Starting /dee2/code/volunteer_pipeline.sh SRR11699625
    current disk space = 2454229942272
    free memory = 1581430340 
SRR11699625 SRAfilesize
7e76cd1d41ff78f0dbde131055b58e58  SRR11699625.sra
SRR11699625.sra file validated
SRR11699625 is single end
SRR11699625 is conventional basespace
SRR11699625 read1 length is 86 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699625_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	49
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.30225	32.0	32.0	32.0	32.0	32.0
2	31.4035	32.0	32.0	32.0	32.0	32.0
3	31.56375	32.0	32.0	32.0	32.0	32.0
4	31.4985	32.0	32.0	32.0	32.0	32.0
5	31.5345	32.0	32.0	32.0	32.0	32.0
6	35.08525	36.0	36.0	36.0	36.0	36.0
7	35.13	36.0	36.0	36.0	36.0	36.0
8	35.0675	36.0	36.0	36.0	36.0	36.0
9	34.703	36.0	36.0	36.0	32.0	36.0
10-11	35.215875	36.0	36.0	36.0	36.0	36.0
12-13	35.080375000000004	36.0	36.0	36.0	36.0	36.0
14-15	34.975875	36.0	36.0	36.0	34.0	36.0
16-17	35.163375	36.0	36.0	36.0	36.0	36.0
18-19	35.225624999999994	36.0	36.0	36.0	36.0	36.0
20-21	34.907250000000005	36.0	36.0	36.0	34.0	36.0
22-23	35.073499999999996	36.0	36.0	36.0	34.0	36.0
24-25	34.929125	36.0	36.0	36.0	36.0	36.0
26-27	34.834500000000006	36.0	36.0	36.0	34.0	36.0
28-29	34.91225	36.0	36.0	36.0	36.0	36.0
30-31	34.90575	36.0	36.0	36.0	36.0	36.0
32-33	34.93675	36.0	36.0	36.0	36.0	36.0
34-35	34.90975	36.0	36.0	36.0	34.0	36.0
36-37	34.81525	36.0	36.0	36.0	34.0	36.0
38-39	34.768	36.0	36.0	36.0	34.0	36.0
40-41	34.860749999999996	36.0	36.0	36.0	36.0	36.0
42-43	34.8435	36.0	36.0	36.0	36.0	36.0
44-45	34.67475	36.0	36.0	36.0	34.0	36.0
46-47	35.052875	36.0	36.0	36.0	36.0	36.0
48-49	34.9555	36.0	36.0	36.0	36.0	36.0
50-51	34.647375	36.0	36.0	36.0	32.0	36.0
52-53	34.642125	36.0	36.0	36.0	34.0	36.0
54-55	33.861625000000004	36.0	36.0	36.0	29.5	36.0
56-57	33.725375	36.0	36.0	36.0	29.5	36.0
58-59	33.640875	36.0	36.0	36.0	29.5	36.0
60-61	33.283125	36.0	36.0	36.0	27.0	36.0
62-63	33.247	36.0	36.0	36.0	27.0	36.0
64-65	33.325125	36.0	36.0	36.0	27.0	36.0
66-67	33.307	36.0	36.0	36.0	27.0	36.0
68-69	33.574749999999995	36.0	36.0	36.0	27.0	36.0
70-71	33.8935	36.0	36.0	36.0	27.0	36.0
72-73	33.962999999999994	36.0	36.0	36.0	32.0	36.0
74-75	34.010875	36.0	36.0	36.0	32.0	36.0
76-77	34.004125	36.0	36.0	36.0	32.0	36.0
78-79	34.18625	36.0	36.0	36.0	32.0	36.0
80-81	34.448875	36.0	36.0	36.0	32.0	36.0
82-83	34.465875	36.0	36.0	36.0	32.0	36.0
84-85	34.29075	36.0	36.0	36.0	32.0	36.0
86	33.702	36.0	36.0	36.0	27.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
19	1.0
20	0.0
21	1.0
22	1.0
23	2.0
24	2.0
25	10.0
26	32.0
27	30.0
28	58.0
29	84.0
30	117.0
31	138.0
32	192.0
33	321.0
34	782.0
35	2229.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	23.65	27.625	24.05	24.675
2	29.325000000000003	22.900000000000002	20.150000000000002	27.625
3	28.7	25.45	18.35	27.500000000000004
4	33.75	25.2	19.525000000000002	21.525
5	23.200000000000003	25.825	22.7	28.275
6	23.200000000000003	20.875	30.75	25.174999999999997
7	33.2	28.000000000000004	19.425	19.375
8	23.674999999999997	21.925	34.75	19.650000000000002
9	26.200000000000003	31.95	21.45	20.4
10-11	31.7875	22.375	24.575	21.2625
12-13	23.5375	20.95	26.775	28.7375
14-15	30.20377547193399	33.391673959244905	18.2522815351919	18.152269033629203
16-17	22.6	25.0	28.6125	23.7875
18-19	35.3875	24.337500000000002	20.05	20.225
20-21	26.1125	31.8625	22.6875	19.3375
22-23	33.7	35.4375	16.175	14.6875
24-25	30.9	37.625	15.1125	16.3625
26-27	28.249999999999996	35.2875	16.025	20.4375
28-29	30.725	32.237500000000004	13.275	23.7625
30-31	34.08352088022005	32.78319579894974	11.652913228307076	21.48037009252313
32-33	27.725	34.949999999999996	13.1625	24.1625
34-35	30.862499999999997	31.6875	15.2375	22.2125
36-37	25.715714464308036	35.76697087135892	12.239029878734842	26.2782847855982
