Starting /dee2/code/volunteer_pipeline.sh SRR11699544
    current disk space = 2462045212672
    free memory = 1581456276 
SRR11699544 SRAfilesize
8684dafae4eb364e76657e5a9deda2ab  SRR11699544.sra
SRR11699544.sra file validated
SRR11699544 is single end
SRR11699544 is conventional basespace
SRR11699544 read1 length is 86 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699544_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	86
%GC	52
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.43275	32.0	32.0	32.0	32.0	32.0
2	31.50175	32.0	32.0	32.0	32.0	32.0
3	31.57125	32.0	32.0	32.0	32.0	32.0
4	31.53175	32.0	32.0	32.0	32.0	32.0
5	31.62025	32.0	32.0	32.0	32.0	32.0
6	35.12725	36.0	36.0	36.0	36.0	36.0
7	35.22825	36.0	36.0	36.0	36.0	36.0
8	35.15975	36.0	36.0	36.0	36.0	36.0
9	34.955	36.0	36.0	36.0	36.0	36.0
10-11	35.181	36.0	36.0	36.0	36.0	36.0
12-13	35.278375	36.0	36.0	36.0	36.0	36.0
14-15	35.12025	36.0	36.0	36.0	36.0	36.0
16-17	35.158249999999995	36.0	36.0	36.0	36.0	36.0
18-19	35.278999999999996	36.0	36.0	36.0	36.0	36.0
20-21	35.17675	36.0	36.0	36.0	36.0	36.0
22-23	35.273624999999996	36.0	36.0	36.0	36.0	36.0
24-25	35.10675	36.0	36.0	36.0	36.0	36.0
26-27	34.949625	36.0	36.0	36.0	36.0	36.0
28-29	35.082	36.0	36.0	36.0	36.0	36.0
30-31	35.0595	36.0	36.0	36.0	36.0	36.0
32-33	35.055375	36.0	36.0	36.0	36.0	36.0
34-35	35.093625	36.0	36.0	36.0	36.0	36.0
36-37	35.047	36.0	36.0	36.0	36.0	36.0
38-39	34.985625	36.0	36.0	36.0	36.0	36.0
40-41	35.027125	36.0	36.0	36.0	36.0	36.0
42-43	35.047875	36.0	36.0	36.0	36.0	36.0
44-45	34.814625	36.0	36.0	36.0	34.0	36.0
46-47	35.082125000000005	36.0	36.0	36.0	36.0	36.0
48-49	35.033	36.0	36.0	36.0	36.0	36.0
50-51	34.878875	36.0	36.0	36.0	34.0	36.0
52-53	34.899249999999995	36.0	36.0	36.0	36.0	36.0
54-55	34.585375	36.0	36.0	36.0	34.0	36.0
56-57	33.982124999999996	36.0	36.0	36.0	32.0	36.0
58-59	33.670125	36.0	36.0	36.0	27.0	36.0
60-61	33.6155	36.0	36.0	36.0	27.0	36.0
62-63	33.582625	36.0	36.0	36.0	27.0	36.0
64-65	33.41325	36.0	36.0	36.0	27.0	36.0
66-67	33.382875	36.0	36.0	36.0	27.0	36.0
68-69	33.683625	36.0	36.0	36.0	27.0	36.0
70-71	33.60825	36.0	36.0	36.0	27.0	36.0
72-73	33.978625	36.0	36.0	36.0	29.5	36.0
74-75	34.059625	36.0	36.0	36.0	32.0	36.0
76-77	33.839625	36.0	36.0	36.0	27.0	36.0
78-79	34.088125000000005	36.0	36.0	36.0	32.0	36.0
80-81	34.505375	36.0	36.0	36.0	32.0	36.0
82-83	34.556875000000005	36.0	36.0	36.0	32.0	36.0
84-85	34.537875	36.0	36.0	36.0	32.0	36.0
86	34.07575	36.0	36.0	36.0	32.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	2.0
22	2.0
23	5.0
24	2.0
25	16.0
26	34.0
27	38.0
28	51.0
29	61.0
30	90.0
31	110.0
32	172.0
33	299.0
34	633.0
35	2485.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	30.95	25.974999999999998	24.775	18.3
2	32.05	23.175	20.25	24.525
3	28.15	28.499999999999996	18.325	25.025
4	35.15	28.425	17.775	18.65
5	22.6	26.150000000000002	26.1	25.15
6	22.35	22.875	31.574999999999996	23.200000000000003
7	37.675	28.125	19.175	15.024999999999999
8	21.575	20.875	40.5	17.05
9	23.075000000000003	37.275000000000006	19.525000000000002	20.125
10-11	34.0125	22.0	25.0	18.987499999999997
12-13	22.112499999999997	18.55	28.000000000000004	31.337500000000002
14-15	30.3	39.8625	16.650000000000002	13.1875
16-17	23.3125	22.112499999999997	35.6	18.975
18-19	41.625	21.349999999999998	21.725	15.299999999999999
20-21	23.3125	30.025000000000002	27.8875	18.775
22-23	33.575	37.8875	14.3625	14.174999999999999
24-25	29.549999999999997	40.0625	15.537500000000001	14.85
26-27	27.187499999999996	31.324999999999996	20.1625	21.325
28-29	30.4375	26.1125	16.9375	26.5125
30-31	34.566820852606575	32.829103637954745	10.888861107638455	21.715214401800225
32-33	27.975	36.5625	13.675	21.7875
34-35	31.724999999999998	30.7375	16.975	20.5625
36-37	28.449999999999996	35.475	11.1375	24.9375
