Starting /dee2/code/volunteer_pipeline.sh SRR11699282
    current disk space = 2469515456512
    free memory = 1575475368 
SRR11699282 SRAfilesize
1b26f72e714c84fcf91279b56d757541  SRR11699282.sra
SRR11699282.sra file validated
SRR11699282 is single end
SRR11699282 is conventional basespace
SRR11699282 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699282_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	31.3265	32.0	32.0	32.0	32.0	32.0
2	31.4385	32.0	32.0	32.0	32.0	32.0
3	31.55475	32.0	32.0	32.0	32.0	32.0
4	31.5425	32.0	32.0	32.0	32.0	32.0
5	31.527	32.0	32.0	32.0	32.0	32.0
6	35.04525	36.0	36.0	36.0	36.0	36.0
7	35.0775	36.0	36.0	36.0	36.0	36.0
8	35.05	36.0	36.0	36.0	36.0	36.0
9	34.94725	36.0	36.0	36.0	36.0	36.0
10-11	35.11625	36.0	36.0	36.0	36.0	36.0
12-13	35.127	36.0	36.0	36.0	36.0	36.0
14-15	35.108375	36.0	36.0	36.0	36.0	36.0
16-17	35.190625	36.0	36.0	36.0	36.0	36.0
18-19	35.257	36.0	36.0	36.0	36.0	36.0
20-21	35.006125	36.0	36.0	36.0	36.0	36.0
22-23	34.981375	36.0	36.0	36.0	36.0	36.0
24-25	35.06525	36.0	36.0	36.0	36.0	36.0
26-27	34.82325	36.0	36.0	36.0	34.0	36.0
28-29	34.983000000000004	36.0	36.0	36.0	36.0	36.0
30-31	34.884875	36.0	36.0	36.0	36.0	36.0
32-33	34.913125	36.0	36.0	36.0	36.0	36.0
34-35	35.005624999999995	36.0	36.0	36.0	36.0	36.0
36-37	35.039125	36.0	36.0	36.0	36.0	36.0
38-39	34.914	36.0	36.0	36.0	36.0	36.0
40-41	34.95975	36.0	36.0	36.0	36.0	36.0
42-43	34.909625	36.0	36.0	36.0	36.0	36.0
44-45	34.821625	36.0	36.0	36.0	34.0	36.0
46-47	34.860375000000005	36.0	36.0	36.0	36.0	36.0
48-49	34.711625	36.0	36.0	36.0	34.0	36.0
50-51	34.487875	36.0	36.0	36.0	32.0	36.0
52-53	34.268	36.0	36.0	36.0	32.0	36.0
54-55	34.079125	36.0	36.0	36.0	32.0	36.0
56-57	33.565250000000006	36.0	36.0	36.0	27.0	36.0
58-59	33.0925	36.0	36.0	36.0	20.5	36.0
60-61	32.944	36.0	36.0	36.0	14.0	36.0
62-63	32.402	36.0	32.0	36.0	14.0	36.0
64-65	31.984375	36.0	32.0	36.0	14.0	36.0
66-67	30.818875	36.0	27.0	36.0	14.0	36.0
68-69	30.925625	36.0	27.0	36.0	14.0	36.0
70-71	31.082375	36.0	32.0	36.0	14.0	36.0
72-73	31.23975	36.0	32.0	36.0	14.0	36.0
74-75	31.5655	36.0	32.0	36.0	14.0	36.0
76	27.884	32.0	14.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
19	1.0
20	0.0
21	2.0
22	1.0
23	4.0
24	11.0
25	17.0
26	41.0
27	48.0
28	82.0
29	98.0
30	146.0
31	189.0
32	287.0
33	409.0
34	1153.0
35	1511.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	23.575	29.049999999999997	23.125	24.25
2	22.925	27.325	27.500000000000004	22.25
3	25.3	33.85	18.7	22.15
4	27.3	34.35	18.7	19.650000000000002
5	21.925	26.575	22.925	28.575
6	27.375	25.75	25.6	21.275
7	32.125	34.1	17.575	16.2
8	22.85	29.275000000000002	27.075	20.8
9	22.225	32.625	19.3	25.85
10-11	31.75	28.199999999999996	21.95	18.099999999999998
12-13	22.237499999999997	25.087500000000002	22.675	30.0
14-15	28.849999999999998	36.8125	17.724999999999998	16.6125
16-17	23.425	23.875	32.8125	19.8875
18-19	35.475	23.525	23.3375	17.6625
20-21	24.6125	35.8125	22.5125	17.0625
22-23	31.5	37.2	14.499999999999998	16.8
24-25	28.549999999999997	37.1125	16.25	18.087500000000002
26-27	29.675	32.175	16.2625	21.8875
28-29	30.175	29.7	15.8	24.325
30-31	33.887499999999996	34.2375	11.3625	20.5125
32-33	28.3875	37.3875	12.174999999999999	22.05
34-35	29.512500000000003	32.5125	13.375	24.6
36-37	26.237500000000004	34.425	11.1	28.237499999999997
38-39	24.5375	33.1125	14.025000000000002	28.325
40-41	25.074999999999996	28.6625	17.05	29.212500000000002
42-43	27.037499999999998	28.0625	19.400000000000002	25.5
44-45	22.05	34.075	16.175	27.700000000000003
46-47	21.3875	31.55	15.937499999999998	31.125000000000004
48-49	16.125	30.475	16.6375	36.762499999999996
50-51	19.15	28.9875	19.8625	32.0
52-53	19.787499999999998	27.650000000000002	21.587500000000002	30.975
54-55	18.4125	28.725	23.0125	29.849999999999998
56-57	18.175	31.5125	21.3625	28.95
58-59	18.8375	32.087500000000006	23.5125	25.5625
60-61	21.875	24.962500000000002	29.5875	23.575
62-63	18.0	25.2	31.912499999999998	24.887500000000003
64-65	16.375	23.4875	32.425	27.712500000000002
