Starting /dee2/code/volunteer_pipeline.sh SRR9060559
    current disk space = 841331792
    free memory = 121962728 
SRR9060559 SRAfilesize
059d20c03e6ff5e73c262fca69ccfa1f  SRR9060559.sra
SRR9060559.sra file validated
SRR9060559 is single end
SRR9060559 is conventional basespace
SRR9060559 read1 length is 49-51 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR9060559_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	49-51
%GC	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.22125	32.0	32.0	32.0	32.0	32.0
2	31.5195	32.0	32.0	32.0	32.0	32.0
3	31.7155	32.0	32.0	32.0	32.0	32.0
4	31.7825	32.0	32.0	32.0	32.0	32.0
5	31.7515	32.0	32.0	32.0	32.0	32.0
6	34.747	36.0	36.0	36.0	36.0	36.0
7	35.30275	36.0	36.0	36.0	36.0	36.0
8	35.2935	36.0	36.0	36.0	36.0	36.0
9	35.39475	36.0	36.0	36.0	36.0	36.0
10	35.424	36.0	36.0	36.0	36.0	36.0
11	35.38675	36.0	36.0	36.0	36.0	36.0
12	35.4135	36.0	36.0	36.0	36.0	36.0
13	35.45575	36.0	36.0	36.0	36.0	36.0
14	35.427	36.0	36.0	36.0	36.0	36.0
15	35.48	36.0	36.0	36.0	36.0	36.0
16	35.426	36.0	36.0	36.0	36.0	36.0
17	35.49	36.0	36.0	36.0	36.0	36.0
18	35.4285	36.0	36.0	36.0	36.0	36.0
19	35.2835	36.0	36.0	36.0	36.0	36.0
20	35.41925	36.0	36.0	36.0	36.0	36.0
21	35.4475	36.0	36.0	36.0	36.0	36.0
22	35.4085	36.0	36.0	36.0	36.0	36.0
23	35.4255	36.0	36.0	36.0	36.0	36.0
24	35.42825	36.0	36.0	36.0	36.0	36.0
25	35.34075	36.0	36.0	36.0	36.0	36.0
26	35.39175	36.0	36.0	36.0	36.0	36.0
27	35.40925	36.0	36.0	36.0	36.0	36.0
28	35.48775	36.0	36.0	36.0	36.0	36.0
29	35.3605	36.0	36.0	36.0	36.0	36.0
30	35.34225	36.0	36.0	36.0	36.0	36.0
31	35.51	36.0	36.0	36.0	36.0	36.0
32	35.3295	36.0	36.0	36.0	36.0	36.0
33	35.37725	36.0	36.0	36.0	36.0	36.0
34	35.33	36.0	36.0	36.0	36.0	36.0
35	35.3115	36.0	36.0	36.0	36.0	36.0
36	35.2915	36.0	36.0	36.0	36.0	36.0
37	35.30125	36.0	36.0	36.0	36.0	36.0
38	35.28925	36.0	36.0	36.0	36.0	36.0
39	35.1445	36.0	36.0	36.0	36.0	36.0
40	35.08225	36.0	36.0	36.0	36.0	36.0
41	35.0645	36.0	36.0	36.0	36.0	36.0
42	34.99525	36.0	36.0	36.0	36.0	36.0
43	35.1215	36.0	36.0	36.0	36.0	36.0
44	35.235	36.0	36.0	36.0	36.0	36.0
45	35.06	36.0	36.0	36.0	36.0	36.0
46	35.16025	36.0	36.0	36.0	36.0	36.0
47	35.08575	36.0	36.0	36.0	36.0	36.0
48	35.0455	36.0	36.0	36.0	36.0	36.0
49	34.8755	36.0	36.0	36.0	36.0	36.0
50	35.03007315090761	36.0	36.0	36.0	36.0	36.0
51	34.81669535283993	36.0	36.0	36.0	36.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
24	3.0
25	6.0
26	10.0
27	23.0
28	25.0
29	43.0
30	57.0
31	62.0
32	107.0
33	175.0
34	455.0
35	3034.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	19.650000000000002	35.425000000000004	15.049999999999999	29.875
2	15.825	32.175	36.1	15.9
3	24.0	15.55	42.125	18.325
4	34.0	16.75	27.400000000000002	21.85
5	51.87500000000001	18.9	15.525	13.700000000000001
6	24.471606824548	18.94576012223071	44.63967405143875	11.942959001782532
7	30.625000000000004	18.224999999999998	19.475	31.674999999999997
8	27.025	27.474999999999998	18.625	26.875
