Starting /dee2/code/volunteer_pipeline.sh SRR11699598
    current disk space = 2456674279424
    free memory = 1580221528 
SRR11699598 SRAfilesize
af30617b3bb1fdfbb48e04ab3b70f8e8  SRR11699598.sra
SRR11699598.sra file validated
SRR11699598 is single end
SRR11699598 is conventional basespace
SRR11699598 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699598_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	50
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	30.7225	32.0	32.0	32.0	32.0	32.0
2	31.0695	32.0	32.0	32.0	32.0	32.0
3	31.468	32.0	32.0	32.0	32.0	32.0
4	31.44275	32.0	32.0	32.0	32.0	32.0
5	31.418	32.0	32.0	32.0	32.0	32.0
6	34.8215	36.0	36.0	36.0	32.0	36.0
7	34.8295	36.0	36.0	36.0	32.0	36.0
8	34.825	36.0	36.0	36.0	32.0	36.0
9	34.66625	36.0	36.0	36.0	32.0	36.0
10-11	34.80175	36.0	36.0	36.0	34.0	36.0
12-13	34.990875	36.0	36.0	36.0	36.0	36.0
14-15	34.847375	36.0	36.0	36.0	34.0	36.0
16-17	34.906125	36.0	36.0	36.0	34.0	36.0
18-19	34.946875	36.0	36.0	36.0	36.0	36.0
20-21	34.794124999999994	36.0	36.0	36.0	36.0	36.0
22-23	34.775375	36.0	36.0	36.0	36.0	36.0
24-25	34.788375	36.0	36.0	36.0	32.0	36.0
26-27	34.686375	36.0	36.0	36.0	32.0	36.0
28-29	34.683875	36.0	36.0	36.0	32.0	36.0
30-31	34.722125000000005	36.0	36.0	36.0	34.0	36.0
32-33	34.67175	36.0	36.0	36.0	34.0	36.0
34-35	34.81125	36.0	36.0	36.0	36.0	36.0
36-37	34.666375	36.0	36.0	36.0	32.0	36.0
38-39	34.675375	36.0	36.0	36.0	32.0	36.0
40-41	34.619375000000005	36.0	36.0	36.0	32.0	36.0
42-43	34.656499999999994	36.0	36.0	36.0	32.0	36.0
44-45	34.724875	36.0	36.0	36.0	32.0	36.0
46-47	34.609	36.0	36.0	36.0	32.0	36.0
48-49	34.557125	36.0	36.0	36.0	32.0	36.0
50-51	34.258125	36.0	36.0	36.0	32.0	36.0
52-53	34.067125000000004	36.0	36.0	36.0	32.0	36.0
54-55	33.90625	36.0	36.0	36.0	32.0	36.0
56-57	33.2695	36.0	34.0	36.0	27.0	36.0
58-59	32.926125	36.0	34.0	36.0	20.5	36.0
60-61	32.281125	36.0	32.0	36.0	14.0	36.0
62-63	31.42275	36.0	32.0	36.0	14.0	36.0
64-65	30.01475	36.0	27.0	36.0	14.0	36.0
66-67	28.335625	32.0	17.5	36.0	14.0	36.0
68-69	28.682875	32.0	14.0	36.0	14.0	36.0
70-71	28.780875	34.0	17.5	36.0	14.0	36.0
72-73	28.8555	34.0	20.5	36.0	14.0	36.0
74-75	29.06025	36.0	14.0	36.0	14.0	36.0
76	24.243	27.0	14.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
19	1.0
20	1.0
21	4.0
22	6.0
23	12.0
24	23.0
25	26.0
26	47.0
27	75.0
28	108.0
29	151.0
30	173.0
31	257.0
32	397.0
33	651.0
34	1327.0
35	741.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	24.9	27.675	18.7	28.725
2	22.225	27.3	31.900000000000002	18.575
3	25.2	37.9	16.25	20.65
4	23.5	41.975	15.75	18.775
5	19.55	24.65	25.2	30.599999999999998
6	32.925	26.325	24.125	16.625
7	30.025000000000002	39.375	15.125	15.475
8	20.3	33.95	26.525	19.225
9	23.200000000000003	31.3	16.55	28.95
10-11	31.65	31.9625	20.65	15.737499999999999
12-13	20.2375	26.950000000000003	22.400000000000002	30.412499999999998
14-15	27.9125	39.15	17.8625	15.075
16-17	20.0	22.7375	39.637499999999996	17.625
18-19	37.525	24.3125	24.2	13.9625
20-21	19.275000000000002	39.75	23.5625	17.4125
22-23	27.962500000000002	38.75	14.4875	18.8
24-25	29.7375	38.8875	15.049999999999999	16.325
26-27	26.25	29.6625	20.2625	23.825
28-29	35.3	27.5875	14.95	22.162499999999998
30-31	31.05	39.375	10.625	18.95
32-33	29.762499999999996	39.0375	10.5375	20.6625
34-35	31.85	30.4	12.35	25.4
36-37	24.3125	35.9	10.5	29.2875
38-39	22.2	34.1625	13.600000000000001	30.0375
40-41	28.9375	28.1	18.987499999999997	23.974999999999998
42-43	25.650000000000002	26.787499999999998	21.337500000000002	26.224999999999998
44-45	25.837500000000002	35.2625	13.850000000000001	25.05
46-47	22.8625	32.225	13.4125	31.5
48-49	15.775	28.8375	17.974999999999998	37.4125
50-51	17.2875	29.599999999999998	16.662499999999998	36.449999999999996
52-53	25.5625	23.4125	21.675	29.349999999999998
54-55	21.9	26.8625	19.525000000000002	31.7125
56-57	29.3875	24.4375	16.412499999999998	29.762499999999996
58-59	29.9375	28.725	17.5625	23.775
60-61	31.125000000000004	20.7125	25.3125	22.85
62-63	29.2	24.637500000000003	22.3	23.8625
64-65	23.7	18.925	28.625	28.749999999999996
66-67	20.375	16.7625	31.837500000000002	31.025000000000002
68-69	26.2875	16.925	31.612499999999997	25.174999999999997
70-71	26.924999999999997	20.6625	31.55	20.8625
