Starting /dee2/code/volunteer_pipeline.sh SRR8404467
    current disk space = 845019624
    free memory = 122949928 
SRR8404467 SRAfilesize
1cc6f56855a3d4dcbcc06957597aa6aa  SRR8404467.sra
SRR8404467.sra file validated
SRR8404467 is single end
SRR8404467 is conventional basespace
SRR8404467 read1 length is 51 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR8404467_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	51
%GC	55
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	30.8935	33.0	31.0	34.0	27.0	34.0
2	31.5855	34.0	31.0	34.0	27.0	34.0
3	31.94275	34.0	31.0	34.0	28.0	34.0
4	35.32625	37.0	35.0	37.0	32.0	37.0
5	35.36575	37.0	35.0	37.0	32.0	37.0
6	35.113	37.0	35.0	37.0	32.0	37.0
7	35.10625	37.0	35.0	37.0	32.0	37.0
8	35.1085	37.0	35.0	37.0	32.0	37.0
9	36.9595	39.0	37.0	39.0	32.0	39.0
10	36.764	39.0	37.0	39.0	32.0	39.0
11	36.787	39.0	37.0	39.0	32.0	39.0
12	36.83775	39.0	37.0	39.0	33.0	39.0
13	36.7275	39.0	37.0	39.0	32.0	39.0
14	38.18225	41.0	38.0	41.0	33.0	41.0
15	38.30175	41.0	38.0	41.0	33.0	41.0
16	38.204	41.0	38.0	41.0	32.0	41.0
17	38.12475	40.0	38.0	41.0	32.0	41.0
18	37.9705	40.0	38.0	41.0	32.0	41.0
19	37.68425	40.0	38.0	41.0	31.0	41.0
20	36.84925	40.0	37.0	41.0	30.0	41.0
21	36.79425	39.0	37.0	41.0	30.0	41.0
22	36.78775	39.0	36.0	41.0	30.0	41.0
23	37.27975	40.0	37.0	41.0	30.0	41.0
24	37.49275	40.0	38.0	41.0	31.0	41.0
25	37.642	40.0	38.0	41.0	31.0	41.0
26	37.61225	40.0	38.0	41.0	31.0	41.0
27	37.645	40.0	38.0	41.0	31.0	41.0
28	37.581	40.0	38.0	41.0	30.0	41.0
29	37.44725	40.0	37.0	41.0	30.0	41.0
30	36.90375	40.0	36.0	41.0	30.0	41.0
31	37.26325	40.0	37.0	41.0	30.0	41.0
32	37.50225	40.0	38.0	41.0	30.0	41.0
33	37.674	40.0	38.0	41.0	30.0	41.0
34	37.71375	40.0	38.0	41.0	31.0	41.0
35	37.6915	40.0	38.0	41.0	32.0	41.0
36	37.6895	40.0	38.0	41.0	31.0	41.0
37	37.6535	40.0	38.0	41.0	31.0	41.0
38	37.81275	40.0	38.0	41.0	31.0	41.0
39	37.9375	40.0	38.0	41.0	31.0	41.0
40	37.7755	40.0	38.0	41.0	32.0	41.0
41	37.55375	40.0	38.0	41.0	31.0	41.0
42	37.414	40.0	37.0	41.0	30.0	41.0
43	37.574	40.0	38.0	41.0	31.0	41.0
44	37.4535	40.0	37.0	41.0	31.0	41.0
45	36.902	40.0	37.0	41.0	29.0	41.0
46	37.138	40.0	37.0	41.0	30.0	41.0
47	37.1495	40.0	37.0	41.0	30.0	41.0
48	37.1165	40.0	37.0	41.0	29.0	41.0
49	37.16	40.0	37.0	41.0	29.0	41.0
50	37.20725	40.0	37.0	41.0	29.0	41.0
51	35.9995	39.0	35.0	40.0	28.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1105	1	0.0
1105	2	0.0
1105	3	0.0
1105	4	0.0
1105	5	0.0
1105	6	0.0
1105	7	0.0
1105	8	0.0
1105	9	0.0
1105	10	0.0
1105	11	0.0
1105	12	0.0
1105	13	0.0
1105	14	0.0
1105	15	0.0
1105	16	0.0
1105	17	0.0
1105	18	0.0
1105	19	0.0
1105	20	0.0
1105	21	0.0
1105	22	0.0
1105	23	0.0
1105	24	0.0
1105	25	0.0
1105	26	0.0
1105	27	0.0
1105	28	0.0
1105	29	0.0
1105	30	0.0
1105	31	0.0
1105	32	0.0
1105	33	0.0
1105	34	0.0
1105	35	0.0
1105	36	0.0
1105	37	0.0
1105	38	0.0
1105	39	0.0
1105	40	0.0
1105	41	0.0
1105	42	0.0
1105	43	0.0
1105	44	0.0
1105	45	0.0
1105	46	0.0
1105	47	0.0
1105	48	0.0
1105	49	0.0
1105	50	0.0
1105	51	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
9	2.0
10	3.0
11	3.0
12	5.0
13	13.0
14	13.0
15	10.0
16	11.0
17	13.0
18	15.0
19	19.0
20	14.0
21	16.0
22	16.0
23	18.0
24	23.0
25	26.0
26	30.0
27	34.0
28	40.0
29	43.0
30	44.0
31	45.0
32	70.0
33	84.0
34	104.0
35	145.0
36	202.0
37	344.0
38	675.0
39	1905.0
40	15.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	14.76891298734831	17.789827007487734	25.380841724761165	42.060418280402786
2	31.474999999999998	12.925	14.575	41.025
3	50.849999999999994	10.05	12.950000000000001	26.150000000000002
4	52.275000000000006	15.1	10.75	21.875
5	33.725	18.125	15.2	32.95
6	29.225	9.55	25.374999999999996	35.85
7	29.075	8.975	32.675	29.275000000000002
