Starting /dee2/code/volunteer_pipeline.sh SRR11699240
    current disk space = 2484239364096
    free memory = 1579689768 
SRR11699240 SRAfilesize
766cf683b6bf948bf2c455ff7d586146  SRR11699240.sra
SRR11699240.sra file validated
SRR11699240 is single end
SRR11699240 is conventional basespace
SRR11699240 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699240_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	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.221	32.0	32.0	32.0	32.0	32.0
2	31.36475	32.0	32.0	32.0	32.0	32.0
3	31.4425	32.0	32.0	32.0	32.0	32.0
4	31.5185	32.0	32.0	32.0	32.0	32.0
5	31.4975	32.0	32.0	32.0	32.0	32.0
6	35.056	36.0	36.0	36.0	36.0	36.0
7	35.04675	36.0	36.0	36.0	36.0	36.0
8	35.01575	36.0	36.0	36.0	36.0	36.0
9	34.88025	36.0	36.0	36.0	32.0	36.0
10-11	35.072	36.0	36.0	36.0	36.0	36.0
12-13	35.093500000000006	36.0	36.0	36.0	36.0	36.0
14-15	35.039125	36.0	36.0	36.0	36.0	36.0
16-17	35.058375	36.0	36.0	36.0	36.0	36.0
18-19	35.1155	36.0	36.0	36.0	36.0	36.0
20-21	34.923249999999996	36.0	36.0	36.0	36.0	36.0
22-23	34.985875	36.0	36.0	36.0	36.0	36.0
24-25	34.98925	36.0	36.0	36.0	36.0	36.0
26-27	34.9045	36.0	36.0	36.0	34.0	36.0
28-29	34.796875	36.0	36.0	36.0	32.0	36.0
30-31	34.849374999999995	36.0	36.0	36.0	36.0	36.0
32-33	34.788875	36.0	36.0	36.0	34.0	36.0
34-35	34.900999999999996	36.0	36.0	36.0	36.0	36.0
36-37	34.8695	36.0	36.0	36.0	36.0	36.0
38-39	34.830875000000006	36.0	36.0	36.0	34.0	36.0
40-41	34.79925	36.0	36.0	36.0	32.0	36.0
42-43	34.689375	36.0	36.0	36.0	34.0	36.0
44-45	34.577875	36.0	36.0	36.0	32.0	36.0
46-47	34.651624999999996	36.0	36.0	36.0	32.0	36.0
48-49	34.345749999999995	36.0	36.0	36.0	32.0	36.0
50-51	33.959500000000006	36.0	36.0	36.0	32.0	36.0
52-53	33.419	36.0	36.0	36.0	26.5	36.0
54-55	33.497875	36.0	36.0	36.0	26.5	36.0
56-57	32.8455	36.0	32.0	36.0	24.0	36.0
58-59	33.006	36.0	32.0	36.0	24.0	36.0
60-61	33.03825	36.0	36.0	36.0	20.5	36.0
62-63	32.812875	36.0	32.0	36.0	14.0	36.0
64-65	32.402375	36.0	32.0	36.0	14.0	36.0
66-67	31.966375	36.0	32.0	36.0	14.0	36.0
68-69	32.502250000000004	36.0	32.0	36.0	14.0	36.0
70-71	32.682500000000005	36.0	32.0	36.0	17.5	36.0
72-73	32.64375	36.0	32.0	36.0	17.5	36.0
74-75	32.99825	36.0	32.0	36.0	17.5	36.0
76	30.384	36.0	27.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	2.0
22	1.0
23	8.0
24	19.0
25	24.0
26	23.0
27	42.0
28	53.0
29	75.0
30	126.0
31	174.0
32	233.0
33	432.0
34	1325.0
35	1463.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	27.150000000000002	30.25	20.95	21.65
2	27.250000000000004	25.025	26.224999999999998	21.5
3	27.500000000000004	31.324999999999996	19.225	21.95
4	28.599999999999998	34.625	18.55	18.224999999999998
5	21.5	26.525	24.474999999999998	27.500000000000004
6	27.725	24.725	27.275	20.275000000000002
7	33.0	33.225	18.45	15.325
8	22.075	26.700000000000003	32.275	18.95
9	23.775	34.849999999999994	18.575	22.8
10-11	33.0625	27.3	21.775	17.8625
12-13	22.112499999999997	23.1875	24.587500000000002	30.112499999999997
14-15	29.51618952369046	38.76734591823978	17.002125265658208	14.714339292411552
16-17	23.5125	22.5875	35.5625	18.337500000000002
18-19	38.95	23.2375	22.5	15.312500000000002
20-21	22.6875	34.6875	25.1	17.525
22-23	30.89136142017752	37.92974121765221	14.039254906863357	17.139642455306912
24-25	30.575000000000003	37.175000000000004	14.4375	17.8125
26-27	26.5125	30.837500000000002	19.625	23.025000000000002
28-29	31.85	27.55	16.412499999999998	24.1875
30-31	31.937500000000004	34.9375	12.0	21.125
32-33	28.212500000000002	35.212500000000006	13.450000000000001	23.125
34-35	30.725	29.7875	14.662500000000001	24.825
36-37	25.124999999999996	35.949999999999996	12.4875	26.437500000000004
38-39	24.0	32.975	14.000000000000002	29.025000000000002
40-41	27.0125	28.375	17.2625	27.35
42-43	28.0875	27.250000000000004	18.6875	25.974999999999998
44-45	23.849999999999998	34.7375	14.762500000000001	26.650000000000002
46-47	22.8625	31.2625	14.1625	31.7125
48-49	18.224999999999998	27.6875	16.675	37.4125
50-51	16.9875	28.65	17.2625	37.1
52-53	22.052756594574323	22.852856607075882	20.44005500687586	34.654331791473936
54-55	19.85	24.4125	22.112499999999997	33.625
56-57	22.5125	22.225	20.2375	35.025
58-59	21.9625	23.474999999999998	19.0125	35.55
60-61	16.575	24.15	24.887500000000003	34.387499999999996
62-63	15.287500000000001	24.2875	24.0	36.425000000000004
64-65	16.2	20.6625	26.437500000000004	36.7
66-67	17.65	16.1375	31.0375	35.175
