Starting /dee2/code/volunteer_pipeline.sh SRR11699271
    current disk space = 2472490655744
    free memory = 1579396352 
SRR11699271 SRAfilesize
8494986fe659a737ea9df3eeb983a4e9  SRR11699271.sra
SRR11699271.sra file validated
SRR11699271 is single end
SRR11699271 is conventional basespace
SRR11699271 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699271_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	52
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.08	32.0	32.0	32.0	32.0	32.0
2	31.2905	32.0	32.0	32.0	32.0	32.0
3	31.43375	32.0	32.0	32.0	32.0	32.0
4	31.44725	32.0	32.0	32.0	32.0	32.0
5	31.4025	32.0	32.0	32.0	32.0	32.0
6	34.7805	36.0	36.0	36.0	32.0	36.0
7	34.98225	36.0	36.0	36.0	36.0	36.0
8	35.01625	36.0	36.0	36.0	36.0	36.0
9	34.80275	36.0	36.0	36.0	32.0	36.0
10-11	34.86725	36.0	36.0	36.0	34.0	36.0
12-13	34.886750000000006	36.0	36.0	36.0	34.0	36.0
14-15	34.943875000000006	36.0	36.0	36.0	36.0	36.0
16-17	34.991875	36.0	36.0	36.0	36.0	36.0
18-19	35.009375	36.0	36.0	36.0	36.0	36.0
20-21	34.83525	36.0	36.0	36.0	36.0	36.0
22-23	34.837875	36.0	36.0	36.0	36.0	36.0
24-25	34.8345	36.0	36.0	36.0	34.0	36.0
26-27	34.761125	36.0	36.0	36.0	34.0	36.0
28-29	34.868750000000006	36.0	36.0	36.0	34.0	36.0
30-31	34.70425	36.0	36.0	36.0	34.0	36.0
32-33	34.73325	36.0	36.0	36.0	34.0	36.0
34-35	34.750375	36.0	36.0	36.0	34.0	36.0
36-37	34.77225	36.0	36.0	36.0	34.0	36.0
38-39	34.713625	36.0	36.0	36.0	32.0	36.0
40-41	34.74725	36.0	36.0	36.0	34.0	36.0
42-43	34.66375	36.0	36.0	36.0	32.0	36.0
44-45	34.72475	36.0	36.0	36.0	32.0	36.0
46-47	34.7355	36.0	36.0	36.0	32.0	36.0
48-49	34.415125	36.0	36.0	36.0	32.0	36.0
50-51	34.106125	36.0	36.0	36.0	32.0	36.0
52-53	34.007	36.0	36.0	36.0	32.0	36.0
54-55	33.254125	36.0	36.0	36.0	20.5	36.0
56-57	32.171625	36.0	32.0	36.0	14.0	36.0
58-59	31.464750000000002	36.0	32.0	36.0	14.0	36.0
60-61	30.877125	36.0	32.0	36.0	14.0	36.0
62-63	30.28425	36.0	27.0	36.0	14.0	36.0
64-65	29.556375	34.0	27.0	36.0	14.0	36.0
66-67	27.7275	32.0	14.0	36.0	14.0	36.0
68-69	27.769750000000002	32.0	14.0	36.0	14.0	36.0
70-71	28.043	32.0	14.0	36.0	14.0	36.0
72-73	27.855249999999998	32.0	14.0	36.0	14.0	36.0
74-75	28.3555	32.0	14.0	36.0	14.0	36.0
76	25.1675	27.0	14.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
20	1.0
21	2.0
22	4.0
23	13.0
24	26.0
25	31.0
26	62.0
27	87.0
28	108.0
29	159.0
30	238.0
31	302.0
32	447.0
33	681.0
34	1269.0
35	570.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	24.224999999999998	31.374999999999996	19.400000000000002	25.0
2	25.674999999999997	26.85	26.224999999999998	21.25
3	27.0	33.074999999999996	17.8	22.125
4	26.3	35.775	17.75	20.175
5	20.974999999999998	27.250000000000004	22.225	29.549999999999997
6	27.200000000000003	26.525	26.174999999999997	20.1
7	31.025000000000002	33.1	18.25	17.625
8	22.475	29.45	29.099999999999998	18.975
9	23.425	32.05	18.4	26.125
10-11	30.5	27.9125	22.975	18.6125
12-13	21.6125	25.724999999999998	23.5375	29.125
14-15	28.825	37.5	18.3625	15.312500000000002
16-17	21.975	24.962500000000002	34.8125	18.25
18-19	35.612500000000004	25.324999999999996	23.325000000000003	15.737499999999999
20-21	24.3625	37.1375	21.587500000000002	16.9125
22-23	30.375000000000004	37.4625	14.6125	17.549999999999997
24-25	29.8375	39.3375	14.0875	16.7375
26-27	29.262500000000003	32.7	16.5	21.5375
28-29	32.550000000000004	27.575	14.774999999999999	25.1
30-31	36.012499999999996	36.512499999999996	8.7625	18.712500000000002
32-33	27.8125	40.45	10.8375	20.9
34-35	32.125	30.662499999999998	12.7625	24.45
36-37	24.6125	34.050000000000004	10.2625	31.075000000000003
38-39	20.0625	33.7	14.174999999999999	32.0625
