Starting /dee2/code/volunteer_pipeline.sh SRR11699288
    current disk space = 2468569948160
    free memory = 1581885612 
SRR11699288 SRAfilesize
223a86f08eea1f072147a5bf16a0cfbd  SRR11699288.sra
SRR11699288.sra file validated
SRR11699288 is single end
SRR11699288 is conventional basespace
SRR11699288 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699288_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	49
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.2325	32.0	32.0	32.0	32.0	32.0
2	31.40525	32.0	32.0	32.0	32.0	32.0
3	31.4115	32.0	32.0	32.0	32.0	32.0
4	31.487	32.0	32.0	32.0	32.0	32.0
5	31.45175	32.0	32.0	32.0	32.0	32.0
6	34.95575	36.0	36.0	36.0	36.0	36.0
7	35.0415	36.0	36.0	36.0	36.0	36.0
8	35.09575	36.0	36.0	36.0	36.0	36.0
9	34.86225	36.0	36.0	36.0	32.0	36.0
10-11	34.99875	36.0	36.0	36.0	36.0	36.0
12-13	34.961124999999996	36.0	36.0	36.0	36.0	36.0
14-15	35.016999999999996	36.0	36.0	36.0	36.0	36.0
16-17	35.004875	36.0	36.0	36.0	36.0	36.0
18-19	35.101875	36.0	36.0	36.0	36.0	36.0
20-21	34.903	36.0	36.0	36.0	36.0	36.0
22-23	35.004999999999995	36.0	36.0	36.0	36.0	36.0
24-25	34.924625000000006	36.0	36.0	36.0	36.0	36.0
26-27	34.765	36.0	36.0	36.0	34.0	36.0
28-29	34.80575	36.0	36.0	36.0	34.0	36.0
30-31	34.8335	36.0	36.0	36.0	34.0	36.0
32-33	34.7555	36.0	36.0	36.0	34.0	36.0
34-35	34.839124999999996	36.0	36.0	36.0	34.0	36.0
36-37	34.811	36.0	36.0	36.0	36.0	36.0
38-39	34.836	36.0	36.0	36.0	36.0	36.0
40-41	34.738375	36.0	36.0	36.0	34.0	36.0
42-43	34.781125	36.0	36.0	36.0	34.0	36.0
44-45	34.616375000000005	36.0	36.0	36.0	32.0	36.0
46-47	34.664375	36.0	36.0	36.0	32.0	36.0
48-49	34.582375	36.0	36.0	36.0	32.0	36.0
50-51	34.380875	36.0	36.0	36.0	32.0	36.0
52-53	34.346625	36.0	36.0	36.0	32.0	36.0
54-55	33.879125	36.0	36.0	36.0	29.5	36.0
56-57	33.31675	36.0	36.0	36.0	24.0	36.0
58-59	33.042249999999996	36.0	36.0	36.0	21.0	36.0
60-61	33.224500000000006	36.0	36.0	36.0	24.0	36.0
62-63	32.656875	36.0	34.0	36.0	14.0	36.0
64-65	32.503249999999994	36.0	32.0	36.0	14.0	36.0
66-67	31.883625000000002	36.0	32.0	36.0	14.0	36.0
68-69	31.851125	36.0	32.0	36.0	14.0	36.0
70-71	32.093625	36.0	32.0	36.0	14.0	36.0
72-73	32.075	36.0	32.0	36.0	14.0	36.0
74-75	32.405625	36.0	32.0	36.0	14.0	36.0
76	29.27825	32.0	21.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
18	1.0
19	2.0
20	1.0
21	1.0
22	3.0
23	8.0
24	14.0
25	24.0
26	41.0
27	53.0
28	57.0
29	92.0
30	130.0
31	177.0
32	258.0
33	429.0
34	1036.0
35	1673.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	26.950000000000003	29.549999999999997	22.7	20.8
2	23.925	25.95	23.525	26.6
3	29.75	31.1	16.900000000000002	22.25
4	28.725	32.275	18.65	20.349999999999998
5	20.525	27.975	24.224999999999998	27.275
6	24.474999999999998	24.275	30.375000000000004	20.875
7	35.05	29.775000000000002	18.65	16.525000000000002
8	21.925	23.925	35.125	19.025
9	24.349999999999998	35.449999999999996	18.15	22.05
10-11	31.837500000000002	25.4375	25.5125	17.2125
12-13	22.2125	22.025	24.462500000000002	31.3
14-15	27.8625	39.8625	17.224999999999998	15.049999999999999
16-17	23.7375	23.9125	31.85	20.5
18-19	36.7375	23.9125	22.900000000000002	16.45
20-21	24.462500000000002	34.449999999999996	24.05	17.0375
22-23	32.6125	37.65	14.7125	15.024999999999999
24-25	29.4375	38.525	16.162499999999998	15.875
26-27	27.3	34.050000000000004	16.8625	21.7875
28-29	30.7375	28.787499999999998	16.5	23.974999999999998
30-31	33.575	33.225	10.65	22.55
32-33	28.9875	37.0625	11.725	22.225
34-35	30.862499999999997	32.4625	13.725000000000001	22.95
36-37	26.9625	33.387499999999996	11.9125	27.737499999999997
38-39	23.9875	33.550000000000004	13.125	29.3375
40-41	23.8125	30.9	15.737499999999999	29.549999999999997
42-43	26.3625	27.450000000000003	19.025	27.1625
44-45	21.725	30.225	17.65	30.4
46-47	19.3125	32.337500000000006	15.125	33.225
48-49	15.5	30.049999999999997	16.7625	37.6875
50-51	16.3375	28.225	19.7625	35.675000000000004
52-53	17.424999999999997	28.799999999999997	20.325	33.45
54-55	16.3	31.9875	20.2375	31.474999999999998
56-57	12.4	31.275	19.7125	36.6125
