Starting /dee2/code/volunteer_pipeline.sh SRR11699545
    current disk space = 2462154244096
    free memory = 1581664860 
SRR11699545 SRAfilesize
8f29184d5f69b37f922f3c8bcfea0b8b  SRR11699545.sra
SRR11699545.sra file validated
SRR11699545 is single end
SRR11699545 is conventional basespace
SRR11699545 read1 length is 86 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699545_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	31.53275	32.0	32.0	32.0	32.0	32.0
2	31.607	32.0	32.0	32.0	32.0	32.0
3	31.66875	32.0	32.0	32.0	32.0	32.0
4	31.67925	32.0	32.0	32.0	32.0	32.0
5	31.695	32.0	32.0	32.0	32.0	32.0
6	35.312	36.0	36.0	36.0	36.0	36.0
7	35.30675	36.0	36.0	36.0	36.0	36.0
8	35.345	36.0	36.0	36.0	36.0	36.0
9	35.23825	36.0	36.0	36.0	36.0	36.0
10-11	35.380125	36.0	36.0	36.0	36.0	36.0
12-13	35.373999999999995	36.0	36.0	36.0	36.0	36.0
14-15	35.251875	36.0	36.0	36.0	36.0	36.0
16-17	35.377125	36.0	36.0	36.0	36.0	36.0
18-19	35.4095	36.0	36.0	36.0	36.0	36.0
20-21	35.28825	36.0	36.0	36.0	36.0	36.0
22-23	35.339	36.0	36.0	36.0	36.0	36.0
24-25	35.29775	36.0	36.0	36.0	36.0	36.0
26-27	35.172250000000005	36.0	36.0	36.0	36.0	36.0
28-29	35.202	36.0	36.0	36.0	36.0	36.0
30-31	35.20825	36.0	36.0	36.0	36.0	36.0
32-33	35.237624999999994	36.0	36.0	36.0	36.0	36.0
34-35	35.23325	36.0	36.0	36.0	36.0	36.0
36-37	35.156375	36.0	36.0	36.0	36.0	36.0
38-39	35.24925	36.0	36.0	36.0	36.0	36.0
40-41	35.26075	36.0	36.0	36.0	36.0	36.0
42-43	35.21375	36.0	36.0	36.0	36.0	36.0
44-45	35.149875	36.0	36.0	36.0	36.0	36.0
46-47	35.28675	36.0	36.0	36.0	36.0	36.0
48-49	35.196375	36.0	36.0	36.0	36.0	36.0
50-51	35.006249999999994	36.0	36.0	36.0	36.0	36.0
52-53	35.153999999999996	36.0	36.0	36.0	36.0	36.0
54-55	34.85125	36.0	36.0	36.0	36.0	36.0
56-57	34.67475	36.0	36.0	36.0	32.0	36.0
58-59	34.688375	36.0	36.0	36.0	32.0	36.0
60-61	34.52875	36.0	36.0	36.0	32.0	36.0
62-63	34.5185	36.0	36.0	36.0	32.0	36.0
64-65	34.39625	36.0	36.0	36.0	32.0	36.0
66-67	34.36225	36.0	36.0	36.0	32.0	36.0
68-69	34.360875	36.0	36.0	36.0	32.0	36.0
70-71	34.448750000000004	36.0	36.0	36.0	32.0	36.0
72-73	34.423249999999996	36.0	36.0	36.0	32.0	36.0
74-75	34.460125000000005	36.0	36.0	36.0	32.0	36.0
76-77	34.321625	36.0	36.0	36.0	32.0	36.0
78-79	34.515	36.0	36.0	36.0	32.0	36.0
80-81	34.66475	36.0	36.0	36.0	32.0	36.0
82-83	34.547875	36.0	36.0	36.0	32.0	36.0
84-85	34.581875	36.0	36.0	36.0	32.0	36.0
86	34.03725	36.0	36.0	36.0	32.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	1.0
22	0.0
23	2.0
24	4.0
25	9.0
26	14.0
27	21.0
28	34.0
29	43.0
30	65.0
31	91.0
32	130.0
33	252.0
34	580.0
35	2754.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	33.550000000000004	20.724999999999998	30.3	15.425
2	29.425	20.1	17.0	33.475
3	30.175	22.975	17.25	29.599999999999998
4	38.35	27.075	16.525000000000002	18.05
5	20.025000000000002	22.7	32.550000000000004	24.725
6	19.825	19.475	39.25	21.45
7	45.5	23.799999999999997	17.95	12.75
8	19.400000000000002	16.5	48.6	15.5
9	20.625	43.55	18.8	17.025000000000002
10-11	36.875	18.675	27.537499999999998	16.9125
12-13	17.825	16.662499999999998	31.7375	33.775
14-15	31.3125	41.05	14.924999999999999	12.712499999999999
16-17	22.7125	18.95	36.325	22.0125
18-19	48.0125	16.8875	19.662499999999998	15.437500000000002
20-21	22.825	27.537499999999998	29.475	20.1625
22-23	35.3	38.5	14.0875	12.112499999999999
24-25	31.087500000000002	37.8125	15.837499999999999	15.262500000000001
26-27	21.349999999999998	33.6625	23.9125	21.075
28-29	26.8125	25.575	19.775000000000002	27.8375
30-31	30.65	30.125	14.1125	25.112499999999997
32-33	30.9375	30.5	15.2	23.3625
34-35	29.975	31.3125	18.1625	20.549999999999997
36-37	31.5125	36.5875	11.3125	20.5875
38-39	27.66941735433858	35.29632408102025	13.178294573643413	23.85596399099775
