Starting /dee2/code/volunteer_pipeline.sh SRR11699298
    current disk space = 2468096786432
    free memory = 702062320 
SRR11699298 SRAfilesize
759b1d39ec41e898f13a5d6cecb6c0e4  SRR11699298.sra
SRR11699298.sra file validated
SRR11699298 is single end
SRR11699298 is conventional basespace
SRR11699298 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699298_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	31.2255	32.0	32.0	32.0	32.0	32.0
2	31.4075	32.0	32.0	32.0	32.0	32.0
3	31.46375	32.0	32.0	32.0	32.0	32.0
4	31.5755	32.0	32.0	32.0	32.0	32.0
5	31.51875	32.0	32.0	32.0	32.0	32.0
6	35.07425	36.0	36.0	36.0	36.0	36.0
7	35.07225	36.0	36.0	36.0	36.0	36.0
8	35.1625	36.0	36.0	36.0	36.0	36.0
9	35.02125	36.0	36.0	36.0	36.0	36.0
10-11	35.127250000000004	36.0	36.0	36.0	36.0	36.0
12-13	35.093875	36.0	36.0	36.0	36.0	36.0
14-15	34.992000000000004	36.0	36.0	36.0	36.0	36.0
16-17	35.117875	36.0	36.0	36.0	36.0	36.0
18-19	35.167874999999995	36.0	36.0	36.0	36.0	36.0
20-21	35.020875000000004	36.0	36.0	36.0	36.0	36.0
22-23	35.046375	36.0	36.0	36.0	36.0	36.0
24-25	35.004875	36.0	36.0	36.0	36.0	36.0
26-27	34.99375	36.0	36.0	36.0	36.0	36.0
28-29	34.91137500000001	36.0	36.0	36.0	34.0	36.0
30-31	34.848875	36.0	36.0	36.0	36.0	36.0
32-33	34.89175	36.0	36.0	36.0	36.0	36.0
34-35	34.9885	36.0	36.0	36.0	36.0	36.0
36-37	34.951625	36.0	36.0	36.0	36.0	36.0
38-39	34.865625	36.0	36.0	36.0	36.0	36.0
40-41	34.915	36.0	36.0	36.0	36.0	36.0
42-43	34.8525	36.0	36.0	36.0	34.0	36.0
44-45	34.841	36.0	36.0	36.0	34.0	36.0
46-47	34.863749999999996	36.0	36.0	36.0	36.0	36.0
48-49	34.677875	36.0	36.0	36.0	34.0	36.0
50-51	34.623625000000004	36.0	36.0	36.0	32.0	36.0
52-53	34.619375000000005	36.0	36.0	36.0	32.0	36.0
54-55	34.5285	36.0	36.0	36.0	32.0	36.0
56-57	33.984125	36.0	36.0	36.0	32.0	36.0
58-59	33.766625000000005	36.0	36.0	36.0	29.5	36.0
60-61	33.96225	36.0	36.0	36.0	29.5	36.0
62-63	33.6105	36.0	36.0	36.0	27.0	36.0
64-65	33.260000000000005	36.0	32.0	36.0	27.0	36.0
66-67	32.633125	36.0	32.0	36.0	27.0	36.0
68-69	32.841	36.0	32.0	36.0	27.0	36.0
70-71	32.7395	36.0	32.0	36.0	24.0	36.0
72-73	32.150125	36.0	32.0	36.0	14.0	36.0
74-75	32.754999999999995	36.0	32.0	36.0	14.0	36.0
76	31.09175	36.0	32.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
16	1.0
17	0.0
18	0.0
19	0.0
20	0.0
21	2.0
22	2.0
23	3.0
24	8.0
25	15.0
26	18.0
27	34.0
28	62.0
29	69.0
30	114.0
31	124.0
32	187.0
33	364.0
34	1120.0
35	1877.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	28.1	25.525	25.25	21.125
2	23.549999999999997	22.525000000000002	23.75	30.175
3	28.449999999999996	30.125	17.375	24.05
4	31.45	28.299999999999997	20.349999999999998	19.900000000000002
5	20.25	24.4	26.025	29.325000000000003
6	24.6	22.825	33.425	19.15
7	38.1	30.175	17.25	14.475
8	19.175	23.625	39.050000000000004	18.15
9	21.9	38.35	18.675	21.075
10-11	33.4	24.05	26.700000000000003	15.85
12-13	19.2	21.712500000000002	25.624999999999996	33.4625
14-15	29.25	40.525	16.325	13.900000000000002
16-17	23.8125	22.3875	32.887499999999996	20.9125
18-19	39.7625	20.7125	25.1	14.424999999999999
20-21	21.7	34.300000000000004	26.687499999999996	17.3125
22-23	33.9875	37.0875	14.0125	14.912500000000001
24-25	27.487499999999997	39.175	17.9375	15.4
26-27	26.150000000000002	34.9875	20.375	18.4875
28-29	28.9875	26.275	22.225	22.5125
30-31	33.5125	34.4375	10.2625	21.7875
32-33	30.7375	40.525	10.337499999999999	18.4
34-35	30.875000000000004	32.337500000000006	14.025000000000002	22.7625
36-37	30.65	32.3625	10.65	26.337500000000002
38-39	25.5375	37.55	10.075000000000001	26.8375
40-41	26.400000000000002	33.625	14.3625	25.6125
42-43	28.599999999999998	27.1625	18.1125	26.125