38-39	23.62431215607804	31.228114057028517	15.632816408204103	29.514757378689342
40-41	21.810905452726363	29.114557278639317	15.32016008004002	33.7543771885943
42-43	25.465683210401302	28.378547318414803	18.789848731091386	27.365920740092513
44-45	18.775	29.15	19.650000000000002	32.425
46-47	18.862499999999997	29.775000000000002	18.45	32.9125
48-49	15.891472868217054	26.219054763690924	24.756189047261813	33.13328332083021
50-51	17.80085063797848	28.546409807355516	20.79059294470853	32.86214660995746
52-53	18.53981747718465	24.415551943992998	23.265408176022003	33.77922240280035
54-55	17.837500000000002	24.875	27.125	30.162499999999998
56-57	16.3125	23.0625	28.425	32.2
58-59	19.422211105552776	23.3991995997999	26.738369184592298	30.440220110055026
60-61	18.587500000000002	24.05	29.6625	27.700000000000003
62-63	23.275000000000002	18.7375	29.775000000000002	28.212500000000002
64-65	18.6625	19.875	27.525	33.9375
66-67	21.41338336460288	15.10944340212633	33.383364602876796	30.093808630393998
68-69	19.4875	15.137500000000001	34.387499999999996	30.9875
70-71	20.025000000000002	12.85	37.125	30.0
72-73	23.902987873484186	12.426553319164896	35.091886485810726	28.57857232154019
74-75	22.112499999999997	9.65	35.4	32.8375
76-77	23.149074537268636	10.055027513756878	37.09354677338669	29.702351175587793
78-79	16.1125	16.55	39.0875	28.249999999999996
80-81	18.9	20.25	36.9	23.95
82-83	17.641910477619405	27.38184546136534	32.38309577394349	22.593148287071767
84-85	17.808904452226113	33.7543771885943	29.427213606803406	19.009504752376188
86	18.099999999999998	38.675	27.825	15.4
>>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	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.5
34	0.5
35	0.5
36	1.0
37	0.5
38	0.0
39	0.5
40	6.5
41	12.5
42	28.0
43	43.0
44	93.0
45	188.0
46	309.5
47	437.0
48	500.5
49	543.5
50	574.0
51	490.5
52	416.5
53	344.5
54	231.5
55	166.0
56	113.0
57	94.0
58	68.0
59	24.5
60	8.0
61	6.0
62	4.0
63	3.5
64	2.0
65	1.5
66	0.5
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	0.0
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	0.0125
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	0.025
32-33	0.0
34-35	0.0
36-37	0.0125
38-39	0.05
40-41	0.05
42-43	0.0125
44-45	0.0
46-47	0.0
48-49	0.025
50-51	0.075
52-53	0.0125
54-55	0.0
56-57	0.0
58-59	0.05
60-61	0.0
62-63	0.0
64-65	0.0
66-67	0.0625
68-69	0.0
70-71	0.0
72-73	0.0125
74-75	0.0
76-77	0.05
78-79	0.0
80-81	0.0
82-83	0.025
84-85	0.05
86	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
86	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	67.2
#Duplication Level	Percentage of deduplicated	Percentage of total
1	88.35565476190477	59.375
2	5.208333333333334	7.000000000000001
3	2.1577380952380953	4.35
4	0.818452380952381	2.1999999999999997
5	0.855654761904762	2.875
6	0.4836309523809524	1.95
7	0.2976190476190476	1.4000000000000001
8	0.4092261904761905	2.1999999999999997
9	0.18601190476190474	1.125
>10	1.0788690476190477	9.925
>50	0.1488095238095238	7.6
>100	0.0	0.0
>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
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTA	87	2.175	TruSeq Adapter, Index 3 (100% over 36bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTA	80	2.0	TruSeq Adapter, Index 3 (100% over 36bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	78	1.95	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC	59	1.4749999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	29	0.7250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	22	0.5499999999999999	No Hit
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	18	0.44999999999999996	No Hit
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	16	0.4	No Hit
CGTTTCCCGGCTGGTGCACCAAGATCGGAAGAGCACACGTCTGAACTCCA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	14	0.35000000000000003	No Hit
