Starting /dee2/code/volunteer_pipeline.sh SRR11699277
    current disk space = 2472646012928
    free memory = 1252656880 
SRR11699277 SRAfilesize
98707e0a5e907cf41e72a8a315210f4c  SRR11699277.sra
SRR11699277.sra file validated
SRR11699277 is single end
SRR11699277 is conventional basespace
SRR11699277 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699277_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	31.297	32.0	32.0	32.0	32.0	32.0
2	31.4885	32.0	32.0	32.0	32.0	32.0
3	31.48125	32.0	32.0	32.0	32.0	32.0
4	31.4355	32.0	32.0	32.0	32.0	32.0
5	31.52525	32.0	32.0	32.0	32.0	32.0
6	34.96125	36.0	36.0	36.0	36.0	36.0
7	35.02875	36.0	36.0	36.0	36.0	36.0
8	35.09225	36.0	36.0	36.0	36.0	36.0
9	34.8605	36.0	36.0	36.0	36.0	36.0
10-11	35.01925	36.0	36.0	36.0	36.0	36.0
12-13	35.032250000000005	36.0	36.0	36.0	36.0	36.0
14-15	34.976875	36.0	36.0	36.0	36.0	36.0
16-17	34.998875	36.0	36.0	36.0	36.0	36.0
18-19	35.079125	36.0	36.0	36.0	36.0	36.0
20-21	34.885999999999996	36.0	36.0	36.0	34.0	36.0
22-23	34.903499999999994	36.0	36.0	36.0	36.0	36.0
24-25	34.971000000000004	36.0	36.0	36.0	36.0	36.0
26-27	34.817875	36.0	36.0	36.0	34.0	36.0
28-29	34.837125	36.0	36.0	36.0	34.0	36.0
30-31	34.8975	36.0	36.0	36.0	36.0	36.0
32-33	34.756125	36.0	36.0	36.0	34.0	36.0
34-35	34.804375	36.0	36.0	36.0	36.0	36.0
36-37	34.809375	36.0	36.0	36.0	34.0	36.0
38-39	34.87075	36.0	36.0	36.0	36.0	36.0
40-41	34.743375	36.0	36.0	36.0	34.0	36.0
42-43	34.738125	36.0	36.0	36.0	34.0	36.0
44-45	34.574	36.0	36.0	36.0	32.0	36.0
46-47	34.62975	36.0	36.0	36.0	32.0	36.0
48-49	34.363749999999996	36.0	36.0	36.0	32.0	36.0
50-51	34.197	36.0	36.0	36.0	32.0	36.0
52-53	33.980625	36.0	36.0	36.0	32.0	36.0
54-55	33.813874999999996	36.0	36.0	36.0	29.5	36.0
56-57	33.2465	36.0	36.0	36.0	24.0	36.0
58-59	33.07925	36.0	36.0	36.0	21.0	36.0
60-61	32.927	36.0	36.0	36.0	17.5	36.0
62-63	32.583875	36.0	34.0	36.0	14.0	36.0
64-65	32.22025	36.0	32.0	36.0	14.0	36.0
66-67	31.0715	36.0	32.0	36.0	14.0	36.0
68-69	30.775	36.0	29.5	36.0	14.0	36.0
70-71	30.813875	36.0	29.5	36.0	14.0	36.0
72-73	30.96275	36.0	29.5	36.0	14.0	36.0
74-75	31.172125	36.0	32.0	36.0	14.0	36.0
76	27.00225	32.0	14.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	4.0
22	3.0
23	6.0
24	11.0
25	35.0
26	47.0
27	48.0
28	83.0
29	123.0
30	163.0
31	209.0
32	311.0
33	449.0
34	967.0
35	1541.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	23.400000000000002	29.225	22.775000000000002	24.6
2	22.900000000000002	27.925	25.674999999999997	23.5
3	26.150000000000002	32.800000000000004	19.975	21.075
4	27.175	31.8	18.099999999999998	22.925
5	22.275	28.1	21.075	28.549999999999997
6	26.0	26.474999999999998	24.099999999999998	23.425
7	30.925000000000004	31.175000000000004	19.325	18.575
8	23.200000000000003	26.6	29.025000000000002	21.175
9	23.95	28.975	21.05	26.025
10-11	30.599999999999998	27.037499999999998	23.799999999999997	18.5625
12-13	23.4875	23.674999999999997	23.724999999999998	29.1125
14-15	29.9625	34.075	18.15	17.8125
16-17	24.75	23.8375	29.212500000000002	22.2
18-19	34.5125	24.9125	22.5125	18.0625
20-21	25.5125	34.300000000000004	22.775000000000002	17.4125
22-23	29.975	35.3375	16.2125	18.475
24-25	26.450000000000003	36.5625	17.837500000000002	19.15
26-27	27.700000000000003	30.4375	18.8125	23.05
28-29	30.7375	28.0625	17.0625	24.1375
30-31	31.7	33.1125	13.237499999999999	21.95
32-33	28.075	35.462500000000006	14.5375	21.925
34-35	28.8875	30.775000000000002	15.0625	25.275
36-37	24.349999999999998	34.5375	13.15	27.962500000000002
38-39	24.6875	32.9	14.4625	27.950000000000003
40-41	25.687500000000004	30.2125	16.8625	27.237499999999997
42-43	27.1125	28.050000000000004	19.6375	25.2
44-45	22.0125	33.775	16.0125	28.199999999999996
46-47	21.625	32.725	14.3375	31.3125
48-49	16.602075259407425	29.378672334041756	16.289536192024006	37.72971621452682
50-51	17.150000000000002	30.1375	16.2625	36.449999999999996
52-53	18.0375	26.5875	19.4375	35.9375
54-55	15.950000000000001	29.062500000000004	18.3	36.6875
56-57	11.975	26.950000000000003	18.075	43.0
58-59	11.55	27.450000000000003	17.1625	43.8375
60-61	10.1125	30.7	21.825	37.3625
62-63	11.0	29.675	25.9875	33.3375
64-65	9.950000000000001	24.3125	28.8375	36.9
66-67	13.0375	19.0125	29.9875	37.9625
68-69	13.389173646705837	21.465183147893487	29.316164520565067	35.8294786848356
70-71	14.9375	21.0375	30.599999999999998	33.425
72-73	14.45	19.787499999999998	29.025000000000002	36.7375
74-75	16.875	17.875	30.675	34.575
76	9.875	16.475	38.1	35.55