40-41	24.275	26.924999999999997	18.425	30.375000000000004
42-43	25.887500000000003	24.7875	23.0	26.325
44-45	22.7	31.025000000000002	17.9	28.375
46-47	22.85	31.887500000000003	14.075	31.1875
48-49	18.6	26.474999999999998	17.05	37.875
50-51	20.1	24.2625	19.75	35.8875
52-53	27.1125	22.1	19.6375	31.15
54-55	25.2625	21.9625	22.4875	30.2875
56-57	29.4875	19.900000000000002	17.375	33.2375
58-59	38.15	16.375	17.8125	27.6625
60-61	35.2375	14.274999999999999	25.8	24.6875
62-63	24.0125	18.8875	27.125	29.975
64-65	18.6	17.7	27.8125	35.8875
66-67	20.200000000000003	11.4125	33.975	34.4125
68-69	23.65	11.9375	34.5125	29.9
70-71	26.474999999999998	14.075	35.3375	24.1125
72-73	25.424999999999997	12.4	32.975	29.2
74-75	25.874999999999996	8.425	29.3875	36.3125
76	13.525	8.725	44.074999999999996	33.675
>>END_MODULE
>>Per sequence GC content	warn
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
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	0.0
36	0.0
37	0.0
38	1.0
39	1.5
40	2.0
41	4.0
42	5.0
43	8.0
44	24.0
45	50.5
46	64.0
47	99.0
48	203.5
49	380.0
50	487.0
51	724.5
52	746.0
53	531.0
54	532.0
55	471.5
56	318.0
57	178.0
58	131.0
59	102.5
60	69.5
61	45.5
62	26.0
63	20.0
64	11.0
65	5.0
66	2.0
67	2.0
68	1.0
69	0.0
70	0.5
71	1.0
72	0.5
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	0.0
32-33	0.0
34-35	0.0
36-37	0.0
38-39	0.0
40-41	0.0
42-43	0.0
44-45	0.0
46-47	0.0
48-49	0.0
50-51	0.0
52-53	0.0
54-55	0.0
56-57	0.0
58-59	0.0
60-61	0.0
62-63	0.0
64-65	0.0
66-67	0.0
68-69	0.0
70-71	0.0
72-73	0.0
74-75	0.0
76	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
76	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	64.67500000000001
#Duplication Level	Percentage of deduplicated	Percentage of total
1	89.2926169308079	57.75
2	4.909161190568226	6.35
3	1.9713954387321222	3.8249999999999997
4	1.0436799381522999	2.7
5	0.6957866254348666	2.25
6	0.30923850019327404	1.2
7	0.27058368766911484	1.225
8	0.23192887514495555	1.2
9	0.11596443757247778	0.675
>10	1.1209895632006184	16.075
>50	0.0	0.0
>100	0.038654812524159254	6.75
>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	270	6.75	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGG	44	1.0999999999999999	TruSeq Adapter, Index 19 (97% over 36bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	43	1.075	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	42	1.05	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	42	1.05	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	39	0.975	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGG	36	0.8999999999999999	TruSeq Adapter, Index 19 (97% over 36bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	36	0.8999999999999999	No Hit
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGT	31	0.775	TruSeq Adapter, Index 11 (97% over 37bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	30	0.75	No Hit
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	25	0.625	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGTGCAT	14	0.35000000000000003	TruSeq Adapter, Index 11 (97% over 37bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGG	13	0.325	TruSeq Adapter, Index 2 (97% over 35bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	12	0.3	No Hit
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	12	0.3	No Hit
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	10	0.25	No Hit
GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGTG	9	0.22499999999999998	TruSeq Adapter, Index 11 (97% over 37bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	9	0.22499999999999998	No Hit
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGTGCA	9	0.22499999999999998	TruSeq Adapter, Index 11 (97% over 37bp)