9	24.775	32.475	30.599999999999998	12.15
10	36.05	16.375	30.275000000000002	17.299999999999997
11	48.525	16.325	19.2	15.950000000000001
12	15.625	15.775	45.75	22.85
13	35.875	17.525	29.425	17.175
14	17.45	18.75	48.65	15.15
15	30.55	13.450000000000001	38.4	17.599999999999998
16	40.575	15.825	20.150000000000002	23.45
17	30.95	16.1	34.725	18.224999999999998
18	33.0	28.825	22.375	15.8
19	22.650000000000002	28.249999999999996	35.325	13.775
20	26.375	16.775000000000002	30.725	26.125
21	32.0	17.1	22.325	28.575
22	22.125	32.375	20.849999999999998	24.65
23	33.050000000000004	18.099999999999998	30.825000000000003	18.025
24	16.925	15.325	47.449999999999996	20.3
25	19.025	33.825	28.225	18.925
26	33.925	17.299999999999997	19.25	29.525000000000002
27	23.7	30.475	32.475	13.350000000000001
28	50.875	18.925	17.4	12.8
29	35.35	21.65	14.099999999999998	28.9
30	20.150000000000002	36.0	30.0	13.850000000000001
31	41.85	19.375	24.125	14.649999999999999
32	20.325	16.55	52.55	10.575
33	22.975	15.65	31.95	29.425
34	31.05	20.3	21.075	27.575
35	34.4	18.075	36.95	10.575
36	24.525	26.650000000000002	36.875	11.95
37	33.6	28.249999999999996	28.225	9.925
38	34.875	20.925	33.15	11.05
39	22.650000000000002	29.825000000000003	33.074999999999996	14.45
40	14.549999999999999	29.25	30.775000000000002	25.424999999999997
41	17.875	15.55	45.5	21.075
42	19.55	6.375	39.7	34.375
43	32.45	4.15	29.5	33.900000000000006
44	39.900000000000006	7.675	27.675	24.75
45	44.2	9.225	18.95	27.625
46	48.199999999999996	8.924999999999999	22.35	20.525
47	57.375	12.9	12.375	17.349999999999998
48	42.925000000000004	16.825000000000003	12.950000000000001	27.3
49	30.25	19.950000000000003	19.45	30.349999999999998
50	33.324302357084804	23.54375507992414	13.979951232728258	29.1519913302628
51	27.925989672977625	0.0	16.00688468158348	56.0671256454389
>>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	0.5
12	1.0
13	1.0
14	1.0
15	0.5
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.5
22	1.0
23	0.5
24	0.0
25	0.0
26	0.5
27	1.5
28	1.5
29	1.0
30	1.0
31	1.5
32	3.5
33	5.0
34	6.0
35	7.0
36	12.0
37	17.5
38	22.5
39	29.0
40	37.5
41	58.0
42	82.0
43	95.5
44	189.5
45	294.0
46	389.5
47	481.5
48	510.5
49	566.0
50	536.5
51	446.5
52	477.5
53	729.0
54	889.0
55	667.0
56	410.0
57	319.0
58	244.5
59	160.0
60	114.0
61	82.0
62	48.0
63	23.0
64	12.5
65	7.0
66	5.5
67	4.0
68	2.0
69	1.0
70	0.5
71	0.0
72	0.0
73	0.0
74	0.0
75	0.0
76	0.0
77	0.0
78	0.0
79	0.0
80	0.0
81	0.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.5
94	1.0
95	0.5
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	0.0
3	0.0
4	0.0
5	0.0
6	1.825
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	warn
#Length	Count
49	309.0
50	1367.0
51	2324.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	53.15
#Duplication Level	Percentage of deduplicated	Percentage of total
1	92.23894637817497	49.025
2	3.3866415804327374	3.5999999999999996
3	1.0818438381937912	1.725
