0	92.3	0.0	0.0	0.0
38	0.0	92.6	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGGTAG	20	6.952051E-4	44.000004	2
GGTGAGT	45	2.728484E-10	44.000004	17
ACTCGAC	20	6.952051E-4	44.000004	12
TCGACTC	20	6.952051E-4	44.000004	14
TAAACAT	20	6.952051E-4	44.000004	3
AAACATC	20	6.952051E-4	44.000004	4
ACCATCA	20	6.952051E-4	44.000004	6
CATCACT	20	6.952051E-4	44.000004	8
AACCATC	20	6.952051E-4	44.000004	5
GAACCAT	20	6.952051E-4	44.000004	4
AGGCTTG	20	6.952051E-4	44.000004	18
GGCTTTG	20	6.952051E-4	44.000004	19
CCATCAC	20	6.952051E-4	44.000004	7
CACTCGA	20	6.952051E-4	44.000004	11
ATCACTC	20	6.952051E-4	44.000004	9
TGAGGTA	20	6.952051E-4	44.000004	1
TCACTCG	20	6.952051E-4	44.000004	10
TGAACCA	20	6.952051E-4	44.000004	3
GCTTTGG	20	6.952051E-4	44.000004	20
GACTCCT	20	6.952051E-4	44.000004	16
>>END_MODULE
Read 298357 spots for SRR5030973.sra
Written 298357 spots for SRR5030973.sra
Read 298357 spots for SRR5030973.sra
Written 298357 spots for SRR5030973.sra
Read 298357 spots for SRR5030973.sra
Written 298357 spots for SRR5030973.sra
Read 298357 spots for SRR5030973.sra
Written 298357 spots for SRR5030973.sra
Read 298357 spots for SRR5030973.sra
Written 298357 spots for SRR5030973.sra
Read 298357 spots for SRR5030973.sra
Written 298357 spots for SRR5030973.sra
Read 298357 spots for SRR5030973.sra
Written 298357 spots for SRR5030973.sra
Read 298357 spots for SRR5030973.sra
Written 298357 spots for SRR5030973.sra
Read 298357 spots for SRR5030973.sra
Written 298357 spots for SRR5030973.sra
Read 298357 spots for SRR5030973.sra
Written 298357 spots for SRR5030973.sra
Read 298357 spots for SRR5030973.sra
Written 298357 spots for SRR5030973.sra
Read 298360 spots for SRR5030973.sra
Written 298360 spots for SRR5030973.sra
SRR ids: ['SRR5030973.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_hqyoijjs
SRR5030973.sra spots: 3580287
blocks: [[1, 298357], [298358, 596714], [596715, 895071], [895072, 1193428], [1193429, 1491785], [1491786, 1790142], [1790143, 2088499], [2088500, 2386856], [2386857, 2685213], [2685214, 2983570], [2983571, 3281927], [3281928, 3580287]]
SRR5030973 file size 619471
SRR5030973 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030973 SRR5030973_1.fastq
Input file:	SRR5030973_1.fastq
trimmed:	SRR5030973-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 06:57:27 2020 >> started

Wed Mar  4 06:57:30 2020 >> done (3.303s)
3580287 reads processed; of these:
    175 ( 0.00%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
3580107 (99.99%) reads available; of these:
 202787 ( 5.66%) trimmed reads available after processing
3377320 (94.34%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     58	  0.00%
 19	     96	  0.00%
 20	    148	  0.00%
 21	    273	  0.01%
 22	    462	  0.01%
 23	    566	  0.02%
 24	    481	  0.01%
 25	    664	  0.02%
 26	    566	  0.02%
 27	    780	  0.02%
 28	    918	  0.03%
 29	   1671	  0.05%
 30	    915	  0.03%
 31	    905	  0.03%
 32	    943	  0.03%
 33	   1431	  0.04%
 34	   1839	  0.05%
 35	   3184	  0.09%
 36	   2832	  0.08%
 37	   2932	  0.08%
 38	   2827	  0.08%
 39	   3043	  0.08%
 40	   3649	  0.10%
 41	   4137	  0.12%
 42	   5861	  0.16%
 43	   8242	  0.23%
 44	  10837	  0.30%
 45	  12891	  0.36%
 46	  17198	  0.48%
 47	  20394	  0.57%
 48	  38498	  1.08%
 49	  53546	  1.50%
 50	3377320	 94.34%
3580107 reads passed initial QC