>>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	0.5
28	0.5
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.5
35	1.0
36	1.0
37	1.0
38	2.5
39	5.5
40	11.0
41	22.5
42	30.0
43	48.0
44	94.5
45	175.0
46	227.0
47	333.0
48	642.5
49	675.5
50	505.0
51	508.0
52	474.5
53	355.0
54	272.0
55	219.5
56	148.0
57	128.0
58	127.0
59	86.0
60	30.0
61	10.5
62	6.0
63	6.5
64	6.5
65	5.5
66	2.5
67	0.0
68	0.5
69	1.0
70	0.5
71	0.0
72	0.5
73	0.5
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	0.5
96	0.0
97	0.5
98	0.5
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	0.0125
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	0.0125
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	65.64999999999999
#Duplication Level	Percentage of deduplicated	Percentage of total
1	87.35719725818736	57.35
2	5.55978674790556	7.3
3	1.942117288651942	3.8249999999999997
4	1.6374714394516376	4.3
5	0.913937547600914	3.0
6	0.49504950495049505	1.95
7	0.26656511805026656	1.225
8	0.3427265803503427	1.7999999999999998
9	0.19040365575019041	1.125
>10	1.2185833968012185	12.975
>50	0.03808073115003808	1.3
>100	0.03808073115003808	3.85
>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	154	3.85	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	52	1.3	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	40	1.0	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	32	0.8	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCC	28	0.7000000000000001	TruSeq Adapter, Index 6 (97% over 36bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	22	0.5499999999999999	No Hit
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	19	0.475	No Hit
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCC	19	0.475	TruSeq Adapter, Index 6 (97% over 36bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCCAATAT	18	0.44999999999999996	TruSeq Adapter, Index 6 (97% over 41bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCCA	16	0.4	TruSeq Adapter, Index 6 (97% over 37bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	14	0.35000000000000003	No Hit
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	13	0.325	No Hit
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAGATC	13	0.325	No Hit
GCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAG	12	0.3	No Hit
CGACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCT	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	12	0.3	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	12	0.3	No Hit
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCCAA	11	0.27499999999999997	TruSeq Adapter, Index 6 (97% over 38bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCCAATA	11	0.27499999999999997	TruSeq Adapter, Index 6 (97% over 40bp)
ATACTGTAGGGGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATC	10	0.25	No Hit
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCGACCCCAGGTCAGTCGGGACTACCCGCTAGATCGGAAGAGCACACGTC	10	0.25	No Hit
CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGAGC	10	0.25	No Hit
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	9	0.22499999999999998	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAGATCGGAAGA	8	0.2	No Hit
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCAGATCGGAAGA	8	0.2	No Hit
CGACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAG	8	0.2	No Hit
CGACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCCAATATC	7	0.17500000000000002	TruSeq Adapter, Index 6 (97% over 42bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GCACCAGTAGTCTAGTGGTAGAATAGTACCCAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
GCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAAAGA	7	0.17500000000000002	No Hit
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	6	0.15	No Hit
CGAGCACCTCTGAGCTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCCAAT	6	0.15	TruSeq Adapter, Index 6 (97% over 39bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCC	6	0.15	TruSeq Adapter, Index 5 (97% over 35bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	6	0.15	No Hit
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	6	0.15	No Hit
ACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAAAGATCGGAAGAG	6	0.15	No Hit
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AGGGATGTAGCGCAGCTTGGTAGCGCTTTTGTTTTAGATCGGAAGAGCAC	6	0.15	No Hit
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	6	0.15	No Hit
CGACACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	5	0.125	No Hit
CTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TCGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCCAA	5	0.125	TruSeq Adapter, Index 6 (97% over 38bp)
ACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
AGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACA	5	0.125	No Hit
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AAGTGGAAGTGCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACG	5	0.125	No Hit
GATGAAGAACGTAGCAAAATGCGATAAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GAGAATTTCTGGAAGGGCTCCCTCTCTTCGGAGAGGGTAAAGCCCTACAG	5	0.125	No Hit
AACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CGACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAAC	5	0.125	No Hit
GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTAGATCGGAAGAGCACA	5	0.125	No Hit
AGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGAT	5	0.125	No Hit
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTAGATCGGAAGAGC	5	0.125	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	5	0.125	No Hit
ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAGAGCA	5	0.125	No Hit
GCCCCCATCGTCTAGTGGTTCAGGACAAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCATTCCAGATCGGA	5	0.125	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTAGATCGGAAGAGCA	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	0.1	0.0	0.0	0.0	0.0
2	0.225	0.0	0.0	0.0	0.0
3	0.325	0.0	0.0	0.0	0.0
4	0.475	0.0	0.0	0.0	0.0
5	0.6	0.0	0.0	0.0	0.0
6	0.7	0.0	0.0	0.0	0.0
7	0.775	0.0	0.0	0.0	0.0
8	1.075	0.0	0.0	0.0	0.0
9	1.7	0.0	0.0	0.0	0.0
10	2.275	0.0	0.0	0.0	0.0
11	2.975	0.0	0.0	0.0	0.0
12	3.95	0.0	0.0	0.0	0.0
13	4.975	0.0	0.0	0.0	0.0
14	7.3	0.0	0.0	0.0	0.0
15	8.1	0.0	0.0	0.0	0.0
16	9.45	0.0	0.0	0.0	0.0
17	11.95	0.0	0.0	0.0	0.0
18	14.15	0.0	0.0	0.0	0.0
19	16.35	0.0	0.0	0.0	0.0
20	18.8	0.0	0.0	0.0	0.0
21	22.025	0.0	0.0	0.0	0.0
22	27.325	0.0	0.0	0.0	0.0
23	35.1	0.0	0.0	0.0	0.0
24	38.225	0.0	0.0	0.0	0.0
25	44.4	0.0	0.0	0.0	0.0
26	47.6	0.0	0.0	0.0	0.0
27	49.9	0.0	0.0	0.0	0.0
28	52.4	0.0	0.0	0.0	0.0
29	54.6	0.0	0.0	0.0	0.0
30	57.025	0.0	0.0	0.0	0.0
31	59.8	0.0	0.0	0.0	0.0
32	62.575	0.0	0.0	0.0	0.0
33	64.95	0.0	0.0	0.0	0.0
34	67.7	0.0	0.0	0.0	0.0
35	70.475	0.0	0.0	0.0	0.0
36	73.975	0.0	0.0	0.0	0.0
37	76.75	0.0	0.0	0.0	0.0
38	79.025	0.0	0.0	0.0	0.0
39	80.7	0.0	0.0	0.0	0.0
40	82.55	0.0	0.0	0.0	0.0
41	83.925	0.0	0.0	0.0	0.0
42	85.925	0.0	0.0	0.0	0.0
43	87.125	0.0	0.0	0.0	0.0
44	88.2	0.0	0.0	0.0	0.0
45	89.075	0.0	0.0	0.0	0.0
46	90.425	0.0	0.0	0.0	0.0
47	91.2	0.0	0.0	0.0	0.0
48	92.025	0.0	0.0	0.0	0.0
49	93.075	0.0	0.0	0.0	0.0
50	93.725	0.0	0.0	0.0	0.0
51	94.0	0.0	0.0	0.0	0.0
52	94.375	0.0	0.0	0.0	0.0
53	94.65	0.0	0.0	0.0	0.0
54	94.825	0.0	0.0	0.0	0.0
55	95.0	0.0	0.0	0.0	0.0
56	95.125	0.0	0.0	0.0	0.0
57	95.225	0.0	0.0	0.0	0.0
58	95.275	0.0	0.0	0.0	0.0
59	95.4	0.0	0.0	0.0	0.0
60	95.45	0.0	0.0	0.0	0.0
61	95.475	0.0	0.0	0.0	0.0
62	95.525	0.0	0.0	0.0	0.0
63	95.55	0.0	0.0	0.0	0.0
64	95.6	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TTGTAGT	20	7.003785E-5	70.0	5
TAGTTCA	20	7.003785E-5	70.0	8
GTAGTTC	20	7.003785E-5	70.0	7
CTGAGAT	20	0.0064587677	52.5	33
AGAGATC	20	0.0064587677	52.5	40
TTCCGTC	35	0.00111172	40.000004	65
CGTATTC	35	0.00111172	40.000004	61
TATTCCG	35	0.00111172	40.000004	63
TCCGTCT	35	0.00111172	40.000004	66
ATTCCGT	35	0.00111172	40.000004	64
GTATTCC	40	0.0021434545	35.0	62
TCGTATT	45	0.003819767	31.111113	60
TATGCCG	80	0.0022346217	21.875	69
ATGCCGT	85	0.0031788175	20.588234	69
>>END_MODULE
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124051 READS because READLEN < 1
Read 124051 spots for SRR11699277.sra
Written 124051 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
Rejected 124039 READS because READLEN < 1
Read 124039 spots for SRR11699277.sra
Written 124039 spots for SRR11699277.sra
SRR ids: ['SRR11699277.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_0370eqh_
SRR11699277.sra spots: 2480792
blocks: [[1, 124039], [124040, 248078], [248079, 372117], [372118, 496156], [496157, 620195], [620196, 744234], [744235, 868273], [868274, 992312], [992313, 1116351], [1116352, 1240390], [1240391, 1364429], [1364430, 1488468], [1488469, 1612507], [1612508, 1736546], [1736547, 1860585], [1860586, 1984624], [1984625, 2108663], [2108664, 2232702], [2232703, 2356741], [2356742, 2480792]]
SRR11699277 file size 470247
SRR11699277 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 SRR11699277 SRR11699277_1.fastq
Input file:	SRR11699277_1.fastq
trimmed:	SRR11699277-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 05:51:13 2025 >> started

