Starting /dee2/code/volunteer_pipeline.sh SRR11699297
    current disk space = 2467277934592
    free memory = 1574523680 
SRR11699297 SRAfilesize
c6da94b0188c5eb71875894e62295b08  SRR11699297.sra
SRR11699297.sra file validated
SRR11699297 is single end
SRR11699297 is conventional basespace
SRR11699297 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699297_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	31.39875	32.0	32.0	32.0	32.0	32.0
2	31.4105	32.0	32.0	32.0	32.0	32.0
3	31.5975	32.0	32.0	32.0	32.0	32.0
4	31.55625	32.0	32.0	32.0	32.0	32.0
5	31.63275	32.0	32.0	32.0	32.0	32.0
6	35.1605	36.0	36.0	36.0	36.0	36.0
7	35.2575	36.0	36.0	36.0	36.0	36.0
8	35.306	36.0	36.0	36.0	36.0	36.0
9	35.0405	36.0	36.0	36.0	36.0	36.0
10-11	35.217	36.0	36.0	36.0	36.0	36.0
12-13	35.164125	36.0	36.0	36.0	36.0	36.0
14-15	35.148125	36.0	36.0	36.0	36.0	36.0
16-17	35.236625000000004	36.0	36.0	36.0	36.0	36.0
18-19	35.268874999999994	36.0	36.0	36.0	36.0	36.0
20-21	35.086875	36.0	36.0	36.0	36.0	36.0
22-23	35.124125	36.0	36.0	36.0	36.0	36.0
24-25	35.144999999999996	36.0	36.0	36.0	36.0	36.0
26-27	35.037499999999994	36.0	36.0	36.0	36.0	36.0
28-29	35.115375	36.0	36.0	36.0	36.0	36.0
30-31	35.06625	36.0	36.0	36.0	36.0	36.0
32-33	34.9825	36.0	36.0	36.0	36.0	36.0
34-35	35.104749999999996	36.0	36.0	36.0	36.0	36.0
36-37	35.068625	36.0	36.0	36.0	36.0	36.0
38-39	35.080375000000004	36.0	36.0	36.0	36.0	36.0
40-41	35.073	36.0	36.0	36.0	36.0	36.0
42-43	35.02475	36.0	36.0	36.0	36.0	36.0
44-45	34.933625000000006	36.0	36.0	36.0	36.0	36.0
46-47	34.9925	36.0	36.0	36.0	36.0	36.0
48-49	34.82475	36.0	36.0	36.0	36.0	36.0
50-51	34.622	36.0	36.0	36.0	32.0	36.0
52-53	34.532	36.0	36.0	36.0	32.0	36.0
54-55	34.257125	36.0	36.0	36.0	32.0	36.0
56-57	34.157875	36.0	36.0	36.0	32.0	36.0
58-59	34.0775	36.0	36.0	36.0	32.0	36.0
60-61	34.05275	36.0	36.0	36.0	32.0	36.0
62-63	33.818	36.0	36.0	36.0	32.0	36.0
64-65	33.704499999999996	36.0	36.0	36.0	27.0	36.0
66-67	33.277625	36.0	32.0	36.0	27.0	36.0
68-69	33.466875	36.0	34.0	36.0	27.0	36.0
70-71	33.557	36.0	34.0	36.0	27.0	36.0
72-73	33.416375	36.0	36.0	36.0	27.0	36.0
74-75	33.62225	36.0	36.0	36.0	29.5	36.0
76	31.6345	36.0	32.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
18	1.0
19	0.0
20	0.0
21	1.0
22	3.0
23	7.0
24	7.0
25	11.0
26	15.0
27	25.0
28	52.0
29	61.0
30	92.0
31	119.0
32	173.0
33	313.0
34	816.0
35	2304.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	25.575	30.025000000000002	21.925	22.475
2	27.375	27.3	23.724999999999998	21.6
3	32.175	30.15	18.025	19.650000000000002
4	28.599999999999998	35.099999999999994	17.75	18.55
5	21.224999999999998	25.6	25.624999999999996	27.55
6	25.874999999999996	24.7	29.45	19.975
7	33.575	32.125	18.05	16.25
8	23.35	25.4	32.0	19.25
9	22.675	35.8	19.45	22.075
10-11	32.2875	26.387500000000003	23.0625	18.2625
12-13	21.6625	22.8	24.7	30.837500000000002
14-15	29.15	36.9375	18.1875	15.725
16-17	23.7125	24.3875	33.5	18.4
18-19	36.1875	23.65	22.375	17.7875
20-21	24.075	35.225	22.3625	18.337500000000002
22-23	32.875	38.0625	13.200000000000001	15.862499999999999
24-25	29.65	38.15	15.375	16.825000000000003
26-27	27.525	33.074999999999996	15.662499999999998	23.7375
28-29	30.562499999999996	29.125	14.000000000000002	26.3125
30-31	34.0125	33.9375	10.35	21.7
32-33	27.400000000000002	36.125	12.4	24.075
34-35	29.4375	31.674999999999997	14.000000000000002	24.887500000000003
36-37	24.462500000000002	36.5	11.65	27.3875
38-39	24.05	30.625000000000004	15.0	30.325000000000003
40-41	25.3	27.712500000000002	16.875	30.112499999999997
42-43	27.437499999999996	29.512500000000003	19.175	23.875
44-45	21.0375	35.475	16.037499999999998	27.450000000000003
46-47	20.0	32.3125	14.625	33.0625
48-49	14.5625	33.6	15.25	36.5875
50-51	18.3625	32.1	16.412499999999998	33.125
52-53	17.1	28.125	22.275	32.5
54-55	15.537500000000001	32.5625	20.7125	31.1875
56-57	12.987499999999999	37.4625	18.8875	30.662499999999998
58-59	15.837499999999999	37.0625	17.0875	30.012499999999996
60-61	13.65	29.775000000000002	24.85	31.724999999999998