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGGATATGGCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAG	13	0.325	TruSeq Adapter, Index 3 (100% over 37bp)
CCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TACCTGGTTGATCCTGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CCACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAG	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
TCCACTGAGATCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCA	11	0.27499999999999997	No Hit
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ATCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
AGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	10	0.25	No Hit
CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGGCCTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTA	9	0.22499999999999998	TruSeq Adapter, Index 3 (100% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATG	9	0.22499999999999998	TruSeq Adapter, Index 3 (100% over 49bp)
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
ACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
AGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGG	9	0.22499999999999998	TruSeq Adapter, Index 3 (100% over 38bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAG	8	0.2	TruSeq Adapter, Index 3 (100% over 37bp)
TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA	8	0.2	No Hit
GCGGCTGGATCACCTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
CGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAG	8	0.2	TruSeq Adapter, Index 3 (97% over 37bp)
CCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	8	0.2	No Hit
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CTGCGGAAGGATCATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAG	7	0.17500000000000002	No Hit
TCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GTGCGGCTGGATCACCTCCTAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TAATTCATGATCTGGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
ACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTT	6	0.15	TruSeq Adapter, Index 1 (97% over 35bp)
TGCGGAAGGATCATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CGACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGG	6	0.15	TruSeq Adapter, Index 3 (100% over 38bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CACTGAGATCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACA	6	0.15	No Hit
GGGGATGTAGCTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTA	6	0.15	TruSeq Adapter, Index 3 (100% over 36bp)
CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TTCCCGGCTGGTGCACCAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CCCGGCTGGTGCACCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	5	0.125	No Hit
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTT	5	0.125	TruSeq Adapter, Index 1 (97% over 35bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AGATGATACGAGCACCTCTGAGCTTAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
AGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACA	5	0.125	No Hit
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	5	0.125	No Hit
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGAGATCGGAAGAGCAC	5	0.125	No Hit
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CGACACGACTCTCGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CTCGTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	5	0.125	No Hit
AAATCATGTGGGCTTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTA	5	0.125	TruSeq Adapter, Index 3 (100% over 36bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	5	0.125	No Hit
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CCGGCTGGTGCACCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAGATCGGAAGAGC	5	0.125	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	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	0.275	0.0	0.0	0.0	0.0