4	0.8466603951081844	1.7999999999999998
5	0.658513640639699	1.7500000000000002
6	0.047036688617121354	0.15
7	0.23518344308560676	0.8750000000000001
8	0.09407337723424271	0.4
9	0.14111006585136407	0.675
>10	0.9877704609595485	14.625
>50	0.09407337723424271	4.25
>100	0.18814675446848542	21.125
>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
GATTGTGCTTGCTTGCGGACGCTTTCTGGTGTTGGAATTCTCGGGTGCCA	322	8.05	No Hit
CTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCCTTGGAATTCTCGGGTGC	237	5.925	No Hit
CTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCCTTTGGAATTCTCGGGTG	179	4.475	No Hit
AAGAGAAGGTGTCTTGCTGGCGGTAGTGGAATTCTCGGGTGCCAAGGAACT	107	2.675	RNA PCR Primer, Index 1 (100% over 25bp)
ATACTGCGATCTGTTGAGACTATCCTTTGATTGAGTGGAATTCTCGGGTGC	97	2.4250000000000003	No Hit
CTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCCTGGAATTCTCGGGTGCC	73	1.825	No Hit
CCTCCAGTTGGTACGTCTGGTTCAGGGTTGTTTTGGAATTCTCGGGTGCC	49	1.225	No Hit
AACTGTGGTCGTGACTTCTAATTTGCTGGTTTGGAATTCTCGGGTGCCA	46	1.15	No Hit
TTGCGGACGCTTTCTGGTGTGTGCTTGGACCTTGGAATTCTCGGGTGCCA	46	1.15	No Hit
AGTGATTGTGCTTGCTTGCGGACGCTTTCTGGTGTTGGAATTCTCGGGTGC	37	0.9249999999999999	No Hit
CGGGGTGCAATTATTAGAACAGACCAAACTGGAATTCTCGGGTGCCAAGG	36	0.8999999999999999	Illumina Small RNA Adapter 2 (100% over 21bp)
TTGCGGACGCTTTCTGGTGTGTGCTTGGACCTCTGGAATTCTCGGGTGCC	36	0.8999999999999999	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC	35	0.8750000000000001	RNA PCR Primer, Index 8 (100% over 51bp)
GATTGTGCTTGCTTGCGGACGCTTTCTGGTGTGGAATTCTCGGGTGCCA	34	0.8500000000000001	No Hit
CTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCCTTTTGGAATTCTCGGGT	28	0.7000000000000001	No Hit
GTGCTTGGACCTCGGTTCTAGTATCCTGATCGCTCTGGAATTCTCGGGTGC	27	0.675	No Hit
GGCCAGTTGGTTGATGCTTGTCCGGCGCAGTTCTGGAATTCTCGGGTGCC	26	0.65	No Hit
TGCGGACGCTTTCTGGTGTGTGCTTGGACCTTGGAATTCTCGGGTGCCA	26	0.65	No Hit
GATTGTGCTTGCTTGCGGACGCTTTCTGGTTGGAATTCTCGGGTGCCAAGG	26	0.65	Illumina Small RNA Adapter 2 (100% over 21bp)
TTGTGATCGTTGCCGGGTGTCGTTTCCTTGGAATTCTCGGGTGCCAAGGA	24	0.6	RNA PCR Primer, Index 1 (100% over 22bp)
AACTGTGGTCGTGACTTCTAATTTGCTGGTTTTGGAATTCTCGGGTGCCA	22	0.5499999999999999	No Hit
GGCCAGTTGGTTGATGCTTGTCCGGCGCAGTGGAATTCTCGGGTGCCAAGG	21	0.525	Illumina Small RNA Adapter 2 (100% over 21bp)
ATTGTGCTTGCTTGCGGACGCTTTCTGGTGTTGGAATTCTCGGGTGCCA	20	0.5	No Hit
TGCGGACGCTTTCTGGTGTGTGCTTGGACCTCTGGAATTCTCGGGTGCCA	13	0.325	No Hit
CTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCTGGAATTCTCGGGTGCC	12	0.3	No Hit
TGTGATCGTTGCCGGGTGTCGTTTCCTTGGAATTCTCGGGTGCCAAGGAAC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 24bp)
AACTGTGGTCGTGACTTCTAATTTGCTGGTGGAATTCTCGGGTGCCAAGG	10	0.25	Illumina Small RNA Adapter 2 (100% over 21bp)
GGCCAGTTGGTTGATGCTTGTCCGGCGCAGTTCTTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
TCTTGGTCAAGGTGTTGTATTCAGTAGAGCAGTCCTTGGAATTCTCGGGTG	9	0.22499999999999998	No Hit
CTTGGTCAAGGTGTTGTATTCAGTAGAGCTGGAATTCTCGGGTGCCAAGG	9	0.22499999999999998	Illumina Small RNA Adapter 2 (100% over 21bp)
