Starting /dee2/code/volunteer_pipeline.sh SRR11699687
    current disk space = 2452110934016
    free memory = 1582323564 
SRR11699687 SRAfilesize
3c2a9572a4e70a2a60a9e583f242bb9c  SRR11699687.sra
SRR11699687.sra file validated
SRR11699687 is single end
SRR11699687 is conventional basespace
SRR11699687 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699687_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	48
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.12125	32.0	32.0	32.0	32.0	32.0
2	31.36575	32.0	32.0	32.0	32.0	32.0
3	31.4825	32.0	32.0	32.0	32.0	32.0
4	31.55625	32.0	32.0	32.0	32.0	32.0
5	31.47075	32.0	32.0	32.0	32.0	32.0
6	35.05875	36.0	36.0	36.0	36.0	36.0
7	35.05125	36.0	36.0	36.0	36.0	36.0
8	35.13475	36.0	36.0	36.0	36.0	36.0
9	34.9465	36.0	36.0	36.0	36.0	36.0
10-11	35.112	36.0	36.0	36.0	36.0	36.0
12-13	35.053625	36.0	36.0	36.0	36.0	36.0
14-15	35.032250000000005	36.0	36.0	36.0	36.0	36.0
16-17	35.1275	36.0	36.0	36.0	36.0	36.0
18-19	35.194125	36.0	36.0	36.0	36.0	36.0
20-21	35.052125000000004	36.0	36.0	36.0	36.0	36.0
22-23	35.051874999999995	36.0	36.0	36.0	36.0	36.0
24-25	35.04025	36.0	36.0	36.0	36.0	36.0
26-27	34.992125	36.0	36.0	36.0	36.0	36.0
28-29	34.93475	36.0	36.0	36.0	36.0	36.0
30-31	34.877125	36.0	36.0	36.0	36.0	36.0
32-33	34.912875	36.0	36.0	36.0	36.0	36.0
34-35	34.940875	36.0	36.0	36.0	36.0	36.0
36-37	34.959375	36.0	36.0	36.0	36.0	36.0
38-39	34.825125	36.0	36.0	36.0	36.0	36.0
40-41	34.884875	36.0	36.0	36.0	36.0	36.0
42-43	34.858875	36.0	36.0	36.0	34.0	36.0
44-45	34.845375000000004	36.0	36.0	36.0	36.0	36.0
46-47	34.826750000000004	36.0	36.0	36.0	36.0	36.0
48-49	34.7375	36.0	36.0	36.0	34.0	36.0
50-51	34.371375	36.0	36.0	36.0	32.0	36.0
52-53	34.37475	36.0	36.0	36.0	32.0	36.0
54-55	34.093875	36.0	36.0	36.0	32.0	36.0
56-57	33.66475	36.0	36.0	36.0	27.0	36.0
58-59	33.551500000000004	36.0	36.0	36.0	27.0	36.0
60-61	33.595125	36.0	36.0	36.0	27.0	36.0
62-63	33.151875000000004	36.0	34.0	36.0	21.0	36.0
64-65	33.180499999999995	36.0	32.0	36.0	27.0	36.0
66-67	32.678125	36.0	32.0	36.0	24.0	36.0
68-69	32.399	36.0	32.0	36.0	14.0	36.0
70-71	32.58625	36.0	32.0	36.0	20.5	36.0
72-73	32.012125	36.0	32.0	36.0	14.0	36.0
74-75	32.8835	36.0	34.0	36.0	14.0	36.0
76	30.14425	36.0	27.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
19	1.0
20	0.0
21	2.0
22	5.0
23	2.0
24	17.0
25	21.0
26	29.0
27	35.0
28	62.0
29	85.0
30	101.0
31	147.0
32	188.0
33	356.0
34	1137.0
35	1812.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	31.025000000000002	24.525	27.725	16.725
2	23.35	21.349999999999998	21.475	33.825
3	28.65	26.525	14.7	30.125
4	36.65	27.200000000000003	17.775	18.375
5	19.875	24.45	31.075000000000003	24.6
6	20.849999999999998	23.175	38.275	17.7
7	43.425000000000004	29.25	15.925	11.4
8	17.25	20.875	45.300000000000004	16.575
9	21.625	45.45	14.075	18.85
10-11	34.599999999999994	23.474999999999998	27.474999999999998	14.45
12-13	17.675	18.5375	28.3375	35.449999999999996
14-15	30.9875	44.275	14.0125	10.725
16-17	22.4625	20.4125	35.15	21.975
18-19	45.475	20.0125	21.837500000000002	12.675
20-21	21.05	32.45	29.3375	17.1625
22-23	37.5625	39.9625	10.212499999999999	12.2625
24-25	30.412499999999998	40.9	14.9875	13.700000000000001
26-27	23.7125	35.275	20.962500000000002	20.05
28-29	27.737499999999997	26.737499999999997	21.275	24.25
30-31	30.312499999999996	34.887499999999996	9.975000000000001	24.825
32-33	30.4	36.725	10.875	22.0
34-35	29.075	28.9875	16.5	25.4375
