Starting /dee2/code/volunteer_pipeline.sh SRR5030993
    current disk space = 160572391424
    free memory = 73924620 
SRR5030993 SRAfilesize
92c65acbab48c47599fdaca319abadde  SRR5030993.sra
SRR5030993.sra file validated
SRR5030993 is single end
SRR5030993 is conventional basespace
SRR5030993 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030993_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	32.318	33.0	31.0	34.0	31.0	34.0
2	32.5685	34.0	31.0	34.0	31.0	34.0
3	32.55625	34.0	31.0	34.0	31.0	34.0
4	36.231	37.0	35.0	37.0	35.0	37.0
5	36.096	37.0	35.0	37.0	35.0	37.0
6	35.91525	37.0	35.0	37.0	35.0	37.0
7	35.9065	37.0	35.0	37.0	35.0	37.0
8	36.03125	37.0	35.0	37.0	35.0	37.0
9	37.648	39.0	37.0	39.0	35.0	39.0
10	37.531	39.0	37.0	39.0	35.0	39.0
11	37.1885	39.0	37.0	39.0	33.0	39.0
12	37.5855	39.0	37.0	39.0	34.0	39.0
13	37.56175	39.0	37.0	39.0	35.0	39.0
14	39.14425	40.0	39.0	41.0	36.0	41.0
15	38.9515	40.0	38.0	41.0	35.0	41.0
16	38.974	40.0	38.0	41.0	35.0	41.0
17	39.11925	40.0	38.0	41.0	36.0	41.0
18	38.86825	40.0	38.0	41.0	35.0	41.0
19	38.73125	40.0	38.0	41.0	34.0	41.0
20	38.808	40.0	38.0	41.0	34.0	41.0
21	38.8995	40.0	38.0	41.0	35.0	41.0
22	38.98175	40.0	39.0	41.0	35.0	41.0
23	38.3985	40.0	38.0	41.0	34.0	41.0
24	38.68675	40.0	38.0	41.0	35.0	41.0
25	38.8125	40.0	38.0	41.0	35.0	41.0
26	38.602	40.0	38.0	41.0	34.0	41.0
27	38.7685	40.0	38.0	41.0	35.0	41.0
28	38.58075	40.0	38.0	41.0	34.0	41.0
29	38.49725	40.0	38.0	41.0	34.0	41.0
30	38.58625	40.0	38.0	41.0	34.0	41.0
31	38.782	40.0	38.0	41.0	35.0	41.0
32	38.7315	40.0	38.0	41.0	35.0	41.0
33	38.1485	40.0	38.0	41.0	34.0	41.0
34	38.1985	40.0	38.0	41.0	34.0	41.0
35	37.90175	40.0	38.0	41.0	33.0	41.0
36	37.85525	40.0	37.0	41.0	33.0	41.0
37	37.37175	40.0	37.0	41.0	31.0	41.0
38	37.43875	39.0	37.0	41.0	32.0	41.0
39	37.89925	40.0	37.0	41.0	33.0	41.0
40	38.03675	40.0	38.0	41.0	33.0	41.0
41	38.30075	40.0	38.0	41.0	34.0	41.0
42	38.2045	40.0	38.0	41.0	34.0	41.0
43	38.0815	40.0	38.0	41.0	33.0	41.0
44	38.208	40.0	38.0	41.0	34.0	41.0
45	38.31575	40.0	38.0	41.0	34.0	41.0
46	37.933	40.0	38.0	41.0	33.0	41.0
47	37.392	40.0	37.0	41.0	32.0	41.0
48	37.151	40.0	37.0	41.0	31.0	41.0
49	37.19625	40.0	36.0	41.0	31.0	41.0
50	36.69975	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
16	2.0
17	0.0
18	2.0
19	1.0
20	2.0
21	2.0
22	4.0
23	7.0
24	5.0
25	9.0
26	15.0
27	13.0
28	19.0
29	44.0
30	49.0
31	58.0
32	79.0
33	101.0
34	149.0
35	199.0
36	269.0
37	432.0
38	719.0
39	1820.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.05	22.875	55.474999999999994	13.600000000000001
2	23.8716148445336	26.83049147442327	23.721163490471415	25.576730190571716
3	18.325	20.150000000000002	21.349999999999998	40.175
4	27.875	37.525	13.225000000000001	21.375
5	23.125	38.550000000000004	27.525	10.8
6	36.85	15.725	34.575	12.85
7	13.5	25.25	25.05	36.199999999999996
8	24.675	40.275	13.925	21.125
9	17.525	38.275	31.0	13.200000000000001
10	19.8	21.099999999999998	26.674999999999997	32.425
11	30.525000000000002	11.450000000000001	16.25	41.775
12	16.400000000000002	17.299999999999997	24.375	41.925000000000004
13	21.425	23.825	36.65	18.099999999999998
14	38.5	23.674999999999997	24.6	13.225000000000001
15	38.95	21.099999999999998	28.075	11.875
16	13.575000000000001	26.700000000000003	23.175	36.55
17	25.525	22.225	39.675	12.575
18	29.075	20.424999999999997	25.424999999999997	25.074999999999996
19	38.425	14.424999999999999	30.049999999999997	17.1
