Starting /dee2/code/volunteer_pipeline.sh SRR5030921
    current disk space = 160635518976
    free memory = 73959468 
SRR5030921 SRAfilesize
134080c72c492e0ef2c4f9f757bed5ce  SRR5030921.sra
SRR5030921.sra file validated
SRR5030921 is single end
SRR5030921 is conventional basespace
SRR5030921 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030921_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	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.3155	33.0	31.0	34.0	31.0	34.0
2	32.6995	34.0	31.0	34.0	31.0	34.0
3	32.651	34.0	31.0	34.0	31.0	34.0
4	36.0945	37.0	35.0	37.0	35.0	37.0
5	36.1685	37.0	37.0	37.0	35.0	37.0
6	35.83175	37.0	35.0	37.0	33.0	37.0
7	36.03525	37.0	35.0	37.0	35.0	37.0
8	36.10425	37.0	35.0	37.0	35.0	37.0
9	37.81775	39.0	38.0	39.0	35.0	39.0
10	37.81375	39.0	38.0	39.0	35.0	39.0
11	37.798	39.0	38.0	39.0	35.0	39.0
12	37.86125	39.0	38.0	39.0	35.0	39.0
13	37.7955	39.0	38.0	39.0	35.0	39.0
14	39.2725	41.0	39.0	41.0	36.0	41.0
15	39.22875	41.0	39.0	41.0	36.0	41.0
16	39.023	40.0	38.0	41.0	36.0	41.0
17	39.23575	40.0	39.0	41.0	36.0	41.0
18	39.157	41.0	39.0	41.0	36.0	41.0
19	38.78375	40.0	38.0	41.0	35.0	41.0
20	39.0615	40.0	39.0	41.0	35.0	41.0
21	39.0925	40.0	39.0	41.0	36.0	41.0
22	39.21275	41.0	39.0	41.0	36.0	41.0
23	38.99675	40.0	39.0	41.0	36.0	41.0
24	38.2665	40.0	38.0	41.0	34.0	41.0
25	38.67375	40.0	38.0	41.0	34.0	41.0
26	38.73	40.0	38.0	41.0	34.0	41.0
27	38.73875	40.0	38.0	41.0	35.0	41.0
28	38.87475	40.0	39.0	41.0	35.0	41.0
29	38.853	40.0	38.0	41.0	35.0	41.0
30	38.604	40.0	38.0	41.0	34.0	41.0
31	38.93925	40.0	38.0	41.0	35.0	41.0
32	39.08625	41.0	39.0	41.0	35.0	41.0
33	37.75175	40.0	38.0	41.0	33.0	41.0
34	37.151	40.0	38.0	41.0	30.0	41.0
35	32.50025	38.0	30.0	40.0	9.0	41.0
36	28.7785	37.0	15.0	40.0	8.0	41.0
37	29.0275	35.0	22.0	39.0	6.0	41.0
38	31.98675	37.0	30.0	40.0	9.0	41.0
39	31.3435	37.0	29.0	40.0	6.0	41.0
40	32.53025	38.0	32.0	40.0	2.0	41.0
41	30.09625	36.0	26.0	40.0	2.0	41.0
42	31.877	37.0	31.0	40.0	2.0	41.0
43	29.5855	36.0	25.0	40.0	2.0	41.0
44	31.02575	37.0	30.0	40.0	2.0	41.0
45	28.919	36.0	24.0	40.0	2.0	41.0
46	26.59625	34.0	8.0	40.0	2.0	41.0
47	26.789	34.0	9.0	39.0	2.0	41.0
48	27.7325	35.0	2.0	39.0	2.0	41.0
49	25.494	34.0	2.0	40.0	2.0	41.0
50	22.4905	29.0	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
12	1.0
13	1.0
14	0.0
15	0.0
16	4.0
17	1.0
18	0.0
19	3.0
20	9.0
21	16.0
22	26.0
23	33.0
24	55.0
25	53.0
26	97.0
27	160.0
28	76.0
29	126.0
30	161.0
31	146.0
32	195.0
33	178.0
34	229.0
35	290.0
36	307.0
37	393.0
38	535.0
39	905.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.058058058058059	25.225225225225223	54.37937937937938	12.337337337337337
2	25.05	28.375	21.925	24.65
3	16.975	20.25	20.424999999999997	42.35
4	26.1	36.975	13.15	23.775
5	22.900000000000002	36.6	29.15	11.35
6	33.525	17.424999999999997	38.224999999999994	10.825
7	15.275	23.875	24.6	36.25
8	25.650000000000002	42.0	12.85	19.5
9	16.425	40.775	31.225	11.575000000000001
10	20.599999999999998	20.849999999999998	25.55	33.0
11	34.475	13.05	13.625000000000002	38.85
12	16.275000000000002	18.325	22.7	42.699999999999996
13	19.85	22.125	38.824999999999996	19.2
14	37.6	22.3	26.6	13.5
15	35.925000000000004	21.3	29.45	13.325000000000001
16	13.375	25.474999999999998	21.825	39.324999999999996
17	24.625	24.825	36.275	14.274999999999999