38-39	24.190523815476936	34.279284910613825	14.039254906863357	27.490936367045883
40-41	26.653331666458307	29.003625453181648	14.47680960120015	29.866233279159893
42-43	28.116014501812725	29.47868483560445	18.12726590823853	24.278034754344294
44-45	23.5875	33.525	15.412500000000001	27.474999999999998
46-47	23.925	31.55	14.499999999999998	30.025000000000002
48-49	18.1375	27.900000000000002	15.825	38.1375
50-51	19.042260565141287	27.7569392348087	17.1167791947987	36.084021005251316
52-53	26.787499999999998	20.875	19.650000000000002	32.6875
54-55	23.525	20.549999999999997	23.95	31.974999999999998
56-57	28.0625	21.9	18.725	31.3125
58-59	30.17877234654332	21.640205025628205	18.56482060257532	29.61620202525316
60-61	29.25	15.462500000000002	24.7375	30.55
62-63	26.474999999999998	17.6125	24.3	31.612499999999997
64-65	23.925	19.925	25.137500000000003	31.0125
66-67	25.14064258032254	12.439054881860233	29.028628578572324	33.391673959244905
68-69	25.25	14.7	28.537499999999998	31.5125
70-71	33.1875	11.4125	31.3125	24.087500000000002
72-73	28.4	10.9	33.037499999999994	27.6625
74-75	26.1625	9.5625	30.099999999999998	34.175
76-77	21.915239404925615	9.73871733966746	36.20452556569571	32.141517689711215
78-79	15.7	9.1	43.3375	31.8625
80-81	21.9375	12.2625	39.6875	26.1125
82-83	18.15	20.8125	35.6	25.4375
84-85	21.327665958244783	22.115264408051004	33.766720840105016	22.7903487935992
86	20.175	26.85	29.849999999999998	23.125
>>END_MODULE
>>Per sequence GC content	pass
#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	0.5
28	0.5
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.5
36	1.0
37	0.5
38	0.0
39	0.0
40	1.0
41	1.5
42	3.0
43	5.0
44	10.5
45	26.5
46	68.5
47	156.0
48	234.0
49	360.5
50	465.0
51	547.5
52	643.5
53	560.0
54	471.0
55	383.0
56	210.0
57	133.0
58	127.5
59	101.5
60	52.5
61	18.5
62	9.0
63	5.0
64	5.0
65	3.5
66	2.0
67	1.0
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	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
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	0.0125
32-33	0.0
34-35	0.0
36-37	0.0
38-39	0.0125
40-41	0.0125
42-43	0.0125
44-45	0.0
46-47	0.0
48-49	0.0
50-51	0.025
52-53	0.0
54-55	0.0
56-57	0.0
58-59	0.0125
60-61	0.0
62-63	0.0
64-65	0.0
66-67	0.0125
68-69	0.0
70-71	0.0
72-73	0.0
74-75	0.0
76-77	0.0125
78-79	0.0
80-81	0.0
82-83	0.0
84-85	0.0125
86	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
86	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	64.225
#Duplication Level	Percentage of deduplicated	Percentage of total
1	88.67263526664073	56.95
2	5.021409108602569	6.45
3	1.7905799922148697	3.45
4	0.9342156481121059	2.4
5	0.8563643441027637	2.75
6	0.46710782405605294	1.7999999999999998
7	0.5838847800700662	2.625
8	0.1946282600233554	1.0
9	0.07785130400934215	0.44999999999999996
>10	1.2845465161541456	15.425
>50	0.07785130400934215	3.5000000000000004
>100	0.038925652004671074	3.2
>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	128	3.2	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	84	2.1	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	56	1.4000000000000001	No Hit
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	41	1.0250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGG	41	1.0250000000000001	TruSeq Adapter, Index 19 (97% over 36bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	38	0.95	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	35	0.8750000000000001	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	32	0.8	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	30	0.75	No Hit
AGCGGAGTAGAGCAGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGAGATCGGAAGAGCAC	27	0.675	No Hit