44-45	22.825	32.324999999999996	15.437500000000002	29.4125
46-47	20.150000000000002	33.475	14.0125	32.3625
48-49	16.4625	28.462500000000002	18.712500000000002	36.3625
50-51	14.662500000000001	27.175	21.8625	36.3
52-53	18.41480185023128	26.96587073384173	21.002625328166022	33.61670208776097
54-55	16.425	29.812499999999996	20.3	33.4625
56-57	11.35	28.325	23.8375	36.4875
58-59	9.1	32.5375	20.8625	37.5
60-61	13.775	29.45	20.3	36.475
62-63	14.9875	27.212500000000002	20.3625	37.4375
64-65	15.25	25.2875	24.637500000000003	34.825
66-67	13.65	22.85	28.625	34.875
68-69	14.5625	21.275	29.212500000000002	34.949999999999996
70-71	19.975	21.1375	30.887500000000003	28.000000000000004
72-73	18.7	18.712500000000002	29.5375	33.050000000000004
74-75	22.975	11.6875	29.025000000000002	36.3125
76	18.3	10.274999999999999	37.15	34.275
>>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	0.5
24	0.5
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.5
33	1.0
34	1.0
35	0.5
36	0.0
37	0.0
38	1.0
39	2.0
40	7.0
41	18.5
42	25.0
43	46.0
44	93.0
45	170.0
46	221.0
47	297.0
48	653.0
49	829.5
50	726.0
51	629.5
52	492.0
53	354.5
54	258.0
55	192.5
56	89.0
57	57.0
58	63.0
59	42.0
60	12.5
61	4.0
62	4.0
63	2.0
64	1.0
65	1.0
66	0.0
67	0.0
68	0.5
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	0.0
92	0.0
93	0.5
94	0.5
95	0.0
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	0.0125
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	60.199999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	88.28903654485049	53.15
2	4.941860465116279	5.949999999999999
3	2.0764119601328903	3.75
4	0.7475083056478405	1.7999999999999998
5	0.7475083056478405	2.25
6	0.6229235880398671	2.25
7	0.33222591362126247	1.4000000000000001
8	0.24916943521594684	1.2
9	0.20764119601328906	1.125
>10	1.7026578073089702	20.575
>50	0.04152823920265781	2.025
>100	0.04152823920265781	4.5249999999999995
>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	181	4.5249999999999995	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	81	2.025	No Hit
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	49	1.225	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	45	1.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTA	44	1.0999999999999999	TruSeq Adapter, Index 7 (97% over 35bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	44	1.0999999999999999	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	39	0.975	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	38	0.95	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	34	0.8500000000000001	No Hit
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	34	0.8500000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	33	0.8250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCAGATCGGAAGAGCACAC	26	0.65	No Hit
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	25	0.625	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	20	0.5	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	20	0.5	No Hit
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	18	0.44999999999999996	No Hit
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	17	0.42500000000000004	No Hit
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	15	0.375	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	15	0.375	No Hit
GCGTTTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	14	0.35000000000000003	No Hit
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	14	0.35000000000000003	No Hit
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	13	0.325	No Hit
