Starting /dee2/code/volunteer_pipeline.sh SRR11699399
    current disk space = 2460346798080
    free memory = 579190412 
SRR11699399 SRAfilesize
a45c9ef786f54b8ff78ba74cb646bdab  SRR11699399.sra
SRR11699399.sra file validated
SRR11699399 is single end
SRR11699399 is conventional basespace
SRR11699399 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699399_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	warn
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.315	32.0	32.0	32.0	32.0	32.0
2	31.464	32.0	32.0	32.0	32.0	32.0
3	31.48675	32.0	32.0	32.0	32.0	32.0
4	31.5095	32.0	32.0	32.0	32.0	32.0
5	31.57125	32.0	32.0	32.0	32.0	32.0
6	35.00925	36.0	36.0	36.0	36.0	36.0
7	35.12275	36.0	36.0	36.0	36.0	36.0
8	35.057	36.0	36.0	36.0	36.0	36.0
9	34.94925	36.0	36.0	36.0	36.0	36.0
10-11	35.12575	36.0	36.0	36.0	36.0	36.0
12-13	35.1875	36.0	36.0	36.0	36.0	36.0
14-15	35.161500000000004	36.0	36.0	36.0	36.0	36.0
16-17	35.1905	36.0	36.0	36.0	36.0	36.0
18-19	35.2345	36.0	36.0	36.0	36.0	36.0
20-21	35.0755	36.0	36.0	36.0	36.0	36.0
22-23	35.04275	36.0	36.0	36.0	36.0	36.0
24-25	35.090625	36.0	36.0	36.0	36.0	36.0
26-27	35.014	36.0	36.0	36.0	36.0	36.0
28-29	35.061625	36.0	36.0	36.0	36.0	36.0
30-31	34.974875	36.0	36.0	36.0	36.0	36.0
32-33	34.91775	36.0	36.0	36.0	36.0	36.0
34-35	35.0345	36.0	36.0	36.0	36.0	36.0
36-37	34.998	36.0	36.0	36.0	36.0	36.0
38-39	34.983125	36.0	36.0	36.0	36.0	36.0
40-41	34.98725	36.0	36.0	36.0	36.0	36.0
42-43	34.899125	36.0	36.0	36.0	36.0	36.0
44-45	34.831	36.0	36.0	36.0	34.0	36.0
46-47	34.778625000000005	36.0	36.0	36.0	34.0	36.0
48-49	34.58825	36.0	36.0	36.0	34.0	36.0
50-51	34.117625000000004	36.0	36.0	36.0	32.0	36.0
52-53	33.89975	36.0	36.0	36.0	29.5	36.0
54-55	33.17575	36.0	36.0	36.0	20.5	36.0
56-57	32.057125	36.0	32.0	36.0	14.0	36.0
58-59	31.06025	36.0	32.0	36.0	14.0	36.0
60-61	30.088875	36.0	20.5	36.0	14.0	36.0
62-63	29.45525	36.0	14.0	36.0	14.0	36.0
64-65	28.058500000000002	34.0	14.0	36.0	14.0	36.0
66-67	26.226125000000003	32.0	14.0	36.0	14.0	36.0
68-69	25.791249999999998	29.5	14.0	36.0	14.0	36.0
70-71	25.81525	32.0	14.0	36.0	14.0	36.0
72-73	25.52375	27.0	14.0	36.0	14.0	36.0
74-75	25.742	29.5	14.0	36.0	14.0	36.0
76	22.97875	21.0	14.0	32.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	1.0
22	4.0
23	11.0
24	21.0
25	29.0
26	50.0
27	79.0
28	122.0
29	218.0
30	338.0
31	449.0
32	500.0
33	716.0
34	903.0
35	559.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	24.7	30.0	20.45	24.85
2	23.45	27.175	26.924999999999997	22.45
3	25.55	35.949999999999996	15.925	22.575
4	26.625	34.0	17.849999999999998	21.525
5	21.975	27.200000000000003	20.674999999999997	30.15
6	26.650000000000002	28.799999999999997	25.424999999999997	19.125
7	30.15	37.974999999999994	15.7	16.175
8	20.65	28.525	29.275000000000002	21.55
9	25.4	33.125	15.65	25.825
10-11	30.625000000000004	30.1375	21.6625	17.575
12-13	21.337500000000002	23.525	23.925	31.2125
14-15	30.675	38.324999999999996	16.1375	14.8625
16-17	22.9875	24.875	32.6125	19.525000000000002
18-19	35.4375	24.9875	23.45	16.125
20-21	24.4375	37.0375	22.2625	16.2625
22-23	32.275	39.4125	12.2125	16.1
24-25	29.799999999999997	38.9375	13.850000000000001	17.4125
26-27	29.299999999999997	31.4625	16.400000000000002	22.8375
28-29	33.4125	30.575000000000003	13.4375	22.575
30-31	31.3125	37.0875	9.8375	21.762500000000003
32-33	29.049999999999997	36.15	11.55	23.25
34-35	29.462500000000002	29.2875	14.149999999999999	27.1
36-37	23.724999999999998	34.7125	11.700000000000001	29.862499999999997
38-39	23.2125	31.424999999999997	15.024999999999999	30.337500000000002
40-41	23.05	27.8125	19.0125	30.125
42-43	23.7625	26.6	20.275000000000002	29.362500000000004
44-45	20.3125	32.5375	16.3625	30.7875
46-47	17.962500000000002	30.3	16.425	35.3125
48-49	14.4625	28.4125	17.4	39.725
50-51	16.3	29.4875	17.8625	36.35
52-53	18.275	26.150000000000002	21.212500000000002	34.362500000000004
54-55	14.887500000000001	30.9625	19.125	35.025
56-57	13.275	26.5625	19.7125	40.45
58-59	18.6625	29.062500000000004	20.549999999999997	31.724999999999998
60-61	14.025000000000002	27.224999999999998	28.3875	30.362499999999997
