Starting /dee2/code/volunteer_pipeline.sh SRR11699281
    current disk space = 2471963267072
    free memory = 738311324 
SRR11699281 SRAfilesize
ce208233748a48bd6ed83c5ba3d804dd  SRR11699281.sra
SRR11699281.sra file validated
SRR11699281 is single end
SRR11699281 is conventional basespace
SRR11699281 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699281_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	31.20375	32.0	32.0	32.0	32.0	32.0
2	31.43325	32.0	32.0	32.0	32.0	32.0
3	31.416	32.0	32.0	32.0	32.0	32.0
4	31.51525	32.0	32.0	32.0	32.0	32.0
5	31.49175	32.0	32.0	32.0	32.0	32.0
6	35.0935	36.0	36.0	36.0	36.0	36.0
7	35.0875	36.0	36.0	36.0	36.0	36.0
8	35.181	36.0	36.0	36.0	36.0	36.0
9	34.98825	36.0	36.0	36.0	36.0	36.0
10-11	35.13075	36.0	36.0	36.0	36.0	36.0
12-13	35.08125	36.0	36.0	36.0	36.0	36.0
14-15	34.948499999999996	36.0	36.0	36.0	34.0	36.0
16-17	35.0955	36.0	36.0	36.0	36.0	36.0
18-19	35.111374999999995	36.0	36.0	36.0	36.0	36.0
20-21	34.976875	36.0	36.0	36.0	36.0	36.0
22-23	35.05575	36.0	36.0	36.0	36.0	36.0
24-25	34.958749999999995	36.0	36.0	36.0	36.0	36.0
26-27	34.973124999999996	36.0	36.0	36.0	36.0	36.0
28-29	34.869625	36.0	36.0	36.0	32.0	36.0
30-31	34.823499999999996	36.0	36.0	36.0	34.0	36.0
32-33	34.953125	36.0	36.0	36.0	36.0	36.0
34-35	34.946124999999995	36.0	36.0	36.0	36.0	36.0
36-37	34.97975	36.0	36.0	36.0	36.0	36.0
38-39	34.8235	36.0	36.0	36.0	34.0	36.0
40-41	34.88575	36.0	36.0	36.0	36.0	36.0
42-43	34.871125	36.0	36.0	36.0	36.0	36.0
44-45	34.67975	36.0	36.0	36.0	32.0	36.0
46-47	34.8675	36.0	36.0	36.0	36.0	36.0
48-49	34.64075	36.0	36.0	36.0	34.0	36.0
50-51	34.179249999999996	36.0	36.0	36.0	32.0	36.0
52-53	33.957625	36.0	36.0	36.0	32.0	36.0
54-55	33.413624999999996	36.0	36.0	36.0	23.0	36.0
56-57	32.040124999999996	36.0	32.0	36.0	14.0	36.0
58-59	30.804875	36.0	32.0	36.0	14.0	36.0
60-61	31.019875	36.0	32.0	36.0	14.0	36.0
62-63	30.2535	36.0	27.0	36.0	14.0	36.0
64-65	29.492125	36.0	20.5	36.0	14.0	36.0
66-67	29.0815	32.0	24.0	36.0	14.0	36.0
68-69	28.83925	34.0	20.5	36.0	14.0	36.0
70-71	28.810875000000003	36.0	14.0	36.0	14.0	36.0
72-73	28.265625	34.0	14.0	36.0	14.0	36.0
74-75	28.213625	32.0	14.0	36.0	14.0	36.0
76	24.9485	27.0	14.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	5.0
22	2.0
23	13.0
24	14.0
25	23.0
26	58.0
27	79.0
28	94.0
29	157.0
30	236.0
31	334.0
32	459.0
33	551.0
34	1093.0
35	882.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	43.075	19.85	21.875	15.2
2	30.725	17.299999999999997	20.375	31.6
3	42.675000000000004	22.575	14.149999999999999	20.599999999999998
4	39.2	23.275000000000002	21.775	15.75
5	17.175	28.575	23.799999999999997	30.45
6	20.1	17.825	45.15	16.925
7	49.65	28.050000000000004	12.45	9.85
8	17.125	17.9	54.7	10.274999999999999
9	18.55	51.975	12.6	16.875
10-11	39.2375	19.225	24.65	16.8875
12-13	13.575000000000001	17.175	28.275	40.975
14-15	27.6	50.0875	13.025	9.2875
16-17	27.025	22.2625	31.837500000000002	18.875
18-19	40.125	16.6375	26.337500000000002	16.900000000000002
20-21	27.500000000000004	34.300000000000004	23.7375	14.4625
22-23	37.5625	42.9375	8.425	11.075
24-25	30.65	41.0625	15.625	12.662499999999998
26-27	26.187500000000004	35.7625	15.85	22.2
28-29	24.275	28.875	20.4875	26.3625
30-31	29.012500000000003	33.4375	8.1875	29.362500000000004
32-33	31.55	32.5375	13.737499999999999	22.175
34-35	27.05	29.762499999999996	17.95	25.2375
36-37	27.487499999999997	33.387499999999996	13.5125	25.6125
38-39	27.8375	32.074999999999996	11.3375	28.749999999999996
40-41	20.8625	32.9625	17.0	29.175
42-43	26.187500000000004	31.775	14.512500000000001	27.525
44-45	23.75	28.775000000000002	17.525	29.95
46-47	13.3	34.2375	14.124999999999998	38.337500000000006
48-49	13.275	33.375	15.962499999999999	37.3875
