Starting /dee2/code/volunteer_pipeline.sh SRR11699259
    current disk space = 2483974672384
    free memory = 926116188 
SRR11699259 SRAfilesize
c44edcf74bb51ce0a180a6c961d70cab  SRR11699259.sra
SRR11699259.sra file validated
SRR11699259 is single end
SRR11699259 is conventional basespace
SRR11699259 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699259_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	47
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.295	32.0	32.0	32.0	32.0	32.0
2	31.36775	32.0	32.0	32.0	32.0	32.0
3	31.519	32.0	32.0	32.0	32.0	32.0
4	31.52975	32.0	32.0	32.0	32.0	32.0
5	31.59075	32.0	32.0	32.0	32.0	32.0
6	35.19175	36.0	36.0	36.0	36.0	36.0
7	35.02775	36.0	36.0	36.0	36.0	36.0
8	35.115	36.0	36.0	36.0	36.0	36.0
9	35.02525	36.0	36.0	36.0	36.0	36.0
10-11	35.128	36.0	36.0	36.0	36.0	36.0
12-13	35.13575	36.0	36.0	36.0	36.0	36.0
14-15	35.090375	36.0	36.0	36.0	36.0	36.0
16-17	35.19975	36.0	36.0	36.0	36.0	36.0
18-19	35.187124999999995	36.0	36.0	36.0	36.0	36.0
20-21	35.103875	36.0	36.0	36.0	36.0	36.0
22-23	35.000375000000005	36.0	36.0	36.0	36.0	36.0
24-25	35.06625	36.0	36.0	36.0	36.0	36.0
26-27	34.948625	36.0	36.0	36.0	36.0	36.0
28-29	34.997625	36.0	36.0	36.0	36.0	36.0
30-31	34.968500000000006	36.0	36.0	36.0	36.0	36.0
32-33	34.975625	36.0	36.0	36.0	36.0	36.0
34-35	34.987375	36.0	36.0	36.0	36.0	36.0
36-37	34.99175	36.0	36.0	36.0	36.0	36.0
38-39	34.882374999999996	36.0	36.0	36.0	36.0	36.0
40-41	34.93925	36.0	36.0	36.0	36.0	36.0
42-43	34.936499999999995	36.0	36.0	36.0	36.0	36.0
44-45	34.839875	36.0	36.0	36.0	34.0	36.0
46-47	34.86825	36.0	36.0	36.0	36.0	36.0
48-49	34.61150000000001	36.0	36.0	36.0	32.0	36.0
50-51	34.2415	36.0	36.0	36.0	32.0	36.0
52-53	33.97525	36.0	36.0	36.0	32.0	36.0
54-55	33.186	36.0	36.0	36.0	17.5	36.0
56-57	31.969375	36.0	32.0	36.0	14.0	36.0
58-59	31.146875	36.0	32.0	36.0	14.0	36.0
60-61	31.143	36.0	32.0	36.0	14.0	36.0
62-63	30.488375	36.0	27.0	36.0	14.0	36.0
64-65	29.680999999999997	36.0	24.0	36.0	14.0	36.0
66-67	29.148249999999997	34.0	24.0	36.0	14.0	36.0
68-69	29.462	36.0	27.0	36.0	14.0	36.0
70-71	29.450125	36.0	27.0	36.0	14.0	36.0
72-73	29.84625	36.0	27.0	36.0	14.0	36.0
74-75	29.947499999999998	36.0	27.0	36.0	14.0	36.0
76	26.2305	32.0	14.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
20	1.0
21	1.0
22	5.0
23	7.0
24	14.0
25	22.0
26	50.0
27	68.0
28	81.0
29	132.0
30	213.0
31	321.0
32	428.0
33	564.0
34	1055.0
35	1038.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	30.75	27.575	21.325	20.349999999999998
2	28.075	24.525	23.35	24.05
3	33.575	27.450000000000003	17.775	21.2
4	34.9	29.75	17.775	17.575
5	19.275000000000002	30.125	24.375	26.224999999999998
6	22.85	22.55	35.25	19.35
7	40.625	28.050000000000004	17.575	13.750000000000002
8	19.85	23.400000000000002	39.550000000000004	17.2
9	20.825	40.025	18.2	20.95
10-11	34.525	22.3875	24.3	18.787499999999998
12-13	19.3375	22.0125	26.8	31.85
14-15	28.4375	41.0	16.275000000000002	14.2875
16-17	23.474999999999998	26.3	31.362499999999997	18.862499999999997
18-19	36.875	23.2875	22.650000000000002	17.1875
20-21	28.037499999999998	32.6375	22.3125	17.0125
22-23	33.1875	40.475	12.775	13.5625
24-25	30.3	40.475	14.2125	15.012500000000001
26-27	29.9	32.775	14.75	22.575
28-29	27.800000000000004	30.837500000000002	14.424999999999999	26.937499999999996