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCACCAGTGGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCACCAGTAGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	11	0.27499999999999997	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AGGGATATAACTCAGCGGTAGAGTAGATCGGAAGAGCACACGTCTGAACT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGGACGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTA	10	0.25	TruSeq Adapter, Index 7 (97% over 35bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	10	0.25	No Hit
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	9	0.22499999999999998	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	9	0.22499999999999998	No Hit
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCACCAGTAGTCTAGTGGTAGAATAGTACCCAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCAGATCGGAAGAGCACACGTCT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CATGCAAATCTAACGAAGTGCTCCTGGACGAGATCGGAAGAGCACACGTC	8	0.2	No Hit
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAG	8	0.2	No Hit
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	8	0.2	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGAGATCGGAAGAGCACACGT	8	0.2	No Hit
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCCCCCATCGTCTAGTGGTTCAGGACAAGATCGGAAGAGCACACGTCTGA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCACCAGTAGTCTAGTGGTAGAATAGTACCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
AAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGTCCCATGGTCTAGCGGTTAGGACATTGGAAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
TCCGTTGTAGTCTAGCTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAAC	7	0.17500000000000002	TruSeq Adapter, Index 4 (97% over 37bp)
CGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAA	7	0.17500000000000002	TruSeq Adapter, Index 3 (97% over 36bp)
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	6	0.15	No Hit
GGGGATGTAGCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	6	0.15	No Hit
ATATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACAC	6	0.15	No Hit
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	6	0.15	No Hit
GGGGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGC	6	0.15	No Hit
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAA	6	0.15	TruSeq Adapter, Index 3 (97% over 36bp)
CACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTCTG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GCACCAGTGGTCTAGTGGTAGAATAGTACCCAGATCGGAAGAGCACACGT	6	0.15	No Hit
TGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GCACCAGTGGTCTAGTGGTAGAATAGTACCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	5	0.125	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	5	0.125	No Hit
TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA	5	0.125	No Hit
ACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTA	5	0.125	TruSeq Adapter, Index 7 (97% over 35bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CGACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAA	5	0.125	TruSeq Adapter, Index 3 (97% over 36bp)
AGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACA	5	0.125	No Hit
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GGGTGTTTGGTCTAGTGGTATGATTCTCAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAACCG	5	0.125	TruSeq Adapter, Index 4 (97% over 38bp)
ATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAA	5	0.125	No Hit
ATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAG	5	0.125	No Hit
GGGCATTTGGTCTAGTGGTATGATTCTCGAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
>>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	0.05	0.0	0.0	0.0	0.0
3	0.05	0.0	0.0	0.0	0.0
4	0.05	0.0	0.0	0.0	0.0
5	0.05	0.0	0.0	0.0	0.0
6	0.1	0.0	0.0	0.0	0.0
7	0.1	0.0	0.0	0.0	0.0
8	0.225	0.0	0.0	0.0	0.0