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTGAGATCGGAAGAGCACAC	21	0.525	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	18	0.44999999999999996	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	18	0.44999999999999996	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG	16	0.4	No Hit
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTAGATCGGAAGAGCACA	15	0.375	No Hit
AGCGGAGTAGAGCAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGGACGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGG	14	0.35000000000000003	TruSeq Adapter, Index 2 (97% over 35bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	14	0.35000000000000003	No Hit
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	13	0.325	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	12	0.3	No Hit
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGG	12	0.3	TruSeq Adapter, Index 19 (97% over 36bp)
GCCCCCATCGTCTAGTGGTTCAGGACATCTCTCTTTAGATCGGAAGAGCA	12	0.3	No Hit
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGG	12	0.3	TruSeq Adapter, Index 2 (97% over 35bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA	10	0.25	No Hit
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAGATCGGAAGAGCACA	10	0.25	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	10	0.25	No Hit
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
GGTAGTTCGACCGTGGATTAGATCGGAAGAGCACACGTCTGAACTCCAGT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGAGATCGGAAGAGCA	8	0.2	No Hit
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	8	0.2	No Hit
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	7	0.17500000000000002	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTAGATCGGAAGAGC	7	0.17500000000000002	No Hit
CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TCTCATGGAGAGTTCGATCCTGGCAGATCGGAAGAGCACACGTCTGAACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCACCAGTAGTCTAGTGGTAGAATAGTACCCAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGGCCTGTAGCTCAGAGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTAGATCGGAAGAGCACAC	7	0.17500000000000002	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAGATCGGAAGAGC	7	0.17500000000000002	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	6	0.15	No Hit
CGACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	6	0.15	No Hit
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	6	0.15	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	6	0.15	No Hit
CAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGATTGTAGTTCAATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGT	5	0.125	TruSeq Adapter, Index 11 (97% over 35bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGGATTGTAGTTCAATTGGTCAGAAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGATTGTAGTTCAATTGGTCAGAGCAAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TTAAATTCAAGTCTCTTGGCTCTTTTCAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CGACACGACTCTCGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTAGATCGGAAGAGCACA	5	0.125	No Hit
GGGTGTTTGGTCTAGTGGTATGATTCTCGCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
TAACTGACTGGTCGTAGGTTCGAATCCTACTTGGGGAGCCAAGATCGGAA	5	0.125	No Hit
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	5	0.125	No Hit
AGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGTG	5	0.125	TruSeq Adapter, Index 11 (97% over 37bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGT	5	0.125	TruSeq Adapter, Index 11 (97% over 37bp)
GGGGATATGGCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGT	5	0.125	TruSeq Adapter, Index 11 (97% over 37bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCACCAGTGGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	5	0.125	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	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	0.05	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	0.075	0.0	0.0	0.0	0.0
6	0.075	0.0	0.0	0.0	0.0
7	0.1	0.0	0.0	0.0	0.0
8	0.15	0.0	0.0	0.0	0.0