40-41	29.1911488936117	31.866483310413802	12.226528316039504	26.715839479934996
42-43	30.275000000000002	33.5	13.087499999999999	23.1375
44-45	26.025	34.0125	13.7125	26.25
46-47	21.875	31.8125	14.4125	31.900000000000002
48-49	20.2375	31.8125	15.737499999999999	32.2125
50-51	15.728932233058265	32.83320830207552	17.504376094023506	33.93348337084271
52-53	19.5625	24.15	22.525000000000002	33.7625
54-55	15.125	27.987499999999997	21.65	35.2375
56-57	14.799999999999999	32.125	20.9125	32.1625
58-59	10.726340792599075	31.66645830728841	20.140017502187774	37.46718339792474
60-61	9.9	26.400000000000002	27.450000000000003	36.25
62-63	10.2875	29.9375	25.112499999999997	34.6625
64-65	11.0875	26.375	26.1625	36.375
66-67	10.438804850606326	23.415426928366045	28.99112389048631	37.154644330541316
68-69	9.4	25.662499999999998	32.3125	32.625
70-71	10.8375	24.837500000000002	31.662499999999998	32.6625
72-73	14.387500000000001	16.2375	34.9125	34.4625
74-75	13.1375	16.425	36.575	33.862500000000004
76-77	17.864733091636452	14.064258032254031	36.69208651081385	31.378922365295665
78-79	14.0375	13.8625	39.025	33.074999999999996
80-81	20.4875	14.8625	36.95	27.700000000000003
82-83	17.939742467808475	18.352294036754593	35.39192399049881	28.316039504938118
84-85	18.725	17.424999999999997	35.475	28.375
86	19.45	19.400000000000002	35.15	26.0
>>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	1.0
33	1.0
34	0.5
35	0.5
36	0.0
37	0.0
38	1.0
39	2.0
40	7.5
41	21.5
42	59.0
43	88.0
44	121.0
45	184.0
46	293.0
47	437.0
48	626.0
49	659.0
50	568.0
51	554.5
52	416.5
53	247.5
54	162.0
55	96.0
56	51.5
57	32.0
58	23.5
59	11.0
60	4.5
61	3.5
62	4.5
63	4.5
64	5.0
65	3.0
66	0.5
67	0.0
68	0.0
69	0.0
70	0.0
71	0.0
72	0.0
73	0.0
74	0.0
75	0.5
76	0.5
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	0.5
99	1.0
100	1.0
>>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	0.025
40-41	0.0125
42-43	0.0
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	0.0125
84-85	0.0
86	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
86	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	61.925
#Duplication Level	Percentage of deduplicated	Percentage of total
1	86.71780379491321	53.7
2	6.0960839725474365	7.55
3	2.1800565199838515	4.05
4	1.2515139281388776	3.1
5	0.8881711748082357	2.75
6	0.5651998385143319	2.1
7	0.44408558740411785	1.925
8	0.28259991925716593	1.4000000000000001
9	0.28259991925716593	1.575
>10	1.1303996770286637	13.200000000000001
>50	0.12111425111021397	4.875
>100	0.04037141703673799	3.775
>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
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	151	3.775	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	74	1.8499999999999999	No Hit
CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC	64	1.6	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	57	1.425	No Hit
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAC	49	1.225	TruSeq Adapter, Index 1 (97% over 36bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	39	0.975	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	32	0.8	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGAGATCGGAAGAGCAC	27	0.675	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	24	0.6	No Hit
TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTGAGATCGGAAGAGCACAC	24	0.6	No Hit
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	21	0.525	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	21	0.525	No Hit
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	21	0.525	No Hit
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAC	21	0.525	TruSeq Adapter, Index 1 (97% over 36bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	20	0.5	No Hit
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAGATCGGAAGAGCACA	17	0.42500000000000004	No Hit