9	0.35	0.0	0.0	0.0	0.0
10	0.375	0.0	0.0	0.0	0.0
11	0.55	0.0	0.0	0.0	0.0
12	0.875	0.0	0.0	0.0	0.0
13	1.275	0.0	0.0	0.0	0.0
14	2.05	0.0	0.0	0.0	0.0
15	4.1	0.0	0.0	0.0	0.0
16	5.15	0.0	0.0	0.0	0.0
17	7.125	0.0	0.0	0.0	0.0
18	9.175	0.0	0.0	0.0	0.0
19	10.6	0.0	0.0	0.0	0.0
20	12.9	0.0	0.0	0.0	0.0
21	15.975	0.0	0.0	0.0	0.0
22	20.5	0.0	0.0	0.0	0.0
23	29.8	0.0	0.0	0.0	0.0
24	32.7	0.0	0.0	0.0	0.0
25	42.475	0.0	0.0	0.0	0.0
26	46.725	0.0	0.0	0.0	0.0
27	50.125	0.0	0.0	0.0	0.0
28	53.9	0.0	0.0	0.0	0.0
29	56.6	0.0	0.0	0.0	0.0
30	60.0	0.0	0.0	0.0	0.0
31	66.65	0.0	0.0	0.0	0.0
32	71.075	0.0	0.0	0.0	0.0
33	75.625	0.0	0.0	0.0	0.0
34	79.575	0.0	0.0	0.0	0.0
35	82.15	0.0	0.0	0.0	0.0
36	85.95	0.0	0.0	0.0	0.0
37	88.125	0.0	0.0	0.0	0.0
38	89.7	0.0	0.0	0.0	0.0
39	90.9	0.0	0.0	0.0	0.0
40	91.925	0.0	0.0	0.0	0.0
41	92.575	0.0	0.0	0.0	0.0
42	93.675	0.0	0.0	0.0	0.0
43	94.475	0.0	0.0	0.0	0.0
44	94.9	0.0	0.0	0.0	0.0
45	95.025	0.0	0.0	0.0	0.0
46	95.575	0.0	0.0	0.0	0.0
47	95.825	0.0	0.0	0.0	0.0
48	95.9	0.0	0.0	0.0	0.0
49	96.025	0.0	0.0	0.0	0.0
50	96.125	0.0	0.0	0.0	0.0
51	96.225	0.0	0.0	0.0	0.0
52	96.275	0.0	0.0	0.0	0.0
53	96.275	0.0	0.0	0.0	0.0
54	96.275	0.0	0.0	0.0	0.0
55	96.275	0.0	0.0	0.0	0.0
56	96.275	0.0	0.0	0.0	0.0
57	96.3	0.0	0.0	0.0	0.0
58	96.325	0.0	0.0	0.0	0.0
59	96.325	0.0	0.0	0.0	0.0
60	96.35	0.0	0.0	0.0	0.0
61	96.35	0.0	0.0	0.0	0.0
62	96.35	0.0	0.0	0.0	0.0
63	96.35	0.0	0.0	0.0	0.0
64	96.35	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTATGAT	15	0.0020658788	70.00001	18
CCAACGG	15	0.0020658788	70.00001	12
TCTAGTG	30	7.878043E-8	70.00001	11
TAGTGGT	30	7.878043E-8	70.00001	13
TGGTATG	15	0.0020658788	70.00001	16
TTGTAGT	30	7.878043E-8	70.00001	5
ATGATTC	15	0.0020658788	70.00001	20
TGATTCT	15	0.0020658788	70.00001	21
TATGATT	15	0.0020658788	70.00001	19
TAGTCTA	30	7.878043E-8	70.00001	8
TAGTCCA	15	0.0020658788	70.00001	8
GGATAAT	15	0.0020658788	70.00001	22
TGTAGTC	35	2.6138878E-9	70.00001	6
GTCCAAC	15	0.0020658788	70.00001	10
CTAGTGG	30	7.878043E-8	70.00001	12
TTTGGTC	15	0.0020658788	70.00001	6
GTCTAGT	30	7.878043E-8	70.00001	10
TTGGTCT	15	0.0020658788	70.00001	7
TCCAACG	15	0.0020658788	70.00001	11
GTGGTAT	15	0.0020658788	70.00001	15
>>END_MODULE
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349766 READS because READLEN < 1
Read 349766 spots for SRR11699298.sra
Written 349766 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
Rejected 349754 READS because READLEN < 1
Read 349754 spots for SRR11699298.sra
Written 349754 spots for SRR11699298.sra
SRR ids: ['SRR11699298.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_azi3b8ed
SRR11699298.sra spots: 6995092
blocks: [[1, 349754], [349755, 699508], [699509, 1049262], [1049263, 1399016], [1399017, 1748770], [1748771, 2098524], [2098525, 2448278], [2448279, 2798032], [2798033, 3147786], [3147787, 3497540], [3497541, 3847294], [3847295, 4197048], [4197049, 4546802], [4546803, 4896556], [4896557, 5246310], [5246311, 5596064], [5596065, 5945818], [5945819, 6295572], [6295573, 6645326], [6645327, 6995092]]
SRR11699298 file size 1329904
SRR11699298 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 SRR11699298 SRR11699298_1.fastq
Input file:	SRR11699298_1.fastq
trimmed:	SRR11699298-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 09:21:48 2025 >> started

Wed Jun 18 09:21:51 2025 >> done (2.692s)
6995092 reads processed; of these:
 759661 (10.86%) short reads filtered out after trimming by size control
    833 ( 0.01%) empty reads filtered out after trimming by size control
6234598 (89.13%) reads available; of these:
6117226 (98.12%) trimmed reads available after processing
 117372 ( 1.88%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 131287	  2.11%