68-69	20.8625	16.8	30.45	31.887500000000003
70-71	23.365420677584698	16.377047130891363	30.991373921740216	29.26615826978372
72-73	20.825	15.2	29.8375	34.137499999999996
74-75	20.5125	15.462500000000002	30.9625	33.0625
76	14.924999999999999	14.374999999999998	37.75	32.95
>>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	0.5
36	0.5
37	0.0
38	0.5
39	3.5
40	4.5
41	12.5
42	22.0
43	27.5
44	50.0
45	91.0
46	115.0
47	168.0
48	312.5
49	661.0
50	918.0
51	739.5
52	535.5
53	498.5
54	487.0
55	389.0
56	217.5
57	114.0
58	84.0
59	84.0
60	53.5
61	15.0
62	7.0
63	7.5
64	6.0
65	3.0
66	1.5
67	1.0
68	1.0
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	0.0
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	0.0125
16-17	0.0
18-19	0.0
20-21	0.0
22-23	0.0125
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	0.0125
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	65.5
#Duplication Level	Percentage of deduplicated	Percentage of total
1	90.07633587786259	59.0
2	4.923664122137405	6.45
3	1.450381679389313	2.85
4	0.5725190839694656	1.5
5	0.5725190839694656	1.875
6	0.4961832061068702	1.95
7	0.3435114503816794	1.575
8	0.19083969465648853	1.0
9	0.19083969465648853	1.125
>10	1.0687022900763359	13.700000000000001
>50	0.07633587786259542	2.9000000000000004
>100	0.03816793893129771	6.075
>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	243	6.075	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	65	1.625	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	51	1.275	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	45	1.125	No Hit
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	35	0.8750000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	33	0.8250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	33	0.8250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCT	28	0.7000000000000001	TruSeq Adapter, Index 11 (100% over 37bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	28	0.7000000000000001	No Hit
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGC	24	0.6	TruSeq Adapter, Index 6 (97% over 36bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACAT	22	0.5499999999999999	TruSeq Adapter, Index 11 (100% over 41bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	22	0.5499999999999999	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	21	0.525	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	17	0.42500000000000004	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	16	0.4	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	15	0.375	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	15	0.375	No Hit
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGC	14	0.35000000000000003	TruSeq Adapter, Index 6 (97% over 36bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTAC	14	0.35000000000000003	TruSeq Adapter, Index 11 (100% over 39bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	13	0.325	No Hit
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTAGATCGGAAGAGCA	13	0.325	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	13	0.325	No Hit
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGTAGATCGGAAGAGCA	10	0.25	No Hit
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	10	0.25	No Hit
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGG	9	0.22499999999999998	TruSeq Adapter, Index 2 (97% over 35bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACA	9	0.22499999999999998	TruSeq Adapter, Index 11 (100% over 40bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AGCGGAGTAGAGCAGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	8	0.2	No Hit
TTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATC	8	0.2	TruSeq Adapter, Index 11 (100% over 42bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	8	0.2	No Hit
AAGATACGGGTTCGATTCCCGTCGCTCGCCCCAAGATCGGAAGAGCACAC	7	0.17500000000000002	No Hit
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTGAGATCGGAAGAGCACAC	7	0.17500000000000002	No Hit
GCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAGATCGGAAGAG	7	0.17500000000000002	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	6	0.15	No Hit
TAAAAGGCTGACGCGGGCTCTAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCT	6	0.15	TruSeq Adapter, Index 11 (97% over 37bp)
TCCTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGAGATCGGAAGAGCAC	6	0.15	No Hit
AGCGTGGAGGTTCGAGTCCTCTTCAAGGCACCAAGATCGGAAGAGCACAC	6	0.15	No Hit
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	6	0.15	No Hit