62-63	13.925	26.075	28.462500000000002	31.5375
64-65	11.2875	19.9125	31.175000000000004	37.625
66-67	15.024999999999999	16.4625	33.75	34.7625
68-69	16.950000000000003	17.6875	34.8375	30.525000000000002
70-71	16.775000000000002	17.4625	36.6	29.1625
72-73	18.4375	14.2	34.2125	33.15
74-75	17.8	11.675	36.1	34.425
76	11.3	10.424999999999999	47.925000000000004	30.349999999999998
>>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	0.0
27	0.5
28	0.5
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	1.5
39	2.5
40	4.0
41	17.0
42	28.0
43	37.5
44	77.0
45	170.5
46	234.0
47	428.5
48	752.0
49	745.0
50	609.0
51	561.0
52	438.5
53	307.0
54	250.0
55	195.5
56	114.0
57	73.0
58	59.0
59	47.0
60	20.0
61	3.5
62	2.0
63	1.5
64	0.5
65	0.5
66	0.5
67	0.0
68	0.0
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	0.5
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	59.75
#Duplication Level	Percentage of deduplicated	Percentage of total
1	88.3682008368201	52.800000000000004
2	5.606694560669457	6.7
3	1.715481171548117	3.075
4	1.00418410041841	2.4
5	0.41841004184100417	1.25
6	0.5439330543933054	1.95
7	0.2928870292887029	1.225
8	0.2928870292887029	1.4000000000000001
9	0.12552301255230125	0.675
>10	1.4644351464435146	17.95
>50	0.12552301255230125	5.0
>100	0.04184100418410042	5.575
>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	223	5.575	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	77	1.925	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	63	1.575	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	60	1.5	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAG	41	1.0250000000000001	TruSeq Adapter, Index 7 (100% over 36bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	39	0.975	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	38	0.95	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGA	36	0.8999999999999999	TruSeq Adapter, Index 7 (100% over 37bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	34	0.8500000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	33	0.8250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAG	31	0.775	TruSeq Adapter, Index 7 (100% over 36bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	29	0.7250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	23	0.575	No Hit
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCAT	23	0.575	TruSeq Adapter, Index 7 (100% over 41bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	20	0.5	TruSeq Adapter, Index 7 (100% over 35bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	19	0.475	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	17	0.42500000000000004	No Hit
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	17	0.42500000000000004	TruSeq Adapter, Index 7 (100% over 35bp)
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCA	16	0.4	TruSeq Adapter, Index 7 (100% over 40bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGACGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	12	0.3	TruSeq Adapter, Index 7 (100% over 35bp)
AGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGAT	11	0.27499999999999997	TruSeq Adapter, Index 7 (100% over 38bp)
AAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAG	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGAT	11	0.27499999999999997	TruSeq Adapter, Index 7 (100% over 38bp)
CTAACGAACGAACGATTTGAACAGATCGGAAGGGCACACGTCTGAACTCC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (96% over 28bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATC	11	0.27499999999999997	TruSeq Adapter, Index 7 (100% over 39bp)
TAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	10	0.25	No Hit
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	10	0.25	No Hit
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	8	0.2	No Hit
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAAAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	7	0.17500000000000002	TruSeq Adapter, Index 7 (100% over 35bp)
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	7	0.17500000000000002	No Hit
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGGGCACACGTCTGAAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (96% over 25bp)
