Starting /dee2/code/volunteer_pipeline.sh SRR11699509
    current disk space = 2464487702528
    free memory = 1581248512 
SRR11699509 SRAfilesize
49b5b9f59a2045bb95f4952ad3969e46  SRR11699509.sra
SRR11699509.sra file validated
SRR11699509 is single end
SRR11699509 is conventional basespace
SRR11699509 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699509_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	76
%GC	50
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.3765	32.0	32.0	32.0	32.0	32.0
2	31.51175	32.0	32.0	32.0	32.0	32.0
3	31.46675	32.0	32.0	32.0	32.0	32.0
4	31.541	32.0	32.0	32.0	32.0	32.0
5	31.5345	32.0	32.0	32.0	32.0	32.0
6	35.01875	36.0	36.0	36.0	36.0	36.0
7	35.17275	36.0	36.0	36.0	36.0	36.0
8	35.2195	36.0	36.0	36.0	36.0	36.0
9	35.01225	36.0	36.0	36.0	36.0	36.0
10-11	35.09075	36.0	36.0	36.0	36.0	36.0
12-13	35.113125	36.0	36.0	36.0	36.0	36.0
14-15	35.052	36.0	36.0	36.0	36.0	36.0
16-17	35.0935	36.0	36.0	36.0	36.0	36.0
18-19	35.21425000000001	36.0	36.0	36.0	36.0	36.0
20-21	35.031	36.0	36.0	36.0	36.0	36.0
22-23	35.034125	36.0	36.0	36.0	36.0	36.0
24-25	35.057375	36.0	36.0	36.0	36.0	36.0
26-27	34.89875	36.0	36.0	36.0	34.0	36.0
28-29	34.96325	36.0	36.0	36.0	36.0	36.0
30-31	34.9705	36.0	36.0	36.0	36.0	36.0
32-33	34.914625	36.0	36.0	36.0	36.0	36.0
34-35	35.008250000000004	36.0	36.0	36.0	36.0	36.0
36-37	35.055375	36.0	36.0	36.0	36.0	36.0
38-39	34.895875000000004	36.0	36.0	36.0	36.0	36.0
40-41	34.980625	36.0	36.0	36.0	36.0	36.0
42-43	34.921875	36.0	36.0	36.0	36.0	36.0
44-45	34.841499999999996	36.0	36.0	36.0	32.0	36.0
46-47	34.920125	36.0	36.0	36.0	36.0	36.0
48-49	34.7365	36.0	36.0	36.0	34.0	36.0
50-51	34.52825	36.0	36.0	36.0	32.0	36.0
52-53	34.41275	36.0	36.0	36.0	32.0	36.0
54-55	34.203625	36.0	36.0	36.0	32.0	36.0
56-57	33.91475	36.0	36.0	36.0	29.5	36.0
58-59	33.683375	36.0	36.0	36.0	27.0	36.0
60-61	33.636125	36.0	36.0	36.0	27.0	36.0
62-63	33.415625000000006	36.0	36.0	36.0	27.0	36.0
64-65	33.1305	36.0	34.0	36.0	24.0	36.0
66-67	32.453500000000005	36.0	32.0	36.0	17.5	36.0
68-69	32.119125000000004	36.0	32.0	36.0	14.0	36.0
70-71	32.559	36.0	32.0	36.0	14.0	36.0
72-73	32.35825	36.0	32.0	36.0	14.0	36.0
74-75	32.841125000000005	36.0	34.0	36.0	14.0	36.0
76	28.98475	32.0	21.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
20	1.0
21	4.0
22	4.0
23	11.0
24	5.0
25	13.0
26	25.0
27	49.0
28	55.0
29	81.0
30	124.0
31	175.0
32	232.0
33	333.0
34	877.0
35	2011.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	23.45	29.775000000000002	24.975	21.8
2	23.125	28.4	22.975	25.5
3	25.074999999999996	30.55	17.599999999999998	26.775
4	27.975	32.225	17.65	22.15
5	20.375	25.324999999999996	27.1	27.200000000000003
6	23.799999999999997	25.324999999999996	28.15	22.725
7	33.675	30.925000000000004	18.45	16.950000000000003
8	22.35	23.1	31.2	23.35
9	22.6	33.625	20.65	23.125
10-11	31.3125	24.887500000000003	25.2875	18.512500000000003
12-13	22.8	21.3625	24.425	31.412499999999998
14-15	30.012499999999996	36.0875	17.1	16.8
16-17	22.9625	24.05	31.0625	21.925
18-19	37.275000000000006	24.087500000000002	20.65	17.9875
20-21	23.7	31.65	25.337500000000002	19.3125
22-23	30.662499999999998	36.35	15.9	17.0875
24-25	29.25	38.587500000000006	15.012500000000001	17.150000000000002
26-27	27.625	33.900000000000006	18.4125	20.0625
28-29	30.049999999999997	25.85	18.1625	25.937500000000004
30-31	35.099999999999994	33.525	10.6375	20.7375
32-33	28.3875	41.375	10.15	20.0875
34-35	32.0375	31.65	12.812499999999998	23.5
36-37	29.912499999999998	32.1375	10.237499999999999	27.712500000000002
38-39	21.987499999999997	37.1375	11.924999999999999	28.95
