Starting /dee2/code/volunteer_pipeline.sh SRR11699279
    current disk space = 2470203949056
    free memory = 1578198728 
SRR11699279 SRAfilesize
a9e94b7231c982e74314c6839a630197  SRR11699279.sra
SRR11699279.sra file validated
SRR11699279 is single end
SRR11699279 is conventional basespace
SRR11699279 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699279_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	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.3405	32.0	32.0	32.0	32.0	32.0
2	31.444	32.0	32.0	32.0	32.0	32.0
3	31.457	32.0	32.0	32.0	32.0	32.0
4	31.55575	32.0	32.0	32.0	32.0	32.0
5	31.49875	32.0	32.0	32.0	32.0	32.0
6	34.971	36.0	36.0	36.0	36.0	36.0
7	34.97225	36.0	36.0	36.0	36.0	36.0
8	35.04975	36.0	36.0	36.0	36.0	36.0
9	34.889	36.0	36.0	36.0	32.0	36.0
10-11	35.03275	36.0	36.0	36.0	36.0	36.0
12-13	35.085375	36.0	36.0	36.0	36.0	36.0
14-15	35.002624999999995	36.0	36.0	36.0	36.0	36.0
16-17	35.092375000000004	36.0	36.0	36.0	36.0	36.0
18-19	35.100375	36.0	36.0	36.0	36.0	36.0
20-21	34.952375	36.0	36.0	36.0	36.0	36.0
22-23	34.932375	36.0	36.0	36.0	36.0	36.0
24-25	35.036125	36.0	36.0	36.0	36.0	36.0
26-27	34.840875	36.0	36.0	36.0	34.0	36.0
28-29	34.953875	36.0	36.0	36.0	36.0	36.0
30-31	34.8155	36.0	36.0	36.0	34.0	36.0
32-33	34.756875	36.0	36.0	36.0	34.0	36.0
34-35	34.945875	36.0	36.0	36.0	36.0	36.0
36-37	34.915000000000006	36.0	36.0	36.0	36.0	36.0
38-39	34.936375	36.0	36.0	36.0	36.0	36.0
40-41	34.863	36.0	36.0	36.0	34.0	36.0
42-43	34.765625	36.0	36.0	36.0	32.0	36.0
44-45	34.69775	36.0	36.0	36.0	32.0	36.0
46-47	34.751374999999996	36.0	36.0	36.0	34.0	36.0
48-49	34.438625	36.0	36.0	36.0	32.0	36.0
50-51	34.05025	36.0	36.0	36.0	32.0	36.0
52-53	33.712500000000006	36.0	36.0	36.0	29.5	36.0
54-55	33.2555	36.0	36.0	36.0	20.5	36.0
56-57	32.122749999999996	36.0	32.0	36.0	14.0	36.0
58-59	31.507375	36.0	32.0	36.0	14.0	36.0
60-61	30.315125000000002	36.0	29.5	36.0	14.0	36.0
62-63	29.359	36.0	17.5	36.0	14.0	36.0
64-65	27.134	32.0	14.0	36.0	14.0	36.0
66-67	24.44375	24.0	14.0	36.0	14.0	36.0
68-69	22.982750000000003	17.5	14.0	36.0	14.0	36.0
70-71	21.965875	14.0	14.0	34.0	14.0	36.0
72-73	21.004375	14.0	14.0	32.0	14.0	36.0
74-75	20.746	14.0	14.0	32.0	14.0	36.0
76	21.7035	14.0	14.0	32.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
16	1.0
17	0.0
18	0.0
19	0.0
20	0.0
21	1.0
22	6.0
23	12.0
24	23.0
25	41.0
26	80.0
27	124.0
28	186.0
29	331.0
30	346.0
31	513.0
32	669.0
33	640.0
34	586.0
35	441.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	22.6	31.65	22.025	23.724999999999998
2	18.975	29.425	28.175	23.425
3	23.599999999999998	33.900000000000006	18.95	23.549999999999997
4	27.725	32.45	18.9	20.925
5	22.025	26.35	23.35	28.275
6	28.525	29.15	24.65	17.675
7	28.975	35.825	18.25	16.950000000000003
8	23.175	29.5	25.674999999999997	21.65
9	25.1	31.825	19.3	23.775
10-11	31.162499999999998	30.675	20.849999999999998	17.3125
12-13	23.0625	25.5375	22.7375	28.6625
14-15	30.062499999999996	35.3	17.8625	16.775000000000002
16-17	23.2875	25.275	30.6375	20.8
18-19	35.525	25.587500000000002	22.475	16.412499999999998
20-21	23.1125	37.2125	22.537499999999998	17.1375
22-23	31.474999999999998	36.125	14.0875	18.3125
24-25	30.1875	37.0375	13.737499999999999	19.037499999999998
26-27	28.5875	32.8125	17.6875	20.9125
28-29	32.487500000000004	31.125000000000004	14.6125	21.775
30-31	30.675	37.237500000000004	11.05	21.0375
32-33	28.425	36.575	12.225	22.775000000000002