20	49.775000000000006	17.7	21.8	10.725
21	21.375	26.35	24.2	28.075
22	31.900000000000002	12.675	48.125	7.3
23	23.674999999999997	12.5	50.4	13.425
24	51.800000000000004	13.350000000000001	28.199999999999996	6.65
25	55.75	21.15	14.975	8.125
26	29.15	49.325	12.225	9.3
27	14.025000000000002	53.525	22.2	10.25
28	9.65	25.85	51.275000000000006	13.225000000000001
29	10.274999999999999	11.425	60.25	18.05
30	10.125	5.45	37.675	46.75
31	12.975	4.05	48.275	34.699999999999996
32	24.65	5.050000000000001	23.3	47.0
33	55.574999999999996	6.45	13.350000000000001	24.625
34	67.225	6.2	13.275	13.3
35	67.55	6.775	16.900000000000002	8.774999999999999
36	41.775	7.5	39.75	10.975
37	47.475	8.975	22.05	21.5
38	24.075	14.05	12.25	49.625
39	13.8	22.125	8.6	55.474999999999994
40	13.05	50.74999999999999	9.1	27.1
41	22.1	54.925000000000004	8.3	14.674999999999999
42	51.15	30.9	9.85	8.1
43	57.05	26.6	6.950000000000001	9.4
44	31.15	50.349999999999994	7.199999999999999	11.3
45	16.175	55.400000000000006	10.625	17.8
46	11.55	27.325	16.975	44.15
47	8.175	13.925	40.825	37.075
48	9.275	10.8	21.4	58.525000000000006
49	10.825	19.0	13.325000000000001	56.85
50	17.9	41.0	10.125	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	0.0
6	0.0
7	0.5
8	1.0
9	0.5
10	0.0
11	1.0
12	2.0
13	1.0
14	0.0
15	0.5
16	1.0
17	0.5
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	1.5
28	3.0
29	2.5
30	2.0
31	7.5
32	13.0
33	12.0
34	11.0
35	13.5
36	16.0
37	18.5
38	21.0
39	25.0
40	29.0
41	40.0
42	51.0
43	92.5
44	134.0
45	180.0
46	226.0
47	453.5
48	681.0
49	676.5
50	672.0
51	826.5
52	981.0
53	659.5
54	338.0
55	333.5
56	329.0
57	284.0
58	239.0
59	145.0
60	51.0
61	42.5
62	34.0
63	52.5
64	71.0
65	48.0
66	25.0
67	14.5
68	4.0
69	9.0
70	14.0
71	29.0
72	44.0
73	24.0
74	4.0
75	3.5
76	3.0
77	1.5
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	0.0
2	0.3
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	37.8
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.25661375661376	28.825
2	9.457671957671957	7.1499999999999995
3	4.166666666666666	4.725
4	2.513227513227513	3.8
5	0.7936507936507936	1.5
6	0.9259259259259258	2.1
7	1.0582010582010581	2.8000000000000003
8	0.6613756613756614	2.0
9	0.5952380952380952	2.025
>10	3.1084656084656084	22.85
>50	0.1984126984126984	4.775
>100	0.26455026455026454	17.45
>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	287	7.175	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	177	4.425	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	123	3.075	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	111	2.775	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	75	1.875	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	58	1.4500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	58	1.4500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	38	0.95	RNA PCR Primer, Index 1 (100% over 30bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	31	0.775	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	30	0.75	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	30	0.75	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	27	0.675	No Hit