18	28.975	18.35	28.299999999999997	24.375
19	34.675	15.75	32.875	16.7
20	48.85	16.975	21.975	12.2
21	21.075	27.525	24.224999999999998	27.175
22	33.050000000000004	11.325000000000001	48.275	7.35
23	24.175	13.675	49.325	12.825000000000001
24	50.9	11.575000000000001	29.9	7.625
25	56.45	21.15	13.875000000000002	8.525
26	31.874999999999996	47.099999999999994	11.075	9.950000000000001
27	13.525	54.87499999999999	21.675	9.925
28	9.55	29.475	49.675000000000004	11.3
29	8.275	11.65	61.45	18.625
30	8.725	5.8999999999999995	41.3	44.074999999999996
31	12.075	4.8500000000000005	45.175	37.9
32	24.15	5.7250000000000005	26.3	43.824999999999996
33	53.949999999999996	6.45	12.925	26.674999999999997
34	69.65	6.075	10.65	13.625000000000002
35	62.925	6.575	20.724999999999998	9.775
36	67.2	7.6	15.4	9.8
37	38.725	10.0	24.95	26.325
38	27.224999999999998	11.275	12.75	48.75
39	15.925	23.45	7.5	53.125
40	13.025	49.2	8.125	29.65
41	27.175	51.025	8.475000000000001	13.325000000000001
42	51.925	32.35	7.124999999999999	8.6
43	50.425	33.875	8.525	7.175
44	33.025	49.5	6.2	11.275
45	15.475	52.15	8.725	23.65
46	8.35	32.324999999999996	26.174999999999997	33.15
47	8.450000000000001	14.075	33.225	44.25
48	9.375	9.425	25.224999999999998	55.974999999999994
49	11.75	25.75	11.899999999999999	50.6
50	31.574999999999996	27.500000000000004	7.324999999999999	33.6
>>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	0.0
18	0.0
19	0.5
20	1.0
21	0.5
22	0.0
23	0.5
24	1.0
25	1.0
26	1.0
27	0.5
28	0.0
29	2.5
30	5.0
31	6.0
32	7.0
33	12.0
34	17.0
35	26.0
36	35.0
37	46.0
38	57.0
39	60.5
40	64.0
41	67.5
42	71.0
43	84.0
44	97.0
45	185.5
46	274.0
47	346.5
48	419.0
49	514.5
50	610.0
51	770.5
52	931.0
53	688.5
54	446.0
55	373.0
56	300.0
57	295.5
58	291.0
59	205.0
60	119.0
61	93.5
62	68.0
63	81.5
64	95.0
65	58.5
66	22.0
67	16.0
68	10.0
69	10.5
70	11.0
71	24.5
72	38.0
73	21.0
74	4.0
75	2.5
76	1.0
77	2.0
78	3.0
79	2.0
80	1.0
81	1.0
82	1.0
83	0.5
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	51.9
#Duplication Level	Percentage of deduplicated	Percentage of total
1	82.5626204238921	42.85
2	7.1772639691714835	7.449999999999999
3	2.842003853564547	4.425
4	1.7822736030828517	3.6999999999999997
5	1.1560693641618496	3.0
6	0.7225433526011561	2.25
7	0.48169556840077066	1.7500000000000002
8	0.5298651252408477	2.1999999999999997
9	0.1445086705202312	0.675
>10	2.5048169556840074	24.099999999999998
>50	0.04816955684007707	2.375
>100	0.04816955684007707	5.225
>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	209	5.225	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	95	2.375	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	40	1.0	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	30	0.75	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	28	0.7000000000000001	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	21	0.525	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGG	17	0.42500000000000004	RNA PCR Primer, Index 2 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	15	0.375	RNA PCR Primer, Index 1 (100% over 30bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	13	0.325	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	13	0.325	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	13	0.325	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	12	0.3	No Hit