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	6	0.15	No Hit
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	5	0.125	No Hit
AGGGATGTAGCGCAGCTTGGTAGCTTTTGTTTTAGATCGGAAGAGCACAC	5	0.125	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG	5	0.125	No Hit
GTCTACGCTGGTTCAAATCCAGCTCGGCCCACCAAGATCGGAAGAGCACA	5	0.125	No Hit
GCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAG	5	0.125	No Hit
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTAGATCGGAAGAGC	5	0.125	No Hit
CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AAAATAGCTCGATGCCAGAATAAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGTCCCATGGTCTAGCGGTTAGGACATTGGACTCTGAGATCGGAAGAGCA	5	0.125	No Hit
TGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTC	5	0.125	TruSeq Adapter, Index 11 (100% over 44bp)
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTAGATCGGAAGAGC	5	0.125	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGAGATCGGAAGAGCACAC	5	0.125	No Hit
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	0.0	0.0	0.0	0.0	0.0
2	0.1	0.0	0.0	0.0	0.0
3	0.225	0.0	0.0	0.0	0.0
4	0.3	0.0	0.0	0.0	0.0
5	0.35	0.0	0.0	0.0	0.0
6	0.6	0.0	0.0	0.0	0.0
7	0.775	0.0	0.0	0.0	0.0
8	1.175	0.0	0.0	0.0	0.0
9	1.85	0.0	0.0	0.0	0.0
10	2.375	0.0	0.0	0.0	0.0
11	3.075	0.0	0.0	0.0	0.0
12	3.625	0.0	0.0	0.0	0.0
13	5.15	0.0	0.0	0.0	0.0
14	7.175	0.0	0.0	0.0	0.0
15	8.35	0.0	0.0	0.0	0.0
16	9.825	0.0	0.0	0.0	0.0
17	12.05	0.0	0.0	0.0	0.0
18	14.925	0.0	0.0	0.0	0.0
19	17.025	0.0	0.0	0.0	0.0
20	20.2	0.0	0.0	0.0	0.0
21	23.2	0.0	0.0	0.0	0.0
22	28.425	0.0	0.0	0.0	0.0
23	39.125	0.0	0.0	0.0	0.0
24	42.05	0.0	0.0	0.0	0.0
25	48.325	0.0	0.0	0.0	0.0
26	52.3	0.0	0.0	0.0	0.0
27	55.325	0.0	0.0	0.0	0.0
28	57.8	0.0	0.0	0.0	0.0
29	60.45	0.0	0.0	0.0	0.0
30	63.025	0.0	0.0	0.0	0.0
31	66.35	0.0	0.0	0.0	0.0
32	68.75	0.0	0.0	0.0	0.0
33	71.125	0.0	0.0	0.0	0.0
34	74.95	0.0	0.0	0.0	0.0
35	78.525	0.0	0.0	0.0	0.0
36	83.3	0.0	0.0	0.0	0.0
37	87.35	0.0	0.0	0.0	0.0
38	89.325	0.0	0.0	0.0	0.0
39	90.475	0.0	0.0	0.0	0.0
40	91.6	0.0	0.0	0.0	0.0
41	92.45	0.0	0.0	0.0	0.0
42	93.625	0.0	0.0	0.0	0.0
43	94.025	0.0	0.0	0.0	0.0
44	94.45	0.0	0.0	0.0	0.0
45	94.65	0.0	0.0	0.0	0.0
46	94.9	0.0	0.0	0.0	0.0
47	95.15	0.0	0.0	0.0	0.0
48	95.35	0.0	0.0	0.0	0.0
49	95.65	0.0	0.0	0.0	0.0
50	95.8	0.0	0.0	0.0	0.0
51	95.85	0.0	0.0	0.0	0.0
52	95.95	0.0	0.0	0.0	0.0
53	95.95	0.0	0.0	0.0	0.0
54	95.95	0.0	0.0	0.0	0.0
55	95.95	0.0	0.0	0.0	0.0
56	95.975	0.0	0.0	0.0	0.0
57	95.975	0.0	0.0	0.0	0.0
58	95.975	0.0	0.0	0.0	0.0
59	96.05	0.0	0.0	0.0	0.0
60	96.05	0.0	0.0	0.0	0.0
61	96.05	0.0	0.0	0.0	0.0
62	96.05	0.0	0.0	0.0	0.0
63	96.05	0.0	0.0	0.0	0.0
64	96.05	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGGTCAG	30	7.878043E-8	70.00001	17
ACACGAC	15	0.0020658788	70.00001	2
TTGTAGT	35	2.6138878E-9	70.00001	5
TAGTTCA	30	7.878043E-8	70.00001	8
GACACGA	15	0.0020658788	70.00001	1
TGTAGTC	15	0.0020658788	70.00001	6
TGTAGCT	15	0.0020658788	70.00001	6
GTCTAGT	15	0.0020658788	70.00001	10
TTGGTCA	30	7.878043E-8	70.00001	16
AACGGAT	15	0.0020658788	70.00001	16
GCTCAGA	15	0.0020658788	70.00001	10
GTAGCTC	15	0.0020658788	70.00001	7
GTAGTTC	30	7.878043E-8	70.00001	7
ACGGATA	15	0.0020658788	70.00001	17
TTCAATT	25	2.3570374E-6	70.0	11
ATTGGTC	25	2.3570374E-6	70.0	15
CACCGCC	25	2.3570374E-6	70.0	26
GGATTGT	25	2.3570374E-6	70.0	2
ACCGCCC	25	2.3570374E-6	70.0	27
CAATTGG	25	2.3570374E-6	70.0	13
>>END_MODULE
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424128 READS because READLEN < 1
Read 424128 spots for SRR11699240.sra
Written 424128 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
Rejected 424117 READS because READLEN < 1
Read 424117 spots for SRR11699240.sra
Written 424117 spots for SRR11699240.sra
SRR ids: ['SRR11699240.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_lab8xqtj
SRR11699240.sra spots: 8482351
blocks: [[1, 424117], [424118, 848234], [848235, 1272351], [1272352, 1696468], [1696469, 2120585], [2120586, 2544702], [2544703, 2968819], [2968820, 3392936], [3392937, 3817053], [3817054, 4241170], [4241171, 4665287], [4665288, 5089404], [5089405, 5513521], [5513522, 5937638], [5937639, 6361755], [6361756, 6785872], [6785873, 7209989], [7209990, 7634106], [7634107, 8058223], [8058224, 8482351]]
SRR11699240 file size 1613122
SRR11699240 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 SRR11699240 SRR11699240_1.fastq
Input file:	SRR11699240_1.fastq
trimmed:	SRR11699240-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 00:23:36 2025 >> started