Wed Jun 18 05:51:14 2025 >> done (1.206s)
2480792 reads processed; of these:
 375990 (15.16%) short reads filtered out after trimming by size control
   3471 ( 0.14%) empty reads filtered out after trimming by size control
2101331 (84.70%) reads available; of these:
1934984 (92.08%) trimmed reads available after processing
 166347 ( 7.92%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  50936	  2.42%
 19	  77645	  3.70%
 20	  90317	  4.30%
 21	 141544	  6.74%
 22	 197137	  9.38%
 23	  81439	  3.88%
 24	 155053	  7.38%
 25	  89982	  4.28%
 26	  66003	  3.14%
 27	  64769	  3.08%
 28	  58052	  2.76%
 29	  63271	  3.01%
 30	  70749	  3.37%
 31	  72182	  3.44%
 32	  61434	  2.92%
 33	  66858	  3.18%
 34	  73149	  3.48%
 35	  83401	  3.97%
 36	  63543	  3.02%
 37	  53129	  2.53%
 38	  42846	  2.04%
 39	  42669	  2.03%
 40	  36550	  1.74%
 41	  50676	  2.41%
 42	  31496	  1.50%
 43	  27350	  1.30%
 44	  22795	  1.08%
 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	      1	  0.00%
 72	      2	  0.00%
 73	      0	  0.00%
 74	      0	  0.00%
 75	      6	  0.00%
 76	 166347	  7.92%
2101331 reads passed initial QC