50-51	15.825	27.3125	26.6125	30.25
52-53	20.4	20.5	26.187500000000004	32.9125
54-55	15.475	35.425000000000004	23.0	26.1
56-57	10.037500000000001	30.475	26.4125	33.074999999999996
58-59	10.5375	21.7	29.599999999999998	38.1625
60-61	19.662499999999998	23.724999999999998	28.4375	28.175
62-63	15.512500000000001	26.4625	34.525	23.5
64-65	11.862499999999999	20.875	30.025000000000002	37.237500000000004
66-67	16.525000000000002	22.225	28.812500000000004	32.4375
68-69	13.55	19.950000000000003	37.15	29.349999999999998
70-71	18.087500000000002	13.750000000000002	42.7125	25.45
72-73	16.3625	14.5875	38.95	30.099999999999998
74-75	19.037499999999998	11.1625	37.0375	32.7625
76	10.7	8.975	51.525	28.799999999999997
>>END_MODULE
>>Per sequence GC content	warn
#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	0.5
23	0.5
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	0.5
36	1.5
37	2.0
38	1.5
39	2.0
40	9.5
41	32.0
42	48.0
43	68.5
44	132.5
45	267.0
46	358.0
47	596.5
48	813.0
49	753.5
50	716.0
51	607.0
52	363.0
53	165.0
54	102.0
55	77.0
56	40.5
57	23.0
58	17.0
59	15.0
60	11.0
61	5.5
62	2.0
63	4.0
64	4.0
65	1.0
66	0.0
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	2.0
95	2.0
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	50.224999999999994
#Duplication Level	Percentage of deduplicated	Percentage of total
1	85.71428571428571	43.05
2	6.072672971627675	6.1
3	2.140368342458935	3.225
4	1.2444001991040319	2.5
5	0.6470881035340966	1.625
6	0.6470881035340966	1.95
7	0.5475360876057741	1.925
8	0.49776007964161273	2.0
9	0.2986560477849677	1.35
>10	1.841712294673967	17.1
>50	0.1991040318566451	7.3999999999999995
>100	0.14932802389248384	11.774999999999999
>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
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA	207	5.175	TruSeq Adapter, Index 7 (97% over 35bp)
CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC	153	3.8249999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	111	2.775	No Hit
GGGGACGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA	80	2.0	TruSeq Adapter, Index 7 (97% over 35bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	75	1.875	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAT	72	1.7999999999999998	TruSeq Adapter, Index 8 (97% over 36bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCAGATCGGAAGAGCACAC	69	1.725	No Hit
GCGTTTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	48	1.2	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	38	0.95	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	37	0.9249999999999999	No Hit
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAT	34	0.8500000000000001	TruSeq Adapter, Index 8 (97% over 36bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	32	0.8	No Hit
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATCGTAT	27	0.675	TruSeq Adapter, Index 9 (97% over 37bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATC	25	0.625	TruSeq Adapter, Index 9 (97% over 37bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGAGATCGGAAGAGCACACGT	21	0.525	No Hit
GGGGATGTAGTTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA	21	0.525	TruSeq Adapter, Index 7 (97% over 35bp)
GCCCCCATCGTCTAGTGGTTCAGGACAAGATCGGAAGAGCACACGTCTGA	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TTAGTGGTGAGAATTCCAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GCACCAGTAGTCTAGTGGTAGAATAGTACCAGATCGGAAGAGCACACGTC	16	0.4	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	15	0.375	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGAGATCGGAAGAGCACACG	14	0.35000000000000003	No Hit
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	12	0.3	No Hit
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	12	0.3	No Hit