34-35	29.65	30.2625	13.450000000000001	26.637499999999996
36-37	25.5375	33.575	12.0	28.8875
38-39	22.662499999999998	32.574999999999996	15.325	29.4375
40-41	25.362499999999997	29.9	17.325	27.4125
42-43	24.775	26.887499999999996	20.1625	28.175
44-45	22.475	32.0625	15.512500000000001	29.95
46-47	22.3625	31.2125	14.787500000000001	31.637500000000003
48-49	20.175	28.9	18.0375	32.887499999999996
50-51	20.962500000000002	28.8875	17.8125	32.337500000000006
52-53	25.637500000000003	27.625	19.4625	27.275
54-55	24.7375	29.575000000000003	17.5625	28.125
56-57	28.999999999999996	25.05	18.625	27.325
58-59	30.9875	28.9125	17.25	22.85
60-61	31.662499999999998	26.674999999999997	21.9625	19.7
62-63	26.8125	26.2625	26.2125	20.7125
64-65	23.6375	18.275	30.112499999999997	27.975
66-67	26.9625	17.2875	30.8	24.95
68-69	29.375	15.137500000000001	32.775	22.7125
70-71	25.974999999999998	15.9125	36.8625	21.25
72-73	22.1375	13.5	36.275	28.0875
74-75	21.075	12.3375	37.4	29.1875
76	17.325	10.674999999999999	46.45	25.55
>>END_MODULE
>>Per sequence GC content	warn
#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	0.0
33	0.0
34	0.0
35	0.5
36	2.0
37	3.0
38	1.5
39	1.0
40	7.5
41	19.5
42	26.0
43	42.5
44	83.5
45	167.0
46	226.0
47	360.0
48	565.5
49	640.0
50	643.0
51	610.0
52	520.0
53	378.5
54	294.0
55	230.5
56	148.0
57	100.0
58	71.0
59	56.5
60	33.0
61	15.5
62	7.0
63	5.0
64	2.5
65	1.5
66	1.5
67	2.0
68	1.0
69	0.5
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	1.0
96	1.0
97	1.0
98	1.0
99	0.5
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	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	60.875
#Duplication Level	Percentage of deduplicated	Percentage of total
1	88.21355236139631	53.7
2	5.420944558521561	6.6000000000000005
3	1.88911704312115	3.45
4	1.0266940451745379	2.5
5	0.9034907597535934	2.75
6	0.41067761806981523	1.5
7	0.41067761806981523	1.7500000000000002
8	0.32854209445585214	1.6
9	0.0	0.0
>10	1.273100616016427	16.0
>50	0.08213552361396304	3.4750000000000005
>100	0.04106776180698152	6.675000000000001
>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	267	6.675000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	82	2.0500000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	57	1.425	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	40	1.0	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGA	40	1.0	TruSeq Adapter, Index 7 (97% over 37bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	35	0.8750000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	33	0.8250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAG	30	0.75	TruSeq Adapter, Index 7 (97% over 36bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	29	0.7250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	29	0.7250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGAGTAT	26	0.65	TruSeq Adapter, Index 7 (97% over 37bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	22	0.5499999999999999	No Hit
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAG	20	0.5	TruSeq Adapter, Index 7 (97% over 36bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	19	0.475	No Hit
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	16	0.4	No Hit
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCA	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	14	0.35000000000000003	No Hit
TGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGAGTATCGG	14	0.35000000000000003	TruSeq Adapter, Index 7 (97% over 37bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGAG	13	0.325	TruSeq Adapter, Index 7 (97% over 37bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGAGTA	12	0.3	TruSeq Adapter, Index 7 (97% over 37bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	11	0.27499999999999997	No Hit
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	11	0.27499999999999997	No Hit
GAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAG	11	0.27499999999999997	TruSeq Adapter, Index 7 (97% over 36bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGAGT	10	0.25	TruSeq Adapter, Index 7 (97% over 37bp)
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	8	0.2	No Hit
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGA	8	0.2	TruSeq Adapter, Index 7 (97% over 35bp)
AAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
ATCCTAACGAACGAACGATTAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCGACCCCAGGTCAGTCGGGAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	8	0.2	No Hit
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
CAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAATCAGATCGGAAGAG	7	0.17500000000000002	No Hit
TCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
TCTCATGGAGAGTTCGATCCTGGCAGATCGGAAGAGCACACGTCTGAACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GATGAAGAACGTAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	6	0.15	No Hit
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	6	0.15	No Hit
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	6	0.15	No Hit
ATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACA	6	0.15	No Hit
AGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAGATCGGAAGAGCACA	6	0.15	No Hit
GTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATC	5	0.125	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	5	0.125	No Hit
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	5	0.125	No Hit
TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGA	5	0.125	TruSeq Adapter, Index 7 (97% over 35bp)
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGAGTATCGGGGGT	5	0.125	TruSeq Adapter, Index 7 (97% over 37bp)
TTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGAGTATC	5	0.125	TruSeq Adapter, Index 7 (97% over 37bp)
ACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CGACACGACTCTCGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCGACCCCAGGTCAGTCGGGACTACCCGCTAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GATGAAGAACGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGA	5	0.125	TruSeq Adapter, Index 7 (97% over 37bp)
GGGCCTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAG	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
GATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGG	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.05	0.0	0.0	0.0	0.0
2	0.325	0.0	0.0	0.0	0.0
3	0.475	0.0	0.0	0.0	0.0
4	0.6	0.0	0.0	0.0	0.0
5	0.7	0.0	0.0	0.0	0.0
6	1.225	0.0	0.0	0.0	0.0
7	1.5	0.0	0.0	0.0	0.0
8	1.975	0.0	0.0	0.0	0.0
9	3.0	0.0	0.0	0.0	0.0
10	3.725	0.0	0.0	0.0	0.0
11	4.7	0.0	0.0	0.0	0.0
12	5.725	0.0	0.0	0.0	0.0
13	7.925	0.0	0.0	0.0	0.0
14	10.775	0.0	0.0	0.0	0.0
15	12.525	0.0	0.0	0.0	0.0
16	14.325	0.0	0.0	0.0	0.0
17	17.35	0.0	0.0	0.0	0.0
18	21.2	0.0	0.0	0.0	0.0
19	23.575	0.0	0.0	0.0	0.0
20	27.425	0.0	0.0	0.0	0.0
21	31.525	0.0	0.0	0.0	0.0
22	36.05	0.0	0.0	0.0	0.0
23	45.85	0.0	0.0	0.0	0.0
24	48.65	0.0	0.0	0.0	0.0
25	54.475	0.0	0.0	0.0	0.0
26	58.525	0.0	0.0	0.0	0.0
27	61.25	0.0	0.0	0.0	0.0
28	63.975	0.0	0.0	0.0	0.0