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	6	0.15	No Hit
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	6	0.15	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	6	0.15	No Hit
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	6	0.15	No Hit
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	6	0.15	No Hit
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGACCCCAGGTCAGTCGGGAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GACACGACTCTCGGCAACGGATATCTCAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAG	6	0.15	TruSeq Adapter, Index 7 (100% over 36bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	6	0.15	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTAGATCGGAAGAGCACAC	6	0.15	No Hit
GAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATC	5	0.125	TruSeq Adapter, Index 7 (100% over 42bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GGGCCTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAG	5	0.125	TruSeq Adapter, Index 7 (100% over 36bp)
GCCCCCATCGTCTAGTGGTTCAGGACAAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
>>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	0.025	0.0	0.0	0.0	0.0
2	0.2	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	0.525	0.0	0.0	0.0	0.0
6	0.825	0.0	0.0	0.0	0.0
7	0.9	0.0	0.0	0.0	0.0
8	1.275	0.0	0.0	0.0	0.0
9	2.225	0.0	0.0	0.0	0.0
10	3.125	0.0	0.0	0.0	0.0
11	3.85	0.0	0.0	0.0	0.0
12	4.9	0.0	0.0	0.0	0.0
13	6.775	0.0	0.0	0.0	0.0
14	10.1	0.0	0.0	0.0	0.0
15	13.05	0.0	0.0	0.0	0.0
16	15.125	0.0	0.0	0.0	0.0
17	19.05	0.0	0.0	0.0	0.0
18	22.7	0.0	0.0	0.0	0.0
19	25.325	0.0	0.0	0.0	0.0
20	29.4	0.0	0.0	0.0	0.0
21	34.0	0.0	0.0	0.0	0.0
22	39.7	0.0	0.0	0.0	0.0
23	49.9	0.0	0.0	0.0	0.0
24	53.125	0.0	0.0	0.0	0.0
25	58.375	0.0	0.0	0.0	0.0
26	62.275	0.0	0.0	0.0	0.0
27	64.725	0.0	0.0	0.0	0.0
28	67.2	0.0	0.0	0.0	0.0
29	69.2	0.0	0.0	0.0	0.0
30	71.275	0.0	0.0	0.0	0.0
31	74.2	0.0	0.0	0.0	0.0
32	76.65	0.0	0.0	0.0	0.0
33	78.725	0.0	0.0	0.0	0.0
34	80.9	0.0	0.0	0.0	0.0
35	82.75	0.0	0.0	0.0	0.0
36	85.0	0.0	0.0	0.0	0.0
37	86.65	0.0	0.0	0.0	0.0
38	87.65	0.0	0.0	0.0	0.0
39	88.125	0.0	0.0	0.0	0.0
40	88.875	0.0	0.0	0.0	0.0
41	89.55	0.0	0.0	0.0	0.0
42	90.2	0.0	0.0	0.0	0.0
43	90.575	0.0	0.0	0.0	0.0
44	90.95	0.0	0.0	0.0	0.0
45	91.075	0.0	0.0	0.0	0.0
46	91.25	0.0	0.0	0.0	0.0
47	91.35	0.0	0.0	0.0	0.0
48	91.475	0.0	0.0	0.0	0.0
49	91.525	0.0	0.0	0.0	0.0
50	91.575	0.0	0.0	0.0	0.0
51	91.575	0.0	0.0	0.0	0.0
52	91.6	0.0	0.0	0.0	0.0
53	91.6	0.0	0.0	0.0	0.0
54	91.6	0.0	0.0	0.0	0.0
55	91.6	0.0	0.0	0.0	0.0
56	91.6	0.0	0.0	0.0	0.0
57	91.6	0.0	0.0	0.0	0.0
58	91.6	0.0	0.0	0.0	0.0
59	91.6	0.0	0.0	0.0	0.0
60	91.6	0.0	0.0	0.0	0.0
61	91.6	0.0	0.0	0.0	0.0
62	91.6	0.0	0.0	0.0	0.0
63	91.6	0.0	0.0	0.0	0.0
64	91.6	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
GGTTAGG	15	0.0020658788	70.00001	17
TGTAGTC	15	0.0020658788	70.00001	6
GTTAGGA	15	0.0020658788	70.00001	18
GTCTAGC	20	7.003785E-5	70.0	10
CGGTTAG	20	0.0064587677	52.5	16
CTAACGA	85	0.0	45.294113	1
GAACGAA	95	1.8189894E-12	40.526318	6
TAACGAA	100	3.6379788E-12	38.5	2
TCTGCTT	40	0.0021434545	35.0	70
GAACGAT	110	4.6020432E-10	31.81818	10
TGCCGTC	45	0.003819767	31.111113	70
AACGATT	125	1.8171704E-9	28.0	11
ATGCCGT	75	4.3394008E-5	28.0	70
ACGATTT	125	1.8171704E-9	28.0	12
TTCTGCT	50	0.0063971295	27.999998	69
CGATTTG	130	2.764864E-9	26.923077	13
GATTTGA	135	4.14002E-9	25.925926	14
TTTGAAC	110	6.588034E-7	25.454544	16
ATTTGAA	140	6.1081664E-9	25.000002	15
>>END_MODULE
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250858 READS because READLEN < 1
Read 250858 spots for SRR11699399.sra
Written 250858 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
Rejected 250851 READS because READLEN < 1
Read 250851 spots for SRR11699399.sra
Written 250851 spots for SRR11699399.sra
SRR ids: ['SRR11699399.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_9yr47jlt
SRR11699399.sra spots: 5017027
blocks: [[1, 250851], [250852, 501702], [501703, 752553], [752554, 1003404], [1003405, 1254255], [1254256, 1505106], [1505107, 1755957], [1755958, 2006808], [2006809, 2257659], [2257660, 2508510], [2508511, 2759361], [2759362, 3010212], [3010213, 3261063], [3261064, 3511914], [3511915, 3762765], [3762766, 4013616], [4013617, 4264467], [4264468, 4515318], [4515319, 4766169], [4766170, 5017027]]