66-67	18.25	18.7	33.0625	29.9875
68-69	18.8	20.1875	34.875	26.137500000000003
70-71	22.45	19.6875	35.675000000000004	22.1875
72-73	19.925	17.1625	34.362500000000004	28.549999999999997
74-75	23.8625	12.6375	34.525	28.975
76	13.775	14.524999999999999	40.849999999999994	30.85
>>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	0.5
32	1.0
33	1.0
34	0.5
35	0.0
36	1.0
37	2.0
38	3.0
39	11.5
40	23.5
41	41.5
42	55.0
43	87.0
44	161.0
45	312.5
46	422.0
47	689.0
48	747.5
49	529.0
50	519.0
51	490.0
52	352.0
53	192.5
54	142.0
55	123.5
56	107.0
57	70.5
58	32.0
59	23.0
60	9.0
61	6.0
62	8.0
63	6.0
64	4.0
65	2.5
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	0.5
86	0.5
87	0.0
88	0.0
89	0.5
90	0.5
91	0.0
92	0.0
93	0.5
94	1.0
95	0.5
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	63.800000000000004
#Duplication Level	Percentage of deduplicated	Percentage of total
1	88.47962382445141	56.45
2	5.054858934169279	6.45
3	2.1551724137931036	4.125
4	1.3322884012539185	3.4000000000000004
5	0.54858934169279	1.7500000000000002
6	0.274294670846395	1.05
7	0.35266457680250785	1.575
8	0.35266457680250785	1.7999999999999998
9	0.07836990595611285	0.44999999999999996
>10	1.2147335423197492	13.3
>50	0.11755485893416928	5.4
>100	0.03918495297805642	4.25
>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	170	4.25	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	96	2.4	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	63	1.575	No Hit
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	57	1.425	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	49	1.225	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	28	0.7000000000000001	No Hit
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGA	27	0.675	TruSeq Adapter, Index 2 (97% over 36bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGAT	20	0.5	TruSeq Adapter, Index 2 (97% over 37bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
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)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATGTAT	17	0.42500000000000004	TruSeq Adapter, Index 2 (97% over 41bp)
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	15	0.375	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	14	0.35000000000000003	No Hit
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	13	0.325	No Hit
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATGT	13	0.325	TruSeq Adapter, Index 2 (97% over 39bp)
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAG	12	0.3	TruSeq Adapter, Index 2 (97% over 35bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATGTA	12	0.3	TruSeq Adapter, Index 2 (97% over 40bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGA	11	0.27499999999999997	TruSeq Adapter, Index 2 (97% over 36bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	10	0.25	No Hit
AAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	9	0.22499999999999998	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	8	0.2	No Hit
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	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)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	8	0.2	No Hit
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
ACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	8	0.2	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATG	7	0.17500000000000002	TruSeq Adapter, Index 2 (97% over 38bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	7	0.17500000000000002	No Hit
TGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
CGACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAG	7	0.17500000000000002	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAATCAGATCGGAAGAG	6	0.15	No Hit
AAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAG	6	0.15	TruSeq Adapter, Index 2 (97% over 35bp)
GAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGA	6	0.15	TruSeq Adapter, Index 2 (97% over 36bp)
AACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	6	0.15	No Hit
CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGAGC	6	0.15	No Hit
GGTAGTTCGACCGTGGATTAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGTAGTTCGACCGTGGATAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GCGACCCCAGGTCAGTCGGGAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	5	0.125	No Hit
GATCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
CAAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCAAAAGAGGAAAGGCTTGCAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	5	0.125	No Hit
TGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGA	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	0.05	0.0	0.0	0.0	0.0
2	0.2	0.0	0.0	0.0	0.0
3	0.3	0.0	0.0	0.0	0.0
4	0.4	0.0	0.0	0.0	0.0
5	0.6	0.0	0.0	0.0	0.0
6	0.8	0.0	0.0	0.0	0.0
7	0.9	0.0	0.0	0.0	0.0
8	1.075	0.0	0.0	0.0	0.0
9	1.675	0.0	0.0	0.0	0.0
10	2.375	0.0	0.0	0.0	0.0
11	3.0	0.0	0.0	0.0	0.0
12	3.85	0.0	0.0	0.0	0.0
13	5.0	0.0	0.0	0.0	0.0
14	7.225	0.0	0.0	0.0	0.0
15	9.15	0.0	0.0	0.0	0.0
16	10.975	0.0	0.0	0.0	0.0
17	13.325	0.0	0.0	0.0	0.0
18	15.95	0.0	0.0	0.0	0.0
19	17.925	0.0	0.0	0.0	0.0
20	20.975	0.0	0.0	0.0	0.0
21	25.4	0.0	0.0	0.0	0.0
22	32.075	0.0	0.0	0.0	0.0
23	39.425	0.0	0.0	0.0	0.0
24	42.85	0.0	0.0	0.0	0.0
25	50.775	0.0	0.0	0.0	0.0
26	54.35	0.0	0.0	0.0	0.0
27	57.175	0.0	0.0	0.0	0.0
28	59.625	0.0	0.0	0.0	0.0
29	62.25	0.0	0.0	0.0	0.0
30	65.575	0.0	0.0	0.0	0.0
31	68.85	0.0	0.0	0.0	0.0
32	71.35	0.0	0.0	0.0	0.0
33	73.825	0.0	0.0	0.0	0.0
34	77.0	0.0	0.0	0.0	0.0
35	79.75	0.0	0.0	0.0	0.0
36	84.125	0.0	0.0	0.0	0.0
37	85.925	0.0	0.0	0.0	0.0
38	87.55	0.0	0.0	0.0	0.0
39	89.025	0.0	0.0	0.0	0.0
40	90.05	0.0	0.0	0.0	0.0
41	90.975	0.0	0.0	0.0	0.0
42	92.1	0.0	0.0	0.0	0.0
43	92.725	0.0	0.0	0.0	0.0
44	93.3	0.0	0.0	0.0	0.0
45	93.8	0.0	0.0	0.0	0.0
46	94.175	0.0	0.0	0.0	0.0
47	94.425	0.0	0.0	0.0	0.0
48	94.575	0.0	0.0	0.0	0.0
49	94.875	0.0	0.0	0.0	0.0
50	95.075	0.0	0.0	0.0	0.0
51	95.15	0.0	0.0	0.0	0.0
52	95.15	0.0	0.0	0.0	0.0
53	95.175	0.0	0.0	0.0	0.0
54	95.225	0.0	0.0	0.0	0.0
55	95.275	0.0	0.0	0.0	0.0
56	95.275	0.0	0.0	0.0	0.0
57	95.275	0.0	0.0	0.0	0.0
58	95.275	0.0	0.0	0.0	0.0
59	95.275	0.0	0.0	0.0	0.0
60	95.275	0.0	0.0	0.0	0.0
61	95.275	0.0	0.0	0.0	0.0
62	95.275	0.0	0.0	0.0	0.0
63	95.3	0.0	0.0	0.0	0.0
64	95.3	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ATCCTAA	15	0.0020658788	70.00001	1
AGCTCAG	15	0.0020658788	70.00001	9
TTGTAGT	15	0.0020658788	70.00001	5
TCCTAAC	15	0.0020658788	70.00001	2
CCTAACG	15	0.0020658788	70.00001	3
TAGCTCA	15	0.0020658788	70.00001	8
TAGTTCA	15	0.0020658788	70.00001	8
GTAGTTC	15	0.0020658788	70.00001	7
TGGTCAG	20	0.0064587677	52.5	17
CTAACGA	65	1.05501385E-10	48.461536	1
TAACGAA	70	2.2009772E-10	45.000004	2
GAACGAA	80	1.4551915E-11	43.75	6
AACGATT	100	0.0	42.0	11
GAACGAT	100	0.0	42.0	10
ACGATTT	100	0.0	42.0	12
CGATTTG	100	0.0	42.0	13
GATTTGA	105	0.0	40.000004	14
ATTTGAA	105	0.0	40.000004	15
GAACAGA	75	2.2724635E-8	37.333332	19
TTGAACA	75	2.2724635E-8	37.333332	17
>>END_MODULE
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407653 READS because READLEN < 1
Read 407653 spots for SRR11699282.sra
Written 407653 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
Rejected 407649 READS because READLEN < 1
Read 407649 spots for SRR11699282.sra
Written 407649 spots for SRR11699282.sra
SRR ids: ['SRR11699282.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_x5yv9471
SRR11699282.sra spots: 8152984
blocks: [[1, 407649], [407650, 815298], [815299, 1222947], [1222948, 1630596], [1630597, 2038245], [2038246, 2445894], [2445895, 2853543], [2853544, 3261192], [3261193, 3668841], [3668842, 4076490], [4076491, 4484139], [4484140, 4891788], [4891789, 5299437], [5299438, 5707086], [5707087, 6114735], [6114736, 6522384], [6522385, 6930033], [6930034, 7337682], [7337683, 7745331], [7745332, 8152984]]
SRR11699282 file size 1550401
SRR11699282 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 SRR11699282 SRR11699282_1.fastq
Input file:	SRR11699282_1.fastq
trimmed:	SRR11699282-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 08:23:31 2025 >> started