30-31	31.374999999999996	34.4125	9.3875	24.825
32-33	28.4125	34.1875	13.825000000000001	23.575
34-35	27.6625	29.375	17.2125	25.75
36-37	26.3625	34.2	12.3875	27.05
38-39	22.325	33.0125	14.299999999999999	30.362499999999997
40-41	20.424999999999997	28.075	18.05	33.45
42-43	24.5	28.4	19.05	28.050000000000004
44-45	19.55	31.887500000000003	18.8125	29.75
46-47	18.087500000000002	32.525	16.6125	32.775
48-49	13.3875	32.824999999999996	17.95	35.8375
50-51	15.537500000000001	34.2875	20.7625	29.4125
52-53	17.2875	35.3	20.5125	26.900000000000002
54-55	15.2125	38.3625	20.962500000000002	25.4625
56-57	13.0375	35.5375	24.5	26.924999999999997
58-59	15.2	34.75	22.8625	27.187499999999996
60-61	16.025	35.6625	27.125	21.1875
62-63	15.6375	34.637499999999996	28.299999999999997	21.425
64-65	13.7875	29.875	26.9125	29.425
66-67	17.9125	21.462500000000002	30.312499999999996	30.312499999999996
68-69	15.8875	22.4375	33.375	28.299999999999997
70-71	17.6375	20.575	38.5375	23.25
72-73	17.724999999999998	18.587500000000002	34.3375	29.349999999999998
74-75	20.849999999999998	15.775	33.0625	30.312499999999996
76	12.875	15.1	44.25	27.775
>>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	0.5
27	0.5
28	0.0
29	0.0
30	0.5
31	0.5
32	0.0
33	0.0
34	0.5
35	1.0
36	2.5
37	4.0
38	8.0
39	16.0
40	43.5
41	90.5
42	114.0
43	161.5
44	320.5
45	622.5
46	813.0
47	729.0
48	625.0
49	548.5
50	492.0
51	375.5
52	188.5
53	101.5
54	85.0
55	86.5
56	53.5
57	10.5
58	2.0
59	3.0
60	3.0
61	2.0
62	2.0
63	2.0
64	1.0
65	0.0
66	1.0
67	2.0
68	1.0
69	0.0
70	0.0
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	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
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	65.17500000000001
#Duplication Level	Percentage of deduplicated	Percentage of total
1	88.60759493670885	57.75
2	5.370157268891447	7.000000000000001
3	1.9562715765247412	3.8249999999999997
4	1.2658227848101267	3.3000000000000003
5	0.5370157268891446	1.7500000000000002
6	0.38358266206367475	1.5
7	0.23014959723820483	1.05
8	0.23014959723820483	1.2
9	0.19179133103183738	1.125
>10	1.0740314537782891	12.174999999999999
>50	0.07671653241273495	3.5999999999999996
>100	0.07671653241273495	5.7250000000000005
>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
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT	126	3.15	TruSeq Adapter, Index 1 (100% over 35bp)
CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC	103	2.5749999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	92	2.3	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATA	52	1.3	TruSeq Adapter, Index 3 (97% over 36bp)
GGGGACGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT	41	1.0250000000000001	TruSeq Adapter, Index 1 (100% over 35bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATA	41	1.0250000000000001	TruSeq Adapter, Index 3 (97% over 36bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	41	1.0250000000000001	No Hit
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	25	0.625	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	20	0.5	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	20	0.5	No Hit
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATAG	18	0.44999999999999996	TruSeq Adapter, Index 3 (97% over 37bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	15	0.375	No Hit