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATCGTA	11	0.27499999999999997	TruSeq Adapter, Index 9 (97% over 37bp)
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
GTTTAGTGGTGAGAATTCCAAGATCGGAAGAGCACACGTCTGAACTCCAG	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCAGATCGGAAGAGCACACGTC	10	0.25	No Hit
GGGGATGTAGCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCAGATCGGAAGAGCACACGTCT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	10	0.25	No Hit
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGTTTGTAGTCCAACGGTTAGGATAGATCGGAAGAGCACACGTCTGAAC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCGAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
GCACCAGTGGTCTAGTGGTAGAATAGATCGGAAGAGCACACGTCTGAACT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGTCCCATGGTCTAGCGGTTAGGACATTGGAGATCGGAAGAGCACACGTC	9	0.22499999999999998	No Hit
AGGGCTATAGCTCAGTTCGGTAGAGCAAGATCGGAAGAGCACACGTCTGA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GCGCATCGGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA	8	0.2	TruSeq Adapter, Index 7 (97% over 35bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GCGTCTGTAGTCCAACGGTTAGGATAGATCGGAAGAGCACACGTCTGAAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGTGTTTGGTCTAGTGGTATGATTCTCAGATCGGAAGAGCACACGTCTG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TAGTGGTGAGAATTCCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGGGATATGGCGAAATCGGTAGACGCTAGATCGGAAGAGCACACGTCTGA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCTAGATCGGAAGAGCACACG	8	0.2	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAAAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGGGCACACG	7	0.17500000000000002	No Hit
GGGCATTTGGTCTAGTGGTATGATTCTCAGATCGGAAGAGCACACGTCTG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGGATGTAGCTCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA	7	0.17500000000000002	TruSeq Adapter, Index 7 (97% over 35bp)
GCACCAGTAGTCTAGTGGTAGAATAGTACCCAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
GCACCAGTAGTCTAGTGGTAGAATAGATCGGAAGAGCACACGTCTGAACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATCGT	7	0.17500000000000002	TruSeq Adapter, Index 9 (97% over 37bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGATGTAGCTCAAGATCGGAAGGGCACACGTCTGAACTCCAGTCACAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (97% over 34bp)
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CTAACGAACGAACGATTTGAACAGATCGGAAGGGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (96% over 28bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGAGATCGGAAGAGCACACG	6	0.15	No Hit
GCACCAGTAGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TTAGTGGTGAGAATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GCGGAACGGCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATCG	6	0.15	TruSeq Adapter, Index 9 (97% over 37bp)
TTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATCGTATC	6	0.15	TruSeq Adapter, Index 9 (97% over 37bp)
GCACCAGTGGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATCG	6	0.15	TruSeq Adapter, Index 9 (97% over 37bp)
GTCGTTGTAGTATAGTGGTGAGTATTCCCGCCAGATCGGAAGAGCACACG	6	0.15	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	6	0.15	No Hit
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCACCAGTGGTCTAGTGGTAGAATAGTACCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	5	0.125	No Hit
AGGGCTATAGCTCAGATCGGAAGGGCACACGTCTGAACTCCAGTCACAAT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (97% over 34bp)
GGGGACGTAGCTCATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCAGATCGGAAGGGCACAC	5	0.125	No Hit
GCGGGTATAGTTTAGTGGTAAAACCAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGGGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (96% over 29bp)
CGACACGACTCTCGGCAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CCCGGCTGGTGCACCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGTCCCATGGTCTAGTGGTTAGGACATTGGAGATCGGAAGAGCACACGTC	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	0.025	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	0.425	0.0	0.0	0.0	0.0
5	0.525	0.0	0.0	0.0	0.0
6	0.725	0.0	0.0	0.0	0.0
7	0.9	0.0	0.0	0.0	0.0
8	1.325	0.0	0.0	0.0	0.0
9	2.375	0.0	0.0	0.0	0.0
10	2.875	0.0	0.0	0.0	0.0
11	3.425	0.0	0.0	0.0	0.0
12	4.475	0.0	0.0	0.0	0.0
13	5.7	0.0	0.0	0.0	0.0
14	9.55	0.0	0.0	0.0	0.0
15	19.525	0.0	0.0	0.0	0.0
16	21.175	0.0	0.0	0.0	0.0
17	24.225	0.0	0.0	0.0	0.0
18	26.95	0.0	0.0	0.0	0.0
19	28.95	0.0	0.0	0.0	0.0
20	31.25	0.0	0.0	0.0	0.0
21	34.35	0.0	0.0	0.0	0.0
22	39.25	0.0	0.0	0.0	0.0
23	45.625	0.0	0.0	0.0	0.0
24	47.35	0.0	0.0	0.0	0.0
25	51.375	0.0	0.0	0.0	0.0
26	54.6	0.0	0.0	0.0	0.0
27	57.425	0.0	0.0	0.0	0.0
28	60.575	0.0	0.0	0.0	0.0
29	62.475	0.0	0.0	0.0	0.0
30	64.175	0.0	0.0	0.0	0.0
31	69.375	0.0	0.0	0.0	0.0
32	73.9	0.0	0.0	0.0	0.0
33	81.35	0.0	0.0	0.0	0.0
34	85.775	0.0	0.0	0.0	0.0
35	87.3	0.0	0.0	0.0	0.0
36	88.975	0.0	0.0	0.0	0.0
37	89.8	0.0	0.0	0.0	0.0
38	90.225	0.0	0.0	0.0	0.0
39	90.575	0.0	0.0	0.0	0.0
40	90.95	0.0	0.0	0.0	0.0
41	91.125	0.0	0.0	0.0	0.0
42	91.475	0.0	0.0	0.0	0.0
43	91.65	0.0	0.0	0.0	0.0
44	91.9	0.0	0.0	0.0	0.0
45	92.025	0.0	0.0	0.0	0.0
46	92.15	0.0	0.0	0.0	0.0
47	92.275	0.0	0.0	0.0	0.0
48	92.35	0.0	0.0	0.0	0.0
49	92.375	0.0	0.0	0.0	0.0
50	92.375	0.0	0.0	0.0	0.0
51	92.375	0.0	0.0	0.0	0.0
52	92.4	0.0	0.0	0.0	0.0
53	92.4	0.0	0.0	0.0	0.0
54	92.425	0.0	0.0	0.0	0.0
55	92.425	0.0	0.0	0.0	0.0
56	92.425	0.0	0.0	0.0	0.0
57	92.45	0.0	0.0	0.0	0.0
58	92.45	0.0	0.0	0.0	0.0
59	92.45	0.0	0.0	0.0	0.0
60	92.475	0.0	0.0	0.0	0.0
61	92.475	0.0	0.0	0.0	0.0
62	92.475	0.0	0.0	0.0	0.0
63	92.475	0.0	0.0	0.0	0.0
64	92.475	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CGTTTGT	15	0.0020658788	70.00001	2
GTTTGTA	15	0.0020658788	70.00001	3
TGGTCAG	35	2.6138878E-9	70.00001	17
TCCCATG	15	0.0020658788	70.00001	3
CCAACGG	35	2.6138878E-9	70.00001	12
CATTGGA	15	0.0020658788	70.00001	25
AGCTCAG	15	0.0020658788	70.00001	9
TAGGACA	15	0.0020658788	70.00001	20
AGGACAT	15	0.0020658788	70.00001	21
TCAGGAT	30	7.878043E-8	70.00001	20
GCTGGTC	30	7.878043E-8	70.00001	15
GGTCCCA	15	0.0020658788	70.00001	1
ATTGGAG	15	0.0020658788	70.00001	26
ATGGTCT	15	0.0020658788	70.00001	7
GGACATT	15	0.0020658788	70.00001	22
CCATGGT	15	0.0020658788	70.00001	5
CCGTTGT	35	2.6138878E-9	70.00001	2
TAGTCTA	35	2.6138878E-9	70.00001	8
GGTCAGG	30	7.878043E-8	70.00001	18
CCCATGG	15	0.0020658788	70.00001	4
>>END_MODULE
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113494 READS because READLEN < 1
Read 113494 spots for SRR11699281.sra
Written 113494 spots for SRR11699281.sra
Rejected 113506 READS because READLEN < 1
Read 113506 spots for SRR11699281.sra
Written 113506 spots for SRR11699281.sra
SRR ids: ['SRR11699281.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_r7qnxvjl
SRR11699281.sra spots: 2269892
blocks: [[1, 113494], [113495, 226988], [226989, 340482], [340483, 453976], [453977, 567470], [567471, 680964], [680965, 794458], [794459, 907952], [907953, 1021446], [1021447, 1134940], [1134941, 1248434], [1248435, 1361928], [1361929, 1475422], [1475423, 1588916], [1588917, 1702410], [1702411, 1815904], [1815905, 1929398], [1929399, 2042892], [2042893, 2156386], [2156387, 2269892]]
SRR11699281 file size 430085
SRR11699281 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 SRR11699281 SRR11699281_1.fastq
Input file:	SRR11699281_1.fastq
trimmed:	SRR11699281-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 06:26:08 2025 >> started

Wed Jun 18 06:26:09 2025 >> done (1.038s)
