Starting /dee2/code/volunteer_pipeline.sh SRR11699487
    current disk space = 2473255911424
    free memory = 1580979328 
SRR11699487 SRAfilesize
7e91ae3b58aac579df45f14b4c451a0e  SRR11699487.sra
SRR11699487.sra file validated
SRR11699487 is single end
SRR11699487 is conventional basespace
SRR11699487 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699487_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	51
>>END_MODULE
>>Per base sequence quality	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	30.707	32.0	32.0	32.0	32.0	32.0
2	31.069	32.0	32.0	32.0	32.0	32.0
3	31.07925	32.0	32.0	32.0	32.0	32.0
4	31.5465	32.0	32.0	32.0	32.0	32.0
5	31.5075	32.0	32.0	32.0	32.0	32.0
6	34.73625	36.0	36.0	36.0	32.0	36.0
7	34.797	36.0	36.0	36.0	36.0	36.0
8	34.98075	36.0	36.0	36.0	36.0	36.0
9	34.5945	36.0	36.0	36.0	32.0	36.0
10-11	34.719625	36.0	36.0	36.0	34.0	36.0
12-13	34.715999999999994	36.0	36.0	36.0	32.0	36.0
14-15	34.205875000000006	36.0	36.0	36.0	28.5	36.0
16-17	34.622749999999996	36.0	36.0	36.0	32.0	36.0
18-19	34.820625	36.0	36.0	36.0	34.0	36.0
20-21	34.784125	36.0	36.0	36.0	34.0	36.0
22-23	34.151125	36.0	36.0	36.0	32.0	36.0
24-25	34.102875	36.0	36.0	36.0	26.5	36.0
26-27	34.612125000000006	36.0	36.0	36.0	32.0	36.0
28-29	34.74575	36.0	36.0	36.0	32.0	36.0
30-31	34.486999999999995	36.0	36.0	36.0	32.0	36.0
32-33	33.894625000000005	36.0	36.0	36.0	23.0	36.0
34-35	34.424125000000004	36.0	36.0	36.0	32.0	36.0
36-37	34.426	36.0	36.0	36.0	32.0	36.0
38-39	34.40025	36.0	36.0	36.0	32.0	36.0
40-41	32.386	36.0	34.0	36.0	23.0	36.0
42-43	23.665374999999997	14.0	14.0	36.0	14.0	36.0
44-45	22.939	14.0	14.0	36.0	14.0	36.0
46-47	25.8415	25.0	14.0	36.0	14.0	36.0
48-49	26.108	25.0	14.0	36.0	14.0	36.0
50-51	22.67675	14.0	14.0	36.0	14.0	36.0
52-53	26.270375	29.5	14.0	36.0	14.0	36.0
54-55	22.280375	14.0	14.0	36.0	14.0	36.0
56-57	25.322375	25.0	14.0	36.0	14.0	36.0
58-59	22.20675	14.0	14.0	36.0	14.0	36.0
60-61	21.445875	14.0	14.0	34.0	14.0	36.0
62-63	22.707250000000002	20.5	14.0	34.0	14.0	36.0
64-65	19.4465	14.0	14.0	27.0	14.0	36.0
66-67	28.965875	34.0	20.5	36.0	14.0	36.0
68-69	30.4295	36.0	27.0	36.0	14.0	36.0
70-71	29.346	36.0	21.0	36.0	14.0	36.0
72-73	22.64875	23.0	14.0	31.5	14.0	36.0
74-75	18.9465	14.0	14.0	20.5	14.0	36.0
76	17.33325	14.0	14.0	14.0	14.0	32.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
19	2.0
20	1.0
21	4.0
22	30.0
23	74.0
24	94.0
25	183.0
26	329.0
27	589.0
28	866.0
29	458.0
30	211.0
31	212.0
32	292.0
33	292.0
34	284.0
35	79.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	24.925	66.7	3.6249999999999996	4.75
2	66.625	5.225	4.725	23.425
3	5.7	67.225	23.75	3.325
4	24.625	5.225	65.925	4.2250000000000005
5	6.0249999999999995	4.2	23.549999999999997	66.225
6	68.35	3.675	5.55	22.425
7	88.35	4.825	3.05	3.775
8	24.95	66.77499999999999	4.45	3.8249999999999997
9	5.475	67.7	23.7	3.125
10-11	47.112500000000004	35.325	13.087499999999999	4.475
12-13	36.7	4.5375	13.112499999999999	45.65
14-15	15.037500000000001	36.987500000000004	12.35	35.625
16-17	16.289536192024006	34.979372421552696	4.150518814851856	44.580572571571444
18-19	47.362500000000004	3.925	44.237500000000004	4.475
20-21	6.05	16.55	42.9	34.5
22-23	44.9375	47.0125	3.2375000000000003	4.8125
24-25	7.9625	36.475	12.825000000000001	42.7375
26-27	26.025	5.7375	33.037499999999994	35.199999999999996
28-29	9.775	55.137499999999996	2.1999999999999997	32.887499999999996
30-31	45.1875	19.537499999999998	30.65	4.625
32-33	17.125	36.4	2.325	44.15
34-35	6.4125000000000005	16.7625	2.4	74.425
36-37	35.55	45.0	2.5875	16.8625
38-39	44.3125	6.6000000000000005	13.125	35.9625
40-41	35.675000000000004	33.4125	15.1	15.812499999999998