62-63	16.6375	27.237499999999997	27.287499999999998	28.8375
64-65	13.3125	23.8875	29.775000000000002	33.025
66-67	16.5625	21.0	29.9875	32.45
68-69	16.3	23.0875	31.5375	29.075
70-71	18.65	23.474999999999998	32.2625	25.6125
72-73	20.625	17.775	30.025000000000002	31.574999999999996
74-75	20.575	14.4625	33.725	31.2375
76	14.099999999999998	14.45	39.75	31.7
>>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	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.5
35	0.5
36	0.5
37	1.0
38	3.0
39	6.0
40	15.5
41	40.5
42	57.0
43	84.0
44	143.0
45	256.0
46	337.0
47	619.0
48	725.5
49	597.0
50	644.0
51	577.0
52	398.5
53	217.5
54	148.0
55	113.5
56	89.5
57	63.5
58	27.0
59	20.0
60	9.5
61	5.0
62	4.0
63	4.0
64	2.5
65	1.0
66	1.0
67	1.0
68	1.0
69	0.5
70	0.5
71	1.0
72	0.5
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	1.0
91	1.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.5
98	0.5
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	63.975
#Duplication Level	Percentage of deduplicated	Percentage of total
1	89.83978116451739	57.475
2	4.337631887456038	5.55
3	1.6412661195779603	3.15
4	1.2504884720593983	3.2
5	0.3907776475185619	1.25
6	0.4298554122704181	1.6500000000000001
7	0.3516998827667058	1.575
8	0.2735443532629933	1.4000000000000001
9	0.15631105900742479	0.8999999999999999
>10	1.1723329425556859	14.174999999999999
>50	0.11723329425556857	5.6000000000000005
>100	0.039077764751856196	4.075
>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	163	4.075	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAA	95	2.375	TruSeq Adapter, Index 5 (97% over 36bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	78	1.95	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAA	51	1.275	TruSeq Adapter, Index 5 (97% over 36bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	45	1.125	No Hit
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	40	1.0	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	29	0.7250000000000001	No Hit
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	27	0.675	No Hit
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	25	0.625	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAAG	24	0.6	TruSeq Adapter, Index 5 (97% over 37bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	22	0.5499999999999999	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	22	0.5499999999999999	No Hit
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	18	0.44999999999999996	No Hit
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAAGCTAT	15	0.375	TruSeq Adapter, Index 5 (97% over 37bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	13	0.325	No Hit
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG	11	0.27499999999999997	No Hit
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	11	0.27499999999999997	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA	9	0.22499999999999998	TruSeq Adapter, Index 7 (97% over 35bp)
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAAGCT	9	0.22499999999999998	TruSeq Adapter, Index 5 (97% over 37bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	9	0.22499999999999998	No Hit
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	8	0.2	No Hit
AAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
ACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	8	0.2	No Hit
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	8	0.2	No Hit
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAAGCTA	8	0.2	TruSeq Adapter, Index 5 (97% over 37bp)
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAGATCGGAAGA	7	0.17500000000000002	No Hit
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAAGC	7	0.17500000000000002	TruSeq Adapter, Index 5 (97% over 37bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	7	0.17500000000000002	No Hit
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	6	0.15	No Hit
CAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CGACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAATCAGATCGGAAGAG	6	0.15	No Hit