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	10	0.25	RNA PCR Primer, Index 1 (95% over 23bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	10	0.25	No Hit
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	10	0.25	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	9	0.22499999999999998	No Hit
CTGACCTATGAATTGACAGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	8	0.2	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	7	0.17500000000000002	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGC	7	0.17500000000000002	RNA PCR Primer, Index 11 (100% over 50bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	6	0.15	RNA PCR Primer, Index 1 (100% over 33bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	6	0.15	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTC	6	0.15	RNA PCR Primer, Index 11 (100% over 44bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	6	0.15	RNA PCR Primer, Index 1 (100% over 32bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	6	0.15	No Hit
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	5	0.125	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	5	0.125	No Hit
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCT	5	0.125	RNA PCR Primer, Index 11 (100% over 37bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	5	0.125	No Hit
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	5	0.125	No Hit
TTAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	5	0.125	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCAA	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	0.225	0.0	0.0	0.0
2	0.0	0.225	0.0	0.0	0.0
3	0.0	0.275	0.0	0.0	0.0
4	0.0	0.275	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	0.6	0.0	0.0	0.0
8	0.0	0.65	0.0	0.0	0.0
9	0.0	0.725	0.0	0.0	0.0
10	0.0	0.75	0.0	0.0	0.0
11	0.0	0.8	0.0	0.0	0.0
12	0.0	0.95	0.0	0.0	0.0
13	0.0	1.025	0.0	0.0	0.0
14	0.0	1.3	0.0	0.0	0.0
15	0.0	1.525	0.0	0.0	0.0
16	0.0	2.275	0.0	0.0	0.0
17	0.0	2.9	0.0	0.0	0.0
18	0.0	3.55	0.0	0.0	0.0
19	0.0	4.25	0.0	0.0	0.0
20	0.0	5.15	0.0	0.0	0.0
21	0.0	8.9	0.0	0.0	0.0
22	0.0	20.1	0.0	0.0	0.0
23	0.0	51.15	0.0	0.0	0.0
24	0.0	69.25	0.0	0.0	0.0
25	0.0	74.8	0.0	0.0	0.0
26	0.0	75.625	0.0	0.0	0.0
27	0.0	75.925	0.0	0.0	0.0
28	0.0	76.5	0.0	0.0	0.0
29	0.0	76.625	0.0	0.0	0.0
30	0.0	77.025	0.0	0.0	0.0
31	0.0	77.6	0.0	0.0	0.0
32	0.0	78.55	0.0	0.0	0.0
33	0.0	79.575	0.0	0.0	0.0
34	0.0	80.925	0.0	0.0	0.0
35	0.0	81.525	0.0	0.0	0.0
36	0.0	81.75	0.0	0.0	0.0
37	0.0	82.25	0.0	0.0	0.0
38	0.0	82.675	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	45	2.728484E-10	44.000004	8
ATCCTAT	20	6.952051E-4	44.000004	12
ACGCTGT	45	2.728484E-10	44.000004	9
TAAACAT	20	6.952051E-4	44.000004	3
AAACATC	20	6.952051E-4	44.000004	4
AGTAGGT	20	6.952051E-4	44.000004	7
TTCAACG	45	2.728484E-10	44.000004	5
GCTGGAA	20	6.952051E-4	44.000004	20
TCAACGC	45	2.728484E-10	44.000004	6
GAGTTGG	40	5.315087E-9	44.000004	20
TAGTAGG	20	6.952051E-4	44.000004	6
GGCCAGG	20	6.952051E-4	44.000004	36
AGTTGGA	45	2.728484E-10	44.000004	21
AGGTTGT	20	6.952051E-4	44.000004	10
GTAGGTT	20	6.952051E-4	44.000004	8
TGTAAAC	20	6.952051E-4	44.000004	1
GTAAACA	20	6.952051E-4	44.000004	2
TAGGTTG	20	6.952051E-4	44.000004	9
AACATCC	20	6.952051E-4	44.000004	5
CAACGCT	45	2.728484E-10	44.000004	7
>>END_MODULE
Read 303458 spots for SRR5030921.sra
