Starting /dee2/code/volunteer_pipeline.sh SRR5030977
    current disk space = 160582877184
    free memory = 73947660 
SRR5030977 SRAfilesize
ab93c90d0cd158aa5b824334405f163f  SRR5030977.sra
SRR5030977.sra file validated
SRR5030977 is single end
SRR5030977 is conventional basespace
SRR5030977 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030977_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	32.49475	34.0	31.0	34.0	31.0	34.0
2	32.80525	34.0	31.0	34.0	31.0	34.0
3	32.7815	34.0	31.0	34.0	31.0	34.0
4	36.27625	37.0	37.0	37.0	35.0	37.0
5	36.17575	37.0	37.0	37.0	35.0	37.0
6	35.9995	37.0	35.0	37.0	35.0	37.0
7	36.01825	37.0	35.0	37.0	35.0	37.0
8	36.18025	37.0	36.0	37.0	35.0	37.0
9	37.77275	39.0	38.0	39.0	35.0	39.0
10	37.975	39.0	38.0	39.0	35.0	39.0
11	37.81775	39.0	38.0	39.0	35.0	39.0
12	37.8225	39.0	38.0	39.0	35.0	39.0
13	37.80025	39.0	38.0	39.0	35.0	39.0
14	39.0055	41.0	38.0	41.0	35.0	41.0
15	39.03475	40.0	39.0	41.0	36.0	41.0
16	39.21675	40.0	39.0	41.0	36.0	41.0
17	39.31575	41.0	39.0	41.0	36.0	41.0
18	39.22025	41.0	39.0	41.0	36.0	41.0
19	39.04325	40.0	39.0	41.0	35.0	41.0
20	39.042	40.0	39.0	41.0	35.0	41.0
21	39.10625	40.0	39.0	41.0	36.0	41.0
22	39.1135	40.0	39.0	41.0	36.0	41.0
23	38.986	40.0	39.0	41.0	36.0	41.0
24	39.1445	40.0	39.0	41.0	36.0	41.0
25	39.182	41.0	39.0	41.0	36.0	41.0
26	38.90625	40.0	39.0	41.0	35.0	41.0
27	38.99275	40.0	39.0	41.0	36.0	41.0
28	38.67875	40.0	38.0	41.0	34.0	41.0
29	38.25775	40.0	38.0	41.0	33.0	41.0
30	38.47525	40.0	38.0	41.0	34.0	41.0
31	38.609	40.0	38.0	41.0	34.0	41.0
32	38.5685	40.0	38.0	41.0	34.0	41.0
33	38.488	40.0	38.0	41.0	34.0	41.0
34	38.50225	40.0	38.0	41.0	35.0	41.0
35	38.26175	40.0	38.0	41.0	34.0	41.0
36	37.73875	40.0	37.0	41.0	33.0	41.0
37	37.52375	40.0	37.0	41.0	32.0	41.0
38	37.5955	40.0	37.0	41.0	32.0	41.0
39	37.93875	40.0	38.0	41.0	33.0	41.0
40	38.0085	40.0	38.0	41.0	33.0	41.0
41	38.02375	40.0	38.0	41.0	33.0	41.0
42	38.0845	40.0	38.0	41.0	34.0	41.0
43	38.21225	40.0	38.0	41.0	34.0	41.0
44	37.9635	40.0	38.0	41.0	33.0	41.0
45	37.8615	40.0	38.0	41.0	33.0	41.0
46	37.30225	40.0	37.0	41.0	32.0	41.0
47	36.84975	40.0	36.0	41.0	30.0	41.0
48	36.382	39.0	35.0	41.0	30.0	41.0
49	36.5605	39.0	36.0	41.0	30.0	41.0
50	36.162	39.0	35.0	41.0	30.0	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
10	1.0
11	0.0
12	0.0
13	1.0
14	0.0
15	0.0
16	2.0
17	1.0
18	2.0
19	2.0
20	3.0
21	1.0
22	5.0
23	8.0
24	12.0
25	7.0
26	8.0
27	14.0
28	17.0
29	34.0
30	38.0
31	58.0
32	78.0
33	96.0
34	130.0
35	173.0
36	255.0
37	425.0
38	854.0
39	1775.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	6.831831831831832	25.8008008008008	53.4034034034034	13.963963963963963
2	23.375	27.700000000000003	19.0	29.925
3	24.7	22.15	21.7	31.45
4	31.85	28.749999999999996	13.100000000000001	26.3
5	20.005001250312578	43.23580895223806	26.756689172293076	10.002500625156289
6	36.65	16.3	32.0	15.049999999999999
7	13.600000000000001	21.375	24.375	40.65
8	24.425	28.299999999999997	17.45	29.825000000000003
9	20.599999999999998	35.099999999999994	27.500000000000004	16.8
10	21.5	24.675	27.725	26.1
11	29.099999999999998	9.0	20.025000000000002	41.875
12	14.149999999999999	17.724999999999998	32.6	35.525
13	32.75	18.925	30.825000000000003	17.5
14	32.275	31.75	19.375	16.6
15	35.575	25.1	26.25	13.075000000000001
16	20.349999999999998	20.175	21.825	37.65
17	23.625	22.925	40.35	13.100000000000001
18	25.85	20.075000000000003	26.85	27.224999999999998