72-73	28.775000000000002	13.737499999999999	28.549999999999997	28.9375
74-75	30.412499999999998	11.325000000000001	27.950000000000003	30.312499999999996
76	16.375	10.475	45.4	27.750000000000004
>>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	1.0
29	2.0
30	1.0
31	0.5
32	0.5
33	0.0
34	0.0
35	1.0
36	1.0
37	0.0
38	0.5
39	2.0
40	5.5
41	11.5
42	15.0
43	30.0
44	67.5
45	114.5
46	139.0
47	207.5
48	415.0
49	827.5
50	1101.0
51	809.0
52	487.5
53	411.5
54	365.0
55	281.5
56	160.5
57	81.5
58	40.0
59	40.5
60	26.5
61	7.5
62	3.0
63	2.5
64	1.0
65	0.0
66	0.0
67	0.0
68	0.0
69	1.0
70	1.0
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	0.5
95	0.5
96	0.0
97	0.0
98	0.0
99	0.5
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	0.0
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	58.650000000000006
#Duplication Level	Percentage of deduplicated	Percentage of total
1	89.30093776641091	52.37500000000001
2	4.859335038363171	5.7
3	1.9607843137254901	3.45
4	0.8525149190110828	2.0
5	0.8525149190110828	2.5
6	0.1278772378516624	0.44999999999999996
7	0.3410059676044331	1.4000000000000001
8	0.1278772378516624	0.6
9	0.17050298380221654	0.8999999999999999
>10	1.278772378516624	16.2
>50	0.08525149190110827	3.7249999999999996
>100	0.042625745950554135	10.7
>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	428	10.7	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	80	2.0	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	69	1.725	No Hit
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	50	1.25	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	48	1.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	48	1.2	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	45	1.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	44	1.0999999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	38	0.95	No Hit
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	33	0.8250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	25	0.625	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	21	0.525	No Hit
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	20	0.5	No Hit
GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	18	0.44999999999999996	No Hit
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	17	0.42500000000000004	No Hit
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	17	0.42500000000000004	No Hit
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGT	16	0.4	TruSeq Adapter, Index 7 (97% over 36bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
AGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACA	14	0.35000000000000003	No Hit
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	13	0.325	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG	13	0.325	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGA	12	0.3	TruSeq Adapter, Index 7 (97% over 36bp)
CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	10	0.25	No Hit
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	10	0.25	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	10	0.25	No Hit
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGAT	9	0.22499999999999998	TruSeq Adapter, Index 7 (97% over 36bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAG	9	0.22499999999999998	TruSeq Adapter, Index 7 (97% over 36bp)
GATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGG	9	0.22499999999999998	No Hit
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGA	7	0.17500000000000002	TruSeq Adapter, Index 7 (97% over 35bp)
AAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	7	0.17500000000000002	No Hit
CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGGATTGTAGTTCAATTGGTCAGAGCAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
ATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAG	7	0.17500000000000002	No Hit
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAGATC	7	0.17500000000000002	No Hit
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	6	0.15	No Hit
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGG	6	0.15	TruSeq Adapter, Index 7 (97% over 36bp)
CGACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAG	6	0.15	No Hit
GTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATC	5	0.125	No Hit
CTAACGAACGAACGATTTGAACAAATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (96% over 28bp)
GCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	5	0.125	No Hit
GCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAG	5	0.125	No Hit
GTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAG	5	0.125	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAGATCGGAAGAGC	5	0.125	No Hit
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACA	5	0.125	No Hit
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
ATATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCAC	5	0.125	No Hit
TCAAAAGAGGAAAGGCTTGCGGTGGATAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAA	5	0.125	No Hit
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTAGATCGGAAGAGC	5	0.125	No Hit
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGAGC	5	0.125	No Hit
GCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCA	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	0.0	0.0	0.0	0.0	0.0
3	0.0	0.0	0.0	0.0	0.0
4	0.0	0.0	0.0	0.0	0.0
5	0.0	0.0	0.0	0.0	0.0
6	0.0	0.0	0.0	0.0	0.0
7	0.05	0.0	0.0	0.0	0.0
8	0.15	0.0	0.0	0.0	0.0
9	0.525	0.0	0.0	0.0	0.0
10	0.95	0.0	0.0	0.0	0.0
11	1.3	0.0	0.0	0.0	0.0
12	1.6	0.0	0.0	0.0	0.0
13	2.6	0.0	0.0	0.0	0.0
14	3.375	0.0	0.0	0.0	0.0
15	3.975	0.0	0.0	0.0	0.0
16	4.925	0.0	0.0	0.0	0.0
17	6.6	0.0	0.0	0.0	0.0
18	9.7	0.0	0.0	0.0	0.0
19	11.1	0.0	0.0	0.0	0.0
20	14.075	0.0	0.0	0.0	0.0
21	17.725	0.0	0.0	0.0	0.0
22	22.575	0.0	0.0	0.0	0.0
23	37.95	0.0	0.0	0.0	0.0
24	40.65	0.0	0.0	0.0	0.0
25	47.675	0.0	0.0	0.0	0.0
26	51.85	0.0	0.0	0.0	0.0
27	54.575	0.0	0.0	0.0	0.0
28	56.875	0.0	0.0	0.0	0.0
29	58.9	0.0	0.0	0.0	0.0
30	61.375	0.0	0.0	0.0	0.0
31	64.225	0.0	0.0	0.0	0.0
32	66.75	0.0	0.0	0.0	0.0
33	69.075	0.0	0.0	0.0	0.0
34	72.3	0.0	0.0	0.0	0.0
35	77.025	0.0	0.0	0.0	0.0
36	81.225	0.0	0.0	0.0	0.0
37	83.975	0.0	0.0	0.0	0.0
38	85.825	0.0	0.0	0.0	0.0
39	87.1	0.0	0.0	0.0	0.0
40	88.325	0.0	0.0	0.0	0.0
41	89.75	0.0	0.0	0.0	0.0
42	90.55	0.0	0.0	0.0	0.0
43	91.225	0.0	0.0	0.0	0.0
44	92.0	0.0	0.0	0.0	0.0
45	92.25	0.0	0.0	0.0	0.0
46	93.0	0.0	0.0	0.0	0.0
47	93.3	0.0	0.0	0.0	0.0
48	93.45	0.0	0.0	0.0	0.0
49	93.65	0.0	0.0	0.0	0.0
50	93.675	0.0	0.0	0.0	0.0
51	93.75	0.0	0.0	0.0	0.0
52	93.775	0.0	0.0	0.0	0.0
53	93.775	0.0	0.0	0.0	0.0
54	93.775	0.0	0.0	0.0	0.0
55	93.775	0.0	0.0	0.0	0.0
56	93.8	0.0	0.0	0.0	0.0
57	93.8	0.0	0.0	0.0	0.0
58	93.8	0.0	0.0	0.0	0.0
59	93.825	0.0	0.0	0.0	0.0
60	93.825	0.0	0.0	0.0	0.0
61	93.825	0.0	0.0	0.0	0.0
62	93.825	0.0	0.0	0.0	0.0
63	93.825	0.0	0.0	0.0	0.0
64	93.825	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGGTCAG	15	0.0020658788	70.00001	17
TTCAATT	15	0.0020658788	70.00001	11
GGATTGT	15	0.0020658788	70.00001	2
GTTCAAT	15	0.0020658788	70.00001	10
GATTGTA	15	0.0020658788	70.00001	3
TAGTTCA	15	0.0020658788	70.00001	8
ATTGTAG	15	0.0020658788	70.00001	4
GGGATTG	15	0.0020658788	70.00001	1
AGTTCAA	15	0.0020658788	70.00001	9
GTAGTTC	15	0.0020658788	70.00001	7
TTGTAGT	20	7.003785E-5	70.0	5
TGTAGTT	20	0.0064587677	52.5	6
GAACAGA	75	4.3291948E-10	42.0	19
AACAGAT	75	4.3291948E-10	42.0	20
TGAACAG	75	4.3291948E-10	42.0	18
ATGCCGT	100	3.6379788E-12	38.5	70
TTTGAAC	85	1.4770194E-9	37.058823	16
ACAGATC	85	1.4770194E-9	37.058823	21
TTGAACA	85	1.4770194E-9	37.058823	17
TAACGAA	105	5.456968E-12	36.666668	2
>>END_MODULE
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
Rejected 206148 READS because READLEN < 1
Read 206148 spots for SRR11699598.sra
Written 206148 spots for SRR11699598.sra
SRR ids: ['SRR11699598.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_7eit1g7b
SRR11699598.sra spots: 4122960
blocks: [[1, 206148], [206149, 412296], [412297, 618444], [618445, 824592], [824593, 1030740], [1030741, 1236888], [1236889, 1443036], [1443037, 1649184], [1649185, 1855332], [1855333, 2061480], [2061481, 2267628], [2267629, 2473776], [2473777, 2679924], [2679925, 2886072], [2886073, 3092220], [3092221, 3298368], [3298369, 3504516], [3504517, 3710664], [3710665, 3916812], [3916813, 4122960]]
SRR11699598 file size 782964
SRR11699598 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 SRR11699598 SRR11699598_1.fastq
Input file:	SRR11699598_1.fastq
trimmed:	SRR11699598-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 08:17:34 2025 >> started