CTTGGNCAAGGTGTTGTATTCAGTAGAGCAGTCCTTGGAATTCTCGGGTGC	8	0.2	No Hit
GGCCAGTTGGTTGATGCTTGTCCGGCGCAGTTTGGAATTCTCGGGTGCCA	8	0.2	No Hit
AACTGTGGTCGTGACTTCTAATTTGCTGGTTTGTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
GTGCTTGGACCTCGGTTCTAGTATCCTGATCGCTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
GCTTGCTTGCGGACGCTTTCTGGTGTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
CTCCGACTTCCCAAGGGTCGTCCTGGCGTGGAATTCTCGGGTGCCAAGGA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 22bp)
GATTGTGCTTGCTTGCGGACGCTTTCTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
AACTGTGGTCGTGACTTCTAATTTGCTGGTTGGAATTCTCGGGTGCCAAGG	6	0.15	Illumina Small RNA Adapter 2 (100% over 21bp)
GAGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTC	5	0.125	RNA PCR Primer, Index 8 (100% over 44bp)
AAGAGAAGGTGTCTTGCTGGCGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCTCAACCTGAACTCAGTCGTGATTACCCTGGAATTCTCGGGTGCCAAGG	5	0.125	Illumina Small RNA Adapter 2 (100% over 21bp)
ACTGCGATCTGTTGAGACTATCCTTTGATTGAGTGGAATTCTCGGGTGCC	5	0.125	No Hit
ATTGTGCTTGCTTGCGGACGCTTTCTGGTTGGAATTCTCGGGTGCCAAGG	5	0.125	Illumina Small RNA Adapter 2 (100% over 21bp)
TTGCGGACGCTTTCTGGTGTGTGCTTGGACCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TCTCAACCTGAACTCAGTCGTGATTACCCGTGGAATTCTCGGGTGCCAAGG	5	0.125	Illumina Small RNA Adapter 2 (100% over 21bp)
CAACTGTGGTCGTGACTTCTAATTTGCTGGTTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
AGGGAATCCGACTGTCTAATTAAAACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
CTGTGGTGTCTCGTGCTCTTTGAACTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GGTTGATGGCGGACTAGTGATTGTGCTTGCTGGAATTCTCGGGTGCCAAGG	5	0.125	Illumina Small RNA Adapter 2 (100% over 21bp)
CGGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGT	5	0.125	RNA PCR Primer, Index 8 (100% over 46bp)
TCAACTGTGGTCGTGACTTCTAATTTGCTGGTTTTGGAATTCTCGGGTGCC	5	0.125	No Hit
CCGGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCG	5	0.125	RNA PCR Primer, Index 8 (100% over 45bp)
>>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	0.975	0.0	0.0	0.0
2	0.0	0.975	0.0	0.0	0.0
3	0.0	0.975	0.0	0.0	0.0
4	0.0	0.975	0.0	0.0	0.0
5	0.0	1.05	0.0	0.0	0.0
6	0.0	1.6	0.0	0.0	0.0
7	0.0	2.625	0.0	0.0	0.0
8	0.0	4.275	0.0	0.0	0.0
9	0.0	4.875	0.0	0.0	0.0
10	0.0	5.35	0.0	0.0	0.0
11	0.0	5.55	0.0	0.0	0.0
12	0.0	5.75	0.0	0.0	0.0
13	0.0	5.925	0.0	0.0	0.0
14	0.0	6.025	0.0	0.0	0.0
15	0.0	6.125	0.0	0.0	0.0
16	0.0	6.225	0.0	0.0	0.0
17	0.0	6.5	0.0	0.0	0.0
18	0.0	6.7	0.0	0.0	0.0
19	0.0	6.85	0.0	0.0	0.0
20	0.0	7.1	0.0	0.0	0.0
21	0.0	7.325	0.0	0.0	0.0
22	0.0	7.5	0.0	0.0	0.0
23	0.0	7.8	0.0	0.0	0.0
24	0.0	7.975	0.0	0.0	0.0
25	0.0	8.725	0.0	0.0	0.0
26	0.0	9.725	0.0	0.0	0.0
27	0.0	14.15	0.0	0.0	0.0
28	0.0	15.95	0.0	0.0	0.0
29	0.0	18.45	0.0	0.0	0.0
30	0.0	22.875	0.0	0.0	0.0
31	0.0	27.6	0.0	0.0	0.0
32	0.0	34.8	0.0	0.0	0.0
33	0.0	50.9	0.0	0.0	0.0
34	0.0	60.225	0.0	0.0	0.0
35	0.0	68.975	0.0	0.0	0.0