8	41.525	13.375	25.650000000000002	19.45
9	48.575	13.65	23.225	14.549999999999999
10	40.050000000000004	28.7	16.125	15.125
11	30.725	36.05	18.85	14.374999999999998
12	23.375	27.950000000000003	38.375	10.299999999999999
13	18.975	21.375	42.725	16.925
14	15.174999999999999	17.724999999999998	36.875	30.225
15	15.55	19.925	40.775	23.75
16	19.400000000000002	13.525	34.175	32.9
17	34.849999999999994	11.55	28.999999999999996	24.6
18	44.275	13.125	18.975	23.625
19	46.725	12.25	21.75	19.275000000000002
20	40.275	8.475000000000001	33.525	17.724999999999998
21	43.475	8.0	26.8	21.725
22	32.85	8.3	25.85	33.0
23	32.5	12.950000000000001	17.974999999999998	36.575
24	27.700000000000003	27.625	13.900000000000002	30.775000000000002
25	26.650000000000002	38.95	13.25	21.15
26	39.675	32.95	10.65	16.725
27	43.925	25.874999999999996	14.875	15.325
28	33.525	37.05	16.45	12.975
29	27.875	40.125	10.075000000000001	21.925
30	19.675	30.825000000000003	20.275000000000002	29.225
31	18.05	23.175	24.425	34.35
32	21.425	21.375	18.05	39.15
33	20.575	23.025000000000002	14.45	41.949999999999996
34	26.5	30.675	12.025	30.8
35	29.7	25.224999999999998	20.849999999999998	24.224999999999998
36	27.3	21.325	27.525	23.849999999999998
37	19.025	22.15	19.45	39.375
38	13.975000000000001	30.85	16.425	38.75
39	18.25	29.349999999999998	13.875000000000002	38.525
40	27.575	31.125000000000004	10.75	30.55
41	27.0	31.324999999999996	15.65	26.025
42	24.5	26.25	24.025	25.224999999999998
43	16.7	31.075000000000003	20.025000000000002	32.2
44	17.849999999999998	38.025	17.0	27.125
45	28.875	30.625000000000004	12.0	28.499999999999996
46	21.625	38.25	20.625	19.5
47	17.474999999999998	29.65	25.45	27.425
48	15.15	23.75	25.25	35.85
49	13.625000000000002	24.875	32.074999999999996	29.425
50	21.45	16.525000000000002	25.25	36.775000000000006
51	25.6	15.55	29.025000000000002	29.825000000000003
>>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	0.0
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	0.5
33	1.0
34	2.5
35	4.0
36	5.5
37	7.0
38	8.0
39	9.0
40	19.0
41	29.0
42	33.5
43	38.0
44	41.0
45	44.0
46	61.0
47	78.0
48	96.5
49	115.0
50	164.5
51	214.0
52	379.0
53	544.0
54	694.0
55	844.0
56	992.5
57	1141.0
58	854.5
59	568.0
60	385.0
61	202.0
62	148.5
63	95.0
64	64.5
65	34.0
66	24.0
67	14.0
68	12.5
69	11.0
70	7.5
71	4.0
72	3.0
73	2.0
74	2.0
75	1.0
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	3.175
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
51	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
51	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	60.925
#Duplication Level	Percentage of deduplicated	Percentage of total
1	84.73533032416906	51.625
2	7.714402954452196	9.4
3	2.5441116126384897	4.65
4	1.5592942141977841	3.8
5	0.943783340172343	2.875
6	0.4924086992203529	1.7999999999999998
7	0.28723840787853916	1.225
8	0.28723840787853916	1.4000000000000001
9	0.2051702913418137	1.125
>10	1.0258514567090684	13.325000000000001
>50	0.16413623307345096	5.4
>100	0.04103405826836274	3.375
>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
TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	135	3.375	RNA PCR Primer, Index 1 (100% over 30bp)
GGGATGGGTCGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATC	58	1.4500000000000002	RNA PCR Primer, Index 9 (100% over 37bp)
CCGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	54	1.35	RNA PCR Primer, Index 9 (100% over 45bp)
CGGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	52	1.3	RNA PCR Primer, Index 9 (100% over 45bp)
CGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	52	1.3	RNA PCR Primer, Index 9 (100% over 45bp)
TCGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	48	1.2	RNA PCR Primer, Index 9 (100% over 45bp)
CGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGT	44	1.0999999999999999	RNA PCR Primer, Index 9 (100% over 46bp)
CCGGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	39	0.975	RNA PCR Primer, Index 9 (100% over 45bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCC	38	0.95	RNA PCR Primer, Index 9 (100% over 51bp)
TCGGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	32	0.8	RNA PCR Primer, Index 9 (100% over 45bp)
CGGACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	29	0.7250000000000001	RNA PCR Primer, Index 9 (100% over 45bp)
CCGGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	28	0.7000000000000001	RNA PCR Primer, Index 9 (100% over 44bp)
TCGGACCAGGCTTCATCCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	27	0.675	RNA PCR Primer, Index 1 (100% over 30bp)
CCCGGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	23	0.575	RNA PCR Primer, Index 9 (100% over 44bp)
CGGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGT	22	0.5499999999999999	RNA PCR Primer, Index 9 (100% over 46bp)
GGATGGGTCGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCA	22	0.5499999999999999	RNA PCR Primer, Index 9 (100% over 38bp)
CGGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGT	18	0.44999999999999996	RNA PCR Primer, Index 9 (100% over 46bp)
CCGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	18	0.44999999999999996	RNA PCR Primer, Index 9 (100% over 44bp)
ACGGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	16	0.4	RNA PCR Primer, Index 9 (100% over 44bp)
TTGGTCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	15	0.375	RNA PCR Primer, Index 9 (100% over 45bp)
CCCGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	14	0.35000000000000003	RNA PCR Primer, Index 9 (100% over 44bp)
GCGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	13	0.325	RNA PCR Primer, Index 9 (100% over 45bp)
ACCGGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	12	0.3	RNA PCR Primer, Index 9 (100% over 44bp)
CCCGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	12	0.3	RNA PCR Primer, Index 9 (100% over 45bp)
TCCGGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	11	0.27499999999999997	RNA PCR Primer, Index 9 (100% over 44bp)
CCGGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	11	0.27499999999999997	RNA PCR Primer, Index 9 (100% over 45bp)
CGGGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	11	0.27499999999999997	RNA PCR Primer, Index 9 (100% over 44bp)
CCGGGCCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCT	10	0.25	RNA PCR Primer, Index 9 (100% over 43bp)
ACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	10	0.25	RNA PCR Primer, Index 1 (100% over 31bp)
CGGGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCT	10	0.25	RNA PCR Primer, Index 9 (100% over 43bp)
CCGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGT	9	0.22499999999999998	RNA PCR Primer, Index 9 (100% over 46bp)
AGGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGT	9	0.22499999999999998	RNA PCR Primer, Index 9 (100% over 46bp)
CGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTA	9	0.22499999999999998	RNA PCR Primer, Index 9 (100% over 47bp)
ACCGGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCT	9	0.22499999999999998	RNA PCR Primer, Index 9 (100% over 43bp)
CGGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	9	0.22499999999999998	RNA PCR Primer, Index 9 (100% over 45bp)
CTGGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	8	0.2	RNA PCR Primer, Index 9 (100% over 45bp)
CGTGGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCT	8	0.2	RNA PCR Primer, Index 9 (100% over 43bp)
CGGGTCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	8	0.2	RNA PCR Primer, Index 9 (100% over 45bp)
CCGGGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCT	8	0.2	RNA PCR Primer, Index 9 (100% over 43bp)
TAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	8	0.2	RNA PCR Primer, Index 9 (100% over 44bp)
AGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	8	0.2	RNA PCR Primer, Index 1 (100% over 33bp)
TGGCGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	7	0.17500000000000002	RNA PCR Primer, Index 9 (100% over 44bp)
AATCCGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGAT	7	0.17500000000000002	RNA PCR Primer, Index 9 (100% over 41bp)
ACGGACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	7	0.17500000000000002	RNA PCR Primer, Index 9 (100% over 44bp)
TTCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACGGACTGGGAATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAG	7	0.17500000000000002	RNA PCR Primer, Index 9 (100% over 39bp)
CGGTGGCGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGA	7	0.17500000000000002	RNA PCR Primer, Index 9 (100% over 40bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATC	7	0.17500000000000002	RNA PCR Primer, Index 9 (100% over 37bp)
CTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	6	0.15	RNA PCR Primer, Index 9 (100% over 44bp)
CCCGGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCT	6	0.15	RNA PCR Primer, Index 9 (100% over 43bp)
CCGGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	6	0.15	RNA PCR Primer, Index 9 (100% over 44bp)
AGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	6	0.15	RNA PCR Primer, Index 9 (100% over 45bp)
TCCCAAATGTAGACAAAGCATGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
GCTGGGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATC	6	0.15	RNA PCR Primer, Index 9 (100% over 42bp)
CTCGGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	6	0.15	RNA PCR Primer, Index 9 (100% over 44bp)
GCGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGT	6	0.15	RNA PCR Primer, Index 9 (100% over 46bp)
TTGGCCGGGTCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGA	6	0.15	RNA PCR Primer, Index 9 (100% over 40bp)
TCGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGT	6	0.15	RNA PCR Primer, Index 9 (100% over 46bp)
CGACGGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATC	6	0.15	RNA PCR Primer, Index 9 (100% over 42bp)
CGGACCGGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGAT	6	0.15	RNA PCR Primer, Index 9 (100% over 41bp)
CCGGGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATC	5	0.125	RNA PCR Primer, Index 9 (100% over 42bp)
AGCCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	5	0.125	RNA PCR Primer, Index 9 (100% over 45bp)
AACGGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	5	0.125	RNA PCR Primer, Index 9 (100% over 44bp)
CCCCGTCGTGCCCGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATC	5	0.125	RNA PCR Primer, Index 9 (100% over 37bp)
CCGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	5	0.125	RNA PCR Primer, Index 9 (100% over 45bp)
TGGCCGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	5	0.125	RNA PCR Primer, Index 9 (100% over 45bp)
TCCCCGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCT	5	0.125	RNA PCR Primer, Index 9 (100% over 43bp)
TGCCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	5	0.125	RNA PCR Primer, Index 9 (100% over 45bp)
CGCGACCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCT	5	0.125	RNA PCR Primer, Index 9 (100% over 43bp)
AGCGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	5	0.125	RNA PCR Primer, Index 9 (100% over 44bp)
TGGCCTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCT	5	0.125	RNA PCR Primer, Index 9 (100% over 43bp)
CGCGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCG	5	0.125	RNA PCR Primer, Index 9 (100% over 45bp)
CGCGGCGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	5	0.125	RNA PCR Primer, Index 9 (100% over 44bp)
CACGGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCT	5	0.125	RNA PCR Primer, Index 9 (100% over 43bp)
TGCCGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCT	5	0.125	RNA PCR Primer, Index 9 (100% over 43bp)
ATCCGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATC	5	0.125	RNA PCR Primer, Index 9 (100% over 42bp)
GGGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGT	5	0.125	RNA PCR Primer, Index 9 (100% over 46bp)
CGCGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCT	5	0.125	RNA PCR Primer, Index 9 (100% over 43bp)
CCGGATCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATC	5	0.125	RNA PCR Primer, Index 9 (100% over 42bp)
TCGGCCGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTC	5	0.125	RNA PCR Primer, Index 9 (100% over 44bp)
CTCGCGTTGACTACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAT	5	0.125	RNA PCR Primer, Index 9 (100% over 36bp)
CCTGGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCT	5	0.125	RNA PCR Primer, Index 9 (100% over 43bp)
TTCCCGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCT	5	0.125	RNA PCR Primer, Index 9 (100% over 43bp)
>>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	1.05	0.0	0.0	0.0
2	0.0	1.05	0.0	0.0	0.0
3	0.0	1.075	0.0	0.0	0.0
4	0.0	1.15	0.0	0.0	0.0
5	0.0	1.75	0.0	0.0	0.0
6	0.0	7.0	0.0	0.0	0.0
7	0.0	23.0	0.0	0.0	0.0
8	0.0	34.6	0.0	0.0	0.0
9	0.0	43.275	0.0	0.0	0.0
10	0.0	48.625	0.0	0.0	0.0
11	0.0	52.95	0.0	0.0	0.0
12	0.0	56.825	0.0	0.0	0.0
13	0.0	59.825	0.0	0.0	0.0
14	0.0	62.65	0.0	0.0	0.0
15	0.0	66.55	0.0	0.0	0.0
16	0.0	68.6	0.0	0.0	0.0
17	0.0	70.45	0.0	0.0	0.0
18	0.0	71.875	0.0	0.0	0.0
19	0.0	73.1	0.0	0.0	0.0
20	0.0	74.55	0.0	0.0	0.0
21	0.0	75.875	0.0	0.0	0.0
22	0.0	82.025	0.0	0.0	0.0
23	0.0	83.75	0.0	0.0	0.0
24	0.0	84.575	0.0	0.0	0.0
25	0.0	85.5	0.0	0.0	0.0
26	0.0	86.575	0.0	0.0	0.0
27	0.0	87.175	0.0	0.0	0.0
28	0.0	87.825	0.0	0.0	0.0
29	0.0	88.55	0.0	0.0	0.0
30	0.0	89.7	0.0	0.0	0.0
31	0.0	90.7	0.0	0.0	0.0
32	0.0	91.6	0.0	0.0	0.0
33	0.0	92.225	0.0	0.0	0.0
34	0.0	92.875	0.0	0.0	0.0
35	0.0	93.575	0.0	0.0	0.0
36	0.0	94.25	0.0	0.0	0.0
37	0.0	94.7	0.0	0.0	0.0
38	0.0	94.9	0.0	0.0	0.0
39	0.0	95.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TCGGACC	40	3.4560799E-9	46.128204	1
CTTCATT	35	8.606912E-8	44.975002	11
TTCATTC	35	8.606912E-8	44.975002	12
GGACCAG	40	4.3783075E-9	44.975002	3
CATTCCC	35	8.606912E-8	44.975002	14
CGGACCA	40	4.3783075E-9	44.975002	2
TTCCCCT	35	8.606912E-8	44.975002	16
GGCTCTG	20	6.2400557E-4	44.975002	3
AGGCTTC	40	4.3783075E-9	44.975002	8
GGCTTCA	40	4.3783075E-9	44.975002	9
CAGGCTT	40	4.3783075E-9	44.975002	7
CCCCTGG	40	4.3783075E-9	44.975002	18
GCTCTGG	20	6.2400557E-4	44.975002	4
ATTCCCC	35	8.606912E-8	44.975002	15
TCATTCC	35	8.606912E-8	44.975002	13
GCTTCAT	40	4.3783075E-9	44.975002	10
GACCAGG	40	4.3783075E-9	44.975002	4
CCAGGCT	40	4.3783075E-9	44.975002	6
TCCCCTG	35	8.606912E-8	44.975002	17
ACCAGGC	40	4.3783075E-9	44.975002	5
>>END_MODULE
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SRR ids: ['SRR8404467.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_tcgy90p1
SRR8404467.sra spots: 36946117