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGTGC	8	0.2	TruSeq Adapter, Index 11 (97% over 37bp)
TCCACAGGCTTTCTTGAACTGAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	6	0.15	No Hit
GGTAGTTCGACCGTGGATTAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CGACACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	6	0.15	No Hit
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	6	0.15	No Hit
AAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CTAACGAACGAACGATTTGAACAAATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (96% over 28bp)
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCAAAAGAGGAAAGGCTTGCGGTGGATAAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
CAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GGGATTGTAGTTCAATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGT	5	0.125	TruSeq Adapter, Index 11 (97% over 35bp)
CCTTATCGGATTGGACGTGCTTCGAAACAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGA	5	0.125	No Hit
CAAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	5	0.125	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	5	0.125	No Hit
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAGATCGGAAGAGCACA	5	0.125	No Hit
AGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGAT	5	0.125	No Hit
TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTGAGATCGGAAGAGCACAC	5	0.125	No Hit
CGACACGACTCTCGGCAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.025	0.0	0.0	0.0	0.0
2	0.075	0.0	0.0	0.0	0.0
3	0.075	0.0	0.0	0.0	0.0
4	0.15	0.0	0.0	0.0	0.0
5	0.175	0.0	0.0	0.0	0.0
6	0.275	0.0	0.0	0.0	0.0
7	0.35	0.0	0.0	0.0	0.0
8	0.55	0.0	0.0	0.0	0.0
9	1.125	0.0	0.0	0.0	0.0
10	1.55	0.0	0.0	0.0	0.0
11	2.125	0.0	0.0	0.0	0.0
12	2.9	0.0	0.0	0.0	0.0
13	4.35	0.0	0.0	0.0	0.0
14	7.825	0.0	0.0	0.0	0.0
15	9.375	0.0	0.0	0.0	0.0
16	11.5	0.0	0.0	0.0	0.0
17	14.225	0.0	0.0	0.0	0.0
18	17.25	0.0	0.0	0.0	0.0
19	18.975	0.0	0.0	0.0	0.0
20	22.5	0.0	0.0	0.0	0.0
21	26.825	0.0	0.0	0.0	0.0
22	31.725	0.0	0.0	0.0	0.0
23	44.15	0.0	0.0	0.0	0.0
24	47.875	0.0	0.0	0.0	0.0
25	59.575	0.0	0.0	0.0	0.0
26	62.85	0.0	0.0	0.0	0.0
27	65.375	0.0	0.0	0.0	0.0
28	67.475	0.0	0.0	0.0	0.0
29	69.2	0.0	0.0	0.0	0.0
30	71.675	0.0	0.0	0.0	0.0
31	74.05	0.0	0.0	0.0	0.0
32	75.925	0.0	0.0	0.0	0.0
33	77.5	0.0	0.0	0.0	0.0
34	79.475	0.0	0.0	0.0	0.0
35	82.5	0.0	0.0	0.0	0.0
36	85.85	0.0	0.0	0.0	0.0
37	87.575	0.0	0.0	0.0	0.0
38	88.975	0.0	0.0	0.0	0.0
39	89.65	0.0	0.0	0.0	0.0
40	90.55	0.0	0.0	0.0	0.0
41	91.075	0.0	0.0	0.0	0.0
42	91.725	0.0	0.0	0.0	0.0
43	92.225	0.0	0.0	0.0	0.0
44	92.625	0.0	0.0	0.0	0.0
45	92.875	0.0	0.0	0.0	0.0
46	93.25	0.0	0.0	0.0	0.0
47	93.45	0.0	0.0	0.0	0.0
48	93.65	0.0	0.0	0.0	0.0
49	93.8	0.0	0.0	0.0	0.0
50	93.925	0.0	0.0	0.0	0.0
51	94.025	0.0	0.0	0.0	0.0
52	94.025	0.0	0.0	0.0	0.0
53	94.05	0.0	0.0	0.0	0.0
54	94.05	0.0	0.0	0.0	0.0
55	94.075	0.0	0.0	0.0	0.0
56	94.1	0.0	0.0	0.0	0.0
57	94.125	0.0	0.0	0.0	0.0
58	94.125	0.0	0.0	0.0	0.0
59	94.125	0.0	0.0	0.0	0.0
60	94.125	0.0	0.0	0.0	0.0
61	94.125	0.0	0.0	0.0	0.0
62	94.125	0.0	0.0	0.0	0.0
63	94.125	0.0	0.0	0.0	0.0
64	94.125	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTAGCTC	15	0.0020658788	70.00001	7
AGCTCAG	20	7.003785E-5	70.0	9
TTGTAGT	20	7.003785E-5	70.0	5
TAGCTCA	20	7.003785E-5	70.0	8
CTAACGA	55	1.4588295E-9	50.90909	1
TAACGAA	60	3.1559466E-9	46.666668	2
GTAGATC	35	0.00111172	40.000004	23
GAACGAA	85	1.4770194E-9	37.058823	6
AACGATT	85	6.8515874E-8	32.941174	11
GAACGAT	85	6.8515874E-8	32.941174	10
GATTTGA	85	6.8515874E-8	32.941174	14
ATTTGAA	85	6.8515874E-8	32.941174	15
ACGATTT	85	6.8515874E-8	32.941174	12
CGATTTG	85	6.8515874E-8	32.941174	13