Sat Jun 21 08:17:36 2025 >> done (2.273s)
4122960 reads processed; of these:
 746357 (18.10%) short reads filtered out after trimming by size control
   1797 ( 0.04%) empty reads filtered out after trimming by size control
3374806 (81.85%) reads available; of these:
3301119 (97.82%) trimmed reads available after processing
  73687 ( 2.18%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  80521	  2.39%
 19	 139666	  4.14%
 20	 160294	  4.75%
 21	 232265	  6.88%
 22	 584016	 17.31%
 23	 134212	  3.98%
 24	 320180	  9.49%
 25	 166579	  4.94%
 26	 113773	  3.37%
 27	 101821	  3.02%
 28	  96572	  2.86%
 29	 110736	  3.28%
 30	 111229	  3.30%
 31	 103345	  3.06%
 32	  95395	  2.83%
 33	 102031	  3.02%
 34	 149548	  4.43%
 35	 134606	  3.99%
 36	  88263	  2.62%
 37	  68755	  2.04%
 38	  45383	  1.34%
 39	  46531	  1.38%
 40	  32162	  0.95%
 41	  33058	  0.98%
 42	  21293	  0.63%
 43	  17019	  0.50%
 44	  11862	  0.35%
 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	      3	  0.00%
 76	  73687	  2.18%
3374806 reads passed initial QC