Wed Jun 18 00:23:40 2025 >> done (3.579s)
8482351 reads processed; of these:
1434088 (16.91%) short reads filtered out after trimming by size control
   3096 ( 0.04%) empty reads filtered out after trimming by size control
7045167 (83.06%) reads available; of these:
6890819 (97.81%) trimmed reads available after processing
 154348 ( 2.19%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 175176	  2.49%
 19	 271290	  3.85%
 20	 304932	  4.33%
 21	 438528	  6.22%
 22	 914715	 12.98%
 23	 257575	  3.66%
 24	 539518	  7.66%
 25	 333069	  4.73%
 26	 225736	  3.20%
 27	 224536	  3.19%
 28	 191023	  2.71%
 29	 205095	  2.91%
 30	 292716	  4.15%
 31	 212600	  3.02%
 32	 204461	  2.90%
 33	 302339	  4.29%
 34	 320464	  4.55%
 35	 452884	  6.43%
 36	 361883	  5.14%
 37	 163143	  2.32%
 38	 101362	  1.44%
 39	  91761	  1.30%
 40	  72222	  1.03%
 41	 111024	  1.58%
 42	  54972	  0.78%
 43	  39392	  0.56%
 44	  28395	  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	      0	  0.00%
 69	      0	  0.00%
 70	      0	  0.00%
 71	      1	  0.00%
 72	      3	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      4	  0.00%
 76	 154348	  2.19%
7045167 reads passed initial QC