42-43	38.5	16.5125	30.887500000000003	14.099999999999998
44-45	32.05	17.6625	15.4	34.887499999999996
46-47	41.7625	7.012500000000001	31.6	19.625
48-49	6.175	37.974999999999994	38.8625	16.9875
50-51	46.4375	6.3625	23.075000000000003	24.125
52-53	32.025	14.85	4.8375	48.2875
54-55	27.05	7.85	22.625	42.475
56-57	23.4625	16.45	49.85	10.237499999999999
58-59	34.2125	10.85	28.8625	26.075
60-61	47.6875	14.099999999999998	14.3625	23.849999999999998
62-63	15.787499999999998	7.2375	63.6875	13.2875
64-65	13.4	24.775	42.0125	19.8125
66-67	13.0375	61.4625	17.2875	8.2125
68-69	5.7875000000000005	72.0375	17.1625	5.0125
70-71	9.65	62.975	11.325000000000001	16.05
72-73	13.450000000000001	55.50000000000001	11.05	20.0
74-75	8.575000000000001	17.6375	44.975	28.812500000000004
76	15.375	5.025	63.14999999999999	16.45
>>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	0.5
36	0.5
37	0.0
38	1.5
39	2.0
40	2.0
41	17.0
42	31.0
43	63.5
44	185.0
45	362.5
46	451.0
47	486.0
48	497.0
49	400.0
50	327.0
51	279.0
52	238.5
53	244.5
54	243.0
55	349.5
56	452.5
57	282.0
58	115.0
59	69.5
60	14.5
61	4.0
62	3.0
63	4.5
64	3.0
65	0.0
66	0.0
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	0.5
89	1.0
90	2.0
91	1.5
92	0.0
93	2.0
94	3.0
95	4.0
96	6.0
97	5.5
98	6.5
99	9.0
100	10.0
>>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	0.0125
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	fail
#Total Deduplicated Percentage	29.099999999999998
#Duplication Level	Percentage of deduplicated	Percentage of total
1	79.20962199312714	23.05
2	8.24742268041237	4.8
3	3.178694158075601	2.775
4	1.9759450171821304	2.3
5	1.1168384879725086	1.625
6	0.6013745704467355	1.05
7	0.6013745704467355	1.225
8	0.5154639175257731	1.2
9	0.25773195876288657	0.675
>10	3.52233676975945	23.1
>50	0.429553264604811	7.175
>100	0.25773195876288657	15.0
>500	0.0859106529209622	16.025
>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
GCTGTCGGTTGCTGTCGGTTAGATCGGAAGAGCACACGTCTGAACTCCAG	641	16.025	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGTCGTATG	267	6.675000000000001	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCTCGTATG	206	5.1499999999999995	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGCGTATG	127	3.175	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTCAGATCGGAAGAGCACACGTCTGAACTCC	60	1.5	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGGGTATT	59	1.4749999999999999	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGGGGATT	57	1.425	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGGGGTTT	56	1.4000000000000001	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCGCGTATG	55	1.375	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGCGTTTG	50	1.25	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGCGGTTG	47	1.175	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGCGGATG	44	1.0999999999999999	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGTGGTATG	43	1.075	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGGGTATG	42	1.05	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGCGTATT	42	1.05	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGTCGTTTG	38	0.95	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGGGGTTG	38	0.95	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGGGGATG	36	0.8999999999999999	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGGGTTTT	32	0.8	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGTCGTATT	29	0.7250000000000001	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGTCGGATG	29	0.7250000000000001	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGGGTTTG	27	0.675	TruSeq Adapter, Index 7 (97% over 36bp)