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCACCAGTAGTCTAGTGGTAGAATAGTACCCAGATCGGAAGAGCACACGT	6	0.15	No Hit
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	6	0.15	No Hit
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	5	0.125	No Hit
GCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	5	0.125	No Hit
CGACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAAGCTATC	5	0.125	TruSeq Adapter, Index 5 (97% over 37bp)
CGACACGACTCTCGGCAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTAGATCGGAAGAGCACAC	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	0.0	0.0	0.0	0.0	0.0
2	0.1	0.0	0.0	0.0	0.0
3	0.15	0.0	0.0	0.0	0.0
4	0.25	0.0	0.0	0.0	0.0
5	0.3	0.0	0.0	0.0	0.0
6	0.5	0.0	0.0	0.0	0.0
7	0.725	0.0	0.0	0.0	0.0
8	0.975	0.0	0.0	0.0	0.0
9	1.675	0.0	0.0	0.0	0.0
10	2.325	0.0	0.0	0.0	0.0
11	3.0	0.0	0.0	0.0	0.0
12	3.8	0.0	0.0	0.0	0.0
13	5.175	0.0	0.0	0.0	0.0
14	9.9	0.0	0.0	0.0	0.0
15	10.925	0.0	0.0	0.0	0.0
16	12.625	0.0	0.0	0.0	0.0
17	15.3	0.0	0.0	0.0	0.0
18	17.725	0.0	0.0	0.0	0.0
19	19.85	0.0	0.0	0.0	0.0
20	23.325	0.0	0.0	0.0	0.0
21	26.475	0.0	0.0	0.0	0.0
22	34.05	0.0	0.0	0.0	0.0
23	42.475	0.0	0.0	0.0	0.0
24	45.475	0.0	0.0	0.0	0.0
25	52.45	0.0	0.0	0.0	0.0
26	55.8	0.0	0.0	0.0	0.0
27	58.25	0.0	0.0	0.0	0.0
28	60.875	0.0	0.0	0.0	0.0
29	63.0	0.0	0.0	0.0	0.0
30	65.7	0.0	0.0	0.0	0.0
31	68.5	0.0	0.0	0.0	0.0
32	70.975	0.0	0.0	0.0	0.0
33	73.525	0.0	0.0	0.0	0.0
34	76.8	0.0	0.0	0.0	0.0
35	80.65	0.0	0.0	0.0	0.0
36	84.5	0.0	0.0	0.0	0.0
37	86.8	0.0	0.0	0.0	0.0
38	88.225	0.0	0.0	0.0	0.0
39	89.575	0.0	0.0	0.0	0.0
40	90.575	0.0	0.0	0.0	0.0
41	91.45	0.0	0.0	0.0	0.0
42	92.8	0.0	0.0	0.0	0.0
43	93.4	0.0	0.0	0.0	0.0
44	93.925	0.0	0.0	0.0	0.0
45	94.475	0.0	0.0	0.0	0.0
46	94.9	0.0	0.0	0.0	0.0
47	95.225	0.0	0.0	0.0	0.0
48	95.4	0.0	0.0	0.0	0.0
49	95.65	0.0	0.0	0.0	0.0
50	95.775	0.0	0.0	0.0	0.0
51	95.825	0.0	0.0	0.0	0.0
52	95.875	0.0	0.0	0.0	0.0
53	95.875	0.0	0.0	0.0	0.0
54	95.875	0.0	0.0	0.0	0.0
55	95.9	0.0	0.0	0.0	0.0
56	95.9	0.0	0.0	0.0	0.0
57	95.9	0.0	0.0	0.0	0.0
58	95.925	0.0	0.0	0.0	0.0
59	95.975	0.0	0.0	0.0	0.0
60	95.975	0.0	0.0	0.0	0.0
61	96.0	0.0	0.0	0.0	0.0
62	96.0	0.0	0.0	0.0	0.0
63	96.0	0.0	0.0	0.0	0.0
64	96.0	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGGTCAG	30	7.878043E-8	70.00001	17
CTATAGC	15	0.0020658788	70.00001	5
AGCTCAG	35	2.6138878E-9	70.00001	9
TTCAATT	30	7.878043E-8	70.00001	11
TTGTAGT	35	2.6138878E-9	70.00001	5
ATTGGTC	30	7.878043E-8	70.00001	15
CCGCCCT	15	0.0020658788	70.00001	28
TAGCTCA	35	2.6138878E-9	70.00001	8
TAAGATC	15	0.0020658788	70.00001	21
CAATTGG	30	7.878043E-8	70.00001	13
TCAATTG	30	7.878043E-8	70.00001	12
GGTCAGA	30	7.878043E-8	70.00001	18
GTTCAAT	30	7.878043E-8	70.00001	10
GATTGTA	30	7.878043E-8	70.00001	3
TAGTTCA	30	7.878043E-8	70.00001	8
GCTATAG	15	0.0020658788	70.00001	4
CAGAGCA	30	7.878043E-8	70.00001	21
TCAGAGC	30	7.878043E-8	70.00001	20
TGTAGTT	30	7.878043E-8	70.00001	6
CTCAGAT	30	7.878043E-8	70.00001	11
>>END_MODULE
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
Rejected 273060 READS because READLEN < 1
Read 273060 spots for SRR11699297.sra
Written 273060 spots for SRR11699297.sra
Rejected 273055 READS because READLEN < 1
Read 273055 spots for SRR11699297.sra
Written 273055 spots for SRR11699297.sra
SRR ids: ['SRR11699297.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_myjoqbsz
SRR11699297.sra spots: 5461105
blocks: [[1, 273055], [273056, 546110], [546111, 819165], [819166, 1092220], [1092221, 1365275], [1365276, 1638330], [1638331, 1911385], [1911386, 2184440], [2184441, 2457495], [2457496, 2730550], [2730551, 3003605], [3003606, 3276660], [3276661, 3549715], [3549716, 3822770], [3822771, 4095825], [4095826, 4368880], [4368881, 4641935], [4641936, 4914990], [4914991, 5188045], [5188046, 5461105]]
SRR11699297 file size 1037787
SRR11699297 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 SRR11699297 SRR11699297_1.fastq
Input file:	SRR11699297_1.fastq
trimmed:	SRR11699297-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 10:37:34 2025 >> started