58-59	15.387500000000001	29.9625	20.325	34.325
60-61	14.787500000000001	34.5875	24.1375	26.487500000000004
62-63	14.1625	33.7	26.825	25.3125
64-65	12.937499999999998	30.5375	25.7375	30.7875
66-67	15.287500000000001	22.375	29.599999999999998	32.737500000000004
68-69	16.675	21.3875	32.337500000000006	29.599999999999998
70-71	18.65	22.412499999999998	33.775	25.162499999999998
72-73	18.3625	20.5	32.5375	28.599999999999998
74-75	20.3125	15.575	32.8625	31.25
76	14.625	13.700000000000001	39.35	32.324999999999996
>>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	0.5
24	0.5
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.5
31	0.5
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	3.5
39	8.5
40	22.0
41	46.5
42	59.0
43	91.5
44	161.5
45	290.0
46	381.0
47	654.0
48	741.0
49	559.0
50	563.0
51	501.0
52	365.5
53	215.5
54	139.0
55	117.5
56	104.0
57	71.5
58	31.0
59	20.5
60	7.5
61	4.5
62	4.0
63	3.0
64	2.0
65	2.0
66	1.5
67	1.0
68	0.5
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	0.5
86	1.0
87	1.0
88	0.5
89	0.0
90	0.5
91	0.5
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.5
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	66.625
#Duplication Level	Percentage of deduplicated	Percentage of total
1	88.51782363977486	58.975
2	5.5159474671669795	7.35
3	2.0637898686679175	4.125
4	1.200750469043152	3.2
5	0.600375234521576	2.0
6	0.33771106941838647	1.35
7	0.18761726078799248	0.8750000000000001
8	0.33771106941838647	1.7999999999999998
9	0.18761726078799248	1.125
>10	0.975609756097561	14.224999999999998
>50	0.0375234521575985	1.35
>100	0.0375234521575985	3.6249999999999996
>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	145	3.6249999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	54	1.35	No Hit
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	48	1.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	45	1.125	No Hit
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	41	1.0250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	33	0.8250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAG	31	0.775	TruSeq Adapter, Index 7 (100% over 36bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	25	0.625	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAG	24	0.6	TruSeq Adapter, Index 7 (100% over 36bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	22	0.5499999999999999	TruSeq Adapter, Index 7 (100% over 35bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGT	17	0.42500000000000004	TruSeq Adapter, Index 16 (97% over 37bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	16	0.4	No Hit
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGACGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	13	0.325	TruSeq Adapter, Index 7 (100% over 35bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	12	0.3	No Hit
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGTAAAT	10	0.25	TruSeq Adapter, Index 16 (97% over 37bp)
GCACCAGTGGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCAGATCGGAAGAGCACAC	9	0.22499999999999998	No Hit
GCGTTTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	8	0.2	No Hit
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	8	0.2	TruSeq Adapter, Index 7 (100% over 35bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	8	0.2	No Hit
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	8	0.2	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	8	0.2	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	8	0.2	No Hit
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGTAA	7	0.17500000000000002	TruSeq Adapter, Index 16 (97% over 37bp)
GCGACCCCAGGTCAGTCGGGACTACCCGCTAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGAGC	7	0.17500000000000002	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	6	0.15	TruSeq Adapter, Index 7 (100% over 35bp)
AAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	6	0.15	No Hit
AACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CGACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAG	6	0.15	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCTAGATCGGAAGAGCACACG	6	0.15	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGCATTTGGTCTAGTGGTATGATTCTCGCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	5	0.125	No Hit