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	16	0.4	No Hit
TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA	15	0.375	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCTAGATCGGAAGAGCACACG	14	0.35000000000000003	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	12	0.3	No Hit
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTAGATCGGAAGAGCACA	11	0.27499999999999997	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTAGATCGGAAGAGCA	11	0.27499999999999997	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	10	0.25	No Hit
GGGCCTGTAGCTCAGAGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TTTGGAACCCTGAACAGACCGCCGGTGTTAAGCCGGAGGAAGGAGATCGG	10	0.25	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCAGATCGGAAGAGCACAC	9	0.22499999999999998	No Hit
GCGACCCCAGGTCAGTCGGGACTACCCGCTGAGTTTAAGCAGATCGGAAG	9	0.22499999999999998	No Hit
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	9	0.22499999999999998	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
GCACCAGTGGTCTAGTGGTAGAATAGTACCCAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGAGATCGGAAGAGCACACG	8	0.2	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTAGATCGGAAGAGCACAC	8	0.2	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	8	0.2	No Hit
GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGAGATCGGAAGAGCAC	8	0.2	No Hit
GGGGACGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA	8	0.2	TruSeq Adapter, Index 7 (97% over 35bp)
GCACCAGTGGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
GCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAG	7	0.17500000000000002	No Hit
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA	7	0.17500000000000002	TruSeq Adapter, Index 7 (97% over 35bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
GCGTTTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTAGATCGGAAGAGCACACGTCT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
TCCATTGTCGTCTAGTCCGGTTAGGATAAGATCGGAAGAGCACACGTCTG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGCCTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAC	6	0.15	TruSeq Adapter, Index 1 (97% over 36bp)
GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGAGATCGGAAGAGCAC	6	0.15	No Hit
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGTTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	6	0.15	No Hit
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGAGATCGGAAGAGCA	6	0.15	No Hit
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	6	0.15	No Hit
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTAGATCGGAAGAGC	6	0.15	No Hit
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGACCCCAGGTCAGTCGGGACTACCCGCTAGATCGGAAGAGCACACGTC	6	0.15	No Hit
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTAGATCGGAAGAGCACA	6	0.15	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTAGATCGGAAGAGCACAC	6	0.15	No Hit
GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	5	0.125	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAGATCGGAAGAGC	5	0.125	No Hit
CGACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GCCCCCATCGTCTAGTGGTTCAGGACATCTCTCTTTAGATCGGAAGAGCA	5	0.125	No Hit
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGAGATCGGAAG	5	0.125	No Hit
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCGTTGTAGTCTAGCTGGTTAGGATAAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GCACCAGTAGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGATTGTAGTTCAATTGGTCAGAGCAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCCATTGTCGTCTAGTCCGGTTAGGATATCTGGCAGATCGGAAGAGCACA	5	0.125	No Hit
GTCGTTGTAGTATAGTGGTGAGTATTCCCGCCAGATCGGAAGAGCACACG	5	0.125	No Hit
TCCGTTGTAGTCTAGTCGGTTAGGATACTCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
GCCCTTTTAACTCAGTGGTAGAGTAATGCCATGAGATCGGAAGAGCACAC	5	0.125	No Hit