TGCCGTC	85	2.820525E-6	28.823528	70
GTCTTCT	50	0.0063971295	27.999998	70
TTTGAAC	80	6.740297E-5	26.25	16
TTGAACA	80	6.740297E-5	26.25	17
TGAACAG	85	1.01866215E-4	24.705881	18
GTATGCC	190	7.2759576E-12	23.94737	70
>>END_MODULE
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150079 READS because READLEN < 1
Read 150079 spots for SRR11699271.sra
Written 150079 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Read 150071 spots for SRR11699271.sra
Rejected 150071 READS because READLEN < 1
Written 150071 spots for SRR11699271.sra
Read 150071 spots for SRR11699271.sra
Written 150071 spots for SRR11699271.sra
SRR ids: ['SRR11699271.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_5tfeaqci
SRR11699271.sra spots: 3001428
blocks: [[1, 150071], [150072, 300142], [300143, 450213], [450214, 600284], [600285, 750355], [750356, 900426], [900427, 1050497], [1050498, 1200568], [1200569, 1350639], [1350640, 1500710], [1500711, 1650781], [1650782, 1800852], [1800853, 1950923], [1950924, 2100994], [2100995, 2251065], [2251066, 2401136], [2401137, 2551207], [2551208, 2701278], [2701279, 2851349], [2851350, 3001428]]
SRR11699271 file size 569391
SRR11699271 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 SRR11699271 SRR11699271_1.fastq
Input file:	SRR11699271_1.fastq
trimmed:	SRR11699271-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 05:57:46 2025 >> started

Wed Jun 18 05:57:48 2025 >> done (1.266s)
3001428 reads processed; of these:
 651893 (21.72%) short reads filtered out after trimming by size control
   1390 ( 0.05%) empty reads filtered out after trimming by size control
2348145 (78.23%) reads available; of these:
2296902 (97.82%) trimmed reads available after processing
  51243 ( 2.18%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  67766	  2.89%
 19	 104131	  4.43%
 20	 116546	  4.96%
 21	 168815	  7.19%
 22	 357246	 15.21%
 23	 109452	  4.66%
 24	 366848	 15.62%
 25	 102216	  4.35%
 26	  70158	  2.99%
 27	  72330	  3.08%
 28	  58636	  2.50%
 29	  65522	  2.79%
 30	  64948	  2.77%
 31	  62587	  2.67%
 32	  56775	  2.42%
 33	  62947	  2.68%
 34	  79087	  3.37%
 35	  89453	  3.81%
 36	  56537	  2.41%
 37	  37964	  1.62%
 38	  25690	  1.09%
 39	  24334	  1.04%
 40	  19342	  0.82%
 41	  21337	  0.91%
 42	  14638	  0.62%
 43	  12393	  0.53%
 44	   9203	  0.39%
 45	      0	  0.00%
 46	      0	  0.00%
 47	      0	  0.00%
 48	      0	  0.00%
 49	      0	  0.00%
 50	      0	  0.00%
 51	      0	  0.00%
 52	      0	  0.00%
 53	      0	  0.00%
 54	      0	  0.00%
 55	      0	  0.00%
 56	      0	  0.00%
 57	      0	  0.00%
 58	      0	  0.00%
 59	      0	  0.00%
 60	      0	  0.00%
 61	      0	  0.00%
 62	      0	  0.00%
 63	      0	  0.00%
 64	      0	  0.00%
 65	      0	  0.00%
 66	      0	  0.00%
 67	      0	  0.00%
 68	      0	  0.00%
 69	      0	  0.00%
 70	      0	  0.00%
 71	      0	  0.00%
 72	      0	  0.00%
 73	      0	  0.00%
 74	      1	  0.00%
 75	      0	  0.00%
 76	  51243	  2.18%
2348145 reads passed initial QC


criterion=sequence-density
sequence-density=3.75
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=0.01
sequence-density-rank=35
fanout-score=60.63
fanout-score-rank=1
prefix-density=0.37
prefix-fanout=1.0
sequence=CCTCGTGTTTAGTTGCCACTATGAGTTTGGAACCCTGAACAGACCGCCGGTGTTAAGCCGGAGGAAGGAGATCGGAA
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 SRR11699271 -
Input file:	STDIN
trimmed:	SRR11699271-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 05:57:52 2025 >> started

Wed Jun 18 05:57:52 2025 >> done (0.738s)
1174073 reads processed; of these:
   2997 ( 0.26%) short reads filtered out after trimming by size control
  44367 ( 3.78%) empty reads filtered out after trimming by size control
1126709 (95.97%) reads available; of these:
   8213 ( 0.73%) trimmed reads available after processing
1118496 (99.27%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  34229	  3.04%
 19	  52568	  4.67%
 20	  57930	  5.14%
 21	  84690	  7.52%
 22	 177991	 15.80%
 23	  54575	  4.84%
 24	 180399	 16.01%
 25	  50998	  4.53%
 26	  33669	  2.99%
 27	  35674	  3.17%
 28	  28956	  2.57%
 29	  29235	  2.59%
 30	  32264	  2.86%
 31	  31008	  2.75%
 32	  25759	  2.29%
 33	  26383	  2.34%
 34	  29437	  2.61%
 35	  30152	  2.68%
 36	  25507	  2.26%
 37	  18004	  1.60%
 38	  12521	  1.11%
 39	  11865	  1.05%
 40	   9076	  0.81%
 41	  10455	  0.93%
 42	   7160	  0.64%
 43	   6057	  0.54%
 44	   4593	  0.41%
 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	      0	  0.00%
 73	    877	  0.08%
 74	      1	  0.00%
 75	      0	  0.00%
 76	  24675	  2.19%


criterion=sequence-density
sequence-density=1.72
sequence-density-rank=1
fanout-score=10.04
fanout-score-rank=3
prefix-density=1.76
prefix-fanout=9.8
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGGTGCATCTCGTATGCCGTCTTCTGC


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=37
fanout-score=64.71
fanout-score-rank=1
prefix-density=0.38
prefix-fanout=1.0
sequence=CCTCGTGTTTAGTTGCCACTATGAGTTTGGAACCCTGAACAGACCGCCGGTGTTAAGCCGGAGGAAGGAGATCGGAA
                                 Started job on |	Jun 18 05:58:14
                             Started mapping on |	Jun 18 05:58:15
                                    Finished on |	Jun 18 05:58:27
       Mapping speed, Million of reads per hour |	690.23

                          Number of input reads |	2300781
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	300205
                        Uniquely mapped reads % |	13.05%
                          Average mapped length |	23.59
                       Number of splices: Total |	6025
            Number of splices: Annotated (sjdb) |	2125
                       Number of splices: GT/AG |	5599
                       Number of splices: GC/AG |	335
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	89
                      Mismatch rate per base, % |	1.24%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.44
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.31
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	296325
             % of reads mapped to multiple loci |	12.88%
        Number of reads mapped to too many loci |	415996
             % of reads mapped to too many loci |	18.08%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.02%
                     % of reads unmapped: other |	48.97%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1704251	1704251	1704251
N_multimapping	296325	296325	296325
N_noFeature	257515	267662	288846
N_ambiguous	1230	15	4
UnstrandedReadsAssigned:41460 PositiveStrandReadsAssigned:32528 NegativeStrandReadsAssigned:11355
Dataset is classified unstranded
MeadianReadLen=24 20thPercentileLength=21 echo kmer=19
SRR11699271 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: SRR11699271-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,300,781 reads, 399,724 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 877 rounds

  72540 SRR11699271.ke.tsv
  44303 SRR11699271.se.tsv
 116843 total
==> SRR11699271.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	2	1.59708
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

==> SRR11699271.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699271 completed mapping pipeline successfully