Written 303458 spots for SRR5030921.sra
Read 303458 spots for SRR5030921.sra
Written 303458 spots for SRR5030921.sra
Read 303458 spots for SRR5030921.sra
Written 303458 spots for SRR5030921.sra
Read 303458 spots for SRR5030921.sra
Written 303458 spots for SRR5030921.sra
Read 303458 spots for SRR5030921.sra
Written 303458 spots for SRR5030921.sra
Read 303458 spots for SRR5030921.sra
Written 303458 spots for SRR5030921.sra
Read 303458 spots for SRR5030921.sra
Written 303458 spots for SRR5030921.sra
Read 303458 spots for SRR5030921.sra
Written 303458 spots for SRR5030921.sra
Read 303458 spots for SRR5030921.sra
Written 303458 spots for SRR5030921.sra
Read 303458 spots for SRR5030921.sra
Written 303458 spots for SRR5030921.sra
Read 303458 spots for SRR5030921.sra
Written 303458 spots for SRR5030921.sra
Read 303459 spots for SRR5030921.sra
Written 303459 spots for SRR5030921.sra
SRR ids: ['SRR5030921.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_u2edm9xg
SRR5030921.sra spots: 3641497
blocks: [[1, 303458], [303459, 606916], [606917, 910374], [910375, 1213832], [1213833, 1517290], [1517291, 1820748], [1820749, 2124206], [2124207, 2427664], [2427665, 2731122], [2731123, 3034580], [3034581, 3338038], [3338039, 3641497]]
SRR5030921 file size 630077
SRR5030921 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030921 SRR5030921_1.fastq
Input file:	SRR5030921_1.fastq
trimmed:	SRR5030921-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 06:45:24 2020 >> started

Wed Mar  4 06:45:27 2020 >> done (3.718s)
3641497 reads processed; of these:
    135 ( 0.00%) short reads filtered out after trimming by size control
      4 ( 0.00%) empty reads filtered out after trimming by size control
3641358 (100.00%) reads available; of these:
 442073 (12.14%) trimmed reads available after processing
3199285 (87.86%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     44	  0.00%
 19	     58	  0.00%
 20	    105	  0.00%
 21	    203	  0.01%
 22	    320	  0.01%
 23	    404	  0.01%
 24	    349	  0.01%
 25	    498	  0.01%
 26	    439	  0.01%
 27	    583	  0.02%
 28	    763	  0.02%
 29	   1486	  0.04%
 30	    887	  0.02%
 31	   1284	  0.04%
 32	   3419	  0.09%
 33	  11260	  0.31%
 34	  35647	  0.98%
 35	   7315	  0.20%
 36	   8495	  0.23%
 37	   4186	  0.11%
 38	   8134	  0.22%
 39	   7507	  0.21%
 40	  17272	  0.47%
 41	   8670	  0.24%
 42	  28446	  0.78%
 43	   8922	  0.25%
 44	  46963	  1.29%
 45	  28238	  0.78%
 46	  22502	  0.62%
 47	  25124	  0.69%
 48	  84850	  2.33%
 49	  77700	  2.13%
 50	3199285	 87.86%
3641358 reads passed initial QC


criterion=sequence-density
sequence-density=81.83
sequence-density-rank=1
fanout-score=18.17
fanout-score-rank=3
prefix-density=84.34
prefix-fanout=17.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCC


criterion=fanout-score
sequence-density=1.41
sequence-density-rank=9
fanout-score=523.17
fanout-score-rank=1
prefix-density=83.65
prefix-fanout=8.8
sequence=GGAATTCTCGGTGCCAAGGA
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCC -o SRR5030921 -
Input file:	STDIN
trimmed:	SRR5030921-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCC
-- 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 06:45:54 2020 >> started

Wed Mar  4 06:46:03 2020 >> done (9.146s)
3552545 reads processed; of these:
 122823 ( 3.46%) short reads filtered out after trimming by size control
  14473 ( 0.41%) empty reads filtered out after trimming by size control
3415249 (96.14%) reads available; of these:
3022119 (88.49%) trimmed reads available after processing
 393130 (11.51%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  19261	  0.56%
 19	  34455	  1.01%
 20	 139836	  4.09%
 21	 372232	 10.90%
 22	1105826	 32.38%
 23	 619245	 18.13%
 24	 216228	  6.33%
 25	  36160	  1.06%
 26	  18159	  0.53%
 27	  17218	  0.50%
 28	  19451	  0.57%
 29	  17100	  0.50%
 30	  26544	  0.78%
 31	  30978	  0.91%
 32	  35846	  1.05%
 33	  60722	  1.78%
 34	  30343	  0.89%
 35	  18230	  0.53%
 36	  25878	  0.76%
 37	  13918	  0.41%
 38	  16123	  0.47%
 39	  16529	  0.48%
 40	  22446	  0.66%
 41	  26269	  0.77%
 42	  33188	  0.97%
 43	  22159	  0.65%
 44	  26980	  0.79%
 45	  24030	  0.70%
 46	  19823	  0.58%
 47	  15419	  0.45%
 48	   6765	  0.20%
 49	  11969	  0.35%
 50	 315919	  9.25%


criterion=sequence-density
sequence-density=4.67
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=20
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.45
sequence-density-rank=33
fanout-score=10.75
fanout-score-rank=1
prefix-density=0.87
prefix-fanout=5.5
sequence=GGAATTCTCGGTGCCCAGGAACTCCAG
                                 Started job on |	Mar 04 06:47:50
                             Started mapping on |	Mar 04 06:47:50
                                    Finished on |	Mar 04 06:48:14
       Mapping speed, Million of reads per hour |	525.61

                          Number of input reads |	3504062
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1689742
                        Uniquely mapped reads % |	48.22%
                          Average mapped length |	26.96
                       Number of splices: Total |	1787
            Number of splices: Annotated (sjdb) |	259
                       Number of splices: GT/AG |	1634
                       Number of splices: GC/AG |	23
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	129
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.31
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.15
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1432552
             % of reads mapped to multiple loci |	40.88%
        Number of reads mapped to too many loci |	64318
             % of reads mapped to too many loci |	1.84%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.52%
                     % of reads unmapped: other |	0.54%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	381768	381768	381768
N_multimapping	1432552	1432552	1432552
N_noFeature	76656	92033	1318503
N_ambiguous	891841	572033	13918
UnstrandedReadsAssigned:721245 PositiveStrandReadsAssigned:1025676 NegativeStrandReadsAssigned:357321
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030921 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: SRR5030921-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,504,062 reads, 659,392 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,114 rounds

 109283 SRR5030921.ke.tsv
  52636 SRR5030921.se.tsv
 161919 total
==> SRR5030921.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

==> SRR5030921.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030921 completed mapping pipeline successfully
