Starting /dee2/code/volunteer_pipeline.sh SRR11699295
    current disk space = 2467307786240
    free memory = 1575360224 
SRR11699295 SRAfilesize
3b9a3e2636054b27350d0c096db2ee8c  SRR11699295.sra
SRR11699295.sra file validated
SRR11699295 is single end
SRR11699295 is conventional basespace
SRR11699295 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699295_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	50
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.17	32.0	32.0	32.0	32.0	32.0
2	31.3795	32.0	32.0	32.0	32.0	32.0
3	31.457	32.0	32.0	32.0	32.0	32.0
4	31.49725	32.0	32.0	32.0	32.0	32.0
5	31.51375	32.0	32.0	32.0	32.0	32.0
6	35.05225	36.0	36.0	36.0	36.0	36.0
7	35.084	36.0	36.0	36.0	36.0	36.0
8	35.14875	36.0	36.0	36.0	36.0	36.0
9	34.978	36.0	36.0	36.0	36.0	36.0
10-11	35.10575	36.0	36.0	36.0	36.0	36.0
12-13	35.1005	36.0	36.0	36.0	36.0	36.0
14-15	35.054125	36.0	36.0	36.0	36.0	36.0
16-17	35.100625	36.0	36.0	36.0	36.0	36.0
18-19	35.229375000000005	36.0	36.0	36.0	36.0	36.0
20-21	35.026875000000004	36.0	36.0	36.0	36.0	36.0
22-23	34.988125	36.0	36.0	36.0	36.0	36.0
24-25	35.043499999999995	36.0	36.0	36.0	36.0	36.0
26-27	34.857	36.0	36.0	36.0	34.0	36.0
28-29	35.014624999999995	36.0	36.0	36.0	36.0	36.0
30-31	34.886375	36.0	36.0	36.0	36.0	36.0
32-33	34.922125	36.0	36.0	36.0	36.0	36.0
34-35	34.8445	36.0	36.0	36.0	36.0	36.0
36-37	34.9315	36.0	36.0	36.0	36.0	36.0
38-39	34.875125	36.0	36.0	36.0	36.0	36.0
40-41	34.8275	36.0	36.0	36.0	36.0	36.0
42-43	34.925250000000005	36.0	36.0	36.0	36.0	36.0
44-45	34.786375	36.0	36.0	36.0	34.0	36.0
46-47	34.795249999999996	36.0	36.0	36.0	36.0	36.0
48-49	34.71725	36.0	36.0	36.0	34.0	36.0
50-51	34.463875	36.0	36.0	36.0	32.0	36.0
52-53	34.38	36.0	36.0	36.0	32.0	36.0
54-55	34.096625	36.0	36.0	36.0	32.0	36.0
56-57	33.515	36.0	36.0	36.0	27.0	36.0
58-59	33.373000000000005	36.0	36.0	36.0	27.0	36.0
60-61	33.48325	36.0	36.0	36.0	27.0	36.0
62-63	33.189375	36.0	34.0	36.0	27.0	36.0
64-65	33.0125	36.0	32.0	36.0	24.0	36.0
66-67	32.429	36.0	32.0	36.0	24.0	36.0
68-69	32.535624999999996	36.0	32.0	36.0	20.5	36.0
70-71	32.64375	36.0	32.0	36.0	17.5	36.0
72-73	32.426249999999996	36.0	32.0	36.0	14.0	36.0
74-75	32.986374999999995	36.0	32.0	36.0	17.5	36.0
76	30.48425	36.0	27.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
22	2.0
23	3.0
24	8.0
25	16.0
26	39.0
27	60.0
28	47.0
29	81.0
30	134.0
31	151.0
32	202.0
33	346.0
34	1009.0
35	1902.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	27.175	30.049999999999997	21.85	20.925
2	26.724999999999998	25.074999999999996	24.95	23.25
3	25.775	30.675	18.05	25.5
4	31.525	30.099999999999998	18.175	20.200000000000003
5	21.9	27.6	23.0	27.500000000000004
6	24.875	26.200000000000003	28.1	20.825
7	34.300000000000004	33.125	17.7	14.875
8	23.75	24.85	34.0	17.4
9	23.799999999999997	36.575	17.925	21.7
10-11	32.800000000000004	28.000000000000004	21.6625	17.5375
12-13	21.712500000000002	21.925	25.05	31.3125
14-15	29.4875	39.2625	17.724999999999998	13.525
16-17	23.875	22.537499999999998	33.862500000000004	19.725
18-19	38.324999999999996	23.0	23.400000000000002	15.275
20-21	23.0125	34.4625	25.9625	16.5625
22-23	32.8375	38.4625	13.2875	15.412500000000001
24-25	30.575000000000003	37.8875	14.05	17.4875
26-27	28.1875	32.587500000000006	18.2	21.025
28-29	29.575000000000003	28.875	15.937499999999998	25.6125
30-31	33.025	34.0	10.6625	22.3125
32-33	27.200000000000003	35.925000000000004	14.174999999999999	22.7
34-35	30.075000000000003	29.65	16.1125	24.1625
36-37	26.5125	34.575	12.1	26.8125
38-39	23.375	33.0625	15.725	27.8375
40-41	25.7625	29.062500000000004	16.325	28.849999999999998
42-43	28.5875	28.050000000000004	18.3125	25.05
44-45	22.8125	33.2625	15.437500000000002	28.487499999999997
46-47	23.425	31.9875	13.8	30.7875
48-49	20.025000000000002	28.287499999999998	15.812499999999998	35.875
50-51	19.650000000000002	28.3875	17.5375	34.425
52-53	24.712500000000002	25.25	19.6875	30.349999999999998