2	0.325	0.0	0.0	0.0	0.0
3	0.325	0.0	0.0	0.0	0.0
4	0.325	0.0	0.0	0.0	0.0
5	0.35	0.0	0.0	0.0	0.0
6	0.375	0.0	0.0	0.0	0.0
7	0.425	0.0	0.0	0.0	0.0
8	0.525	0.0	0.0	0.0	0.0
9	0.775	0.0	0.0	0.0	0.0
10	1.075	0.0	0.0	0.0	0.0
11	1.65	0.0	0.0	0.0	0.0
12	2.625	0.0	0.0	0.0	0.0
13	4.15	0.0	0.0	0.0	0.0
14	10.625	0.0	0.0	0.0	0.0
15	12.15	0.0	0.0	0.0	0.0
16	14.175	0.0	0.0	0.0	0.0
17	18.225	0.0	0.0	0.0	0.0
18	21.4	0.0	0.0	0.0	0.0
19	24.95	0.0	0.0	0.0	0.0
20	28.9	0.0	0.0	0.0	0.0
21	33.025	0.0	0.0	0.0	0.0
22	38.25	0.0	0.0	0.0	0.0
23	44.825	0.0	0.0	0.0	0.0
24	49.025	0.0	0.0	0.0	0.0
25	56.3	0.0	0.0	0.0	0.0
26	59.875	0.0	0.0	0.0	0.0
27	63.4	0.0	0.0	0.0	0.0
28	68.175	0.0	0.0	0.0	0.0
29	70.575	0.0	0.0	0.0	0.0
30	73.375	0.0	0.0	0.0	0.0
31	76.175	0.0	0.0	0.0	0.0
32	78.45	0.0	0.0	0.0	0.0
33	80.375	0.0	0.0	0.0	0.0
34	82.4	0.0	0.0	0.0	0.0
35	84.2	0.0	0.0	0.0	0.0
36	87.2	0.0	0.0	0.0	0.0
37	89.35	0.0	0.0	0.0	0.0
38	90.7	0.0	0.0	0.0	0.0
39	91.25	0.0	0.0	0.0	0.0
40	92.025	0.0	0.0	0.0	0.0
41	92.55	0.0	0.0	0.0	0.0
42	93.225	0.0	0.0	0.0	0.0
43	93.6	0.0	0.0	0.0	0.0
44	93.95	0.0	0.0	0.0	0.0
45	94.2	0.0	0.0	0.0	0.0
46	94.375	0.0	0.0	0.0	0.0
47	94.625	0.0	0.0	0.0	0.0
48	94.675	0.0	0.0	0.0	0.0
49	94.725	0.0	0.0	0.0	0.0
50	94.775	0.0	0.0	0.0	0.0
51	94.8	0.0	0.0	0.0	0.0
52	94.825	0.0	0.0	0.0	0.0
53	94.875	0.0	0.0	0.0	0.0
54	94.9	0.0	0.0	0.0	0.0
55	94.9	0.0	0.0	0.0	0.0
56	94.9	0.0	0.0	0.0	0.0
57	94.9	0.0	0.0	0.0	0.0
58	94.9	0.0	0.0	0.0	0.0
59	94.9	0.0	0.0	0.0	0.0
60	94.9	0.0	0.0	0.0	0.0
61	94.9	0.0	0.0	0.0	0.0
62	94.9	0.0	0.0	0.0	0.0
63	94.9	0.0	0.0	0.0	0.0
64	94.9	0.0	0.0	0.0	0.0
65	94.9	0.0	0.0	0.0	0.0
66	94.9	0.0	0.0	0.0	0.0
67	94.9	0.0	0.0	0.0	0.0
68	94.9	0.0	0.0	0.0	0.0
69	94.9	0.0	0.0	0.0	0.0
70	94.9	0.0	0.0	0.0	0.0
71	94.9	0.0	0.0	0.0	0.0
72	94.9	0.0	0.0	0.0	0.0
73	94.9	0.0	0.0	0.0	0.0
74	94.9	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTTGATC	15	0.0012159165	80.00001	7
TGGTTGA	15	0.0012159165	80.00001	5
GGTTGAT	15	0.0012159165	80.00001	6
TGATCCT	15	0.0012159165	80.00001	9
CCGTTGT	15	0.0012159165	80.00001	2
TAGTCTA	20	3.6123936E-5	80.00001	8
TAGTTCA	15	0.0012159165	80.00001	8
CTGGTTG	15	0.0012159165	80.00001	4
ACCTGGT	15	0.0012159165	80.00001	2
TGTAGTC	15	0.0012159165	80.00001	6
TGTAGCT	20	3.6123936E-5	80.00001	6
TTGATCC	15	0.0012159165	80.00001	8
TCCGTTG	15	0.0012159165	80.00001	1
TACCTGG	15	0.0012159165	80.00001	1
CGTTGTA	15	0.0012159165	80.00001	3
AGTCTAG	20	3.6123936E-5	80.00001	9
GTAGCTC	15	0.0012159165	80.00001	7
GTAGTTC	15	0.0012159165	80.00001	7
CCTGGTT	15	0.0012159165	80.00001	3
GTAGTCT	20	3.6123936E-5	80.00001	7
>>END_MODULE
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295346 READS because READLEN < 1
Read 295346 spots for SRR11699625.sra
Written 295346 spots for SRR11699625.sra
Rejected 295351 READS because READLEN < 1
Read 295351 spots for SRR11699625.sra
Written 295351 spots for SRR11699625.sra
SRR ids: ['SRR11699625.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_rh7v65k7
SRR11699625.sra spots: 5906925
blocks: [[1, 295346], [295347, 590692], [590693, 886038], [886039, 1181384], [1181385, 1476730], [1476731, 1772076], [1772077, 2067422], [2067423, 2362768], [2362769, 2658114], [2658115, 2953460], [2953461, 3248806], [3248807, 3544152], [3544153, 3839498], [3839499, 4134844], [4134845, 4430190], [4430191, 4725536], [4725537, 5020882], [5020883, 5316228], [5316229, 5611574], [5611575, 5906925]]
SRR11699625 file size 1238054
SRR11699625 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 SRR11699625 SRR11699625_1.fastq
Input file:	SRR11699625_1.fastq
trimmed:	SRR11699625-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
Sat Jun 21 14:40:53 2025 >> started

Sat Jun 21 14:40:56 2025 >> done (2.524s)
5906925 reads processed; of these:
1328230 (22.49%) short reads filtered out after trimming by size control
  18945 ( 0.32%) empty reads filtered out after trimming by size control
4559750 (77.19%) reads available; of these:
4542691 (99.63%) trimmed reads available after processing
  17059 ( 0.37%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 236334	  5.18%
 19	 255370	  5.60%
 20	 272863	  5.98%
 21	 349819	  7.67%
 22	 377982	  8.29%
 23	 257088	  5.64%
 24	 447624	  9.82%
 25	 216134	  4.74%
 26	 205502	  4.51%
 27	 311456	  6.83%
 28	 158230	  3.47%
 29	 162024	  3.55%
 30	 180210	  3.95%
 31	 127961	  2.81%
 32	 117710	  2.58%
 33	 112801	  2.47%
 34	 119338	  2.62%
 35	 179580	  3.94%
 36	 128199	  2.81%
 37	  70946	  1.56%
 38	  45870	  1.01%
 39	  43375	  0.95%
 40	  31215	  0.68%
 41	  44428	  0.97%
 42	  23079	  0.51%
 43	  17521	  0.38%
 44	  14413	  0.32%
 45	  11927	  0.26%
 46	   7094	  0.16%
 47	   5473	  0.12%
 48	   4600	  0.10%
 49	   2804	  0.06%
 50	   1512	  0.03%
 51	    932	  0.02%
 52	    565	  0.01%
 53	    431	  0.01%
 54	    278	  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	  17059	  0.37%
4559750 reads passed initial QC


criterion=sequence-density
sequence-density=5.45
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=14
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGAAAGACCCGGGTT


criterion=fanout-score
sequence-density=0.13
sequence-density-rank=21
fanout-score=21.53
fanout-score-rank=1
prefix-density=1.95
prefix-fanout=1.4
sequence=GTCAGGATAGCTCAGTTGGTAGAGC
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 21 14:41:33
                             Started mapping on |	Jun 21 14:41:33
                                    Finished on |	Jun 21 14:41:47
       Mapping speed, Million of reads per hour |	1172.51

                          Number of input reads |	4559750
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	471934
                        Uniquely mapped reads % |	10.35%
                          Average mapped length |	23.60
                       Number of splices: Total |	12526
            Number of splices: Annotated (sjdb) |	4602
                       Number of splices: GT/AG |	11929
                       Number of splices: GC/AG |	456
                       Number of splices: AT/AC |	4
               Number of splices: Non-canonical |	137
                      Mismatch rate per base, % |	1.22%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.53
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.32
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	595528
             % of reads mapped to multiple loci |	13.06%
        Number of reads mapped to too many loci |	1130583
             % of reads mapped to too many loci |	24.79%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.66%
                     % of reads unmapped: other |	46.13%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3492288	3492288	3492288
N_multimapping	595528	595528	595528
N_noFeature	373190	391319	450815
N_ambiguous	3062	44	34
UnstrandedReadsAssigned:95682 PositiveStrandReadsAssigned:80571 NegativeStrandReadsAssigned:21085
Dataset is classified unstranded
MeadianReadLen=25 20thPercentileLength=21 echo kmer=19
SRR11699625 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: SRR11699625-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,559,750 reads, 980,752 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 934 rounds

  72540 SRR11699625.ke.tsv
  44303 SRR11699625.se.tsv
 116843 total
==> SRR11699625.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	7	2.14595
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	1	0.439766

==> SRR11699625.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	1
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699625 completed mapping pipeline successfully