9	0.175	0.0	0.0	0.0	0.0
10	0.25	0.0	0.0	0.0	0.0
11	0.425	0.0	0.0	0.0	0.0
12	0.75	0.0	0.0	0.0	0.0
13	1.225	0.0	0.0	0.0	0.0
14	3.35	0.0	0.0	0.0	0.0
15	4.875	0.0	0.0	0.0	0.0
16	6.05	0.0	0.0	0.0	0.0
17	9.65	0.0	0.0	0.0	0.0
18	12.3	0.0	0.0	0.0	0.0
19	14.5	0.0	0.0	0.0	0.0
20	17.15	0.0	0.0	0.0	0.0
21	20.325	0.0	0.0	0.0	0.0
22	25.425	0.0	0.0	0.0	0.0
23	33.375	0.0	0.0	0.0	0.0
24	36.85	0.0	0.0	0.0	0.0
25	45.925	0.0	0.0	0.0	0.0
26	49.425	0.0	0.0	0.0	0.0
27	52.425	0.0	0.0	0.0	0.0
28	57.125	0.0	0.0	0.0	0.0
29	59.675	0.0	0.0	0.0	0.0
30	62.4	0.0	0.0	0.0	0.0
31	65.625	0.0	0.0	0.0	0.0
32	68.475	0.0	0.0	0.0	0.0
33	71.275	0.0	0.0	0.0	0.0
34	74.725	0.0	0.0	0.0	0.0
35	79.55	0.0	0.0	0.0	0.0
36	86.5	0.0	0.0	0.0	0.0
37	90.075	0.0	0.0	0.0	0.0
38	91.6	0.0	0.0	0.0	0.0
39	92.55	0.0	0.0	0.0	0.0
40	93.25	0.0	0.0	0.0	0.0
41	93.925	0.0	0.0	0.0	0.0
42	94.95	0.0	0.0	0.0	0.0
43	95.35	0.0	0.0	0.0	0.0
44	95.75	0.0	0.0	0.0	0.0
45	96.0	0.0	0.0	0.0	0.0
46	96.1	0.0	0.0	0.0	0.0
47	96.275	0.0	0.0	0.0	0.0
48	96.3	0.0	0.0	0.0	0.0
49	96.325	0.0	0.0	0.0	0.0
50	96.475	0.0	0.0	0.0	0.0
51	96.525	0.0	0.0	0.0	0.0
52	96.55	0.0	0.0	0.0	0.0
53	96.55	0.0	0.0	0.0	0.0
54	96.55	0.0	0.0	0.0	0.0
55	96.55	0.0	0.0	0.0	0.0
56	96.575	0.0	0.0	0.0	0.0
57	96.575	0.0	0.0	0.0	0.0
58	96.575	0.0	0.0	0.0	0.0
59	96.575	0.0	0.0	0.0	0.0
60	96.575	0.0	0.0	0.0	0.0
61	96.575	0.0	0.0	0.0	0.0
62	96.575	0.0	0.0	0.0	0.0
63	96.575	0.0	0.0	0.0	0.0
64	96.575	0.0	0.0	0.0	0.0
65	96.575	0.0	0.0	0.0	0.0
66	96.575	0.0	0.0	0.0	0.0
67	96.575	0.0	0.0	0.0	0.0
68	96.575	0.0	0.0	0.0	0.0
69	96.6	0.0	0.0	0.0	0.0
70	96.6	0.0	0.0	0.0	0.0
71	96.6	0.0	0.0	0.0	0.0
72	96.6	0.0	0.0	0.0	0.0
73	96.6	0.0	0.0	0.0	0.0
74	96.6	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AGCTCAG	20	3.6123936E-5	80.00001	9
TAGCTCA	20	3.6123936E-5	80.00001	8
GGATTGT	20	3.6123936E-5	80.00001	2
GATTGTA	20	3.6123936E-5	80.00001	3
ATTGTAG	20	3.6123936E-5	80.00001	4
TGTAGCT	15	0.0012159165	80.00001	6
GGGATTG	20	3.6123936E-5	80.00001	1
GGGATGT	15	0.0012159165	80.00001	2
GGGGATG	15	0.0012159165	80.00001	1
AGTTCAA	20	3.6123936E-5	80.00001	9
GTAGCTC	15	0.0012159165	80.00001	7
TTGTAGT	45	0.0	80.0	5
CCGTTGT	25	1.0653384E-6	80.0	2
TAGTCTA	25	1.0653384E-6	80.0	8
TAGTTCA	25	1.0653384E-6	80.0	8
TCCGTTG	25	1.0653384E-6	80.0	1
CGTTGTA	25	1.0653384E-6	80.0	3
AGTCTAG	25	1.0653384E-6	80.0	9
GTAGTTC	25	1.0653384E-6	80.0	7
GTAGTCT	25	1.0653384E-6	80.0	7
>>END_MODULE
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183232 READS because READLEN < 1
Read 183232 spots for SRR11699544.sra
Written 183232 spots for SRR11699544.sra
Rejected 183238 READS because READLEN < 1
Read 183238 spots for SRR11699544.sra
Written 183238 spots for SRR11699544.sra
SRR ids: ['SRR11699544.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ne4wlpyq
SRR11699544.sra spots: 3664646
blocks: [[1, 183232], [183233, 366464], [366465, 549696], [549697, 732928], [732929, 916160], [916161, 1099392], [1099393, 1282624], [1282625, 1465856], [1465857, 1649088], [1649089, 1832320], [1832321, 2015552], [2015553, 2198784], [2198785, 2382016], [2382017, 2565248], [2565249, 2748480], [2748481, 2931712], [2931713, 3114944], [3114945, 3298176], [3298177, 3481408], [3481409, 3664646]]
SRR11699544 file size 767263
SRR11699544 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 SRR11699544 SRR11699544_1.fastq
Input file:	SRR11699544_1.fastq
trimmed:	SRR11699544-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
Fri Jun 20 20:31:53 2025 >> started

Fri Jun 20 20:31:55 2025 >> done (1.796s)
3664646 reads processed; of these:
 476035 (12.99%) short reads filtered out after trimming by size control
    916 ( 0.02%) empty reads filtered out after trimming by size control
3187695 (86.99%) reads available; of these:
3177001 (99.66%) trimmed reads available after processing