36-37	30.4	32.237500000000004	11.2875	26.075
38-39	25.724999999999998	37.0	12.2125	25.0625
40-41	24.9875	33.5875	14.825	26.6
42-43	28.349999999999998	26.674999999999997	17.0	27.975
44-45	21.575	32.175	14.637500000000001	31.612499999999997
46-47	17.4125	32.65	15.037500000000001	34.9
48-49	18.025	28.125	20.974999999999998	32.875
50-51	16.0875	26.4625	23.9875	33.4625
52-53	19.6	26.0625	23.3875	30.95
54-55	15.037500000000001	32.0625	20.125	32.775
56-57	12.0	29.262500000000003	25.424999999999997	33.3125
58-59	15.15	25.825	25.775	33.25
60-61	15.0875	24.762500000000003	30.525000000000002	29.625
62-63	14.549999999999999	29.2875	28.050000000000004	28.1125
64-65	11.700000000000001	27.8375	26.5	33.9625
66-67	17.925	18.6875	33.1875	30.2
68-69	16.7125	16.85	37.175000000000004	29.262500000000003
70-71	15.862499999999999	24.087500000000002	34.375	25.674999999999997
72-73	18.587500000000002	17.025000000000002	33.1	31.2875
74-75	17.7625	12.950000000000001	35.325	33.9625
76	19.925	11.475	41.3	27.3
>>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	0.5
31	0.5
32	0.0
33	0.0
34	0.0
35	0.0
36	2.0
37	4.0
38	3.5
39	4.5
40	12.5
41	37.5
42	56.0
43	62.0
44	120.0
45	275.0
46	378.0
47	677.5
48	882.0
49	691.0
50	595.0
51	505.5
52	324.5
53	167.5
54	102.0
55	92.5
56	69.0
57	35.0
58	15.0
59	13.0
60	8.0
61	4.5
62	4.0
63	2.0
64	2.5
65	3.5
66	1.0
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	0.0
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	0.5
95	1.0
96	1.0
97	0.5
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	56.699999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	87.61022927689595	49.675000000000004
2	5.64373897707231	6.4
3	2.204585537918871	3.75
4	0.7495590828924161	1.7000000000000002
5	0.6613756613756614	1.875
6	0.4409171075837742	1.5
7	0.48500881834215165	1.925
8	0.26455026455026454	1.2
9	0.04409171075837742	0.22499999999999998
>10	1.6313932980599646	18.825
>50	0.2204585537918871	8.975
>100	0.04409171075837742	3.95
>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	158	3.95	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	85	2.125	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	83	2.075	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	70	1.7500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	63	1.575	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATG	58	1.4500000000000002	TruSeq Adapter, Index 15 (100% over 36bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	48	1.2	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	44	1.0999999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	41	1.0250000000000001	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	40	1.0	No Hit
TCCGTTGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC	37	0.9249999999999999	No Hit
TCCGTTGTAGTCTAGTCGGTTAGGATACTCAGATCGGAAGAGCACACGTC	36	0.8999999999999999	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	33	0.8250000000000001	No Hit
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	31	0.775	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGT	25	0.625	TruSeq Adapter, Index 15 (100% over 37bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	25	0.625	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	24	0.6	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCAGATCGGAAGAGCACAC	22	0.5499999999999999	No Hit
TCCGTTGTAGTCTAGCTGGTGAGGATACTCAGATCGGAAGAGCACACGTC	21	0.525	No Hit
