Starting /dee2/code/volunteer_pipeline.sh SRR11699278
    current disk space = 2469679247360
    free memory = 1581674688 
SRR11699278 SRAfilesize
7f782e5a314b9c256883cf67d4d722e7  SRR11699278.sra
SRR11699278.sra file validated
SRR11699278 is single end
SRR11699278 is conventional basespace
SRR11699278 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699278_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	31.2205	32.0	32.0	32.0	32.0	32.0
2	31.299	32.0	32.0	32.0	32.0	32.0
3	31.5095	32.0	32.0	32.0	32.0	32.0
4	31.46475	32.0	32.0	32.0	32.0	32.0
5	31.5455	32.0	32.0	32.0	32.0	32.0
6	35.061	36.0	36.0	36.0	36.0	36.0
7	35.08025	36.0	36.0	36.0	36.0	36.0
8	35.11475	36.0	36.0	36.0	36.0	36.0
9	34.9595	36.0	36.0	36.0	36.0	36.0
10-11	35.093375	36.0	36.0	36.0	36.0	36.0
12-13	35.08925	36.0	36.0	36.0	36.0	36.0
14-15	35.055625	36.0	36.0	36.0	36.0	36.0
16-17	35.122625	36.0	36.0	36.0	36.0	36.0
18-19	35.198875	36.0	36.0	36.0	36.0	36.0
20-21	35.034875	36.0	36.0	36.0	36.0	36.0
22-23	34.982625	36.0	36.0	36.0	36.0	36.0
24-25	35.00325	36.0	36.0	36.0	36.0	36.0
26-27	34.858999999999995	36.0	36.0	36.0	36.0	36.0
28-29	34.935874999999996	36.0	36.0	36.0	36.0	36.0
30-31	34.94425	36.0	36.0	36.0	36.0	36.0
32-33	34.830875	36.0	36.0	36.0	34.0	36.0
34-35	34.963625	36.0	36.0	36.0	36.0	36.0
36-37	34.98025	36.0	36.0	36.0	36.0	36.0
38-39	34.89575	36.0	36.0	36.0	36.0	36.0
40-41	34.881625	36.0	36.0	36.0	34.0	36.0
42-43	34.86825	36.0	36.0	36.0	34.0	36.0
44-45	34.84225	36.0	36.0	36.0	32.0	36.0
46-47	34.871375	36.0	36.0	36.0	36.0	36.0
48-49	34.47387500000001	36.0	36.0	36.0	32.0	36.0
50-51	33.806125	36.0	36.0	36.0	29.5	36.0
52-53	33.661875	36.0	36.0	36.0	29.5	36.0
54-55	33.17075	36.0	36.0	36.0	17.5	36.0
56-57	32.894125	36.0	34.0	36.0	17.5	36.0
58-59	32.885999999999996	36.0	32.0	36.0	17.5	36.0
60-61	33.221625	36.0	36.0	36.0	20.5	36.0
62-63	33.071625	36.0	36.0	36.0	20.5	36.0
64-65	33.062	36.0	32.0	36.0	27.0	36.0
66-67	32.439375	36.0	32.0	36.0	24.0	36.0
68-69	32.8635	36.0	32.0	36.0	27.0	36.0
70-71	33.5115	36.0	36.0	36.0	27.0	36.0
72-73	33.435125	36.0	36.0	36.0	27.0	36.0
74-75	33.847	36.0	36.0	36.0	32.0	36.0
76	31.0325	36.0	32.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
18	1.0
19	0.0
20	0.0
21	2.0
22	2.0
23	3.0
24	8.0
25	13.0
26	26.0
27	49.0
28	71.0
29	80.0
30	116.0
31	130.0
32	239.0
33	385.0
34	1059.0
35	1816.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	22.075	35.425000000000004	18.925	23.575
2	23.45	30.525000000000002	23.95	22.075
3	27.3	31.75	18.25	22.7
4	31.2	30.2	19.05	19.55
5	23.375	28.749999999999996	21.4	26.474999999999998
6	25.45	28.575	26.25	19.725
7	27.825	34.775	19.725	17.675
8	22.025	27.150000000000002	29.825000000000003	21.0
9	26.55	33.25	18.8	21.4
10-11	30.55	28.475	22.162499999999998	18.8125
12-13	22.7125	24.8625	24.975	27.450000000000003
14-15	31.3125	35.949999999999996	18.1125	14.625
16-17	23.775	29.7	28.175	18.35
18-19	36.1875	28.5625	19.375	15.875
20-21	28.425	37.5	18.2	15.875
22-23	33.5125	38.775	11.1	16.6125
24-25	30.4375	41.05	11.225	17.2875
26-27	31.075000000000003	34.150000000000006	12.475	22.3
28-29	31.337500000000002	31.574999999999996	12.1625	24.925
30-31	32.2875	36.15	8.875	22.6875
32-33	25.900000000000002	37.012499999999996	12.0625	25.025
34-35	28.275	28.499999999999996	15.0	28.225
36-37	21.05	32.6625	12.962499999999999	33.324999999999996
38-39	19.0625	29.6375	17.5625	33.7375
40-41	17.5375	26.724999999999998	20.0875	35.65
42-43	21.912499999999998	23.549999999999997	23.7	30.837500000000002