29	66.125	0.0	0.0	0.0	0.0
30	68.8	0.0	0.0	0.0	0.0
31	72.825	0.0	0.0	0.0	0.0
32	74.85	0.0	0.0	0.0	0.0
33	76.975	0.0	0.0	0.0	0.0
34	78.8	0.0	0.0	0.0	0.0
35	81.6	0.0	0.0	0.0	0.0
36	83.85	0.0	0.0	0.0	0.0
37	85.75	0.0	0.0	0.0	0.0
38	87.1	0.0	0.0	0.0	0.0
39	88.575	0.0	0.0	0.0	0.0
40	89.825	0.0	0.0	0.0	0.0
41	90.4	0.0	0.0	0.0	0.0
42	91.125	0.0	0.0	0.0	0.0
43	91.7	0.0	0.0	0.0	0.0
44	92.3	0.0	0.0	0.0	0.0
45	92.825	0.0	0.0	0.0	0.0
46	93.375	0.0	0.0	0.0	0.0
47	93.675	0.0	0.0	0.0	0.0
48	93.925	0.0	0.0	0.0	0.0
49	94.225	0.0	0.0	0.0	0.0
50	94.575	0.0	0.0	0.0	0.0
51	94.6	0.0	0.0	0.0	0.0
52	94.8	0.0	0.0	0.0	0.0
53	94.85	0.0	0.0	0.0	0.0
54	94.925	0.0	0.0	0.0	0.0
55	94.95	0.0	0.0	0.0	0.0
56	94.975	0.0	0.0	0.0	0.0
57	95.0	0.0	0.0	0.0	0.0
58	95.05	0.0	0.0	0.0	0.0
59	95.1	0.0	0.0	0.0	0.0
60	95.1	0.0	0.0	0.0	0.0
61	95.1	0.0	0.0	0.0	0.0
62	95.1	0.0	0.0	0.0	0.0
63	95.1	0.0	0.0	0.0	0.0
64	95.1	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TTGTAGT	15	0.0020658788	70.00001	5
AGTCTAG	15	0.0020658788	70.00001	9
TAGCTCA	20	7.003785E-5	70.0	8
TGGTCAG	20	0.0064587677	52.5	17
AGCTCAG	20	0.0064587677	52.5	9
CGTATTC	30	5.201195E-4	46.666668	67
CTAACGA	85	0.0	45.294113	1
TAACGAA	90	1.8189894E-12	42.77778	2
GAACGAA	115	1.8189894E-11	33.47826	6
GATTTGA	115	1.8189894E-11	33.47826	14
ATTTGAA	115	1.8189894E-11	33.47826	15
ACGATTT	115	1.8189894E-11	33.47826	12
CGATTTG	115	1.8189894E-11	33.47826	13
TTTGAAC	105	2.7830538E-10	33.333336	16
TTGAACA	105	2.7830538E-10	33.333336	17
AACGATT	120	2.910383E-11	32.083336	11
GAACGAT	120	2.910383E-11	32.083336	10
GTATTCC	45	0.003819767	31.111113	68
ACAGATC	105	1.1683369E-8	30.000002	21
GAACAGA	110	1.839362E-8	28.636362	19
>>END_MODULE
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195719 READS because READLEN < 1
Read 195719 spots for SRR11699279.sra
Written 195719 spots for SRR11699279.sra
Rejected 195730 READS because READLEN < 1
Read 195730 spots for SRR11699279.sra
Written 195730 spots for SRR11699279.sra
SRR ids: ['SRR11699279.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_lgqj6mju
SRR11699279.sra spots: 3914391
blocks: [[1, 195719], [195720, 391438], [391439, 587157], [587158, 782876], [782877, 978595], [978596, 1174314], [1174315, 1370033], [1370034, 1565752], [1565753, 1761471], [1761472, 1957190], [1957191, 2152909], [2152910, 2348628], [2348629, 2544347], [2544348, 2740066], [2740067, 2935785], [2935786, 3131504], [3131505, 3327223], [3327224, 3522942], [3522943, 3718661], [3718662, 3914391]]
SRR11699279 file size 743247
SRR11699279 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 SRR11699279 SRR11699279_1.fastq
Input file:	SRR11699279_1.fastq
trimmed:	SRR11699279-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
Wed Jun 18 07:43:27 2025 >> started

Wed Jun 18 07:43:30 2025 >> done (2.432s)
3914391 reads processed; of these:
 915743 (23.39%) short reads filtered out after trimming by size control
   3377 ( 0.09%) empty reads filtered out after trimming by size control
2995271 (76.52%) reads available; of these:
2894470 (96.63%) trimmed reads available after processing
 100801 ( 3.37%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 100162	  3.34%
 19	 159834	  5.34%
 20	 171275	  5.72%
 21	 188539	  6.29%
 22	 371299	 12.40%
 23	 117693	  3.93%
 24	 236124	  7.88%
 25	 176779	  5.90%
 26	 109054	  3.64%
 27	 109205	  3.65%
 28	  89759	  3.00%
 29	  94879	  3.17%
 30	 166212	  5.55%
 31	  88238	  2.95%
 32	  87503	  2.92%