19	38.525	13.350000000000001	30.4	17.724999999999998
20	42.5	14.875	29.025000000000002	13.600000000000001
21	23.875	18.35	30.3	27.474999999999998
22	29.725	11.600000000000001	49.6	9.075
23	27.950000000000003	11.975	46.075	14.000000000000002
24	54.425000000000004	13.700000000000001	25.424999999999997	6.45
25	51.225	26.875	14.124999999999998	7.775
26	26.674999999999997	49.95	13.375	10.0
27	14.899999999999999	49.875	25.074999999999996	10.15
28	10.0	24.3	51.1	14.6
29	11.375	11.65	58.175	18.8
30	9.049999999999999	5.425	38.2	47.325
31	13.850000000000001	4.0	47.949999999999996	34.2
32	28.9	4.6	20.125	46.375
33	57.599999999999994	8.525	12.6	21.275
34	65.425	6.75	15.1	12.725
35	67.85	5.800000000000001	18.875	7.475
36	44.1	5.8500000000000005	38.0	12.049999999999999
37	46.975	10.05	17.8	25.174999999999997
38	21.175	17.724999999999998	10.825	50.275000000000006
39	13.100000000000001	25.8	9.1	52.0
40	14.05	51.05	10.125	24.775
41	24.85	51.425	7.000000000000001	16.725
42	50.449999999999996	30.55	9.45	9.55
43	51.800000000000004	32.15	6.1	9.950000000000001
44	29.25	52.575	5.475	12.7
45	16.775000000000002	51.5	12.8	18.925
46	10.475	25.35	19.400000000000002	44.775
47	6.35	14.649999999999999	40.775	38.224999999999994
48	8.275	12.625	19.875	59.22500000000001
49	11.25	19.575	14.000000000000002	55.175
50	17.75	39.775	12.525	29.95
>>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	0.5
14	1.0
15	0.5
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	0.5
26	0.0
27	0.0
28	0.0
29	0.5
30	1.0
31	4.5
32	8.0
33	10.5
34	13.0
35	9.0
36	5.0
37	11.0
38	17.0
39	21.5
40	26.0
41	34.5
42	43.0
43	81.0
44	119.0
45	183.5
46	248.0
47	379.5
48	511.0
49	659.0
50	807.0
51	824.0
52	841.0
53	626.5
54	412.0
55	428.5
56	445.0
57	328.0
58	211.0
59	130.5
60	50.0
61	43.0
62	36.0
63	80.5
64	125.0
65	75.0
66	25.0
67	15.5
68	6.0
69	9.0
70	12.0
71	23.5
72	35.0
73	18.0
74	1.0
75	0.5
76	0.0
77	0.0
78	0.0
79	0.5
80	1.0
81	0.5
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	0.1
2	0.0
3	0.0
4	0.0
5	0.025
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	35.0
#Duplication Level	Percentage of deduplicated	Percentage of total
1	73.78571428571429	25.825
2	10.5	7.35
3	4.857142857142857	5.1
4	2.357142857142857	3.3000000000000003
5	1.9285714285714284	3.375
6	0.9285714285714286	1.95
7	0.9285714285714286	2.275
8	0.7857142857142858	2.1999999999999997
9	0.5	1.575
>10	2.7142857142857144	20.5
>50	0.5	14.774999999999999
>100	0.2142857142857143	11.774999999999999
>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
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	196	4.9	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	165	4.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	110	2.75	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	99	2.475	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	95	2.375	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	94	2.35	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	83	2.075	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	65	1.625	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	58	1.4500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	50	1.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	45	1.