criterion=sequence-density
sequence-density=6.98
sequence-density-rank=1
fanout-score=19.20
fanout-score-rank=2
prefix-density=7.10
prefix-fanout=18.9
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCCAATATCTCGTATGCCGTCTTCT


criterion=fanout-score
sequence-density=0.30
sequence-density-rank=12
fanout-score=22.06
fanout-score-rank=1
prefix-density=1.49
prefix-fanout=4.5
sequence=GTCTAGTGGTATGATTCTCGCTT
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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCCAATATCTCGTATGCCGTCTTCT -o SRR11699277 -
Input file:	STDIN
trimmed:	SRR11699277-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCCAATATCTCGTATGCCGTCTTCT
-- 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 05:51:20 2025 >> started

Wed Jun 18 05:51:21 2025 >> done (1.116s)
1500951 reads processed; of these:
   1887 ( 0.13%) short reads filtered out after trimming by size control
      4 ( 0.00%) empty reads filtered out after trimming by size control
1499060 (99.87%) reads available; of these:
 130455 ( 8.70%) trimmed reads available after processing
1368605 (91.30%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  36980	  2.47%
 19	  56397	  3.76%
 20	  66387	  4.43%
 21	 102097	  6.81%
 22	 139860	  9.33%
 23	  56837	  3.79%
 24	 109466	  7.30%
 25	  64097	  4.28%
 26	  47326	  3.16%
 27	  45796	  3.05%
 28	  41664	  2.78%
 29	  45388	  3.03%
 30	  50502	  3.37%
 31	  51339	  3.42%
 32	  43692	  2.91%
 33	  47750	  3.19%
 34	  52091	  3.47%
 35	  59600	  3.98%
 36	  45226	  3.02%
 37	  37974	  2.53%
 38	  30545	  2.04%
 39	  30729	  2.05%
 40	  28284	  1.89%
 41	  37575	  2.51%
 42	  22115	  1.48%
 43	  17524	  1.17%
 44	  14805	  0.99%
 45	  23771	  1.59%
 46	  13085	  0.87%
 47	  11889	  0.79%
 48	  17424	  1.16%
 49	   9478	  0.63%
 50	   7033	  0.47%
 51	   5789	  0.39%
 52	   4161	  0.28%
 53	   3746	  0.25%
 54	   2780	  0.19%
 55	   2115	  0.14%
 56	   1571	  0.10%
 57	   1778	  0.12%
 58	   2012	  0.13%
 59	    478	  0.03%
 60	    465	  0.03%
 61	    578	  0.04%
 62	    433	  0.03%
 63	    187	  0.01%
 64	     89	  0.01%
 65	     76	  0.01%
 66	     81	  0.01%
 67	     56	  0.00%
 68	     94	  0.01%
 69	     50	  0.00%
 70	     80	  0.01%
 71	     14	  0.00%
 72	     12	  0.00%
 73	     34	  0.00%
 74	      0	  0.00%
 75	      1	  0.00%
 76	   7654	  0.51%


criterion=sequence-density
sequence-density=2.06
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=19
prefix-density=0.00
prefix-fanout=1.0
sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCG


criterion=fanout-score
sequence-density=0.30
sequence-density-rank=14
fanout-score=21.95
fanout-score-rank=1
prefix-density=1.49
prefix-fanout=4.5
sequence=GTCTAGTGGTATGATTCTCGCTT
                                 Started job on |	Jun 18 05:51:51
                             Started mapping on |	Jun 18 05:51:51
                                    Finished on |	Jun 18 05:52:02
       Mapping speed, Million of reads per hour |	687.09

                          Number of input reads |	2099440
                      Average input read length |	30
                                    UNIQUE READS:
                   Uniquely mapped reads number |	173529
                        Uniquely mapped reads % |	8.27%
                          Average mapped length |	27.14
                       Number of splices: Total |	4243
            Number of splices: Annotated (sjdb) |	2241
                       Number of splices: GT/AG |	3843
                       Number of splices: GC/AG |	230
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	169
                      Mismatch rate per base, % |	1.44%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.43
                        Insertion rate per base |	0.01%
                       Insertion average length |	1.18
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	165799
             % of reads mapped to multiple loci |	7.90%
        Number of reads mapped to too many loci |	427339
             % of reads mapped to too many loci |	20.35%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.57%
                     % of reads unmapped: other |	55.91%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1760112	1760112	1760112
N_multimapping	165799	165799	165799
N_noFeature	137209	141696	167878
N_ambiguous	1184	16	10
UnstrandedReadsAssigned:35136 PositiveStrandReadsAssigned:31817 NegativeStrandReadsAssigned:5641
Dataset is classified positive stranded
MeadianReadLen=28 20thPercentileLength=22 echo kmer=19
SRR11699277 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: SRR11699277-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,099,440 reads, 278,213 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 740 rounds

  72540 SRR11699277.ke.tsv
  44303 SRR11699277.se.tsv
 116843 total
==> SRR11699277.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	3	3.13609
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

==> SRR11699277.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	1
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699277 completed mapping pipeline successfully