Wed Jun 18 08:23:34 2025 >> done (3.423s)
8152984 reads processed; of these:
1351110 (16.57%) short reads filtered out after trimming by size control
   6795 ( 0.08%) empty reads filtered out after trimming by size control
6795079 (83.34%) reads available; of these:
6631404 (97.59%) trimmed reads available after processing
 163675 ( 2.41%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 207139	  3.05%
 19	 292415	  4.30%
 20	 404603	  5.95%
 21	 530952	  7.81%
 22	 679768	 10.00%
 23	 301681	  4.44%
 24	 684567	 10.07%
 25	 290900	  4.28%
 26	 242389	  3.57%
 27	 244328	  3.60%
 28	 212995	  3.13%
 29	 231614	  3.41%
 30	 296964	  4.37%
 31	 204840	  3.01%
 32	 213840	  3.15%
 33	 251593	  3.70%
 34	 220322	  3.24%
 35	 316629	  4.66%
 36	 184278	  2.71%
 37	 132887	  1.96%
 38	 103062	  1.52%
 39	  96026	  1.41%
 40	  72566	  1.07%
 41	  86430	  1.27%
 42	  53606	  0.79%
 43	  42309	  0.62%
 44	  32699	  0.48%
 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	      1	  0.00%
 72	      0	  0.00%
 73	      0	  0.00%
 74	      1	  0.00%
 75	      0	  0.00%
 76	 163675	  2.41%
6795079 reads passed initial QC