criterion=sequence-density
sequence-density=92.77
sequence-density-rank=1
fanout-score=17.55
fanout-score-rank=1
prefix-density=94.30
prefix-fanout=17.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTCGTATGCC


criterion=fanout-score
sequence-density=92.77
sequence-density-rank=1
fanout-score=17.55
fanout-score-rank=1
prefix-density=94.30
prefix-fanout=17.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTCGTATGCC -o SRR5030973 -
Input file:	STDIN
trimmed:	SRR5030973-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTCAGAATCTCGTATGCC
-- 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 06:57:50 2020 >> started

Wed Mar  4 06:57:59 2020 >> done (8.192s)
3503116 reads processed; of these:
 169205 ( 4.83%) short reads filtered out after trimming by size control
   8752 ( 0.25%) empty reads filtered out after trimming by size control
3325159 (94.92%) reads available; of these:
3266242 (98.23%) trimmed reads available after processing
  58917 ( 1.77%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  19426	  0.58%
 19	  42670	  1.28%
 20	 179358	  5.39%
 21	 441944	 13.29%
 22	1294369	 38.93%
 23	 645672	 19.42%
 24	 210203	  6.32%
 25	  36468	  1.10%
 26	  17581	  0.53%
 27	  16522	  0.50%
 28	  18636	  0.56%
 29	  13809	  0.42%
 30	  23957	  0.72%
 31	  26064	  0.78%
 32	  31800	  0.96%
 33	  58137	  1.75%
 34	  23578	  0.71%
 35	  14053	  0.42%
 36	  14541	  0.44%
 37	  11020	  0.33%
 38	  11755	  0.35%
 39	  11859	  0.36%
 40	  16410	  0.49%
 41	  21170	  0.64%
 42	  21187	  0.64%
 43	  16076	  0.48%
 44	  12123	  0.36%
 45	  13124	  0.39%
 46	   9876	  0.30%
 47	   6554	  0.20%
 48	    721	  0.02%
 49	   1176	  0.04%
 50	  43320	  1.30%


criterion=sequence-density
sequence-density=6.19
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.42
sequence-density-rank=28
fanout-score=15.78
fanout-score-rank=1
prefix-density=6.69
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 06:58:26
                             Started mapping on |	Mar 04 06:58:27
                                    Finished on |	Mar 04 06:58:53
       Mapping speed, Million of reads per hour |	471.07

                          Number of input reads |	3402150
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1645104
                        Uniquely mapped reads % |	48.35%
                          Average mapped length |	23.25
                       Number of splices: Total |	1476
            Number of splices: Annotated (sjdb) |	158
                       Number of splices: GT/AG |	1391
                       Number of splices: GC/AG |	13
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	70
                      Mismatch rate per base, % |	0.12%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.68
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1492816
             % of reads mapped to multiple loci |	43.88%
        Number of reads mapped to too many loci |	45882
             % of reads mapped to too many loci |	1.35%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.80%
                     % of reads unmapped: other |	0.62%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	264230	264230	264230
N_multimapping	1492816	1492816	1492816
N_noFeature	59663	72129	1236427
N_ambiguous	885379	533352	10732
UnstrandedReadsAssigned:700062 PositiveStrandReadsAssigned:1039623 NegativeStrandReadsAssigned:397945
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030973 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: SRR5030973-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,402,150 reads, 679,458 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,110 rounds

 109283 SRR5030973.ke.tsv
  52636 SRR5030973.se.tsv
 161919 total
==> SRR5030973.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

==> SRR5030973.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030973 completed mapping pipeline successfully