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	34	0.8500000000000001	RNA PCR Primer, Index 7 (97% over 35bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	25	0.625	RNA PCR Primer, Index 1 (100% over 33bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTC	24	0.6	RNA PCR Primer, Index 44 (100% over 44bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	21	0.525	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGC	16	0.4	RNA PCR Primer, Index 44 (100% over 50bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	9	0.22499999999999998	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	9	0.22499999999999998	RNA PCR Primer, Index 3 (100% over 34bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGCATTCTCGGGTGCC	8	0.2	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	8	0.2	RNA PCR Primer, Index 1 (100% over 31bp)
TAGCACCATCTGAAATCGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	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
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	7	0.17500000000000002	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATA	7	0.17500000000000002	RNA PCR Primer, Index 43 (97% over 37bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	6	0.15	RNA PCR Primer, Index 3 (100% over 34bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	6	0.15	RNA PCR Primer, Index 7 (97% over 35bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	6	0.15	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
CTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCTTATCAGACTGATGTTGATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCG	5	0.125	RNA PCR Primer, Index 44 (100% over 45bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	5	0.125	No Hit
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATTCAGGATAGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	5	0.125	RNA PCR Primer, Index 3 (100% over 34bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTGGAATTCTCGGGTGC	5	0.125	No Hit
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	5	0.125	No Hit
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCAGTGCACTACAGAACTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAACAGTCTACAGCCATGGTCGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	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	0.425	0.0	0.0	0.0
2	0.0	0.425	0.0	0.0	0.0
3	0.0	0.55	0.0	0.0	0.0
4	0.0	0.6	0.0	0.0	0.0
5	0.0	0.65	0.0	0.0	0.0
6	0.0	0.8	0.0	0.0	0.0
7	0.0	1.475	0.0	0.0	0.0
8	0.0	1.65	0.0	0.0	0.0
9	0.0	1.8	0.0	0.0	0.0
10	0.0	2.05	0.0	0.0	0.0
11	0.0	2.375	0.0	0.0	0.0
12	0.0	2.675	0.0	0.0	0.0
13	0.0	2.9	0.0	0.0	0.0
14	0.0	3.2	0.0	0.0	0.0
15	0.0	3.575	0.0	0.0	0.0
16	0.0	5.25	0.0	0.0	0.0
17	0.0	6.175	0.0	0.0	0.0
18	0.0	7.325	0.0	0.0	0.0
19	0.0	7.95	0.0	0.0	0.0
20	0.0	9.125	0.0	0.0	0.0
21	0.0	15.475	0.0	0.0	0.0
22	0.0	29.1	0.0	0.0	0.0
23	0.0	61.675	0.0	0.0	0.0
24	0.0	75.25	0.0	0.0	0.0
25	0.0	81.625	0.0	0.0	0.0
26	0.0	83.0	0.0	0.0	0.0
27	0.0	83.625	0.0	0.0	0.0
28	0.0	84.175	0.0	0.0	0.0
29	0.0	84.775	0.0	0.0	0.0
30	0.0	85.175	0.0	0.0	0.0
31	0.0	85.7	0.0	0.0	0.0
32	0.0	86.275	0.0	0.0	0.0
33	0.0	87.225	0.0	0.0	0.0
34	0.0	90.2	0.0	0.0	0.0
35	0.0	91.2	0.0	0.0	0.0
36	0.0	91.825	0.0	0.0	0.0
37	0.0	92.175	0.0	0.0	0.0
38	0.0	92.55	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CGCGACC	20	6.952051E-4	44.000004	1
GTTGAAG	20	6.952051E-4	44.000004	10
AAGTAAT	40	5.315087E-9	44.000004	4
TCAAGTA	40	5.315087E-9	44.000004	2
AATCCAG	40	5.315087E-9	44.000004	8
CAGTTGA	20	6.952051E-4	44.000004	8
CTGAGCT	20	6.952051E-4	44.000004	11
AGCTTGG	20	6.952051E-4	44.000004	14
ATCCAGG	40	5.315087E-9	44.000004	9
CCAGTTG	20	6.952051E-4	44.000004	7
AACTGTT	20	6.952051E-4	44.000004	17