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCGTTGTAGTCTAGTTGGTCAGGATAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
>>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	0.05	0.0	0.0	0.0	0.0
6	0.05	0.0	0.0	0.0	0.0
7	0.05	0.0	0.0	0.0	0.0
8	0.125	0.0	0.0	0.0	0.0
9	0.15	0.0	0.0	0.0	0.0
10	0.275	0.0	0.0	0.0	0.0
11	0.325	0.0	0.0	0.0	0.0
12	0.6	0.0	0.0	0.0	0.0
13	0.85	0.0	0.0	0.0	0.0
14	3.525	0.0	0.0	0.0	0.0
15	4.45	0.0	0.0	0.0	0.0
16	5.375	0.0	0.0	0.0	0.0
17	6.925	0.0	0.0	0.0	0.0
18	8.05	0.0	0.0	0.0	0.0
19	9.2	0.0	0.0	0.0	0.0
20	11.325	0.0	0.0	0.0	0.0
21	13.15	0.0	0.0	0.0	0.0
22	16.65	0.0	0.0	0.0	0.0
23	21.6	0.0	0.0	0.0	0.0
24	24.0	0.0	0.0	0.0	0.0
25	28.7	0.0	0.0	0.0	0.0
26	31.8	0.0	0.0	0.0	0.0
27	35.25	0.0	0.0	0.0	0.0
28	41.75	0.0	0.0	0.0	0.0
29	44.525	0.0	0.0	0.0	0.0
30	47.075	0.0	0.0	0.0	0.0
31	53.375	0.0	0.0	0.0	0.0
32	56.625	0.0	0.0	0.0	0.0
33	60.825	0.0	0.0	0.0	0.0
34	65.375	0.0	0.0	0.0	0.0
35	70.825	0.0	0.0	0.0	0.0
36	77.025	0.0	0.0	0.0	0.0
37	81.0	0.0	0.0	0.0	0.0
38	82.75	0.0	0.0	0.0	0.0
39	84.0	0.0	0.0	0.0	0.0
40	85.6	0.0	0.0	0.0	0.0
41	86.9	0.0	0.0	0.0	0.0
42	88.975	0.0	0.0	0.0	0.0
43	90.05	0.0	0.0	0.0	0.0
44	91.225	0.0	0.0	0.0	0.0
45	91.7	0.0	0.0	0.0	0.0
46	92.275	0.0	0.0	0.0	0.0
47	92.9	0.0	0.0	0.0	0.0
48	93.475	0.0	0.0	0.0	0.0
49	94.4	0.0	0.0	0.0	0.0
50	94.625	0.0	0.0	0.0	0.0
51	94.85	0.0	0.0	0.0	0.0
52	95.05	0.0	0.0	0.0	0.0
53	95.05	0.0	0.0	0.0	0.0
54	95.125	0.0	0.0	0.0	0.0
55	95.15	0.0	0.0	0.0	0.0
56	95.175	0.0	0.0	0.0	0.0
57	95.225	0.0	0.0	0.0	0.0
58	95.325	0.0	0.0	0.0	0.0
59	95.35	0.0	0.0	0.0	0.0
60	95.35	0.0	0.0	0.0	0.0
61	95.375	0.0	0.0	0.0	0.0
62	95.375	0.0	0.0	0.0	0.0
63	95.375	0.0	0.0	0.0	0.0
64	95.4	0.0	0.0	0.0	0.0
65	95.4	0.0	0.0	0.0	0.0
66	95.4	0.0	0.0	0.0	0.0
67	95.4	0.0	0.0	0.0	0.0
68	95.4	0.0	0.0	0.0	0.0
69	95.4	0.0	0.0	0.0	0.0
70	95.4	0.0	0.0	0.0	0.0
71	95.4	0.0	0.0	0.0	0.0
72	95.4	0.0	0.0	0.0	0.0
73	95.4	0.0	0.0	0.0	0.0
74	95.4	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
TAGTCTA	30	3.1202944E-8	80.00001	8
TGTAGTC	40	2.5465852E-11	80.00001	6
AGTCTAG	30	3.1202944E-8	80.00001	9
GTAGCTC	15	0.0012159165	80.00001	7
GTAGTCT	30	3.1202944E-8	80.00001	7
GTTGTAG	30	3.1202944E-8	80.00001	4
TTGTAGT	75	0.0	80.0	5
TAGCTCA	25	1.0653384E-6	80.0	8
GGATTGT	45	0.0	80.0	2
CCGTTGT	25	1.0653384E-6	80.0	2
GATTGTA	45	0.0	80.0	3
TAGTTCA	50	0.0	80.0	8
ATTGTAG	45	0.0	80.0	4
GGGATTG	45	0.0	80.0	1
TCCGTTG	25	1.0653384E-6	80.0	1
CGTTGTA	25	1.0653384E-6	80.0	3
AGTTCAA	45	0.0	80.0	9
GTAGTTC	50	0.0	80.0	7
TGTAGTT	50	1.8189894E-12	72.0	6
>>END_MODULE
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242551 READS because READLEN < 1
Read 242551 spots for SRR11699545.sra
Written 242551 spots for SRR11699545.sra
Rejected 242555 READS because READLEN < 1
Read 242555 spots for SRR11699545.sra
Written 242555 spots for SRR11699545.sra
SRR ids: ['SRR11699545.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_1i5mgwfr
SRR11699545.sra spots: 4851024
blocks: [[1, 242551], [242552, 485102], [485103, 727653], [727654, 970204], [970205, 1212755], [1212756, 1455306], [1455307, 1697857], [1697858, 1940408], [1940409, 2182959], [2182960, 2425510], [2425511, 2668061], [2668062, 2910612], [2910613, 3153163], [3153164, 3395714], [3395715, 3638265], [3638266, 3880816], [3880817, 4123367], [4123368, 4365918], [4365919, 4608469], [4608470, 4851024]]
SRR11699545 file size 1016356
SRR11699545 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 SRR11699545 SRR11699545_1.fastq
Input file:	SRR11699545_1.fastq
trimmed:	SRR11699545-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 21:05:54 2025 >> started

Fri Jun 20 21:05:56 2025 >> done (2.619s)
4851024 reads processed; of these:
 430337 ( 8.87%) short reads filtered out after trimming by size control