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAAT	20	0.5	TruSeq Adapter, Index 15 (97% over 41bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATG	16	0.4	TruSeq Adapter, Index 15 (100% over 36bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	13	0.325	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	12	0.3	No Hit
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT	12	0.3	TruSeq Adapter, Index 1 (100% over 35bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGAGATCGGAAGAGCACACGT	12	0.3	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCTAGATCGGAAGAGCACACG	12	0.3	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	11	0.27499999999999997	No Hit
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GGGTGTTTGGTCTAGTGGTATGATTCTCAGATCGGAAGAGCACACGTCTG	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	10	0.25	No Hit
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	10	0.25	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACAGATCGGAAGAGCACACGT	10	0.25	No Hit
GCGTTTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGAGATCGGAAGAGCACACG	8	0.2	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	8	0.2	No Hit
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCAGATCGGAAGAGCACACGTCT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
AGGGCTATAGCTCAGTTCGGTAGAGCAAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT	7	0.17500000000000002	TruSeq Adapter, Index 1 (100% over 35bp)
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	7	0.17500000000000002	No Hit
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GCACCAGTGGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGATTGTAGTTCAATCGGAAGAGCACACGTCTGAACTCCAGTCACATGT	7	0.17500000000000002	TruSeq Adapter, Index 15 (97% over 37bp)
GGTAGTTCGACCGTGGATTAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCA	6	0.15	No Hit
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAA	6	0.15	TruSeq Adapter, Index 15 (97% over 39bp)
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCCGTTGTAGTCTAGCTGGTTAGGATAAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GCACCAGTAGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATG	6	0.15	TruSeq Adapter, Index 15 (100% over 36bp)
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTAGATCGGAAGAGC	6	0.15	No Hit
TCCGTTGTAGTCTAGCTGGTCAGGATAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	6	0.15	No Hit
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	5	0.125	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	5	0.125	No Hit
GGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
AAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CTAACGAACGAACGATTTGAACAGATCGGAAGGGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (96% over 28bp)
GCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCA	5	0.125	TruSeq Adapter, Index 15 (100% over 39bp)
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	5	0.125	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	5	0.125	No Hit
GTCGTTGTAGTATAGTGGTGAGTATTCCCAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GTCGTTGTAGTATAGTGGTGAGTATTCCCGCCAGATCGGAAGAGCACACG	5	0.125	No Hit
GTTTAGTGGTGAGAATTCCAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGG	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	0.0	0.0	0.0	0.0	0.0
2	0.025	0.0	0.0	0.0	0.0
3	0.075	0.0	0.0	0.0	0.0
4	0.125	0.0	0.0	0.0	0.0
5	0.175	0.0	0.0	0.0	0.0
6	0.225	0.0	0.0	0.0	0.0
7	0.25	0.0	0.0	0.0	0.0
8	0.375	0.0	0.0	0.0	0.0
9	1.0	0.0	0.0	0.0	0.0
10	1.4	0.0	0.0	0.0	0.0