criterion=sequence-density
sequence-density=3.53
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=20
prefix-density=0.00
prefix-fanout=1.0
sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGC


criterion=fanout-score
sequence-density=1.92
sequence-density-rank=3
fanout-score=17.71
fanout-score-rank=1
prefix-density=1.97
prefix-fanout=17.3
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATGTATCTCGTATGCCGTCTTCTGCTTG
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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGC -o SRR11699282 -
Input file:	STDIN
trimmed:	SRR11699282-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGC
-- 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 08:23:43 2025 >> started

Wed Jun 18 08:23:45 2025 >> done (2.308s)
3397540 reads processed; of these:
   9228 ( 0.27%) short reads filtered out after trimming by size control
 122564 ( 3.61%) empty reads filtered out after trimming by size control
3265748 (96.12%) reads available; of these:
  24490 ( 0.75%) trimmed reads available after processing
3241258 (99.25%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 104758	  3.21%
 19	 146256	  4.48%
 20	 199555	  6.11%
 21	 264986	  8.11%
 22	 339459	 10.39%
 23	 150874	  4.62%
 24	 338519	 10.37%
 25	 144450	  4.42%
 26	 120241	  3.68%
 27	 122267	  3.74%
 28	 105944	  3.24%
 29	 114443	  3.50%
 30	 148437	  4.55%
 31	 102071	  3.13%
 32	 103217	  3.16%
 33	  89639	  2.74%
 34	  98821	  3.03%
 35	  95461	  2.92%
 36	  87857	  2.69%
 37	  65751	  2.01%
 38	  51468	  1.58%
 39	  47808	  1.46%
 40	  36064	  1.10%
 41	  42607	  1.30%
 42	  26223	  0.80%
 43	  20604	  0.63%
 44	  16186	  0.50%
 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	      1	  0.00%
 69	      0	  0.00%
 70	      1	  0.00%
 71	      1	  0.00%
 72	      1	  0.00%
 73	   2843	  0.09%
 74	      1	  0.00%
 75	      0	  0.00%
 76	  78934	  2.42%


criterion=sequence-density
sequence-density=2.31
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAAGACCCGGGTT


criterion=fanout-score
sequence-density=1.99
sequence-density-rank=2
fanout-score=17.48
fanout-score-rank=1
prefix-density=2.04
prefix-fanout=17.1
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATGTATCTCGTATGCCGTCTTCTGCTT
                                 Started job on |	Jun 18 08:23:57
                             Started mapping on |	Jun 18 08:23:57
                                    Finished on |	Jun 18 08:24:13
       Mapping speed, Million of reads per hour |	1499.24

                          Number of input reads |	6663287
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	627563
                        Uniquely mapped reads % |	9.42%
                          Average mapped length |	24.67
                       Number of splices: Total |	14634
            Number of splices: Annotated (sjdb) |	5352
                       Number of splices: GT/AG |	13397
                       Number of splices: GC/AG |	818
                       Number of splices: AT/AC |	6
               Number of splices: Non-canonical |	413
                      Mismatch rate per base, % |	1.51%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.31
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.21
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	679364
             % of reads mapped to multiple loci |	10.20%
        Number of reads mapped to too many loci |	1199308
             % of reads mapped to too many loci |	18.00%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.88%
                     % of reads unmapped: other |	54.50%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	5356360	5356360	5356360
N_multimapping	679364	679364	679364
N_noFeature	531021	548257	607095
N_ambiguous	3325	64	41
UnstrandedReadsAssigned:93217 PositiveStrandReadsAssigned:79242 NegativeStrandReadsAssigned:20427
Dataset is classified unstranded
MeadianReadLen=25 20thPercentileLength=21 echo kmer=19
SRR11699282 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: SRR11699282-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 6,663,287 reads, 1,101,691 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 906 rounds

  72540 SRR11699282.ke.tsv
  44303 SRR11699282.se.tsv
 116843 total
==> SRR11699282.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	1	0.470101
Zm00001eb321680_T001	3417	3318	1	0.27883
Zm00001eb323640_T001	3273	3174	1	0.29148
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

==> SRR11699282.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699282 completed mapping pipeline successfully