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CGACACGACTCTCGGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGGTGTTTGGTCTAGTGGTATGATTCTCAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGTA	5	0.125	TruSeq Adapter, Index 16 (97% over 37bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
AGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGAGATCGGAA	5	0.125	No Hit
GAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAG	5	0.125	TruSeq Adapter, Index 7 (100% over 36bp)
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	0.05	0.0	0.0	0.0	0.0
2	0.225	0.0	0.0	0.0	0.0
3	0.25	0.0	0.0	0.0	0.0
4	0.3	0.0	0.0	0.0	0.0
5	0.375	0.0	0.0	0.0	0.0
6	0.4	0.0	0.0	0.0	0.0
7	0.55	0.0	0.0	0.0	0.0
8	0.725	0.0	0.0	0.0	0.0
9	1.125	0.0	0.0	0.0	0.0
10	1.375	0.0	0.0	0.0	0.0
11	1.975	0.0	0.0	0.0	0.0
12	2.8	0.0	0.0	0.0	0.0
13	4.05	0.0	0.0	0.0	0.0
14	7.025	0.0	0.0	0.0	0.0
15	9.5	0.0	0.0	0.0	0.0
16	11.55	0.0	0.0	0.0	0.0
17	14.35	0.0	0.0	0.0	0.0
18	17.125	0.0	0.0	0.0	0.0
19	19.85	0.0	0.0	0.0	0.0
20	23.1	0.0	0.0	0.0	0.0
21	26.475	0.0	0.0	0.0	0.0
22	31.55	0.0	0.0	0.0	0.0
23	39.875	0.0	0.0	0.0	0.0
24	43.425	0.0	0.0	0.0	0.0
25	51.65	0.0	0.0	0.0	0.0
26	55.95	0.0	0.0	0.0	0.0
27	58.85	0.0	0.0	0.0	0.0
28	62.4	0.0	0.0	0.0	0.0
29	64.825	0.0	0.0	0.0	0.0
30	66.875	0.0	0.0	0.0	0.0
31	70.55	0.0	0.0	0.0	0.0
32	73.65	0.0	0.0	0.0	0.0
33	77.3	0.0	0.0	0.0	0.0
34	80.175	0.0	0.0	0.0	0.0
35	82.425	0.0	0.0	0.0	0.0
36	85.675	0.0	0.0	0.0	0.0
37	87.35	0.0	0.0	0.0	0.0
38	88.75	0.0	0.0	0.0	0.0
39	89.7	0.0	0.0	0.0	0.0
40	90.625	0.0	0.0	0.0	0.0
41	91.35	0.0	0.0	0.0	0.0
42	92.6	0.0	0.0	0.0	0.0
43	92.925	0.0	0.0	0.0	0.0
44	93.225	0.0	0.0	0.0	0.0
45	93.55	0.0	0.0	0.0	0.0
46	93.9	0.0	0.0	0.0	0.0
47	94.15	0.0	0.0	0.0	0.0
48	94.375	0.0	0.0	0.0	0.0
49	94.65	0.0	0.0	0.0	0.0
50	94.725	0.0	0.0	0.0	0.0
51	94.75	0.0	0.0	0.0	0.0
52	94.75	0.0	0.0	0.0	0.0
53	94.775	0.0	0.0	0.0	0.0
54	94.775	0.0	0.0	0.0	0.0
55	94.775	0.0	0.0	0.0	0.0
56	94.775	0.0	0.0	0.0	0.0
57	94.775	0.0	0.0	0.0	0.0
58	94.775	0.0	0.0	0.0	0.0
59	94.775	0.0	0.0	0.0	0.0
60	94.775	0.0	0.0	0.0	0.0
61	94.775	0.0	0.0	0.0	0.0
62	94.775	0.0	0.0	0.0	0.0
63	94.775	0.0	0.0	0.0	0.0
64	94.775	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGGTCAG	30	7.878043E-8	70.00001	17
CCAACGG	15	0.0020658788	70.00001	12
TTGTAGT	30	7.878043E-8	70.00001	5
CCAGTGG	15	0.0020658788	70.00001	4
TCAGGAT	30	7.878043E-8	70.00001	20
AGTGGTC	15	0.0020658788	70.00001	6
GATAATT	15	0.0020658788	70.00001	23
GTCTGTA	15	0.0020658788	70.00001	3
TAGTCTA	30	7.878043E-8	70.00001	8
GGTCAGG	30	7.878043E-8	70.00001	18
TAGTCCA	15	0.0020658788	70.00001	8
ATAATTG	15	0.0020658788	70.00001	24
GGATAAT	15	0.0020658788	70.00001	22
TCTGTAG	15	0.0020658788	70.00001	4
TGTAGTC	45	3.6379788E-12	70.00001	6
TAATTGC	15	0.0020658788	70.00001	25
GTCCAAC	15	0.0020658788	70.00001	10
GTCTAGT	30	7.878043E-8	70.00001	10
TCCAACG	15	0.0020658788	70.00001	11
GTGGTCT	15	0.0020658788	70.00001	7
>>END_MODULE
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275320 READS because READLEN < 1
Read 275320 spots for SRR11699288.sra
Written 275320 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
Rejected 275302 READS because READLEN < 1
Read 275302 spots for SRR11699288.sra
Written 275302 spots for SRR11699288.sra
SRR ids: ['SRR11699288.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_0_vf96t_
SRR11699288.sra spots: 5506058
blocks: [[1, 275302], [275303, 550604], [550605, 825906], [825907, 1101208], [1101209, 1376510], [1376511, 1651812], [1651813, 1927114], [1927115, 2202416], [2202417, 2477718], [2477719, 2753020], [2753021, 3028322], [3028323, 3303624], [3303625, 3578926], [3578927, 3854228], [3854229, 4129530], [4129531, 4404832], [4404833, 4680134], [4680135, 4955436], [4955437, 5230738], [5230739, 5506058]]
SRR11699288 file size 1046347
SRR11699288 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 SRR11699288 SRR11699288_1.fastq