54-55	23.3375	26.825	21.275	28.5625
56-57	25.587500000000002	25.4	20.7125	28.299999999999997
58-59	27.1125	28.7	18.7625	25.424999999999997
60-61	21.6125	26.974999999999998	27.0625	24.349999999999998
62-63	18.5625	29.2	25.2	27.037499999999998
64-65	19.525000000000002	26.150000000000002	26.1	28.225
66-67	22.875	17.4125	31.05	28.6625
68-69	21.95	19.675	30.337500000000002	28.037499999999998
70-71	28.225	18.625	30.65	22.5
72-73	24.3125	19.0875	30.275000000000002	26.325
74-75	20.7875	16.475	34.0125	28.725
76	15.55	17.05	40.2	27.200000000000003
>>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	0.0
35	0.0
36	0.0
37	0.0
38	0.5
39	3.5
40	5.0
41	10.0
42	16.0
43	36.5
44	70.0
45	130.5
46	178.0
47	292.5
48	693.0
49	795.0
50	611.0
51	575.0
52	500.0
53	389.5
54	318.0
55	227.5
56	107.0
57	82.0
58	87.0
59	53.0
60	12.0
61	4.0
62	3.0
63	3.5
64	3.0
65	1.5
66	1.5
67	2.0
68	1.5
69	0.5
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	0.5
92	1.0
93	0.5
94	0.0
95	0.0
96	0.0
97	0.5
98	0.5
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10-11	0.0
12-13	0.0
14-15	0.0
16-17	0.0
18-19	0.0
20-21	0.0
22-23	0.0
24-25	0.0
26-27	0.0
28-29	0.0
30-31	0.0
32-33	0.0
34-35	0.0
36-37	0.0
38-39	0.0
40-41	0.0
42-43	0.0
44-45	0.0
46-47	0.0
48-49	0.0
50-51	0.0
52-53	0.0
54-55	0.0
56-57	0.0
58-59	0.0
60-61	0.0
62-63	0.0
64-65	0.0
66-67	0.0
68-69	0.0
70-71	0.0
72-73	0.0
74-75	0.0
76	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
76	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	60.775
#Duplication Level	Percentage of deduplicated	Percentage of total
1	87.28918140682846	53.05
2	6.129164952694365	7.449999999999999
3	1.9333607568901685	3.5249999999999995
4	1.2340600575894694	3.0
5	0.6170300287947347	1.875
6	0.4113533525298231	1.5
7	0.3702180172768408	1.575
8	0.24681201151789386	1.2
9	0.20567667626491154	1.125
>10	1.3986013986013985	16.45
>50	0.12340600575894693	4.875
>100	0.04113533525298231	4.375
>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	175	4.375	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	71	1.775	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	70	1.7500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	54	1.35	No Hit
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	48	1.2	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	38	0.95	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGG	35	0.8750000000000001	TruSeq Adapter, Index 19 (97% over 36bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	35	0.8750000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGG	31	0.775	TruSeq Adapter, Index 19 (97% over 36bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGA	26	0.65	TruSeq Adapter, Index 19 (97% over 37bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	22	0.5499999999999999	No Hit
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGATAAT	19	0.475	TruSeq Adapter, Index 19 (97% over 37bp)
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGG	18	0.44999999999999996	TruSeq Adapter, Index 2 (97% over 35bp)
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	18	0.44999999999999996	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	16	0.4	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	16	0.4	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	14	0.35000000000000003	No Hit
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGTAGATCGGAAGAGCA	13	0.325	No Hit
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	13	0.325	No Hit
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	13	0.325	No Hit
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	11	0.27499999999999997	No Hit
GGGCCTGTAGCTCAGAGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	11	0.27499999999999997	No Hit
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGCGGAGTAGAGCAGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	9	0.22499999999999998	No Hit