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAG	22	0.5499999999999999	RNA PCR Primer, Index 2 (97% over 35bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	21	0.525	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 33bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	18	0.44999999999999996	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	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)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTC	11	0.27499999999999997	RNA PCR Primer, Index 13 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	9	0.22499999999999998	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	9	0.22499999999999998	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	8	0.2	No Hit
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	8	0.2	RNA PCR Primer, Index 1 (100% over 31bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	8	0.2	No Hit
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	8	0.2	No Hit
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TATGCAAGGGCAAGCTCTCTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CGACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	6	0.15	RNA PCR Primer, Index 1 (100% over 34bp)
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CAGCAGCACACTGTGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTGTGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
CATGCTCAATAGGATTACGCTGAGGCCCTGGAATTCTCGGGTGCCAAGGA	6	0.15	RNA PCR Primer, Index 1 (100% over 22bp)
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	6	0.15	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CTCAATAGGATTACGCTGAGGCCCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAG	5	0.125	RNA PCR Primer, Index 2 (97% over 35bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTGGAATTCTCGGGTGC	5	0.125	No Hit
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTGTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTTGGAATT	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTAT	5	0.125	RNA PCR Primer, Index 13 (100% over 48bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.075	0.0	0.0	0.0
2	0.0	0.125	0.0	0.0	0.0
3	0.0	0.275	0.0	0.0	0.0
4	0.0	0.3	0.0	0.0	0.0
5	0.0	0.325	0.0	0.0	0.0
6	0.0	0.35	0.0	0.0	0.0
7	0.0	0.725	0.0	0.0	0.0
8	0.0	0.875	0.0	0.0	0.0
9	0.0	0.95	0.0	0.0	0.0
10	0.0	1.075	0.0	0.0	0.0
11	0.0	1.275	0.0	0.0	0.0
12	0.0	1.525	0.0	0.0	0.0
13	0.0	1.7	0.0	0.0	0.0
14	0.0	2.05	0.0	0.0	0.0
15	0.0	2.375	0.0	0.0	0.0
16	0.0	3.325	0.0	0.0	0.0
17	0.0	3.975	0.0	0.0	0.0
18	0.0	5.15	0.0	0.0	0.0
19	0.0	5.625	0.0	0.0	0.0
20	0.0	6.85	0.0	0.0	0.0
21	0.0	11.275	0.0	0.0	0.0
22	0.0	22.2	0.0	0.0	0.0
23	0.0	55.475	0.0	0.0	0.0
24	0.0	71.25	0.0	0.0	0.0
25	0.0	77.3	0.0	0.0	0.0
26	0.0	78.375	0.0	0.0	0.0
27	0.0	78.825	0.0	0.0	0.0
28	0.0	79.475	0.0	0.0	0.0
29	0.0	80.125	0.0	0.0	0.0
30	0.0	80.5	0.0	0.0	0.0
31	0.0	81.325	0.0	0.0	0.0
32	0.0	82.45	0.0	0.0	0.0
33	0.0	83.65	0.0	0.0	0.0
34	0.0	85.65	0.0	0.0	0.0
35	0.0	86.775	0.0	0.0	0.0
36	0.0	87.675	0.0	0.0	0.0
37	0.0	88.375	0.0	0.0	0.0
38	0.0	88.9	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ATCCCCG	20	6.952051E-4	44.000004	8
AACGCTG	20	6.952051E-4	44.000004	8
TGTTGGA	20	6.952051E-4	44.000004	20
ACGCTGT	20	6.952051E-4	44.000004	9
TTCAACG	20	6.952051E-4	44.000004	5
CATCCCC	20	6.952051E-4	44.000004	7
ATAGGCT	65	0.0	44.000004	16
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
ACATCCC	20	6.952051E-4	44.000004	6
CCCCGAC	20	6.952051E-4	44.000004	10
CTGGAAG	20	6.952051E-4	44.000004	16
CCCGACT	20	6.952051E-4	44.000004	11
GACTGGA	20	6.952051E-4	44.000004	14
TGGTGGT	20	6.952051E-4	44.000004	5
ACTGGAA	20	6.952051E-4	44.000004	15
CCGACTG	20	6.952051E-4	44.000004	12
ATTCAAC	20	6.952051E-4	44.000004	4