blocks: [[1, 577283], [577284, 1154566], [1154567, 1731849], [1731850, 2309132], [2309133, 2886415], [2886416, 3463698], [3463699, 4040981], [4040982, 4618264], [4618265, 5195547], [5195548, 5772830], [5772831, 6350113], [6350114, 6927396], [6927397, 7504679], [7504680, 8081962], [8081963, 8659245], [8659246, 9236528], [9236529, 9813811], [9813812, 10391094], [10391095, 10968377], [10968378, 11545660], [11545661, 12122943], [12122944, 12700226], [12700227, 13277509], [13277510, 13854792], [13854793, 14432075], [14432076, 15009358], [15009359, 15586641], [15586642, 16163924], [16163925, 16741207], [16741208, 17318490], [17318491, 17895773], [17895774, 18473056], [18473057, 19050339], [19050340, 19627622], [19627623, 20204905], [20204906, 20782188], [20782189, 21359471], [21359472, 21936754], [21936755, 22514037], [22514038, 23091320], [23091321, 23668603], [23668604, 24245886], [24245887, 24823169], [24823170, 25400452], [25400453, 25977735], [25977736, 26555018], [26555019, 27132301], [27132302, 27709584], [27709585, 28286867], [28286868, 28864150], [28864151, 29441433], [29441434, 30018716], [30018717, 30595999], [30596000, 31173282], [31173283, 31750565], [31750566, 32327848], [32327849, 32905131], [32905132, 33482414], [33482415, 34059697], [34059698, 34636980], [34636981, 35214263], [35214264, 35791546], [35791547, 36368829], [36368830, 36946117]]
SRR8404467 file size 5955888
SRR8404467 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 64 -o SRR8404467 SRR8404467_1.fastq
Input file:	SRR8404467_1.fastq
trimmed:	SRR8404467-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):	32
Mon Feb  3 21:27:56 2020 >> started

Mon Feb  3 21:28:26 2020 >> done (29.961s)
36946117 reads processed; of these:
     164 ( 0.00%) short reads filtered out after trimming by size control
       0 ( 0.00%) empty reads filtered out after trimming by size control
36945953 (100.00%) reads available; of these:
  604052 ( 1.63%) trimmed reads available after processing
36341901 (98.37%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	       1	  0.00%
 19	       2	  0.00%
 20	       8	  0.00%
 21	       7	  0.00%
 22	      45	  0.00%
 23	       6	  0.00%
 24	      13	  0.00%
 25	       7	  0.00%
 26	      17	  0.00%
 27	      12	  0.00%
 28	      11	  0.00%
 29	      23	  0.00%
 30	      22	  0.00%
 31	      38	  0.00%
 32	      74	  0.00%
 33	     125	  0.00%
 34	     106	  0.00%
 35	     116	  0.00%
 36	     171	  0.00%
 37	     254	  0.00%
 38	     352	  0.00%
 39	     534	  0.00%
 40	     795	  0.00%
 41	    1261	  0.00%
 42	    1565	  0.00%
 43	    2340	  0.01%
 44	    3749	  0.01%
 45	    5669	  0.02%
 46	   10751	  0.03%
 47	   18542	  0.05%
 48	   44738	  0.12%
 49	  102948	  0.28%
 50	  409750	  1.11%
 51	36341901	 98.37%
36945953 reads passed initial QC


criterion=sequence-density
sequence-density=94.59
sequence-density-rank=1
fanout-score=18.60
fanout-score-rank=4
prefix-density=94.52
prefix-fanout=18.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTGAAAAA


criterion=fanout-score
sequence-density=1.52
sequence-density-rank=5
fanout-score=176.25
fanout-score-rank=1
prefix-density=94.32
prefix-fanout=2.8
sequence=GAATTCTCGGGGGCCAAGGAACT
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 64 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTGAAAAA -o SRR8404467 -
Input file:	STDIN
trimmed:	SRR8404467-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTGA
-- 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):	32
Mon Feb  3 21:29:38 2020 >> started

Mon Feb  3 21:30:28 2020 >> done (50.401s)
36168144 reads processed; of these:
25421023 (70.29%) short reads filtered out after trimming by size control
  353803 ( 0.98%) empty reads filtered out after trimming by size control
10393318 (28.74%) reads available; of these:
 8697326 (83.68%) trimmed reads available after processing
 1695992 (16.32%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  490466	  4.72%
 19	  455105	  4.38%
 20	  502091	  4.83%
 21	 2160396	 20.79%
 22	  495940	  4.77%