GCTGTCGGTTGCTGTCGGTCAGATCGGAAGAGCACACGTCTGAACTCCAG	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AGATCGGAAGAGCACACGTCAGATCGGAAGAGCACACGTCTGAACTCCAG	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AGATCGGAAGAGCACACGTAGATCGGAAGAGCACACGTCTGAACTCCAGT	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AGATCGGAAGAGCACACGTCTTAGATCGGAAGAGCACACGTCTGAACTCC	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGCGGATT	20	0.5	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGTCGGTTG	19	0.475	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCTGGTATG	19	0.475	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGCGGTTT	18	0.44999999999999996	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCGGGTATG	16	0.4	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGAGGGCGGTTG	15	0.375	TruSeq Adapter, Index 7 (97% over 36bp)
CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCTCGTATT	15	0.375	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGCGTTTT	15	0.375	TruSeq Adapter, Index 7 (97% over 36bp)
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG	14	0.35000000000000003	No Hit
CCATCTCATCCCTGCGTGTCTCCGACTCAGAGATCGGAAGAGCACACGTC	14	0.35000000000000003	No Hit
GTTCAGAGTTCTACAGTCCGACGATCGTTCAGAGATCGGAAGAGCACACG	13	0.325	Illumina DpnII expression Sequencing Primer (100% over 26bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCGCGGATG	13	0.325	TruSeq Adapter, Index 7 (97% over 36bp)
AGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG	13	0.325	No Hit
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCGGGTATT	12	0.3	TruSeq Adapter, Index 7 (97% over 36bp)
AGAGTTCTACAGTCCGACGATCAGATCGGAAGAGCACACGTCTGAACTCC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCTCGGATG	12	0.3	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCTCGTTTG	12	0.3	TruSeq Adapter, Index 7 (97% over 36bp)
TGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG	11	0.27499999999999997	No Hit
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGTCGGATT	11	0.27499999999999997	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGTCGTTTT	10	0.25	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGTGGTATT	10	0.25	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCGGGGATT	10	0.25	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCGGGGATG	10	0.25	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCGCGTTTG	9	0.22499999999999998	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCGCGTATT	9	0.22499999999999998	TruSeq Adapter, Index 7 (97% over 36bp)
GCTGTCGGTTGCTGTCGGTTAGATCGGAAGGGCACACGTCTGAACTCCAG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (96% over 30bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGAGGGCGGTTT	8	0.2	TruSeq Adapter, Index 7 (97% over 36bp)
TTCAGAGTTCTACAGTCCGACGATCTTCAGAGATCGGAAGAGCACACGTC	8	0.2	Illumina DpnII expression Sequencing Primer (100% over 25bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGTGGGATG	8	0.2	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGAGTATT	8	0.2	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCGGGTTTG	8	0.2	TruSeq Adapter, Index 7 (97% over 36bp)
GTTCAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGG	8	0.2	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGTGGTTTG	7	0.17500000000000002	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGTGGGATT	7	0.17500000000000002	TruSeq Adapter, Index 7 (97% over 36bp)
GTTCTACAGTCCGACGATCAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CAGAGTTCTACAGTCCGACGATCAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AGTTCTACAGTCCGACGATCAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCGGGTTTT	7	0.17500000000000002	TruSeq Adapter, Index 7 (97% over 36bp)
CTACAGTCCGACGATCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGAGGGCGGATG	6	0.15	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCGCGTTTT	6	0.15	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGTGGGTTG	6	0.15	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCGCGGTTT	6	0.15	TruSeq Adapter, Index 7 (97% over 36bp)
GCTGTCGGTTGCTGTGGTTAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCTGGTATT	6	0.15	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGTCGTAAG	6	0.15	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGCGGTAG	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGCGGTAT	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCGCGGATT	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGAGGGCGTATG	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGTGGTTTT	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGAGGGCGGAAG	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTAGATCGGAAGGGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (96% over 31bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCGCGGAAT	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGCGTAAG	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGGGGTAAT	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
GTTCAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATGT	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
AGATCGGAAGGGCACACGTCTGAACTCCAGTCACCAGGCGATCTCGTATG	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
>>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	58.475	0.0	0.0	0.0	0.0
2	58.75	0.0	0.0	0.0	0.0
3	58.925	0.0	0.0	0.0	0.0
4	58.975	0.0	0.0	0.0	0.0
5	59.05	0.0	0.0	0.0	0.0
6	59.075	0.0	0.0	0.0	0.0
7	59.65	0.0	0.0	0.0	0.0
8	59.725	0.0	0.0	0.0	0.0
9	59.85	0.0	0.0	0.0	0.0
10	60.025	0.0	0.0	0.0	0.0
11	60.3	0.0	0.0	0.0	0.0
12	60.55	0.0	0.0	0.0	0.0
13	60.925	0.0	0.0	0.0	0.0
14	61.525	0.0	0.0	0.0	0.0
15	61.8	0.0	0.0	0.0	0.0
16	62.275	0.0	0.0	0.0	0.0
17	62.925	0.0	0.0	0.0	0.0
18	63.425	0.0	0.0	0.0	0.0
19	63.925	0.0	0.0	0.0	0.0
20	65.15	0.0	0.0	0.0	0.0
21	84.15	0.0	0.0	0.0	0.0
22	84.95	0.0	0.0	0.0	0.0
23	86.225	0.0	0.0	0.0	0.0
24	86.575	0.0	0.0	0.0	0.0
25	87.05	0.0	0.0	0.0	0.0
26	87.5	0.0	0.0	0.0	0.0
27	87.825	0.0	0.0	0.0	0.0
28	88.175	0.0	0.0	0.0	0.0
29	88.425	0.0	0.0	0.0	0.0
30	88.725	0.0	0.0	0.0	0.0
31	89.65	0.0	0.0	0.0	0.0
32	89.75	0.0	0.0	0.0	0.0
33	90.375	0.0	0.0	0.0	0.0
34	90.525	0.0	0.0	0.0	0.0
35	90.75	0.0	0.0	0.0	0.0
36	91.125	0.0	0.0	0.0	0.0
37	91.25	0.0	0.0	0.0	0.0
38	91.25	0.0	0.0	0.0	0.0
39	91.35	0.0	0.0	0.0	0.0
40	91.5	0.0	0.0	0.0	0.0
41	91.6	0.0	0.0	0.0	0.0
42	91.7	0.0	0.0	0.0	0.0
43	91.7	0.0	0.0	0.0	0.0
44	91.75	0.0	0.0	0.0	0.0
45	91.75	0.0	0.0	0.0	0.0
46	91.75	0.0	0.0	0.0	0.0
47	91.75	0.0	0.0	0.0	0.0
48	91.75	0.0	0.0	0.0	0.0
49	91.75	0.0	0.0	0.0	0.0
50	91.75	0.0	0.0	0.0	0.0
51	91.75	0.0	0.0	0.0	0.0
52	91.75	0.0	0.0	0.0	0.0
53	91.75	0.0	0.0	0.0	0.0
54	91.75	0.0	0.0	0.0	0.0
55	91.75	0.0	0.0	0.0	0.0
56	91.75	0.0	0.0	0.0	0.0
57	91.75	0.0	0.0	0.0	0.0
58	91.75	0.0	0.0	0.0	0.0
59	91.75	0.0	0.0	0.0	0.0
60	91.75	0.0	0.0	0.0	0.0
61	91.75	0.0	0.0	0.0	0.0
62	91.75	0.0	0.0	0.0	0.0
63	91.75	0.0	0.0	0.0	0.0
64	91.75	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGTTGTG	15	0.0020658788	70.00001	54
CCGTGTT	15	0.0020658788	70.00001	51
GCCTCTT	15	0.0020658788	70.00001	51
GATCGGG	15	0.0020658788	70.00001	40
GATCGCG	30	7.878043E-8	70.00001	40
GGTTTAA	15	0.0020658788	70.00001	61
TTCCCTC	15	0.0020658788	70.00001	69
TTCTTTA	15	0.0020658788	70.00001	59
ATCGGGG	15	0.0020658788	70.00001	41
TCGTTTG	15	0.0020658788	70.00001	44
GCTTGAA	30	7.878043E-8	70.00001	60
CTGCTTT	15	0.0020658788	70.00001	58
AAAATTC	15	0.0020658788	70.00001	70