40-41	25.2375	31.825	14.274999999999999	28.6625
42-43	27.237499999999997	25.2625	20.599999999999998	26.900000000000002
44-45	21.725	29.975	17.75	30.55
46-47	21.975	34.225	13.4	30.4
48-49	15.775	30.275000000000002	17.3875	36.5625
50-51	14.224999999999998	26.325	19.662499999999998	39.787499999999994
52-53	18.125	28.212500000000002	18.425	35.2375
54-55	17.925	27.537499999999998	20.1	34.4375
56-57	12.0875	28.0625	18.787499999999998	41.0625
58-59	11.625	27.8875	16.1375	44.35
60-61	15.325	30.162499999999998	20.8125	33.7
62-63	17.0625	30.049999999999997	23.6125	29.275000000000002
64-65	11.8125	25.2875	29.625	33.275
66-67	12.587499999999999	19.6125	31.275	36.525
68-69	17.3625	18.875	30.7625	33.0
70-71	18.85	21.1625	33.6875	26.3
72-73	18.587500000000002	18.85	32.324999999999996	30.2375
74-75	21.1375	13.8375	30.65	34.375
76	15.725	12.35	36.25	35.675000000000004
>>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	0.5
23	0.5
24	0.0
25	0.0
26	0.0
27	0.5
28	0.5
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.5
35	1.0
36	1.5
37	2.0
38	2.0
39	4.5
40	10.0
41	25.0
42	37.0
43	49.0
44	80.5
45	138.0
46	176.0
47	283.0
48	593.5
49	650.5
50	504.0
51	548.0
52	535.0
53	408.5
54	339.0
55	248.5
56	158.0
57	134.0
58	110.0
59	74.5
60	25.5
61	9.0
62	6.0
63	4.5
64	3.5
65	3.5
66	1.5
67	0.0
68	0.5
69	1.0
70	0.5
71	0.0
72	0.0
73	0.5
74	0.5
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	0.5
95	0.0
96	0.0
97	0.0
98	0.0
99	0.5
100	1.0
>>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	0.0
7	0.0
8	0.0
9	0.0
10-11	0.0
12-13	0.0
14-15	0.0
16-17	0.0
18-19	0.0
20-21	0.0
22-23	0.0
24-25	0.0
26-27	0.0
28-29	0.0
30-31	0.0
32-33	0.0
34-35	0.0
36-37	0.0
38-39	0.0
40-41	0.0
42-43	0.0
44-45	0.0
46-47	0.0
48-49	0.0
50-51	0.0
52-53	0.0
54-55	0.0
56-57	0.0
58-59	0.0
60-61	0.0
62-63	0.0
64-65	0.0
66-67	0.0
68-69	0.0
70-71	0.0
72-73	0.0
74-75	0.0
76	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
76	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	65.05
#Duplication Level	Percentage of deduplicated	Percentage of total
1	89.73866256725596	58.375
2	4.650269023827825	6.05
3	1.5757109915449656	3.075
4	1.1145272867025366	2.9000000000000004
5	0.4611837048424289	1.5
6	0.49961568024596464	1.95
7	0.3074558032282859	1.4000000000000001
8	0.3074558032282859	1.6
9	0.2690238278247502	1.575
>10	0.9223674096848578	12.55
>50	0.11529592621060722	4.775
>100	0.03843197540353574	4.25
>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
CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC	170	4.25	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	76	1.9	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	62	1.55	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	53	1.325	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	49	1.225	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	43	1.075	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAC	36	0.8999999999999999	TruSeq Adapter, Index 7 (97% over 35bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	30	0.75	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	29	0.7250000000000001	No Hit
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	25	0.625	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACGATAT	18	0.44999999999999996	TruSeq Adapter, Index 7 (97% over 35bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	16	0.4	No Hit
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAC	16	0.4	TruSeq Adapter, Index 7 (97% over 35bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	15	0.375	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	15	0.375	No Hit
GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	12	0.3	No Hit
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACG	11	0.27499999999999997	TruSeq Adapter, Index 7 (97% over 35bp)
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGAGC	10	0.25	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	9	0.22499999999999998	No Hit
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACGATA	9	0.22499999999999998	TruSeq Adapter, Index 7 (97% over 35bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	8	0.2	No Hit
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	8	0.2	TruSeq Adapter, Index 7 (100% over 35bp)
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AGATCATGTTGCAGCTTCACTAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	8	0.2	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	8	0.2	No Hit
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GGGGACGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	7	0.17500000000000002	TruSeq Adapter, Index 7 (100% over 35bp)
CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
CGACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GCGACCCCAGGTCAGTCGGGAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CGACACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	6	0.15	TruSeq Adapter, Index 7 (100% over 35bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	6	0.15	No Hit
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	6	0.15	No Hit
ACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGACCCCAGGTCAGTCGGGACTACCCGCTGAGTAGATCGGAAGAGCACA	6	0.15	No Hit
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	6	0.15	No Hit
CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	6	0.15	No Hit
AGTTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	5	0.125	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGAGATCGGAAGAGCACACG	5	0.125	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG	5	0.125	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAATCAGATCGGAAGAG	5	0.125	No Hit
CTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	5	0.125	No Hit
CACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGAGATCGGAAGA	5	0.125	No Hit
CGACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGT	5	0.125	No Hit
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	5	0.125	No Hit
CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
>>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	0.1	0.0	0.0	0.0	0.0
2	0.225	0.0	0.0	0.0	0.0
3	0.225	0.0	0.0	0.0	0.0
4	0.325	0.0	0.0	0.0	0.0
5	0.375	0.0	0.0	0.0	0.0
6	0.425	0.0	0.0	0.0	0.0
7	0.5	0.0	0.0	0.0	0.0
8	0.7	0.0	0.0	0.0	0.0
9	1.275	0.0	0.0	0.0	0.0
10	1.675	0.0	0.0	0.0	0.0
11	2.125	0.0	0.0	0.0	0.0
12	2.55	0.0	0.0	0.0	0.0
13	3.3	0.0	0.0	0.0	0.0
14	5.375	0.0	0.0	0.0	0.0
15	6.6	0.0	0.0	0.0	0.0
16	7.775	0.0	0.0	0.0	0.0
17	10.425	0.0	0.0	0.0	0.0
18	12.85	0.0	0.0	0.0	0.0
19	14.8	0.0	0.0	0.0	0.0
20	17.55	0.0	0.0	0.0	0.0
21	20.4	0.0	0.0	0.0	0.0
22	24.6	0.0	0.0	0.0	0.0
23	33.375	0.0	0.0	0.0	0.0
24	37.35	0.0	0.0	0.0	0.0
25	49.3	0.0	0.0	0.0	0.0
26	53.825	0.0	0.0	0.0	0.0
27	56.4	0.0	0.0	0.0	0.0
28	60.4	0.0	0.0	0.0	0.0
29	62.425	0.0	0.0	0.0	0.0
30	64.925	0.0	0.0	0.0	0.0
31	70.325	0.0	0.0	0.0	0.0
32	73.125	0.0	0.0	0.0	0.0
33	75.55	0.0	0.0	0.0	0.0
34	78.3	0.0	0.0	0.0	0.0
35	80.85	0.0	0.0	0.0	0.0
36	84.75	0.0	0.0	0.0	0.0
37	86.375	0.0	0.0	0.0	0.0
38	88.3	0.0	0.0	0.0	0.0
39	89.7	0.0	0.0	0.0	0.0
40	90.975	0.0	0.0	0.0	0.0
41	91.625	0.0	0.0	0.0	0.0
42	93.075	0.0	0.0	0.0	0.0
43	93.575	0.0	0.0	0.0	0.0
44	94.125	0.0	0.0	0.0	0.0
45	94.525	0.0	0.0	0.0	0.0
46	94.85	0.0	0.0	0.0	0.0
47	95.1	0.0	0.0	0.0	0.0