 33	  75903	  2.53%
 34	  88380	  2.95%
 35	  98496	  3.29%
 36	  75147	  2.51%
 37	  57977	  1.94%
 38	  47614	  1.59%
 39	  43528	  1.45%
 40	  31327	  1.05%
 41	  36555	  1.22%
 42	  30077	  1.00%
 43	  25818	  0.86%
 44	  17089	  0.57%
 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	      0	  0.00%
 69	      0	  0.00%
 70	      0	  0.00%
 71	      0	  0.00%
 72	      2	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      2	  0.00%
 76	 100801	  3.37%
2995271 reads passed initial QC


criterion=sequence-density
sequence-density=3.82
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=22
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATA


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=30
fanout-score=1820.99
fanout-score-rank=1
prefix-density=19.90
prefix-fanout=1.0
sequence=CGATTTGAACTCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGGAAGTGGTGTTTCCAGTGGCGAACGGGTGAGTAACGCGTAAGAACCTGCCCTTGGGAGGGGAACAACAACTGGAAACGGTTGCTAATACCCCGTAGGCTGAGGAGCAAAAGGAGAAATCC
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 18 07:43:41
                             Started mapping on |	Jun 18 07:43:41
                                    Finished on |	Jun 18 07:43:59
       Mapping speed, Million of reads per hour |	599.05

                          Number of input reads |	2995271
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	222641
                        Uniquely mapped reads % |	7.43%
                          Average mapped length |	25.11
                       Number of splices: Total |	5389
            Number of splices: Annotated (sjdb) |	2469
                       Number of splices: GT/AG |	4881
                       Number of splices: GC/AG |	266
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	239
                      Mismatch rate per base, % |	1.08%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.42
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	280388
             % of reads mapped to multiple loci |	9.36%
        Number of reads mapped to too many loci |	510905
             % of reads mapped to too many loci |	17.06%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.38%
                     % of reads unmapped: other |	58.77%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2492242	2492242	2492242
N_multimapping	280388	280388	280388
N_noFeature	181190	186818	215556
N_ambiguous	1482	17	13
UnstrandedReadsAssigned:39969 PositiveStrandReadsAssigned:35806 NegativeStrandReadsAssigned:7072
Dataset is classified positive stranded
MeadianReadLen=25 20thPercentileLength=21 echo kmer=19
SRR11699279 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: SRR11699279-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,995,271 reads, 302,732 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 848 rounds

  72540 SRR11699279.ke.tsv
  44303 SRR11699279.se.tsv
 116843 total
==> SRR11699279.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	2	3.15148
Zm00001eb321680_T001	3417	3318	1	0.934617
Zm00001eb323640_T001	3273	3174	0	0
Zm00001eb314140_T001	893	794	0	0
Zm00001eb080260_T001	3529	3430	0	0
Zm00001eb026490_T001	2433	2334	0	0
Zm00001eb026490_T002	2229	2130	0	0
Zm00001eb026490_T003	2220	2121	0	0
Zm00001eb281360_T001	2412	2313	0	0

==> SRR11699279.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	1
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699279 completed mapping pipeline successfully