CGACTGG	20	6.952051E-4	44.000004	13
GATAGGC	65	0.0	44.000004	15
>>END_MODULE
Read 341787 spots for SRR5030993.sra
Written 341787 spots for SRR5030993.sra
Read 341787 spots for SRR5030993.sra
Written 341787 spots for SRR5030993.sra
Read 341787 spots for SRR5030993.sra
Written 341787 spots for SRR5030993.sra
Read 341787 spots for SRR5030993.sra
Written 341787 spots for SRR5030993.sra
Read 341787 spots for SRR5030993.sra
Written 341787 spots for SRR5030993.sra
Read 341787 spots for SRR5030993.sra
Written 341787 spots for SRR5030993.sra
Read 341787 spots for SRR5030993.sra
Written 341787 spots for SRR5030993.sra
Read 341787 spots for SRR5030993.sra
Written 341787 spots for SRR5030993.sra
Read 341787 spots for SRR5030993.sra
Written 341787 spots for SRR5030993.sra
Read 341787 spots for SRR5030993.sra
Written 341787 spots for SRR5030993.sra
Read 341787 spots for SRR5030993.sra
Written 341787 spots for SRR5030993.sra
Read 341791 spots for SRR5030993.sra
Written 341791 spots for SRR5030993.sra
SRR ids: ['SRR5030993.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_15vpm15r
SRR5030993.sra spots: 4101448
blocks: [[1, 341787], [341788, 683574], [683575, 1025361], [1025362, 1367148], [1367149, 1708935], [1708936, 2050722], [2050723, 2392509], [2392510, 2734296], [2734297, 3076083], [3076084, 3417870], [3417871, 3759657], [3759658, 4101448]]
SRR5030993 file size 709810
SRR5030993 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030993 SRR5030993_1.fastq
Input file:	SRR5030993_1.fastq
trimmed:	SRR5030993-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- end quality threshold (-q):		10
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ (auto detected)
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	12
Wed Mar  4 07:01:30 2020 >> started

Wed Mar  4 07:01:32 2020 >> done (2.462s)
4101448 reads processed; of these:
    314 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
4101128 (99.99%) reads available; of these:
 214423 ( 5.23%) trimmed reads available after processing
3886705 (94.77%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     95	  0.00%
 19	    109	  0.00%
 20	    212	  0.01%
 21	    260	  0.01%
 22	    513	  0.01%
 23	    573	  0.01%
 24	    517	  0.01%
 25	    783	  0.02%
 26	    545	  0.01%
 27	    732	  0.02%
 28	    875	  0.02%
 29	   1588	  0.04%
 30	    913	  0.02%
 31	   1032	  0.03%
 32	   1214	  0.03%
 33	   1443	  0.04%
 34	   1825	  0.04%
 35	   3361	  0.08%
 36	   2888	  0.07%
 37	   3410	  0.08%
 38	   3170	  0.08%
 39	   3478	  0.08%
 40	   3956	  0.10%
 41	   4246	  0.10%
 42	   5667	  0.14%
 43	   8403	  0.20%
 44	  11635	  0.28%
 45	  15462	  0.38%
 46	  20412	  0.50%
 47	  25600	  0.62%
 48	  41007	  1.00%
 49	  48499	  1.18%
 50	3886705	 94.77%
4101128 reads passed initial QC


criterion=sequence-density
sequence-density=88.53
sequence-density-rank=1
fanout-score=18.71
fanout-score-rank=1
prefix-density=90.54
prefix-fanout=18.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCC


criterion=fanout-score
sequence-density=88.53
sequence-density-rank=1
fanout-score=18.71
fanout-score-rank=1
prefix-density=90.54
prefix-fanout=18.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCC -o SRR5030993 -
Input file:	STDIN
trimmed:	SRR5030993-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCC
-- 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 07:01:51 2020 >> started