48	95.425	0.0	0.0	0.0	0.0
49	95.725	0.0	0.0	0.0	0.0
50	95.875	0.0	0.0	0.0	0.0
51	95.9	0.0	0.0	0.0	0.0
52	95.95	0.0	0.0	0.0	0.0
53	95.975	0.0	0.0	0.0	0.0
54	95.975	0.0	0.0	0.0	0.0
55	95.975	0.0	0.0	0.0	0.0
56	96.0	0.0	0.0	0.0	0.0
57	96.0	0.0	0.0	0.0	0.0
58	96.0	0.0	0.0	0.0	0.0
59	96.0	0.0	0.0	0.0	0.0
60	96.0	0.0	0.0	0.0	0.0
61	96.0	0.0	0.0	0.0	0.0
62	96.0	0.0	0.0	0.0	0.0
63	96.0	0.0	0.0	0.0	0.0
64	96.0	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTGTCCT	15	0.0020658788	70.00001	8
AGCTCAG	15	0.0020658788	70.00001	9
TCTAGCT	30	7.878043E-8	70.00001	11
TGTCCTA	15	0.0020658788	70.00001	9
TCCTAGG	15	0.0020658788	70.00001	11
TCAGGAT	30	7.878043E-8	70.00001	20
GCTGGTC	30	7.878043E-8	70.00001	15
TAGCTGG	30	7.878043E-8	70.00001	13
TAGCTCA	15	0.0020658788	70.00001	8
TTCTGGT	15	0.0020658788	70.00001	3
CCGTTGT	35	2.6138878E-9	70.00001	2
TAGTCTA	35	2.6138878E-9	70.00001	8
GGTCAGG	30	7.878043E-8	70.00001	18
CTGGTGT	15	0.0020658788	70.00001	5
CTGGTCA	30	7.878043E-8	70.00001	16
GTCCTAG	15	0.0020658788	70.00001	10
TATTCTG	15	0.0020658788	70.00001	1
TGTAGTC	35	2.6138878E-9	70.00001	6
CTAGCTG	30	7.878043E-8	70.00001	12
GTCTAGC	30	7.878043E-8	70.00001	10
>>END_MODULE
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
Rejected 234708 READS because READLEN < 1
Read 234708 spots for SRR11699509.sra
Written 234708 spots for SRR11699509.sra
Rejected 234702 READS because READLEN < 1
Read 234702 spots for SRR11699509.sra
Written 234702 spots for SRR11699509.sra
SRR ids: ['SRR11699509.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_hgqfjl_h
SRR11699509.sra spots: 4694046
blocks: [[1, 234702], [234703, 469404], [469405, 704106], [704107, 938808], [938809, 1173510], [1173511, 1408212], [1408213, 1642914], [1642915, 1877616], [1877617, 2112318], [2112319, 2347020], [2347021, 2581722], [2581723, 2816424], [2816425, 3051126], [3051127, 3285828], [3285829, 3520530], [3520531, 3755232], [3755233, 3989934], [3989935, 4224636], [4224637, 4459338], [4459339, 4694046]]
SRR11699509 file size 891716
SRR11699509 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -f sanger -l 18 -q 10 -k inf -t 20 -o SRR11699509 SRR11699509_1.fastq
Input file:	SRR11699509_1.fastq
trimmed:	SRR11699509-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 
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	20
Fri Jun 20 13:25:59 2025 >> started

Fri Jun 20 13:26:02 2025 >> done (2.704s)
4694046 reads processed; of these:
 618063 (13.17%) short reads filtered out after trimming by size control
   6076 ( 0.13%) empty reads filtered out after trimming by size control
4069907 (86.70%) reads available; of these:
3981009 (97.82%) trimmed reads available after processing
  88898 ( 2.18%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  94341	  2.32%
 19	 151099	  3.71%
 20	 153996	  3.78%
 21	 234629	  5.76%
 22	 451197	 11.09%
 23	 178950	  4.40%
 24	 554178	 13.62%
 25	 199459	  4.90%
 26	 130030	  3.19%
 27	 175092	  4.30%
 28	 112457	  2.76%
 29	 125152	  3.08%
 30	 295025	  7.25%
 31	 124638	  3.06%
 32	 111087	  2.73%
 33	 137378	  3.38%
 34	 114779	  2.82%
 35	 174237	  4.28%
 36	  86913	  2.14%
 37	  73566	  1.81%
 38	  56406	  1.39%
 39	  59034	  1.45%
 40	  40941	  1.01%
 41	  70697	  1.74%
 42	  30719	  0.75%
 43	  27071	  0.67%
 44	  17934	  0.44%
 45	      0	  0.00%
 46	      0	  0.00%
 47	      0	  0.00%
 48	      0	  0.00%
 49	      0	  0.00%
 50	      0	  0.00%
 51	      0	  0.00%
 52	      0	  0.00%
 53	      0	  0.00%
 54	      0	  0.00%
 55	      0	  0.00%
 56	      0	  0.00%
 57	      0	  0.00%
 58	      0	  0.00%