  10694 ( 0.34%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  73801	  2.32%
 19	 109701	  3.44%
 20	 120544	  3.78%
 21	 194678	  6.11%
 22	 326213	 10.23%
 23	 126839	  3.98%
 24	 309477	  9.71%
 25	 129737	  4.07%
 26	 116151	  3.64%
 27	 208518	  6.54%
 28	  96702	  3.03%
 29	 107928	  3.39%
 30	 121085	  3.80%
 31	  99150	  3.11%
 32	 105868	  3.32%
 33	 130066	  4.08%
 34	 170259	  5.34%
 35	 239992	  7.53%
 36	 151927	  4.77%
 37	  60582	  1.90%
 38	  34956	  1.10%
 39	  26924	  0.84%
 40	  25578	  0.80%
 41	  37824	  1.19%
 42	  15750	  0.49%
 43	  10360	  0.32%
 44	   6743	  0.21%
 45	   5842	  0.18%
 46	   3853	  0.12%
 47	   2706	  0.08%
 48	   3433	  0.11%
 49	   1358	  0.04%
 50	    849	  0.03%
 51	    646	  0.02%
 52	    367	  0.01%
 53	    358	  0.01%
 54	    233	  0.01%
 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	      0	  0.00%
 76	      0	  0.00%
 77	      0	  0.00%
 78	      0	  0.00%
 79	      0	  0.00%
 80	      0	  0.00%
 81	      0	  0.00%
 82	      0	  0.00%
 83	      0	  0.00%
 84	      0	  0.00%
 85	      3	  0.00%
 86	  10694	  0.34%
3187695 reads passed initial QC


criterion=sequence-density
sequence-density=6.58
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=13
prefix-density=0.02
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAAGACCCGGGTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=41
fanout-score=180.40
fanout-score-rank=1
prefix-density=0.93
prefix-fanout=1.0
sequence=TAGCCAAGTGTGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTCCGACTTCC
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 20 20:32:58
                             Started mapping on |	Jun 20 20:32:58
                                    Finished on |	Jun 20 20:33:09
       Mapping speed, Million of reads per hour |	1043.25

                          Number of input reads |	3187695
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	325949
                        Uniquely mapped reads % |	10.23%
                          Average mapped length |	24.82
                       Number of splices: Total |	7824
            Number of splices: Annotated (sjdb) |	4250
                       Number of splices: GT/AG |	7319
                       Number of splices: GC/AG |	385
                       Number of splices: AT/AC |	4
               Number of splices: Non-canonical |	116
                      Mismatch rate per base, % |	0.94%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.42
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.36
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	457406
             % of reads mapped to multiple loci |	14.35%
        Number of reads mapped to too many loci |	1061394
             % of reads mapped to too many loci |	33.30%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	4.49%
                     % of reads unmapped: other |	37.63%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2404340	2404340	2404340
N_multimapping	457406	457406	457406
N_noFeature	241680	254957	310136
N_ambiguous	2574	29	16
UnstrandedReadsAssigned:81695 PositiveStrandReadsAssigned:70963 NegativeStrandReadsAssigned:15797
Dataset is classified unstranded
MeadianReadLen=27 20thPercentileLength=22 echo kmer=19
SRR11699544 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: SRR11699544-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,187,695 reads, 873,523 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 808 rounds

  72540 SRR11699544.ke.tsv
  44303 SRR11699544.se.tsv
 116843 total
==> SRR11699544.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	3	1.2121
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

==> SRR11699544.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699544 completed mapping pipeline successfully