Wed Mar  4 07:01:56 2020 >> done (5.432s)
4008968 reads processed; of these:
 215995 ( 5.39%) short reads filtered out after trimming by size control
  11722 ( 0.29%) empty reads filtered out after trimming by size control
3781251 (94.32%) reads available; of these:
3645926 (96.42%) trimmed reads available after processing
 135325 ( 3.58%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  22620	  0.60%
 19	  48126	  1.27%
 20	 182319	  4.82%
 21	 448288	 11.86%
 22	1316391	 34.81%
 23	 657440	 17.39%
 24	 244971	  6.48%
 25	  41663	  1.10%
 26	  22919	  0.61%
 27	  22126	  0.59%
 28	  24516	  0.65%
 29	  18712	  0.49%
 30	  32621	  0.86%
 31	  47633	  1.26%
 32	  43213	  1.14%
 33	  82286	  2.18%
 34	  44677	  1.18%
 35	  34872	  0.92%
 36	  39459	  1.04%
 37	  20623	  0.55%
 38	  22681	  0.60%
 39	  19986	  0.53%
 40	  25431	  0.67%
 41	  36275	  0.96%
 42	  41061	  1.09%
 43	  32769	  0.87%
 44	  26899	  0.71%
 45	  27283	  0.72%
 46	  21700	  0.57%
 47	  15560	  0.41%
 48	   1506	  0.04%
 49	   2708	  0.07%
 50	 111917	  2.96%


criterion=sequence-density
sequence-density=9.54
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=22
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.41
sequence-density-rank=32
fanout-score=8.41
fanout-score-rank=1
prefix-density=3.41
prefix-fanout=1.0
sequence=TAGTAGGTTGTGTGGTTTT
                                 Started job on |	Mar 04 07:02:17
                             Started mapping on |	Mar 04 07:02:17
                                    Finished on |	Mar 04 07:02:44
       Mapping speed, Million of reads per hour |	516.45

                          Number of input reads |	3873411
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1823175
                        Uniquely mapped reads % |	47.07%
                          Average mapped length |	24.32
                       Number of splices: Total |	1909
            Number of splices: Annotated (sjdb) |	306
                       Number of splices: GT/AG |	1743
                       Number of splices: GC/AG |	22
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	144
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.73
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.02
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1629645
             % of reads mapped to multiple loci |	42.07%
        Number of reads mapped to too many loci |	106953
             % of reads mapped to too many loci |	2.76%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.15%
                     % of reads unmapped: other |	0.95%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	420591	420591	420591
N_multimapping	1629645	1629645	1629645
N_noFeature	100085	117436	1395897
N_ambiguous	953590	590278	15726
UnstrandedReadsAssigned:769500 PositiveStrandReadsAssigned:1115461 NegativeStrandReadsAssigned:411552
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5030993 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: SRR5030993-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,873,411 reads, 727,321 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,178 rounds

 109283 SRR5030993.ke.tsv
  52636 SRR5030993.se.tsv
 161919 total
==> SRR5030993.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

==> SRR5030993.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030993 completed mapping pipeline successfully