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	12	0.3	No Hit
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	12	0.3	No Hit
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
GCGTTTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGATGTAGTTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT	11	0.27499999999999997	TruSeq Adapter, Index 1 (100% over 35bp)
GCACCAGTGGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATAGAAAT	10	0.25	TruSeq Adapter, Index 3 (97% over 37bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATAGAA	9	0.22499999999999998	TruSeq Adapter, Index 3 (97% over 37bp)
GCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATAGAAA	9	0.22499999999999998	TruSeq Adapter, Index 3 (97% over 37bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT	8	0.2	TruSeq Adapter, Index 1 (100% over 35bp)
GCACCAGTAGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCGTTTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	8	0.2	No Hit
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT	7	0.17500000000000002	TruSeq Adapter, Index 1 (100% over 35bp)
GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCAGATCGGAAGAGCACAC	7	0.17500000000000002	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
ACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATAG	6	0.15	TruSeq Adapter, Index 3 (97% over 37bp)
GATGAAGAACGTAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATAGAAATG	6	0.15	TruSeq Adapter, Index 3 (97% over 37bp)
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	6	0.15	No Hit
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	6	0.15	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	6	0.15	No Hit
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGGATGTAGCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCAAAAGAGGAAAGGCTTGCGGTGGATAAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
ACTTGACGGATCGCACGGCCTTCGTGCCGGCAGATCGGAAGAGCACACGT	5	0.125	No Hit
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTAGATCGGAAGAGCACA	5	0.125	No Hit
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGAGATCGGAAGAGCAC	5	0.125	No Hit
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	5	0.125	No Hit
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAGATCGGAAGAGCACA	5	0.125	No Hit
GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GCACCAGTGGTCTAGTGGTAGAATAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTAGATCGGAAGAGC	5	0.125	No Hit
TTTGTACCGCGCATATTACTAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
>>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	0.075	0.0	0.0	0.0	0.0
2	0.15	0.0	0.0	0.0	0.0
3	0.2	0.0	0.0	0.0	0.0
4	0.275	0.0	0.0	0.0	0.0
5	0.425	0.0	0.0	0.0	0.0
6	0.65	0.0	0.0	0.0	0.0
7	0.85	0.0	0.0	0.0	0.0
8	1.4	0.0	0.0	0.0	0.0
9	2.1	0.0	0.0	0.0	0.0
10	2.8	0.0	0.0	0.0	0.0
11	3.825	0.0	0.0	0.0	0.0
12	5.175	0.0	0.0	0.0	0.0
13	7.025	0.0	0.0	0.0	0.0
14	11.45	0.0	0.0	0.0	0.0
15	18.1	0.0	0.0	0.0	0.0
16	20.625	0.0	0.0	0.0	0.0
17	25.225	0.0	0.0	0.0	0.0
18	28.35	0.0	0.0	0.0	0.0
19	31.05	0.0	0.0	0.0	0.0
20	34.125	0.0	0.0	0.0	0.0
21	38.125	0.0	0.0	0.0	0.0
22	44.575	0.0	0.0	0.0	0.0
23	50.95	0.0	0.0	0.0	0.0
24	53.825	0.0	0.0	0.0	0.0
25	61.15	0.0	0.0	0.0	0.0
26	64.275	0.0	0.0	0.0	0.0
27	66.975	0.0	0.0	0.0	0.0
28	69.95	0.0	0.0	0.0	0.0