Input file:	SRR11699288_1.fastq
trimmed:	SRR11699288-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 09:10:01 2025 >> started

Wed Jun 18 09:10:03 2025 >> done (2.335s)
5506058 reads processed; of these:
1070491 (19.44%) short reads filtered out after trimming by size control
   3467 ( 0.06%) empty reads filtered out after trimming by size control
4432100 (80.49%) reads available; of these:
4352290 (98.20%) trimmed reads available after processing
  79810 ( 1.80%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 139205	  3.14%
 19	 195782	  4.42%
 20	 236584	  5.34%
 21	 326644	  7.37%
 22	 486005	 10.97%
 23	 198350	  4.48%
 24	 449171	 10.13%
 25	 213665	  4.82%
 26	 164126	  3.70%
 27	 185512	  4.19%
 28	 129181	  2.91%
 29	 143337	  3.23%
 30	 222935	  5.03%
 31	 176794	  3.99%
 32	 196185	  4.43%
 33	 154578	  3.49%
 34	 125221	  2.83%
 35	 177463	  4.00%
 36	  93430	  2.11%
 37	  73814	  1.67%
 38	  55873	  1.26%
 39	  51641	  1.17%
 40	  40959	  0.92%
 41	  47855	  1.08%
 42	  29399	  0.66%
 43	  22964	  0.52%
 44	  15609	  0.35%
 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	      1	  0.00%
 66	      0	  0.00%
 67	      0	  0.00%
 68	      0	  0.00%
 69	      0	  0.00%
 70	      0	  0.00%
 71	      1	  0.00%
 72	      1	  0.00%
 73	      0	  0.00%
 74	      1	  0.00%
 75	      4	  0.00%
 76	  79810	  1.80%
4432100 reads passed initial QC


criterion=sequence-density
sequence-density=3.82
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAAGACCCGGGTT


criterion=fanout-score
sequence-density=0.14
sequence-density-rank=21
fanout-score=23.08
fanout-score-rank=1
prefix-density=2.24
prefix-fanout=1.5
sequence=GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTG
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 09:10:30
                             Started mapping on |	Jun 18 09:10:30
                                    Finished on |	Jun 18 09:10:43
       Mapping speed, Million of reads per hour |	1227.35

                          Number of input reads |	4432100
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	419446
                        Uniquely mapped reads % |	9.46%
                          Average mapped length |	24.16
                       Number of splices: Total |	8633
            Number of splices: Annotated (sjdb) |	3820
                       Number of splices: GT/AG |	7936
                       Number of splices: GC/AG |	504
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	191
                      Mismatch rate per base, % |	1.01%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.34
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.24
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	605659
             % of reads mapped to multiple loci |	13.67%
        Number of reads mapped to too many loci |	1002603
             % of reads mapped to too many loci |	22.62%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.91%
                     % of reads unmapped: other |	48.34%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3406995	3406995	3406995
N_multimapping	605659	605659	605659
N_noFeature	346742	360558	403300
N_ambiguous	2380	35	23
UnstrandedReadsAssigned:70324 PositiveStrandReadsAssigned:58853 NegativeStrandReadsAssigned:16123
Dataset is classified unstranded
MeadianReadLen=25 20thPercentileLength=21 echo kmer=19
SRR11699288 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: SRR11699288-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,432,100 reads, 891,774 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,025 rounds

  72540 SRR11699288.ke.tsv
  44303 SRR11699288.se.tsv
 116843 total
==> SRR11699288.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	1	0.362187
Zm00001eb323640_T001	3273	3174	1	0.378619
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

==> SRR11699288.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	1
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699288 completed mapping pipeline successfully