   2082 ( 0.04%) empty reads filtered out after trimming by size control
4418605 (91.09%) reads available; of these:
4396384 (99.50%) trimmed reads available after processing
  22221 ( 0.50%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  63567	  1.44%
 19	  95198	  2.15%
 20	 104656	  2.37%
 21	 178997	  4.05%
 22	 246276	  5.57%
 23	 115305	  2.61%
 24	 235069	  5.32%
 25	 147208	  3.33%
 26	 148761	  3.37%
 27	 366609	  8.30%
 28	 120897	  2.74%
 29	 137983	  3.12%
 30	 305683	  6.92%
 31	 173781	  3.93%
 32	 227044	  5.14%
 33	 228281	  5.17%
 34	 257836	  5.84%
 35	 317792	  7.19%
 36	 181498	  4.11%
 37	 108495	  2.46%
 38	  76406	  1.73%
 39	  71880	  1.63%
 40	  65953	  1.49%
 41	 134207	  3.04%
 42	  48373	  1.09%
 43	  48035	  1.09%
 44	  34449	  0.78%
 45	  31774	  0.72%
 46	  25100	  0.57%
 47	  22216	  0.50%
 48	  31760	  0.72%
 49	  14636	  0.33%
 50	  10487	  0.24%
 51	   8007	  0.18%
 52	   5390	  0.12%
 53	   4097	  0.09%
 54	   2668	  0.06%
 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	     10	  0.00%
 86	  22221	  0.50%
4418605 reads passed initial QC


criterion=sequence-density
sequence-density=12.25
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=12
prefix-density=0.02
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATA


criterion=fanout-score
sequence-density=0.38
sequence-density-rank=25
fanout-score=27.89
fanout-score-rank=1
prefix-density=10.45
prefix-fanout=1.0
sequence=GTCTAGCTGGTTAGGATATTCGG
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 21:06:34
                             Started mapping on |	Jun 20 21:06:34
                                    Finished on |	Jun 20 21:06:53
       Mapping speed, Million of reads per hour |	837.21

                          Number of input reads |	4418605
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	341574
                        Uniquely mapped reads % |	7.73%
                          Average mapped length |	24.46
                       Number of splices: Total |	9900
            Number of splices: Annotated (sjdb) |	3398
                       Number of splices: GT/AG |	9288
                       Number of splices: GC/AG |	458
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	151
                      Mismatch rate per base, % |	0.95%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.31
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.37
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	686901
             % of reads mapped to multiple loci |	15.55%
        Number of reads mapped to too many loci |	1572805
             % of reads mapped to too many loci |	35.60%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.92%
                     % of reads unmapped: other |	35.21%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3390130	3390130	3390130
N_multimapping	686901	686901	686901
N_noFeature	282553	293543	328247
N_ambiguous	2378	25	20
UnstrandedReadsAssigned:56643 PositiveStrandReadsAssigned:48006 NegativeStrandReadsAssigned:13307
Dataset is classified unstranded
MeadianReadLen=26 20thPercentileLength=20 echo kmer=19
SRR11699545 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: SRR11699545-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,418,605 reads, 1,006,327 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,000 rounds

  72540 SRR11699545.ke.tsv
  44303 SRR11699545.se.tsv
 116843 total
==> SRR11699545.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	5	1.75763
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

==> SRR11699545.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	1
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	1
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699545 completed mapping pipeline successfully