 59	      0	  0.00%
 60	      0	  0.00%
 61	      0	  0.00%
 62	      0	  0.00%
 63	      0	  0.00%
 64	      0	  0.00%
 65	      0	  0.00%
 66	      0	  0.00%
 67	      0	  0.00%
 68	      1	  0.00%
 69	      0	  0.00%
 70	      0	  0.00%
 71	      0	  0.00%
 72	      0	  0.00%
 73	      0	  0.00%
 74	      1	  0.00%
 75	      2	  0.00%
 76	  88898	  2.18%
4069907 reads passed initial QC


criterion=sequence-density
sequence-density=6.39
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATACTCGGCTCTCAC


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=33
fanout-score=84.13
fanout-score-rank=1
prefix-density=0.50
prefix-fanout=1.0
sequence=CCTCGTGTTTAGTTGCCACTATGAGTTTGGAACCCTGAACAGACCGCCGGTGTTAAGCCGGAGGAAGGAGATCGGAA
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:
    0 (0.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    1 (100.00%) aligned >1 times
100.00% overall alignment rate
Potential adapter found in reference sequence. Continuing without clipping.
                                 Started job on |	Jun 20 13:26:36
                             Started mapping on |	Jun 20 13:26:52
                                    Finished on |	Jun 20 13:27:08
       Mapping speed, Million of reads per hour |	915.73

                          Number of input reads |	4069907
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	426236
                        Uniquely mapped reads % |	10.47%
                          Average mapped length |	24.21
                       Number of splices: Total |	9307
            Number of splices: Annotated (sjdb) |	3547
                       Number of splices: GT/AG |	8702
                       Number of splices: GC/AG |	445
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	157
                      Mismatch rate per base, % |	1.18%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.44
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.25
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	571805
             % of reads mapped to multiple loci |	14.05%
        Number of reads mapped to too many loci |	804978
             % of reads mapped to too many loci |	19.78%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	6.86%
                     % of reads unmapped: other |	48.84%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3071866	3071866	3071866
N_multimapping	571805	571805	571805
N_noFeature	362004	374462	411513
N_ambiguous	2321	39	33
UnstrandedReadsAssigned:61911 PositiveStrandReadsAssigned:51735 NegativeStrandReadsAssigned:14690
Dataset is classified unstranded
MeadianReadLen=26 20thPercentileLength=22 echo kmer=19
SRR11699509 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: 72,539
[index] number of k-mers: 56,563,136
[index] number of equivalence classes: 414,827
[quant] running in single-end mode
[quant] will process file 1: SRR11699509-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,069,907 reads, 869,739 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 931 rounds

  72540 SRR11699509.ke.tsv
  44303 SRR11699509.se.tsv
 116843 total
==> SRR11699509.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	1	0.378596
Zm00001eb323640_T001	3273	3174	0	0
Zm00001eb314140_T001	893	794	0	0
Zm00001eb080260_T001	3529	3430	1	0.366234
Zm00001eb026490_T001	2433	2334	0	0
Zm00001eb026490_T002	2229	2130	0	0
Zm00001eb026490_T003	2220	2121	0	0
Zm00001eb281360_T001	2412	2313	1	0.543096

==> SRR11699509.se.tsv <==
Zm00001eb015280	3
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699509 completed mapping pipeline successfully