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGAGATCGGAAGAGCAC	9	0.22499999999999998	No Hit
CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	8	0.2	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAGATCGGAAGAGCACA	8	0.2	No Hit
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
AAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	7	0.17500000000000002	No Hit
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CTAACGAACGAACGATTTGAACAGATCGGAAGGGCACACGTCTGAACTCC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (96% over 28bp)
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCAGATCGGAAGA	7	0.17500000000000002	No Hit
AGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGAT	7	0.17500000000000002	TruSeq Adapter, Index 19 (97% over 37bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGAGATCGGAAGAGCACACG	6	0.15	No Hit
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGA	6	0.15	TruSeq Adapter, Index 11 (97% over 35bp)
GGGGACGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGG	6	0.15	TruSeq Adapter, Index 2 (97% over 35bp)
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGAGATCGGAAGAGCAC	6	0.15	No Hit
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	6	0.15	No Hit
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGATAA	6	0.15	TruSeq Adapter, Index 19 (97% over 37bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	6	0.15	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTAGATCGGAAGAGCACA	6	0.15	No Hit
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	5	0.125	No Hit
TCAAAAGAGGAAAGGCTTGCGGTGGATAAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGG	5	0.125	TruSeq Adapter, Index 2 (97% over 35bp)
GCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGG	5	0.125	TruSeq Adapter, Index 2 (97% over 35bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	5	0.125	No Hit
GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
ATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GGCGGATGTAGCCAAGTGGAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGTGTTTGGTCTAGTGGTATGATTCTCAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTAGATCGGAAGAGCACA	5	0.125	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGAGATCGGAAGAGCACACGT	5	0.125	No Hit
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	5	0.125	No Hit
AGCGGAGTAGAGCAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
>>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	0.1	0.0	0.0	0.0	0.0
3	0.125	0.0	0.0	0.0	0.0
4	0.175	0.0	0.0	0.0	0.0
5	0.275	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	0.7	0.0	0.0	0.0	0.0
9	1.25	0.0	0.0	0.0	0.0
10	1.625	0.0	0.0	0.0	0.0
11	1.95	0.0	0.0	0.0	0.0
12	2.825	0.0	0.0	0.0	0.0
13	4.0	0.0	0.0	0.0	0.0
14	6.95	0.0	0.0	0.0	0.0
15	8.625	0.0	0.0	0.0	0.0
16	10.0	0.0	0.0	0.0	0.0
17	12.8	0.0	0.0	0.0	0.0
18	16.525	0.0	0.0	0.0	0.0
19	18.775	0.0	0.0	0.0	0.0
20	22.325	0.0	0.0	0.0	0.0
21	26.075	0.0	0.0	0.0	0.0
22	31.375	0.0	0.0	0.0	0.0
23	39.225	0.0	0.0	0.0	0.0
24	42.3	0.0	0.0	0.0	0.0
25	48.925	0.0	0.0	0.0	0.0
26	52.95	0.0	0.0	0.0	0.0
27	55.125	0.0	0.0	0.0	0.0
28	57.775	0.0	0.0	0.0	0.0
29	59.9	0.0	0.0	0.0	0.0
30	62.25	0.0	0.0	0.0	0.0
31	65.8	0.0	0.0	0.0	0.0
32	68.15	0.0	0.0	0.0	0.0
33	71.025	0.0	0.0	0.0	0.0
34	73.9	0.0	0.0	0.0	0.0
35	77.4	0.0	0.0	0.0	0.0
36	83.125	0.0	0.0	0.0	0.0
37	86.375	0.0	0.0	0.0	0.0
38	88.1	0.0	0.0	0.0	0.0
39	89.3	0.0	0.0	0.0	0.0
40	90.05	0.0	0.0	0.0	0.0
41	90.85	0.0	0.0	0.0	0.0
42	91.825	0.0	0.0	0.0	0.0
43	92.175	0.0	0.0	0.0	0.0
44	92.725	0.0	0.0	0.0	0.0
45	92.975	0.0	0.0	0.0	0.0
46	93.325	0.0	0.0	0.0	0.0
47	93.425	0.0	0.0	0.0	0.0
48	93.575	0.0	0.0	0.0	0.0
49	93.775	0.0	0.0	0.0	0.0
50	93.925	0.0	0.0	0.0	0.0
51	93.95	0.0	0.0	0.0	0.0
52	93.975	0.0	0.0	0.0	0.0
53	94.025	0.0	0.0	0.0	0.0
54	94.05	0.0	0.0	0.0	0.0
55	94.05	0.0	0.0	0.0	0.0
56	94.075	0.0	0.0	0.0	0.0
57	94.075	0.0	0.0	0.0	0.0
58	94.075	0.0	0.0	0.0	0.0
59	94.075	0.0	0.0	0.0	0.0
60	94.075	0.0	0.0	0.0	0.0
61	94.075	0.0	0.0	0.0	0.0
62	94.075	0.0	0.0	0.0	0.0