11	1.875	0.0	0.0	0.0	0.0
12	2.3	0.0	0.0	0.0	0.0
13	3.525	0.0	0.0	0.0	0.0
14	6.55	0.0	0.0	0.0	0.0
15	8.3	0.0	0.0	0.0	0.0
16	9.825	0.0	0.0	0.0	0.0
17	12.65	0.0	0.0	0.0	0.0
18	15.375	0.0	0.0	0.0	0.0
19	17.2	0.0	0.0	0.0	0.0
20	19.875	0.0	0.0	0.0	0.0
21	23.225	0.0	0.0	0.0	0.0
22	27.775	0.0	0.0	0.0	0.0
23	36.325	0.0	0.0	0.0	0.0
24	38.825	0.0	0.0	0.0	0.0
25	44.225	0.0	0.0	0.0	0.0
26	48.175	0.0	0.0	0.0	0.0
27	50.875	0.0	0.0	0.0	0.0
28	55.15	0.0	0.0	0.0	0.0
29	56.95	0.0	0.0	0.0	0.0
30	59.475	0.0	0.0	0.0	0.0
31	68.85	0.0	0.0	0.0	0.0
32	71.85	0.0	0.0	0.0	0.0
33	77.2	0.0	0.0	0.0	0.0
34	79.775	0.0	0.0	0.0	0.0
35	81.7	0.0	0.0	0.0	0.0
36	84.725	0.0	0.0	0.0	0.0
37	86.575	0.0	0.0	0.0	0.0
38	87.85	0.0	0.0	0.0	0.0
39	88.675	0.0	0.0	0.0	0.0
40	89.75	0.0	0.0	0.0	0.0
41	90.425	0.0	0.0	0.0	0.0
42	91.45	0.0	0.0	0.0	0.0
43	92.0	0.0	0.0	0.0	0.0
44	92.4	0.0	0.0	0.0	0.0
45	92.5	0.0	0.0	0.0	0.0
46	92.9	0.0	0.0	0.0	0.0
47	93.175	0.0	0.0	0.0	0.0
48	93.325	0.0	0.0	0.0	0.0
49	93.45	0.0	0.0	0.0	0.0
50	93.5	0.0	0.0	0.0	0.0
51	93.525	0.0	0.0	0.0	0.0
52	93.525	0.0	0.0	0.0	0.0
53	93.525	0.0	0.0	0.0	0.0
54	93.55	0.0	0.0	0.0	0.0
55	93.55	0.0	0.0	0.0	0.0
56	93.55	0.0	0.0	0.0	0.0
57	93.55	0.0	0.0	0.0	0.0
58	93.575	0.0	0.0	0.0	0.0
59	93.575	0.0	0.0	0.0	0.0
60	93.575	0.0	0.0	0.0	0.0
61	93.575	0.0	0.0	0.0	0.0
62	93.575	0.0	0.0	0.0	0.0
63	93.575	0.0	0.0	0.0	0.0
64	93.575	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TTCAATT	15	0.0020658788	70.00001	11
CAATTGG	15	0.0020658788	70.00001	13
TCAATTG	15	0.0020658788	70.00001	12
GTTCAAT	15	0.0020658788	70.00001	10
TAGTTCA	15	0.0020658788	70.00001	8
ATTGCCA	15	0.0020658788	70.00001	27
CGTTGTA	30	7.878043E-8	70.00001	3
AGTTCAA	15	0.0020658788	70.00001	9
AATTGGT	15	0.0020658788	70.00001	14
AATTGCC	15	0.0020658788	70.00001	26
GTTGTAG	30	7.878043E-8	70.00001	4
TTGCCAG	15	0.0020658788	70.00001	28
TGGTCAG	40	8.54925E-11	70.0	17
CCAACGG	20	7.003785E-5	70.0	12
TCTAGCT	20	7.003785E-5	70.0	11
GATACTC	20	7.003785E-5	70.0	24
AGGATAC	20	7.003785E-5	70.0	22
TCAGGAT	20	7.003785E-5	70.0	20
GCTGGTC	20	7.003785E-5	70.0	15
ATTGGTC	20	7.003785E-5	70.0	15
>>END_MODULE
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335807 READS because READLEN < 1
Read 335807 spots for SRR11699687.sra
Written 335807 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
Rejected 335806 READS because READLEN < 1
Read 335806 spots for SRR11699687.sra
Written 335806 spots for SRR11699687.sra
SRR ids: ['SRR11699687.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_6yced3f6
SRR11699687.sra spots: 6716121
blocks: [[1, 335806], [335807, 671612], [671613, 1007418], [1007419, 1343224], [1343225, 1679030], [1679031, 2014836], [2014837, 2350642], [2350643, 2686448], [2686449, 3022254], [3022255, 3358060], [3358061, 3693866], [3693867, 4029672], [4029673, 4365478], [4365479, 4701284], [4701285, 5037090], [5037091, 5372896], [5372897, 5708702], [5708703, 6044508], [6044509, 6380314], [6380315, 6716121]]
SRR11699687 file size 1276779
SRR11699687 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 SRR11699687 SRR11699687_1.fastq
Input file:	SRR11699687_1.fastq
trimmed:	SRR11699687-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
Sun Jun 22 00:47:34 2025 >> started

Sun Jun 22 00:47:38 2025 >> done (4.221s)
6716121 reads processed; of these:
1217436 (18.13%) short reads filtered out after trimming by size control
   3827 ( 0.06%) empty reads filtered out after trimming by size control