2269892 reads processed; of these:
 662936 (29.21%) short reads filtered out after trimming by size control
    811 ( 0.04%) empty reads filtered out after trimming by size control
1606145 (70.76%) reads available; of these:
1585500 (98.71%) trimmed reads available after processing
  20645 ( 1.29%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  44472	  2.77%
 19	  57307	  3.57%
 20	  67733	  4.22%
 21	 118298	  7.37%
 22	 166673	 10.38%
 23	  42370	  2.64%
 24	 113557	  7.07%
 25	  80230	  5.00%
 26	  62606	  3.90%
 27	  64807	  4.03%
 28	  42483	  2.65%
 29	  53490	  3.33%
 30	 115863	  7.21%
 31	 112275	  6.99%
 32	 175251	 10.91%
 33	 105890	  6.59%
 34	  38300	  2.38%
 35	  35808	  2.23%
 36	  21555	  1.34%
 37	  14291	  0.89%
 38	  12591	  0.78%
 39	  11788	  0.73%
 40	   7612	  0.47%
 41	   7660	  0.48%
 42	   5150	  0.32%
 43	   4328	  0.27%
 44	   3111	  0.19%
 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	      0	  0.00%
 75	      1	  0.00%
 76	  20645	  1.29%
1606145 reads passed initial QC


criterion=sequence-density
sequence-density=9.13
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAA


criterion=fanout-score
sequence-density=0.26
sequence-density-rank=25
fanout-score=65.65
fanout-score-rank=1
prefix-density=12.44
prefix-fanout=1.4
sequence=CGGTTAGGATACCTGGCT
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    1 (100.00%) aligned >1 times
100.00% overall alignment rate
Potential adapter found in reference sequence. Continuing without clipping.
                                 Started job on |	Jun 18 06:26:35
                             Started mapping on |	Jun 18 06:26:36
                                    Finished on |	Jun 18 06:26:47
       Mapping speed, Million of reads per hour |	525.65

                          Number of input reads |	1606145
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	118777
                        Uniquely mapped reads % |	7.40%
                          Average mapped length |	24.58
                       Number of splices: Total |	2565
            Number of splices: Annotated (sjdb) |	897
                       Number of splices: GT/AG |	2307
                       Number of splices: GC/AG |	161
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	97
                      Mismatch rate per base, % |	1.22%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.58
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.21
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	412902
             % of reads mapped to multiple loci |	25.71%
        Number of reads mapped to too many loci |	454442
             % of reads mapped to too many loci |	28.29%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	4.75%
                     % of reads unmapped: other |	33.85%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1074466	1074466	1074466
N_multimapping	412902	412902	412902
N_noFeature	101589	105479	114370
N_ambiguous	536	10	11
UnstrandedReadsAssigned:16652 PositiveStrandReadsAssigned:13288 NegativeStrandReadsAssigned:4396
Dataset is classified unstranded
MeadianReadLen=27 20thPercentileLength=22 echo kmer=19
SRR11699281 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: SRR11699281-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,606,145 reads, 385,514 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 825 rounds

  72540 SRR11699281.ke.tsv
  44303 SRR11699281.se.tsv
 116843 total
==> SRR11699281.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	0	0
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

==> SRR11699281.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699281 completed mapping pipeline successfully