63	94.075	0.0	0.0	0.0	0.0
64	94.075	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGGTCAG	35	2.6138878E-9	70.00001	17
CCGTTGT	15	0.0020658788	70.00001	2
TAGTCTA	15	0.0020658788	70.00001	8
TAGTTCA	30	7.878043E-8	70.00001	8
GAGCACC	30	7.878043E-8	70.00001	23
TGTAGTC	15	0.0020658788	70.00001	6
TGTAGCT	15	0.0020658788	70.00001	6
TCCGTTG	15	0.0020658788	70.00001	1
AGTCTAG	15	0.0020658788	70.00001	9
GGGGATG	15	0.0020658788	70.00001	1
GTAGTCT	15	0.0020658788	70.00001	7
CGCCCTG	20	7.003785E-5	70.0	29
TTCAATT	25	2.3570374E-6	70.0	11
TTGTAGT	40	8.54925E-11	70.0	5
ATTGGTC	25	2.3570374E-6	70.0	15
CCGCCCT	20	7.003785E-5	70.0	28
CACCGCC	25	2.3570374E-6	70.0	26
ACCGCCC	20	7.003785E-5	70.0	27
CAATTGG	25	2.3570374E-6	70.0	13
CCTGAGA	20	7.003785E-5	70.0	32
>>END_MODULE
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335514 READS because READLEN < 1
Read 335514 spots for SRR11699295.sra
Written 335514 spots for SRR11699295.sra
Rejected 335531 READS because READLEN < 1
Read 335531 spots for SRR11699295.sra
Written 335531 spots for SRR11699295.sra
SRR ids: ['SRR11699295.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_mrjyq3li
SRR11699295.sra spots: 6710297
blocks: [[1, 335514], [335515, 671028], [671029, 1006542], [1006543, 1342056], [1342057, 1677570], [1677571, 2013084], [2013085, 2348598], [2348599, 2684112], [2684113, 3019626], [3019627, 3355140], [3355141, 3690654], [3690655, 4026168], [4026169, 4361682], [4361683, 4697196], [4697197, 5032710], [5032711, 5368224], [5368225, 5703738], [5703739, 6039252], [6039253, 6374766], [6374767, 6710297]]
SRR11699295 file size 1275670
SRR11699295 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 SRR11699295 SRR11699295_1.fastq
Input file:	SRR11699295_1.fastq
trimmed:	SRR11699295-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 10:36:53 2025 >> started

Wed Jun 18 10:36:56 2025 >> done (2.873s)
6710297 reads processed; of these:
1259815 (18.77%) short reads filtered out after trimming by size control
   2682 ( 0.04%) empty reads filtered out after trimming by size control
5447800 (81.19%) reads available; of these:
5338031 (97.99%) trimmed reads available after processing
 109769 ( 2.01%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 156065	  2.86%
 19	 239341	  4.39%
 20	 271220	  4.98%
 21	 362916	  6.66%
 22	 604238	 11.09%
 23	 217677	  4.00%
 24	 470790	  8.64%
 25	 283766	  5.21%
 26	 178746	  3.28%
 27	 184646	  3.39%
 28	 151888	  2.79%
 29	 160687	  2.95%
 30	 260617	  4.78%
 31	 157736	  2.90%
 32	 160559	  2.95%
 33	 199578	  3.66%
 34	 226300	  4.15%
 35	 363591	  6.67%
 36	 213471	  3.92%
 37	 117954	  2.17%
 38	  79535	  1.46%
 39	  68649	  1.26%
 40	  53658	  0.98%
 41	  63075	  1.16%
 42	  39521	  0.73%
 43	  30738	  0.56%
 44	  21059	  0.39%
 45	      0	  0.00%
 46	      0	  0.00%
 47	      0	  0.00%
 48	      0	  0.00%
 49	      0	  0.00%
 50	      0	  0.00%
 51	      0	  0.00%
 52	      0	  0.00%
 53	      0	  0.00%
 54	      0	  0.00%
 55	      0	  0.00%
 56	      0	  0.00%
 57	      0	  0.00%
 58	      0	  0.00%
 59	      0	  0.00%
 60	      0	  0.00%
 61	      0	  0.00%
 62	      0	  0.00%
 63	      0	  0.00%
 64	      0	  0.00%
 65	      0	  0.00%
 66	      0	  0.00%
 67	      0	  0.00%
 68	      0	  0.00%
 69	      0	  0.00%
 70	      0	  0.00%
 71	      0	  0.00%
 72	      0	  0.00%
 73	      0	  0.00%
 74	      2	  0.00%
 75	      8	  0.00%
 76	 109769	  2.01%
5447800 reads passed initial QC


criterion=sequence-density
sequence-density=3.82
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=1.52
sequence-density-rank=5
fanout-score=15.97
fanout-score-rank=1
prefix-density=1.58
prefix-fanout=15.4
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGATAATCTCGTATGCCGTCTTCTGCTTGA
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 SRR11699295 -
Input file:	STDIN
trimmed:	SRR11699295-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 10:37:02 2025 >> started