5494858 (81.82%) reads available; of these:
5396172 (98.20%) trimmed reads available after processing
  98686 ( 1.80%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 128407	  2.34%
 19	 193096	  3.51%
 20	 222496	  4.05%
 21	 314840	  5.73%
 22	 562277	 10.23%
 23	 181376	  3.30%
 24	 395930	  7.21%
 25	 304830	  5.55%
 26	 207732	  3.78%
 27	 272926	  4.97%
 28	 149371	  2.72%
 29	 178762	  3.25%
 30	 673678	 12.26%
 31	 252094	  4.59%
 32	 305092	  5.55%
 33	 214735	  3.91%
 34	 150125	  2.73%
 35	 191558	  3.49%
 36	 116690	  2.12%
 37	  81745	  1.49%
 38	  59162	  1.08%
 39	  54486	  0.99%
 40	  40177	  0.73%
 41	  65774	  1.20%
 42	  32381	  0.59%
 43	  27990	  0.51%
 44	  18436	  0.34%
 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	      1	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      5	  0.00%
 76	  98686	  1.80%
5494858 reads passed initial QC


criterion=sequence-density
sequence-density=13.79
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=15
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATA


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=36
fanout-score=62.68
fanout-score-rank=1
prefix-density=0.37
prefix-fanout=1.0
sequence=AGCCAAGTGTGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTC
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 22 00:48:07
                             Started mapping on |	Jun 22 00:48:07
                                    Finished on |	Jun 22 00:48:21
       Mapping speed, Million of reads per hour |	1412.96

                          Number of input reads |	5494858
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	477383
                        Uniquely mapped reads % |	8.69%
                          Average mapped length |	22.94
                       Number of splices: Total |	6350
            Number of splices: Annotated (sjdb) |	2596
                       Number of splices: GT/AG |	5663
                       Number of splices: GC/AG |	540
                       Number of splices: AT/AC |	4
               Number of splices: Non-canonical |	143
                      Mismatch rate per base, % |	0.62%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.49
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	917080
             % of reads mapped to multiple loci |	16.69%
        Number of reads mapped to too many loci |	1611173
             % of reads mapped to too many loci |	29.32%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	4.06%
                     % of reads unmapped: other |	41.24%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	4100395	4100395	4100395
N_multimapping	917080	917080	917080
N_noFeature	420910	431533	465008
N_ambiguous	1791	21	20
UnstrandedReadsAssigned:54682 PositiveStrandReadsAssigned:45829 NegativeStrandReadsAssigned:12355
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=18 echo kmer=19
SRR11699687 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: SRR11699687-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 5,494,858 reads, 1,037,350 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 913 rounds

  72540 SRR11699687.ke.tsv
  44303 SRR11699687.se.tsv
 116843 total
==> SRR11699687.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	2	0.726382
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

==> SRR11699687.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699687 completed mapping pipeline successfully