36	0.0	85.15	0.0	0.0	0.0
37	0.0	94.05	0.0	0.0	0.0
38	0.0	97.125	0.0	0.0	0.0
39	0.0	97.825	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGGTCAA	30	1.6497997E-6	45.063293	3
TCAAGGT	30	1.6497997E-6	45.063293	6
GTCAAGG	30	1.6497997E-6	45.063293	5
GGTCAAG	30	1.6497997E-6	45.063293	4
CTTGGTC	30	1.6497997E-6	45.063293	1
TTGGTCA	30	1.6497997E-6	45.063293	2
GTAGAGC	30	1.8053379E-6	44.5	23
GTGTTGT	30	1.8053379E-6	44.5	11
CAGTCCT	30	1.8053379E-6	44.5	29
TTGTATT	30	1.8053379E-6	44.5	14
AGTAGAG	30	1.8053379E-6	44.5	22
CAGTAGA	30	1.8053379E-6	44.5	21
GTATTCA	30	1.8053379E-6	44.5	16
AGGTGTT	30	1.8053379E-6	44.5	9
AGCAGTC	30	1.8053379E-6	44.5	27
GAGCAGT	30	1.8053379E-6	44.5	26
TCAGTAG	30	1.8053379E-6	44.5	20
GCAGTCC	30	1.8053379E-6	44.5	28
AGAGCAG	30	1.8053379E-6	44.5	25
TATTCAG	30	1.8053379E-6	44.5	17
>>END_MODULE
Rejected 365082 READS because READLEN < 1
Read 365082 spots for SRR9060559.sra
Written 365082 spots for SRR9060559.sra
Rejected 365082 READS because READLEN < 1
Read 365082 spots for SRR9060559.sra
Written 365082 spots for SRR9060559.sra
Rejected 365082 READS because READLEN < 1
Read 365082 spots for SRR9060559.sra
Written 365082 spots for SRR9060559.sra
Rejected 365082 READS because READLEN < 1
Read 365082 spots for SRR9060559.sra
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SRR ids: ['SRR9060559.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_skvi4q75
SRR9060559.sra spots: 23365281
blocks: [[1, 365082], [365083, 730164], [730165, 1095246], [1095247, 1460328], [1460329, 1825410], [1825411, 2190492], [2190493, 2555574], [2555575, 2920656], [2920657, 3285738], [3285739, 3650820], [3650821, 4015902], [4015903, 4380984], [4380985, 4746066], [4746067, 5111148], [5111149, 5476230], [5476231, 5841312], [5841313, 6206394], [6206395, 6571476], [6571477, 6936558], [6936559, 7301640], [7301641, 7666722], [7666723, 8031804], [8031805, 8396886], [8396887, 8761968], [8761969, 9127050], [9127051, 9492132], [9492133, 9857214], [9857215, 10222296], [10222297, 10587378], [10587379, 10952460], [10952461, 11317542], [11317543, 11682624], [11682625, 12047706], [12047707, 12412788], [12412789, 12777870], [12777871, 13142952], [13142953, 13508034], [13508035, 13873116], [13873117, 14238198], [14238199, 14603280], [14603281, 14968362], [14968363, 15333444], [15333445, 15698526], [15698527, 16063608], [16063609, 16428690], [16428691, 16793772], [16793773, 17158854], [17158855, 17523936], [17523937, 17889018], [17889019, 18254100], [18254101, 18619182], [18619183, 18984264], [18984265, 19349346], [19349347, 19714428], [19714429, 20079510], [20079511, 20444592], [20444593, 20809674], [20809675, 21174756], [21174757, 21539838], [21539839, 21904920], [21904921, 22270002], [22270003, 22635084], [22635085, 23000166], [23000167, 23365281]]
SRR9060559 file size 3286536
SRR9060559 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 64 -o SRR9060559 SRR9060559_1.fastq