Wed Jun 18 10:37:37 2025 >> done (3.070s)
5461105 reads processed; of these:
1040055 (19.04%) short reads filtered out after trimming by size control
   2779 ( 0.05%) empty reads filtered out after trimming by size control
4418271 (80.90%) reads available; of these:
4300494 (97.33%) trimmed reads available after processing
 117777 ( 2.67%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 121085	  2.74%
 19	 178038	  4.03%
 20	 194793	  4.41%
 21	 383172	  8.67%
 22	 535798	 12.13%
 23	 174799	  3.96%
 24	 367274	  8.31%
 25	 173946	  3.94%
 26	 142430	  3.22%
 27	 142639	  3.23%
 28	 129085	  2.92%
 29	 148045	  3.35%
 30	 145135	  3.28%
 31	 136974	  3.10%
 32	 139159	  3.15%
 33	 180180	  4.08%
 34	 199111	  4.51%
 35	 219521	  4.97%
 36	 126071	  2.85%
 37	  91155	  2.06%
 38	  66490	  1.50%
 39	  64731	  1.47%
 40	  52882	  1.20%
 41	  92541	  2.09%
 42	  38065	  0.86%
 43	  32238	  0.73%
 44	  25134	  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	      1	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      2	  0.00%
 76	 117777	  2.67%
4418271 reads passed initial QC