GGGGTTG	15	0.0020658788	70.00001	44
AAAAATA	15	0.0020658788	70.00001	68
TTGTGCT	35	2.6138878E-9	70.00001	56
TGTGCTT	45	3.6379788E-12	70.00001	57
CGTCTTG	30	7.878043E-8	70.00001	52
CTTCTGG	15	0.0020658788	70.00001	55
GTTGTGG	15	0.0020658788	70.00001	55
>>END_MODULE
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1059 READS because READLEN < 1
Read 1059 spots for SRR11699487.sra
Written 1059 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
Rejected 1054 READS because READLEN < 1
Read 1054 spots for SRR11699487.sra
Written 1054 spots for SRR11699487.sra
SRR ids: ['SRR11699487.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_v5q5ho2f
SRR11699487.sra spots: 21085
blocks: [[1, 1054], [1055, 2108], [2109, 3162], [3163, 4216], [4217, 5270], [5271, 6324], [6325, 7378], [7379, 8432], [8433, 9486], [9487, 10540], [10541, 11594], [11595, 12648], [12649, 13702], [13703, 14756], [14757, 15810], [15811, 16864], [16865, 17918], [17919, 18972], [18973, 20026], [20027, 21085]]
SRR11699487 file size 3912
SRR11699487 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 SRR11699487 SRR11699487_1.fastq
Input file:	SRR11699487_1.fastq
trimmed:	SRR11699487-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 08:58:04 2025 >> started

Fri Jun 20 08:58:04 2025 >> done (0.019s)
21085 reads processed; of these:
 1129 ( 5.35%) short reads filtered out after trimming by size control
12513 (59.35%) empty reads filtered out after trimming by size control
 7443 (35.30%) reads available; of these:
 7044 (94.64%) trimmed reads available after processing
  399 ( 5.36%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  96	  1.29%
 19	 383	  5.15%
 20	4296	 57.72%
 21	 200	  2.69%
 22	 753	 10.12%
 23	 129	  1.73%
 24	 132	  1.77%
 25	  74	  0.99%
 26	  91	  1.22%
 27	  55	  0.74%
 28	  77	  1.03%
 29	  53	  0.71%
 30	 208	  2.79%
 31	  38	  0.51%
 32	 106	  1.42%
 33	  39	  0.52%
 34	  54	  0.73%
 35	  78	  1.05%
 36	  36	  0.48%
 37	  35	  0.47%
 38	  28	  0.38%
 39	  18	  0.24%
 40	  13	  0.17%
 41	  21	  0.28%
 42	   8	  0.11%
 43	  10	  0.13%
 44	  13	  0.17%
 45	   0	  0.00%
 46	   0	  0.00%
 47	   0	  0.00%
 48	   0	  0.00%
 49	   0	  0.00%
 50	   0	  0.00%
 51	   0	  0.00%
 52	   0	  0.00%
 53	   0	  0.00%
 54	   0	  0.00%
 55	   0	  0.00%
 56	   0	  0.00%
 57	   0	  0.00%
 58	   0	  0.00%
 59	   0	  0.00%
 60	   0	  0.00%
 61	   0	  0.00%
 62	   0	  0.00%
 63	   0	  0.00%
 64	   0	  0.00%
 65	   0	  0.00%
 66	   0	  0.00%
 67	   0	  0.00%
 68	   0	  0.00%
 69	   0	  0.00%
 70	   0	  0.00%
 71	   0	  0.00%
 72	   0	  0.00%
 73	   0	  0.00%
 74	   0	  0.00%
 75	   0	  0.00%
 76	 399	  5.36%
7443 reads passed initial QC


criterion=sequence-density
sequence-density=53.24
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=7
prefix-density=52.83
prefix-fanout=1.0
sequence=GCTGTCGGTTGCTGTCGGTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=11
fanout-score=3951.00
fanout-score-rank=1
prefix-density=53.08
prefix-fanout=1.0
sequence=TTGCTGTCGGTC
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 GCTGTCGGTTGCTGTCGGTT -o SRR11699487 -
Input file:	STDIN
trimmed:	SRR11699487-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	GCTGTCGGTTGCTGTCGGTT
-- 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
Fri Jun 20 08:58:05 2025 >> started

Fri Jun 20 08:58:05 2025 >> done (0.006s)
7167 reads processed; of these:
  98 ( 1.37%) short reads filtered out after trimming by size control
3843 (53.62%) empty reads filtered out after trimming by size control
3226 (45.01%) reads available; of these:
  16 ( 0.50%) trimmed reads available after processing