criterion=sequence-density
sequence-density=4.84
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCG


criterion=fanout-score
sequence-density=1.75
sequence-density-rank=3
fanout-score=15.59
fanout-score-rank=1
prefix-density=1.79
prefix-fanout=15.3
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTGA
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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCG -o SRR11699240 -
Input file:	STDIN
trimmed:	SRR11699240-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCG
-- 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 00:23:53 2025 >> started

Wed Jun 18 00:23:56 2025 >> done (2.781s)
4227100 reads processed; of these:
   9508 ( 0.22%) short reads filtered out after trimming by size control
 206405 ( 4.88%) empty reads filtered out after trimming by size control
4011187 (94.89%) reads available; of these:
  25469 ( 0.63%) trimmed reads available after processing
3985718 (99.37%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 106252	  2.65%
 19	 163544	  4.08%
 20	 180599	  4.50%
 21	 262176	  6.54%
 22	 548069	 13.66%
 23	 154287	  3.85%
 24	 320311	  7.99%
 25	 199100	  4.96%
 26	 133790	  3.34%
 27	 134182	  3.35%
 28	 114445	  2.85%
 29	 119231	  2.97%
 30	 174828	  4.36%
 31	 126922	  3.16%
 32	 113278	  2.82%
 33	 136998	  3.42%
 34	 156813	  3.91%
 35	 198543	  4.95%
 36	 186155	  4.64%
 37	  95414	  2.38%
 38	  60292	  1.50%
 39	  54700	  1.36%
 40	  42633	  1.06%
 41	  65003	  1.62%
 42	  31621	  0.79%
 43	  22843	  0.57%
 44	  16822	  0.42%
 45	      0	  0.00%
 46	      0	  0.00%
 47	      0	  0.00%
 48	      0	  0.00%
 49	      0	  0.00%
 50	      0	  0.00%
 51	      0	  0.00%
 52	      0	  0.00%
 53	      0	  0.00%
 54	      0	  0.00%
 55	      0	  0.00%
 56	      0	  0.00%
 57	      0	  0.00%
 58	      0	  0.00%
 59	      0	  0.00%
 60	      0	  0.00%
 61	      0	  0.00%
 62	      0	  0.00%
 63	      0	  0.00%
 64	      0	  0.00%
 65	      0	  0.00%
 66	      0	  0.00%
 67	      0	  0.00%
 68	      1	  0.00%
 69	      0	  0.00%
 70	      0	  0.00%
 71	      0	  0.00%
 72	      3	  0.00%
 73	   2512	  0.06%
 74	      0	  0.00%
 75	      2	  0.00%
 76	  89818	  2.24%


criterion=sequence-density
sequence-density=2.77
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=11
prefix-density=0.02
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAA


criterion=fanout-score
sequence-density=1.83
sequence-density-rank=2
fanout-score=15.40
fanout-score-rank=1
prefix-density=1.87
prefix-fanout=15.1
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTGA
                                 Started job on |	Jun 18 00:24:20
                             Started mapping on |	Jun 18 00:24:20
                                    Finished on |	Jun 18 00:24:42
       Mapping speed, Million of reads per hour |	1117.51

                          Number of input reads |	6829254
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	591126
                        Uniquely mapped reads % |	8.66%
                          Average mapped length |	25.45
                       Number of splices: Total |	14654
            Number of splices: Annotated (sjdb) |	7772
                       Number of splices: GT/AG |	13360
                       Number of splices: GC/AG |	740
                       Number of splices: AT/AC |	6
               Number of splices: Non-canonical |	548
                      Mismatch rate per base, % |	1.05%
                         Deletion rate per base |	0.02%
                        Deletion average length |	1.58
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.25
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	723676
             % of reads mapped to multiple loci |	10.60%
        Number of reads mapped to too many loci |	1828727
             % of reads mapped to too many loci |	26.78%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.06%
                     % of reads unmapped: other |	46.91%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	5514452	5514452	5514452
N_multimapping	723676	723676	723676
N_noFeature	461744	475734	572854
N_ambiguous	4357	53	38
UnstrandedReadsAssigned:125025 PositiveStrandReadsAssigned:115339 NegativeStrandReadsAssigned:18234
Dataset is classified positive stranded
MeadianReadLen=26 20thPercentileLength=22 echo kmer=19
SRR11699240 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: SRR11699240-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 6,829,254 reads, 1,014,382 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 893 rounds

  72540 SRR11699240.ke.tsv
  44303 SRR11699240.se.tsv
 116843 total
==> SRR11699240.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	4	1.19534
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

==> SRR11699240.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	1
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699240 completed mapping pipeline successfully