Input file:	SRR9060559_1.fastq
trimmed:	SRR9060559-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
Thu Feb 13 06:34:11 2020 >> started

Thu Feb 13 06:34:35 2020 >> done (24.065s)
23365281 reads processed; of these:
       0 ( 0.00%) short reads filtered out after trimming by size control
       0 ( 0.00%) empty reads filtered out after trimming by size control
23365281 (100.00%) reads available; of these:
     197 ( 0.00%) trimmed reads available after processing
23365084 (100.00%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 40	       2	  0.00%
 41	       4	  0.00%
 42	       2	  0.00%
 43	       1	  0.00%
 44	      10	  0.00%
 45	     132	  0.00%
 46	     142	  0.00%
 47	     202	  0.00%
 48	    2753	  0.01%
 49	 1762420	  7.54%
 50	 8313161	 35.58%
 51	13286452	 56.86%
23365281 reads passed initial QC


criterion=sequence-density
sequence-density=97.60
sequence-density-rank=1
fanout-score=21.89
fanout-score-rank=1
prefix-density=97.63
prefix-fanout=21.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCCG


criterion=fanout-score
sequence-density=97.60
sequence-density-rank=1
fanout-score=21.89
fanout-score-rank=1
prefix-density=97.63
prefix-fanout=21.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCCG
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCCG -o SRR9060559 -
Input file:	STDIN
trimmed:	SRR9060559-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCCG
-- 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
Thu Feb 13 06:35:30 2020 >> started

Thu Feb 13 06:36:07 2020 >> done (37.332s)
22888439 reads processed; of these:
 1343640 ( 5.87%) short reads filtered out after trimming by size control
  169872 ( 0.74%) empty reads filtered out after trimming by size control
21374927 (93.39%) reads available; of these:
21137674 (98.89%) trimmed reads available after processing
  237253 ( 1.11%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   52983	  0.25%
 19	   58294	  0.27%
 20	   66556	  0.31%
 21	   73413	  0.34%
 22	   73276	  0.34%
 23	   59975	  0.28%
 24	  154559	  0.72%
 25	  218660	  1.02%
 26	  909289	  4.25%
 27	  411182	  1.92%
 28	  564523	  2.64%
 29	  936349	  4.38%
 30	 1151764	  5.39%
 31	 1635083	  7.65%
 32	 3873337	 18.12%
 33	 2381253	 11.14%
 34	 1901170	  8.89%
 35	 3617416	 16.92%
 36	 2021511	  9.46%
 37	  662234	  3.10%
 38	  188458	  0.88%
 39	   53204	  0.25%
 40	   24330	  0.11%
 41	   22620	  0.11%
 42	    5339	  0.02%
 43	    6528	  0.03%
 44	    3908	  0.02%
 45	    2265	  0.01%
 46	    2321	  0.01%
 47	    2921	  0.01%
 48	    4356	  0.02%
 49	   15918	  0.07%
 50	   85946	  0.40%
 51	  133986	  0.63%


criterion=sequence-density
sequence-density=0.24
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=CTCCGACTTCCCAAGGGTCGTCCTGGCGTT


criterion=fanout-score
sequence-density=0.08
sequence-density-rank=10
fanout-score=23.57
fanout-score-rank=1
prefix-density=1.88
prefix-fanout=1.0
sequence=TTGCTGGTTTGCCC