 19	 201260	  3.23%
 20	 242962	  3.90%
 21	 354999	  5.69%
 22	 642532	 10.31%
 23	 228637	  3.67%
 24	 648692	 10.40%
 25	 288982	  4.64%
 26	 236126	  3.79%
 27	 281813	  4.52%
 28	 192953	  3.09%
 29	 228943	  3.67%
 30	 475738	  7.63%
 31	 286666	  4.60%
 32	 353173	  5.66%
 33	 239497	  3.84%
 34	 197232	  3.16%
 35	 240763	  3.86%
 36	 163594	  2.62%
 37	 107329	  1.72%
 38	  77635	  1.25%
 39	  70027	  1.12%
 40	  55502	  0.89%
 41	  78244	  1.25%
 42	  40801	  0.65%
 43	  29540	  0.47%
 44	  22294	  0.36%
 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	      1	  0.00%
 71	      0	  0.00%
 72	      1	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      3	  0.00%
 76	 117372	  1.88%
6234598 reads passed initial QC


criterion=sequence-density
sequence-density=7.53
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=17
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAAGACCCGGGTT


criterion=fanout-score
sequence-density=0.30
sequence-density-rank=18
fanout-score=24.19
fanout-score-rank=1
prefix-density=0.94
prefix-fanout=7.8
sequence=TAGCTCAGTGGTAGAGCGGTCGGCTGTT
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 09:22:31
                             Started mapping on |	Jun 18 09:22:32
                                    Finished on |	Jun 18 09:22:44
       Mapping speed, Million of reads per hour |	1870.38

                          Number of input reads |	6234598
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	573434
                        Uniquely mapped reads % |	9.20%
                          Average mapped length |	24.99
                       Number of splices: Total |	12554
            Number of splices: Annotated (sjdb) |	5811
                       Number of splices: GT/AG |	11603
                       Number of splices: GC/AG |	630
                       Number of splices: AT/AC |	7
               Number of splices: Non-canonical |	314
                      Mismatch rate per base, % |	1.16%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.52
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.16
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1061926
             % of reads mapped to multiple loci |	17.03%
        Number of reads mapped to too many loci |	1508052
             % of reads mapped to too many loci |	24.19%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.29%
                     % of reads unmapped: other |	44.29%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	4599238	4599238	4599238
N_multimapping	1061926	1061926	1061926
N_noFeature	465297	484591	550494
N_ambiguous	3712	47	45
UnstrandedReadsAssigned:104425 PositiveStrandReadsAssigned:88796 NegativeStrandReadsAssigned:22895
Dataset is classified unstranded
MeadianReadLen=27 20thPercentileLength=22 echo kmer=19
SRR11699298 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: SRR11699298-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 6,234,598 reads, 1,377,867 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 992 rounds

  72540 SRR11699298.ke.tsv
  44303 SRR11699298.se.tsv
 116843 total
==> SRR11699298.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	3	0.774491
Zm00001eb323640_T001	3273	3174	0	0
Zm00001eb314140_T001	893	794	0	0
Zm00001eb080260_T001	3529	3430	1	0.249734
Zm00001eb026490_T001	2433	2334	1	0.367004
Zm00001eb026490_T002	2229	2130	0	0
Zm00001eb026490_T003	2220	2121	0	0
Zm00001eb281360_T001	2412	2313	0	0

==> SRR11699298.se.tsv <==
Zm00001eb015280	2
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699298 completed mapping pipeline successfully