Wed Jun 18 10:37:04 2025 >> done (1.854s)
2723900 reads processed; of these:
   6781 ( 0.25%) short reads filtered out after trimming by size control
 106174 ( 3.90%) empty reads filtered out after trimming by size control
2610945 (95.85%) reads available; of these:
  17166 ( 0.66%) trimmed reads available after processing
2593779 (99.34%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  78591	  3.01%
 19	 120549	  4.62%
 20	 133823	  5.13%
 21	 180727	  6.92%
 22	 301607	 11.55%
 23	 108609	  4.16%
 24	 232769	  8.92%
 25	 141298	  5.41%
 26	  89030	  3.41%
 27	  92176	  3.53%
 28	  75767	  2.90%
 29	  79332	  3.04%
 30	 129952	  4.98%
 31	  78393	  3.00%
 32	  77785	  2.98%
 33	  81258	  3.11%
 34	 103838	  3.98%
 35	 121550	  4.66%
 36	  94976	  3.64%
 37	  58142	  2.23%
 38	  39322	  1.51%
 39	  34245	  1.31%
 40	  26799	  1.03%
 41	  30921	  1.18%
 42	  19170	  0.73%
 43	  14947	  0.57%
 44	  10501	  0.40%
 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	      2	  0.00%
 69	      0	  0.00%
 70	      3	  0.00%
 71	     81	  0.00%
 72	     62	  0.00%
 73	   1982	  0.08%
 74	      0	  0.00%
 75	      4	  0.00%
 76	  52734	  2.02%


criterion=sequence-density
sequence-density=3.62
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=17
prefix-density=0.02
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATA


criterion=fanout-score
sequence-density=1.60
sequence-density-rank=4
fanout-score=16.00
fanout-score-rank=1
prefix-density=1.66
prefix-fanout=15.5
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGATAATCTCGTATGCCGTCTTCTGCTTGA
                                 Started job on |	Jun 18 10:37:22
                             Started mapping on |	Jun 18 10:37:27
                                    Finished on |	Jun 18 10:37:39
       Mapping speed, Million of reads per hour |	1600.45

                          Number of input reads |	5334845
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	490437
                        Uniquely mapped reads % |	9.19%
                          Average mapped length |	25.06
                       Number of splices: Total |	8851
            Number of splices: Annotated (sjdb) |	4272
                       Number of splices: GT/AG |	7929
                       Number of splices: GC/AG |	567
                       Number of splices: AT/AC |	4
               Number of splices: Non-canonical |	351
                      Mismatch rate per base, % |	0.76%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.57
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.47
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	602706
             % of reads mapped to multiple loci |	11.30%
        Number of reads mapped to too many loci |	1224967
             % of reads mapped to too many loci |	22.96%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	6.28%
                     % of reads unmapped: other |	50.27%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	4241702	4241702	4241702
N_multimapping	602706	602706	602706
N_noFeature	406252	423298	471051
N_ambiguous	2392	36	22
UnstrandedReadsAssigned:81793 PositiveStrandReadsAssigned:67103 NegativeStrandReadsAssigned:19364
Dataset is classified unstranded
MeadianReadLen=26 20thPercentileLength=22 echo kmer=19
SRR11699295 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: SRR11699295-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 5,334,845 reads, 1,102,667 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 877 rounds

  72540 SRR11699295.ke.tsv
  44303 SRR11699295.se.tsv
 116843 total
==> SRR11699295.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	3	0.90085
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

==> SRR11699295.se.tsv <==
Zm00001eb015280	1
Zm00001eb000610	0
Zm00001eb033210	1
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699295 completed mapping pipeline successfully