 23	  385721	  3.71%
 24	  358928	  3.45%
 25	  337789	  3.25%
 26	  334552	  3.22%
 27	  323248	  3.11%
 28	  346392	  3.33%
 29	  359151	  3.46%
 30	  332945	  3.20%
 31	  379855	  3.65%
 32	  348725	  3.36%
 33	  300283	  2.89%
 34	  234769	  2.26%
 35	  192765	  1.85%
 36	  122682	  1.18%
 37	   56655	  0.55%
 38	   32889	  0.32%
 39	   26509	  0.26%
 40	   21130	  0.20%
 41	   17970	  0.17%
 42	   16082	  0.15%
 43	   12911	  0.12%
 44	   11529	  0.11%
 45	   11256	  0.11%
 46	   12243	  0.12%
 47	   16931	  0.16%
 48	   43313	  0.42%
 49	   27226	  0.26%
 50	   51617	  0.50%
 51	 1573254	 15.14%


criterion=sequence-density
sequence-density=2.84
sequence-density-rank=1
fanout-score=5.40
fanout-score-rank=6
prefix-density=15.24
prefix-fanout=1.0
sequence=CCAGGCTTCATCCCCCTGGAATT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=33
fanout-score=30.13
fanout-score-rank=1
prefix-density=0.08
prefix-fanout=2.2
sequence=ACCATAAACGATGCCGACCAGGGATCAGCGGATGTTGCTTATAGGACTCCGCTGGCACCTTATGAGAAATCAAAGT
                                 Started job on |	Feb 03 21:31:13
                             Started mapping on |	Feb 03 21:31:14
                                    Finished on |	Feb 03 21:32:00
       Mapping speed, Million of reads per hour |	874.26

                          Number of input reads |	11171127
                      Average input read length |	30
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1961397
                        Uniquely mapped reads % |	17.56%
                          Average mapped length |	26.05
                       Number of splices: Total |	21733
            Number of splices: Annotated (sjdb) |	9733
                       Number of splices: GT/AG |	21076
                       Number of splices: GC/AG |	195
                       Number of splices: AT/AC |	27
               Number of splices: Non-canonical |	435
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.31
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	6376721
             % of reads mapped to multiple loci |	57.08%
        Number of reads mapped to too many loci |	213882
             % of reads mapped to too many loci |	1.91%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	22.75%
                     % of reads unmapped: other |	0.70%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2833009	2833009	2833009
N_multimapping	6376721	6376721	6376721
N_noFeature	1108376	1207534	1824118
N_ambiguous	77427	39212	1344
UnstrandedReadsAssigned:775594 PositiveStrandReadsAssigned:714651 NegativeStrandReadsAssigned:135935
Dataset is classified positive stranded
MeadianReadLen=26 20thPercentileLength=21 echo kmer=19
SRR8404467 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: 48,359
[index] number of k-mers: 44,957,248
[index] number of equivalence classes: 195,259
[quant] running in single-end mode
[quant] will process file 1: SRR8404467-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 11,171,127 reads, 330,006 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,004 rounds

  48360 SRR8404467.ke.tsv
  32833 SRR8404467.se.tsv
  81193 total
==> SRR8404467.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
AT1G19090.1	2509	2410	127	89.7024
AT1G18320.1	699	600	0.93617	2.65596
AT5G11100.1	1709	1610	0	0
AT4G35335.1	1280	1181	4	5.76538
AT1G60930.1	3876	3777	0	0
AT1G17000.1	2351	2252	1	0.755874
AT3G55270.1	3130	3031	7	3.93124
AT4G16150.1	3181	3082	19.7531	10.9099
AT3G18150.1	1370	1271	0	0

==> SRR8404467.se.tsv <==
AT1G01010	5
AT1G01020	0
AT1G03987	0
AT1G01030	1
AT1G01040	11
AT1G03993	0
AT1G01046	5
AT1G01050	11
AT1G03997	0
AT1G01060	1
SRR8404467 completed mapping pipeline successfully