criterion=sequence-density
sequence-density=5.03
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCG


criterion=fanout-score
sequence-density=0.21
sequence-density-rank=14
fanout-score=10.28
fanout-score-rank=1
prefix-density=0.52
prefix-fanout=4.3
sequence=GTCTAGTGGTAGAATAGTACCCTGCCACGG
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 SRR11699598 -
Input file:	STDIN
trimmed:	SRR11699598-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
Sat Jun 21 08:17:41 2025 >> started

Sat Jun 21 08:17:43 2025 >> done (2.192s)
2249871 reads processed; of these:
   4956 ( 0.22%) short reads filtered out after trimming by size control
 113687 ( 5.05%) empty reads filtered out after trimming by size control
2131228 (94.73%) reads available; of these:
  14719 ( 0.69%) trimmed reads available after processing
2116509 (99.31%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  54474	  2.56%
 19	  93632	  4.39%
 20	 106336	  4.99%
 21	 153762	  7.21%
 22	 388206	 18.22%
 23	  88751	  4.16%
 24	 207481	  9.74%
 25	 110853	  5.20%
 26	  70704	  3.32%
 27	  65629	  3.08%
 28	  63960	  3.00%
 29	  64037	  3.00%
 30	  73666	  3.46%
 31	  68191	  3.20%
 32	  57186	  2.68%
 33	  56483	  2.65%
 34	  61020	  2.86%
 35	  69791	  3.27%
 36	  54170	  2.54%
 37	  42004	  1.97%
 38	  28965	  1.36%
 39	  29949	  1.41%
 40	  18605	  0.87%
 41	  21670	  1.02%
 42	  13865	  0.65%
 43	  11065	  0.52%
 44	   7800	  0.37%
 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	      1	  0.00%
 58	      0	  0.00%
 59	      0	  0.00%
 60	      0	  0.00%
 61	      0	  0.00%
 62	      1	  0.00%
 63	      0	  0.00%
 64	      1	  0.00%
 65	      0	  0.00%
 66	      0	  0.00%
 67	      0	  0.00%
 68	      0	  0.00%
 69	      0	  0.00%
 70	      2	  0.00%
 71	      2	  0.00%
 72	      5	  0.00%
 73	   1886	  0.09%
 74	      0	  0.00%
 75	      3	  0.00%
 76	  47072	  2.21%


criterion=sequence-density
sequence-density=1.60
sequence-density-rank=1
fanout-score=9.86
fanout-score-rank=3
prefix-density=1.63
prefix-fanout=9.6
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGATCTCGTATGCCGTCTTCTGC


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=38
fanout-score=28.19
fanout-score-rank=1
prefix-density=0.14
prefix-fanout=1.1
sequence=GGGACGGACCGGGAACGGCCCCCTCGGGGGCCTTCCCCGGGCGTCGAACAACCGACTCAGAACTGGTACGGACAAGGGGAATCCGACTGTTTAATTAAAACAAAGCATTGCGACGGTCCTCGAGGATGCTGACGCAATGTGATTTCTGCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAACCAAGCGCGGGTAAACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCC
                                 Started job on |	Jun 21 08:18:14
                             Started mapping on |	Jun 21 08:18:14
                                    Finished on |	Jun 21 08:18:29
       Mapping speed, Million of reads per hour |	781.48

                          Number of input reads |	3256163
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	304442
                        Uniquely mapped reads % |	9.35%
                          Average mapped length |	24.30
                       Number of splices: Total |	6692
            Number of splices: Annotated (sjdb) |	2940
                       Number of splices: GT/AG |	6218
                       Number of splices: GC/AG |	279
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	193
                      Mismatch rate per base, % |	1.26%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.42
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.20
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	290714
             % of reads mapped to multiple loci |	8.93%
        Number of reads mapped to too many loci |	515168
             % of reads mapped to too many loci |	15.82%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.30%
                     % of reads unmapped: other |	58.60%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2661007	2661007	2661007
N_multimapping	290714	290714	290714
N_noFeature	250089	259570	293320
N_ambiguous	1683	27	24
UnstrandedReadsAssigned:52670 PositiveStrandReadsAssigned:44845 NegativeStrandReadsAssigned:11098
Dataset is classified unstranded
MeadianReadLen=24 20thPercentileLength=22 echo kmer=19
SRR11699598 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: SRR11699598-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,256,163 reads, 494,391 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 834 rounds

  72540 SRR11699598.ke.tsv
  44303 SRR11699598.se.tsv
 116843 total
==> SRR11699598.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	2	1.21605
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

==> SRR11699598.se.tsv <==
Zm00001eb015280	1
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699598 completed mapping pipeline successfully