SRR11699399 file size 953221
SRR11699399 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 SRR11699399 SRR11699399_1.fastq
Input file:	SRR11699399_1.fastq
trimmed:	SRR11699399-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
Thu Jun 19 03:21:51 2025 >> started

Thu Jun 19 03:32:50 2025 >> done (659.115s)
5017027 reads processed; of these:
1302109 (25.95%) short reads filtered out after trimming by size control
   1989 ( 0.04%) empty reads filtered out after trimming by size control
3712929 (74.01%) reads available; of these:
3666247 (98.74%) trimmed reads available after processing
  46682 ( 1.26%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 144788	  3.90%
 19	 229777	  6.19%
 20	 247695	  6.67%
 21	 318702	  8.58%
 22	 523350	 14.10%
 23	 176443	  4.75%
 24	 338598	  9.12%
 25	 234901	  6.33%
 26	 125156	  3.37%
 27	 129788	  3.50%
 28	 100669	  2.71%
 29	 106005	  2.86%
 30	 152914	  4.12%
 31	 109784	  2.96%
 32	 115832	  3.12%
 33	 114585	  3.09%
 34	  99708	  2.69%
 35	 113568	  3.06%
 36	  71771	  1.93%
 37	  50753	  1.37%
 38	  36094	  0.97%
 39	  31932	  0.86%
 40	  23139	  0.62%
 41	  34206	  0.92%
 42	  16299	  0.44%
 43	  12192	  0.33%
 44	   7596	  0.20%
 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	      1	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      1	  0.00%
 76	  46682	  1.26%
3712929 reads passed initial QC


criterion=sequence-density
sequence-density=2.57
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=15
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAA


criterion=fanout-score
sequence-density=0.39
sequence-density-rank=14
fanout-score=14.92
fanout-score-rank=1
prefix-density=1.25
prefix-fanout=4.6
sequence=GTCTAGTGGTATGATTCTCGCTT
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 19 03:35:49
                             Started mapping on |	Jun 19 03:35:52
                                    Finished on |	Jun 19 03:38:12
       Mapping speed, Million of reads per hour |	95.48

                          Number of input reads |	3712929
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	276696
                        Uniquely mapped reads % |	7.45%
                          Average mapped length |	23.13
                       Number of splices: Total |	6116
            Number of splices: Annotated (sjdb) |	2236
                       Number of splices: GT/AG |	5554
                       Number of splices: GC/AG |	418
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	142
                      Mismatch rate per base, % |	1.23%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.43
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.07
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	365109
             % of reads mapped to multiple loci |	9.83%
        Number of reads mapped to too many loci |	732405
             % of reads mapped to too many loci |	19.73%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.42%
                     % of reads unmapped: other |	57.57%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3071124	3071124	3071124
N_multimapping	365109	365109	365109
N_noFeature	233815	241886	267443
N_ambiguous	1210	16	16
UnstrandedReadsAssigned:41671 PositiveStrandReadsAssigned:34794 NegativeStrandReadsAssigned:9237
Dataset is classified unstranded
MeadianReadLen=24 20thPercentileLength=21 echo kmer=19
SRR11699399 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: SRR11699399-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,712,929 reads, 573,314 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 908 rounds

  72540 SRR11699399.ke.tsv
  44303 SRR11699399.se.tsv
 116843 total
==> SRR11699399.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	1	0.937887
Zm00001eb321680_T001	3417	3318	1	0.556288
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

==> SRR11699399.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699399 completed mapping pipeline successfully