                                 Started job on |	Feb 13 06:36:59
                             Started mapping on |	Feb 13 06:36:59
                                    Finished on |	Feb 13 06:38:10
       Mapping speed, Million of reads per hour |	1107.98

                          Number of input reads |	21851769
                      Average input read length |	32
                                    UNIQUE READS:
                   Uniquely mapped reads number |	14062915
                        Uniquely mapped reads % |	64.36%
                          Average mapped length |	31.82
                       Number of splices: Total |	729300
            Number of splices: Annotated (sjdb) |	716699
                       Number of splices: GT/AG |	722162
                       Number of splices: GC/AG |	3809
                       Number of splices: AT/AC |	91
               Number of splices: Non-canonical |	3238
                      Mismatch rate per base, % |	0.08%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.27
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	7001038
             % of reads mapped to multiple loci |	32.04%
        Number of reads mapped to too many loci |	378850
             % of reads mapped to too many loci |	1.73%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	1.87%
                     % of reads unmapped: other |	0.00%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	787816	787816	787816
N_multimapping	7001038	7001038	7001038
N_noFeature	40864	47128	13990446
N_ambiguous	79267	13521	149
UnstrandedReadsAssigned:13942784 PositiveStrandReadsAssigned:14002266 NegativeStrandReadsAssigned:72320
Dataset is classified positive stranded
MeadianReadLen=33 20thPercentileLength=30 echo kmer=25
SRR9060559 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=25

[quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20
[index] k-mer length: 25
[index] number of targets: 33,746
[index] number of k-mers: 28,932,940
[index] number of equivalence classes: 56,957
[quant] running in single-end mode
[quant] will process file 1: SRR9060559-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 21,851,769 reads, 7,946,923 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,294 rounds

  33747 SRR9060559.ke.tsv
  46739 SRR9060559.se.tsv
  80486 total
==> SRR9060559.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Y110A7A.10	1787	1688	256	16.9635
F27C8.1	1940	1841	25	1.51892
F07C3.7	1728	1629	17	1.16728
F52H2.2a	1739	1640	32	2.1825
F52H2.2b	1840	1741	0	0
T13A10.10a	1734	1635	35.7306	2.4444
T13A10.10b	1598	1499	0.269383	0.020101
C55C2.5a	1840	1741	7.84234	0.503844
C55C2.5b	1606	1507	0	0

==> SRR9060559.se.tsv <==
WBGene00197333	0
WBGene00198386	0
WBGene00015153	7
WBGene00002061	4520
WBGene00255704	3
WBGene00235314	0
WBGene00001177	184
WBGene00169236	0
WBGene00219784	0
WBGene00015152	1
SRR9060559 completed mapping pipeline successfully