29	72.05	0.0	0.0	0.0	0.0
30	74.25	0.0	0.0	0.0	0.0
31	77.925	0.0	0.0	0.0	0.0
32	80.125	0.0	0.0	0.0	0.0
33	82.725	0.0	0.0	0.0	0.0
34	84.425	0.0	0.0	0.0	0.0
35	86.95	0.0	0.0	0.0	0.0
36	89.5	0.0	0.0	0.0	0.0
37	91.5	0.0	0.0	0.0	0.0
38	92.275	0.0	0.0	0.0	0.0
39	92.775	0.0	0.0	0.0	0.0
40	93.525	0.0	0.0	0.0	0.0
41	93.95	0.0	0.0	0.0	0.0
42	94.4	0.0	0.0	0.0	0.0
43	94.6	0.0	0.0	0.0	0.0
44	94.825	0.0	0.0	0.0	0.0
45	94.875	0.0	0.0	0.0	0.0
46	95.075	0.0	0.0	0.0	0.0
47	95.25	0.0	0.0	0.0	0.0
48	95.35	0.0	0.0	0.0	0.0
49	95.35	0.0	0.0	0.0	0.0
50	95.425	0.0	0.0	0.0	0.0
51	95.5	0.0	0.0	0.0	0.0
52	95.5	0.0	0.0	0.0	0.0
53	95.55	0.0	0.0	0.0	0.0
54	95.575	0.0	0.0	0.0	0.0
55	95.575	0.0	0.0	0.0	0.0
56	95.6	0.0	0.0	0.0	0.0
57	95.6	0.0	0.0	0.0	0.0
58	95.6	0.0	0.0	0.0	0.0
59	95.6	0.0	0.0	0.0	0.0
60	95.6	0.0	0.0	0.0	0.0
61	95.6	0.0	0.0	0.0	0.0
62	95.6	0.0	0.0	0.0	0.0
63	95.6	0.0	0.0	0.0	0.0
64	95.6	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TCTAGTG	15	0.0020658788	70.00001	11
TCTAGCT	15	0.0020658788	70.00001	11
GATATTC	15	0.0020658788	70.00001	24
AGGATAT	15	0.0020658788	70.00001	22
GCTGGTC	15	0.0020658788	70.00001	15
AGTGGTA	15	0.0020658788	70.00001	14
TAACGAA	30	7.878043E-8	70.00001	2
TAGCTCA	30	7.878043E-8	70.00001	8
GGATATT	15	0.0020658788	70.00001	23
CTGGTCA	15	0.0020658788	70.00001	16
CTAACGA	30	7.878043E-8	70.00001	1
CTAGCTG	15	0.0020658788	70.00001	12
CTAGTGG	15	0.0020658788	70.00001	12
GTCTAGC	15	0.0020658788	70.00001	10
TTGAAAG	15	0.0020658788	70.00001	17
AGCTGGT	15	0.0020658788	70.00001	14
AGCTCAG	25	2.3570374E-6	70.0	9
TTGTAGT	25	2.3570374E-6	70.0	5
CCGTTGT	20	7.003785E-5	70.0	2
TAGTCTA	25	2.3570374E-6	70.0	8
>>END_MODULE
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272910 READS because READLEN < 1
Read 272910 spots for SRR11699259.sra
Written 272910 spots for SRR11699259.sra
Rejected 272929 READS because READLEN < 1
Read 272929 spots for SRR11699259.sra
Written 272929 spots for SRR11699259.sra
SRR ids: ['SRR11699259.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_l5ntlnj7
SRR11699259.sra spots: 5458219
blocks: [[1, 272910], [272911, 545820], [545821, 818730], [818731, 1091640], [1091641, 1364550], [1364551, 1637460], [1637461, 1910370], [1910371, 2183280], [2183281, 2456190], [2456191, 2729100], [2729101, 3002010], [3002011, 3274920], [3274921, 3547830], [3547831, 3820740], [3820741, 4093650], [4093651, 4366560], [4366561, 4639470], [4639471, 4912380], [4912381, 5185290], [5185291, 5458219]]
SRR11699259 file size 1037237
SRR11699259 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 SRR11699259 SRR11699259_1.fastq
Input file:	SRR11699259_1.fastq
trimmed:	SRR11699259-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 01:49:05 2025 >> started

Wed Jun 18 01:49:07 2025 >> done (2.258s)
5458219 reads processed; of these:
1637615 (30.00%) short reads filtered out after trimming by size control
   2619 ( 0.05%) empty reads filtered out after trimming by size control
3817985 (69.95%) reads available; of these:
3763695 (98.58%) trimmed reads available after processing
  54290 ( 1.42%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 152396	  3.99%
 19	 190572	  4.99%
 20	 210274	  5.51%
 21	 371084	  9.72%
 22	 380082	  9.96%
 23	 187141	  4.90%
 24	 416812	 10.92%
 25	 171434	  4.49%
 26	 145344	  3.81%