GCGACCT	20	6.952051E-4	44.000004	2
GCGACCC	20	6.952051E-4	44.000004	22
TTCAAGT	40	5.315087E-9	44.000004	1
TTCAACG	20	6.952051E-4	44.000004	5
AGGATAG	40	5.315087E-9	44.000004	13
CCGCTGA	20	6.952051E-4	44.000004	27
ATAGGCT	40	5.315087E-9	44.000004	16
GAGCTTG	20	6.952051E-4	44.000004	13
GGATCCG	20	6.952051E-4	44.000004	3
>>END_MODULE
Read 232238 spots for SRR5030977.sra
Written 232238 spots for SRR5030977.sra
Read 232238 spots for SRR5030977.sra
Written 232238 spots for SRR5030977.sra
Read 232238 spots for SRR5030977.sra
Written 232238 spots for SRR5030977.sra
Read 232238 spots for SRR5030977.sra
Written 232238 spots for SRR5030977.sra
Read 232238 spots for SRR5030977.sra
Written 232238 spots for SRR5030977.sra
Read 232238 spots for SRR5030977.sra
Written 232238 spots for SRR5030977.sra
Read 232238 spots for SRR5030977.sra
Written 232238 spots for SRR5030977.sra
Read 232238 spots for SRR5030977.sra
Written 232238 spots for SRR5030977.sra
Read 232238 spots for SRR5030977.sra
Written 232238 spots for SRR5030977.sra
Read 232238 spots for SRR5030977.sra
Written 232238 spots for SRR5030977.sra
Read 232244 spots for SRR5030977.sra
Written 232244 spots for SRR5030977.sra
Read 232238 spots for SRR5030977.sra
Written 232238 spots for SRR5030977.sra
SRR ids: ['SRR5030977.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_fb93cafe
SRR5030977.sra spots: 2786862
blocks: [[1, 232238], [232239, 464476], [464477, 696714], [696715, 928952], [928953, 1161190], [1161191, 1393428], [1393429, 1625666], [1625667, 1857904], [1857905, 2090142], [2090143, 2322380], [2322381, 2554618], [2554619, 2786862]]
SRR5030977 file size 481956
SRR5030977 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030977 SRR5030977_1.fastq
Input file:	SRR5030977_1.fastq
trimmed:	SRR5030977-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 06:58:01 2020 >> started

Wed Mar  4 06:58:03 2020 >> done (1.441s)
2786862 reads processed; of these:
    136 ( 0.00%) short reads filtered out after trimming by size control
      1 ( 0.00%) empty reads filtered out after trimming by size control
2786725 (100.00%) reads available; of these:
 172874 ( 6.20%) trimmed reads available after processing
2613851 (93.80%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     50	  0.00%
 19	     83	  0.00%
 20	    145	  0.01%
 21	    178	  0.01%
 22	    299	  0.01%
 23	    336	  0.01%
 24	    372	  0.01%
 25	    539	  0.02%
 26	    418	  0.01%
 27	    603	  0.02%
 28	    758	  0.03%
 29	   1014	  0.04%
 30	    740	  0.03%
 31	    738	  0.03%
 32	    792	  0.03%
 33	   1223	  0.04%
 34	   1512	  0.05%
 35	   2724	  0.10%
 36	   2470	  0.09%
 37	   2412	  0.09%
 38	   2476	  0.09%
 39	   2629	  0.09%
 40	   2973	  0.11%
 41	   3221	  0.12%
 42	   4561	  0.16%
 43	   6515	  0.23%
 44	   9425	  0.34%
 45	  11752	  0.42%
 46	  17636	  0.63%
 47	  18403	  0.66%
 48	  32037	  1.15%
 49	  43840	  1.57%
 50	2613851	 93.80%
2786725 reads passed initial QC


criterion=sequence-density
sequence-density=92.50
sequence-density-rank=1
fanout-score=19.21
fanout-score-rank=1
prefix-density=93.67
prefix-fanout=19.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGCC


criterion=fanout-score
sequence-density=92.50
sequence-density-rank=1
fanout-score=19.21
fanout-score-rank=1
prefix-density=93.67
prefix-fanout=19.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGCC -o SRR5030977 -
Input file:	STDIN