3210 (99.50%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  89	  2.76%
 19	 294	  9.11%
 20	 300	  9.30%
 21	 190	  5.89%
 22	 715	 22.16%
 23	 120	  3.72%
 24	 127	  3.94%
 25	  70	  2.17%
 26	  89	  2.76%
 27	  55	  1.70%
 28	  71	  2.20%
 29	  53	  1.64%
 30	 202	  6.26%
 31	  36	  1.12%
 32	 102	  3.16%
 33	  36	  1.12%
 34	  52	  1.61%
 35	  79	  2.45%
 36	  32	  0.99%
 37	  34	  1.05%
 38	  26	  0.81%
 39	  17	  0.53%
 40	  13	  0.40%
 41	  18	  0.56%
 42	   8	  0.25%
 43	   9	  0.28%
 44	  13	  0.40%
 45	   0	  0.00%
 46	   0	  0.00%
 47	   0	  0.00%
 48	   0	  0.00%
 49	   0	  0.00%
 50	   0	  0.00%
 51	   0	  0.00%
 52	   0	  0.00%
 53	   0	  0.00%
 54	   0	  0.00%
 55	   0	  0.00%
 56	   0	  0.00%
 57	   0	  0.00%
 58	   0	  0.00%
 59	   0	  0.00%
 60	   0	  0.00%
 61	   0	  0.00%
 62	   0	  0.00%
 63	   0	  0.00%
 64	   0	  0.00%
 65	   0	  0.00%
 66	   0	  0.00%
 67	   0	  0.00%
 68	   0	  0.00%
 69	   0	  0.00%
 70	   0	  0.00%
 71	   0	  0.00%
 72	   0	  0.00%
 73	   0	  0.00%
 74	   0	  0.00%
 75	   0	  0.00%
 76	 376	 11.66%


criterion=sequence-density
sequence-density=23.56
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=6
prefix-density=0.00
prefix-fanout=1.0
sequence=AGATCGGAAGAGCACACGTCTC


criterion=fanout-score
sequence-density=0.11
sequence-density-rank=9
fanout-score=192.50
fanout-score-rank=1
prefix-density=21.99
prefix-fanout=1.0
sequence=AGCACACGTCTT
                                 Started job on |	Jun 20 08:58:22
                             Started mapping on |	Jun 20 08:58:26
                                    Finished on |	Jun 20 08:58:26
       Mapping speed, Million of reads per hour |	inf

                          Number of input reads |	3502
                      Average input read length |	30
                                    UNIQUE READS:
                   Uniquely mapped reads number |	598
                        Uniquely mapped reads % |	17.08%
                          Average mapped length |	18.94
                       Number of splices: Total |	26
            Number of splices: Annotated (sjdb) |	2
                       Number of splices: GT/AG |	25
                       Number of splices: GC/AG |	1
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	0
                      Mismatch rate per base, % |	1.62%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.00
                        Insertion rate per base |	0.00%
                       Insertion average length |	0.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1103
             % of reads mapped to multiple loci |	31.50%
        Number of reads mapped to too many loci |	426
             % of reads mapped to too many loci |	12.16%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	26.16%
                     % of reads unmapped: other |	13.11%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1801	1801	1801
N_multimapping	1103	1103	1103
N_noFeature	546	575	569
N_ambiguous	0	0	0
UnstrandedReadsAssigned:52 PositiveStrandReadsAssigned:23 NegativeStrandReadsAssigned:29
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=20 echo kmer=19
SRR11699487 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: SRR11699487-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,502 reads, 347 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 394 rounds

  72540 SRR11699487.ke.tsv
  44303 SRR11699487.se.tsv
 116843 total
==> SRR11699487.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	0	0
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

==> SRR11699487.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699487 completed mapping pipeline successfully