 27	 162028	  4.24%
 28	 117005	  3.06%
 29	 125239	  3.28%
 30	 180121	  4.72%
 31	 122483	  3.21%
 32	 141547	  3.71%
 33	 106831	  2.80%
 34	 118664	  3.11%
 35	 142245	  3.73%
 36	 110694	  2.90%
 37	  51976	  1.36%
 38	  36451	  0.95%
 39	  34065	  0.89%
 40	  26940	  0.71%
 41	  24720	  0.65%
 42	  16084	  0.42%
 43	  12276	  0.32%
 44	   9187	  0.24%
 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	      0	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      0	  0.00%
 76	  54290	  1.42%
3817985 reads passed initial QC


criterion=sequence-density
sequence-density=4.94
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=16
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAAGACCCGGGTT


criterion=fanout-score
sequence-density=0.27
sequence-density-rank=21
fanout-score=24.88
fanout-score-rank=1
prefix-density=1.04
prefix-fanout=6.5
sequence=TAGCTCAGTGGTAGAGC
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 01:49:34
                             Started mapping on |	Jun 18 01:49:34
                                    Finished on |	Jun 18 01:49:47
       Mapping speed, Million of reads per hour |	1057.29

                          Number of input reads |	3817985
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	450050
                        Uniquely mapped reads % |	11.79%
                          Average mapped length |	24.20
                       Number of splices: Total |	9876
            Number of splices: Annotated (sjdb) |	4326
                       Number of splices: GT/AG |	9170
                       Number of splices: GC/AG |	541
                       Number of splices: AT/AC |	5
               Number of splices: Non-canonical |	160
                      Mismatch rate per base, % |	1.25%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.54
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.37
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	573816
             % of reads mapped to multiple loci |	15.03%
        Number of reads mapped to too many loci |	855974
             % of reads mapped to too many loci |	22.42%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	6.32%
                     % of reads unmapped: other |	44.44%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2794119	2794119	2794119
N_multimapping	573816	573816	573816
N_noFeature	362542	375653	433860
N_ambiguous	3162	49	42
UnstrandedReadsAssigned:84346 PositiveStrandReadsAssigned:74348 NegativeStrandReadsAssigned:16148
Dataset is classified unstranded
MeadianReadLen=25 20thPercentileLength=21 echo kmer=19
SRR11699259 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: SRR11699259-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,817,985 reads, 855,790 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 841 rounds

  72540 SRR11699259.ke.tsv
  44303 SRR11699259.se.tsv
 116843 total
==> SRR11699259.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	3	1.16913
Zm00001eb323640_T001	3273	3174	0	0
Zm00001eb314140_T001	893	794	1	1.62853
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

==> SRR11699259.se.tsv <==
Zm00001eb015280	1
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	1
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699259 completed mapping pipeline successfully