trimmed:	SRR5030977-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGCC
-- 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 06:58:16 2020 >> started

Wed Mar  4 06:58:18 2020 >> done (2.925s)
2726796 reads processed; of these:
 207590 ( 7.61%) short reads filtered out after trimming by size control
  12848 ( 0.47%) empty reads filtered out after trimming by size control
2506358 (91.92%) reads available; of these:
2459818 (98.14%) trimmed reads available after processing
  46540 ( 1.86%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  15950	  0.64%
 19	  34041	  1.36%
 20	 176587	  7.05%
 21	 384679	 15.35%
 22	 876609	 34.98%
 23	 362942	 14.48%
 24	 171517	  6.84%
 25	  39143	  1.56%
 26	  19753	  0.79%
 27	  17035	  0.68%
 28	  16209	  0.65%
 29	  11649	  0.46%
 30	  18668	  0.74%
 31	  21415	  0.85%
 32	  27170	  1.08%
 33	  96816	  3.86%
 34	  21896	  0.87%
 35	  14785	  0.59%
 36	  16188	  0.65%
 37	   9603	  0.38%
 38	   9489	  0.38%
 39	   9170	  0.37%
 40	  12580	  0.50%
 41	  16471	  0.66%
 42	  19048	  0.76%
 43	  13449	  0.54%
 44	  10276	  0.41%
 45	  11960	  0.48%
 46	   8896	  0.35%
 47	   6516	  0.26%
 48	    541	  0.02%
 49	    887	  0.04%
 50	  34420	  1.37%


criterion=sequence-density
sequence-density=6.20
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=40
fanout-score=169.17
fanout-score-rank=1
prefix-density=2.00
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:58:38
                             Started mapping on |	Mar 04 06:58:38
                                    Finished on |	Mar 04 06:59:04
       Mapping speed, Million of reads per hour |	355.33

                          Number of input reads |	2566287
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1394045
                        Uniquely mapped reads % |	54.32%
                          Average mapped length |	23.16
                       Number of splices: Total |	1233
            Number of splices: Annotated (sjdb) |	391
                       Number of splices: GT/AG |	1186
                       Number of splices: GC/AG |	9
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	38
                      Mismatch rate per base, % |	0.13%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.70
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.02
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	893908
             % of reads mapped to multiple loci |	34.83%
        Number of reads mapped to too many loci |	45130
             % of reads mapped to too many loci |	1.76%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.54%
                     % of reads unmapped: other |	0.54%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	278334	278334	278334
N_multimapping	893908	893908	893908
N_noFeature	49248	59886	957047
N_ambiguous	792595	408589	10791
UnstrandedReadsAssigned:552202 PositiveStrandReadsAssigned:925570 NegativeStrandReadsAssigned:426207
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030977 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: SRR5030977-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,566,287 reads, 694,439 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,096 rounds

 109283 SRR5030977.ke.tsv
  52636 SRR5030977.se.tsv
 161919 total
==> SRR5030977.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

==> SRR5030977.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030977 completed mapping pipeline successfully