criterion=sequence-density
sequence-density=6.30
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGG


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=40
fanout-score=70.78
fanout-score-rank=1
prefix-density=0.37
prefix-fanout=1.0
sequence=CCTCGTGTTTAGTTGCCACTATGAGTTTGGAACCCTGAACAGACCGCCGGTGTTAAGCCGGAGGAAGGAGATCGGAA
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -f sanger -l 18 -t 20 -x GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGG -o SRR11699297 -
Input file:	STDIN
trimmed:	SRR11699297-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGG
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ 
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	20
Wed Jun 18 10:37:43 2025 >> started

Wed Jun 18 10:37:45 2025 >> done (2.068s)
3155908 reads processed; of these:
   8484 ( 0.27%) short reads filtered out after trimming by size control
 201975 ( 6.40%) empty reads filtered out after trimming by size control
2945449 (93.33%) reads available; of these:
  22806 ( 0.77%) trimmed reads available after processing
2922643 (99.23%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  87593	  2.97%
 19	 127784	  4.34%
 20	 137372	  4.66%
 21	 272025	  9.24%
 22	 381311	 12.95%
 23	 124223	  4.22%
 24	 257229	  8.73%
 25	 123896	  4.21%
 26	  97414	  3.31%
 27	 100408	  3.41%
 28	  91662	  3.11%
 29	  96127	  3.26%
 30	 103215	  3.50%
 31	  97130	  3.30%
 32	  89993	  3.06%
 33	  83146	  2.82%
 34	  95194	  3.23%
 35	  92629	  3.14%
 36	  83964	  2.85%
 37	  60908	  2.07%
 38	  46382	  1.57%
 39	  45189	  1.53%
 40	  34898	  1.18%
 41	  65059	  2.21%
 42	  26437	  0.90%
 43	  22427	  0.76%
 44	  17825	  0.61%
 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	      2	  0.00%
 62	      0	  0.00%
 63	      1	  0.00%
 64	      0	  0.00%
 65	      0	  0.00%
 66	      1	  0.00%
 67	      0	  0.00%
 68	      1	  0.00%
 69	      0	  0.00%
 70	      0	  0.00%
 71	      0	  0.00%
 72	      1	  0.00%
 73	   2313	  0.08%
 74	      0	  0.00%
 75	      2	  0.00%
 76	  81688	  2.77%


criterion=sequence-density
sequence-density=2.20
sequence-density-rank=1
fanout-score=16.74
fanout-score-rank=3
prefix-density=2.24
prefix-fanout=16.4
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAAGCTATCTCGTATGCCGTCTTCTGCTTGA


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=34
fanout-score=67.65
fanout-score-rank=1
prefix-density=0.40
prefix-fanout=1.0
sequence=CCTCGTGTTTAGTTGCCACTATGAGTTTGGAACCCTGAACAGACCGCCGGTGTTAAGCCGGAGGAAGGAGATCGGAA
                                 Started job on |	Jun 18 10:37:56
                             Started mapping on |	Jun 18 10:37:56
                                    Finished on |	Jun 18 10:38:10
       Mapping speed, Million of reads per hour |	1082.01

                          Number of input reads |	4207812
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	374941
                        Uniquely mapped reads % |	8.91%
                          Average mapped length |	24.50
                       Number of splices: Total |	10024
            Number of splices: Annotated (sjdb) |	3426
                       Number of splices: GT/AG |	9188
                       Number of splices: GC/AG |	538
                       Number of splices: AT/AC |	6
               Number of splices: Non-canonical |	292
                      Mismatch rate per base, % |	1.40%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.47
                        Insertion rate per base |	0.01%
                       Insertion average length |	1.22
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	434241
             % of reads mapped to multiple loci |	10.32%
        Number of reads mapped to too many loci |	786813
             % of reads mapped to too many loci |	18.70%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.87%
                     % of reads unmapped: other |	52.20%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3398630	3398630	3398630
N_multimapping	434241	434241	434241
N_noFeature	310967	324074	359711
N_ambiguous	2203	38	53
UnstrandedReadsAssigned:61771 PositiveStrandReadsAssigned:50829 NegativeStrandReadsAssigned:15177
Dataset is classified unstranded
MeadianReadLen=25 20thPercentileLength=21 echo kmer=19
SRR11699297 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: SRR11699297-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,207,812 reads, 704,574 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 996 rounds

  72540 SRR11699297.ke.tsv
  44303 SRR11699297.se.tsv
 116843 total
==> SRR11699297.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	3	1.27776
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

==> SRR11699297.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	1
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699297 completed mapping pipeline successfully