44-45	16.8	28.425	21.4375	33.3375
46-47	17.625	28.4125	20.225	33.7375
48-49	14.224999999999998	27.375	22.95	35.449999999999996
50-51	12.975	24.2375	29.549999999999997	33.2375
52-53	14.3625	23.6625	30.675	31.3
54-55	14.674999999999999	23.65	32.625	29.049999999999997
56-57	14.0875	21.9625	33.25	30.7
58-59	15.575	19.3125	35.975	29.1375
60-61	12.425	19.8125	40.575	27.187499999999996
62-63	15.6125	16.975	40.2125	27.200000000000003
64-65	14.1375	15.0875	38.6125	32.1625
66-67	19.075	9.6125	39.287499999999994	32.025
68-69	18.462500000000002	9.9125	40.325	31.3
70-71	19.7	10.6625	42.325	27.3125
72-73	21.099999999999998	11.1625	38.025	29.7125
74-75	21.375	10.6375	35.65	32.337500000000006
76	15.725	13.100000000000001	44.0	27.175
>>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	0.5
25	1.0
26	0.5
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.5
37	1.0
38	1.5
39	4.0
40	12.5
41	36.0
42	53.0
43	76.0
44	177.5
45	332.5
46	409.0
47	727.0
48	795.5
49	516.5
50	487.0
51	448.0
52	361.0
53	233.0
54	153.0
55	123.0
56	85.5
57	46.5
58	15.0
59	9.0
60	4.5
61	3.5
62	1.0
63	1.0
64	0.5
65	0.5
66	0.5
67	0.0
68	0.0
69	0.0
70	0.0
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	0.0
92	0.0
93	1.0
94	1.0
95	0.0
96	0.0
97	0.0
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	63.14999999999999
#Duplication Level	Percentage of deduplicated	Percentage of total
1	89.86539984164688	56.75
2	5.186064924782265	6.550000000000001
3	1.583531274742676	3.0
4	0.6730007917656373	1.7000000000000002
5	0.4750593824228029	1.5
6	0.3167062549485352	1.2
7	0.435471100554236	1.925
8	0.0791765637371338	0.4
9	0.1979414093428345	1.125
>10	0.9501187648456058	13.8
>50	0.1979414093428345	7.55
>100	0.0395882818685669	4.5
>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	180	4.5	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	74	1.8499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAT	60	1.5	TruSeq Adapter, Index 9 (100% over 36bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATT	59	1.4749999999999999	TruSeq Adapter, Index 21 (97% over 37bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAT	56	1.4000000000000001	TruSeq Adapter, Index 9 (100% over 36bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTCTAT	53	1.325	TruSeq Adapter, Index 21 (97% over 38bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	42	1.05	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	40	1.0	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	40	1.0	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	38	0.95	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTCTA	37	0.9249999999999999	TruSeq Adapter, Index 21 (97% over 38bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	31	0.775	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTCT	29	0.7250000000000001	TruSeq Adapter, Index 21 (97% over 38bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	27	0.675	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGA	23	0.575	TruSeq Adapter, Index 7 (97% over 35bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGA	20	0.5	TruSeq Adapter, Index 7 (97% over 35bp)
ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTC	20	0.5	TruSeq Adapter, Index 21 (97% over 38bp)
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTCTATC	18	0.44999999999999996	TruSeq Adapter, Index 21 (97% over 38bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAT	14	0.35000000000000003	TruSeq Adapter, Index 9 (100% over 36bp)
GGGCCTGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAT	13	0.325	TruSeq Adapter, Index 9 (100% over 36bp)
CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	12	0.3	No Hit
TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGA	11	0.27499999999999997	TruSeq Adapter, Index 7 (97% over 35bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTCTATCTC	9	0.22499999999999998	TruSeq Adapter, Index 21 (97% over 38bp)
AGATAAAAGGCTGACGCGGGCTCTAGATCGGAAGAGCACACGTCTGAACT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AAATCATGTGGGCTTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATCGGAAGAGCACACGTCTGAACTCCAGTCACGATT	9	0.22499999999999998	TruSeq Adapter, Index 9 (97% over 36bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	8	0.2	No Hit
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTCTATCT	7	0.17500000000000002	TruSeq Adapter, Index 21 (97% over 38bp)
AAAGGCTGACGCGGGCTCTAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTCTATCTCGTATG	7	0.17500000000000002	TruSeq Adapter, Index 21 (97% over 38bp)
CGACACGACTCTCGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCACCAGTGGTCTAGTGGTAGAATAAGATCGGAAGAGCACACGTCTGAAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	6	0.15	No Hit
ACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATTCT	6	0.15	TruSeq Adapter, Index 21 (97% over 38bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CGACACGACTCTCGGCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
CACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CACGACTCTCGGCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	5	0.125	No Hit
TCCACAGGCTTTCTTGAACTGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
CCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATT	5	0.125	TruSeq Adapter, Index 21 (97% over 37bp)
TACCTGGTTGATCCTGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CCCGGCTGGTGCACCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
>>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	0.2	0.0	0.0	0.0	0.0
2	0.275	0.0	0.0	0.0	0.0
3	0.425	0.0	0.0	0.0	0.0
4	0.6	0.0	0.0	0.0	0.0
5	0.775	0.0	0.0	0.0	0.0
6	1.075	0.0	0.0	0.0	0.0
7	1.45	0.0	0.0	0.0	0.0
8	2.375	0.0	0.0	0.0	0.0
9	4.5	0.0	0.0	0.0	0.0
10	6.225	0.0	0.0	0.0	0.0
11	8.25	0.0	0.0	0.0	0.0
12	10.55	0.0	0.0	0.0	0.0
13	14.2	0.0	0.0	0.0	0.0
14	20.475	0.0	0.0	0.0	0.0
15	25.025	0.0	0.0	0.0	0.0
16	28.575	0.0	0.0	0.0	0.0
17	34.075	0.0	0.0	0.0	0.0
18	39.375	0.0	0.0	0.0	0.0
19	42.525	0.0	0.0	0.0	0.0
20	47.375	0.0	0.0	0.0	0.0
21	52.15	0.0	0.0	0.0	0.0
22	58.275	0.0	0.0	0.0	0.0
23	67.275	0.0	0.0	0.0	0.0
24	70.8	0.0	0.0	0.0	0.0
25	78.8	0.0	0.0	0.0	0.0
26	82.2	0.0	0.0	0.0	0.0
27	83.8	0.0	0.0	0.0	0.0
28	86.275	0.0	0.0	0.0	0.0
29	87.225	0.0	0.0	0.0	0.0
30	88.5	0.0	0.0	0.0	0.0
31	90.0	0.0	0.0	0.0	0.0
32	91.025	0.0	0.0	0.0	0.0
33	91.775	0.0	0.0	0.0	0.0
34	92.2	0.0	0.0	0.0	0.0
35	93.05	0.0	0.0	0.0	0.0
36	93.75	0.0	0.0	0.0	0.0
37	94.55	0.0	0.0	0.0	0.0
38	94.725	0.0	0.0	0.0	0.0
39	94.875	0.0	0.0	0.0	0.0
40	94.875	0.0	0.0	0.0	0.0
41	94.975	0.0	0.0	0.0	0.0
42	95.025	0.0	0.0	0.0	0.0
43	95.075	0.0	0.0	0.0	0.0
44	95.1	0.0	0.0	0.0	0.0
45	95.1	0.0	0.0	0.0	0.0
46	95.1	0.0	0.0	0.0	0.0
47	95.1	0.0	0.0	0.0	0.0
48	95.1	0.0	0.0	0.0	0.0
49	95.1	0.0	0.0	0.0	0.0
50	95.1	0.0	0.0	0.0	0.0
51	95.1	0.0	0.0	0.0	0.0
52	95.1	0.0	0.0	0.0	0.0
53	95.1	0.0	0.0	0.0	0.0
54	95.1	0.0	0.0	0.0	0.0
55	95.1	0.0	0.0	0.0	0.0
56	95.1	0.0	0.0	0.0	0.0
57	95.1	0.0	0.0	0.0	0.0
58	95.1	0.0	0.0	0.0	0.0
59	95.1	0.0	0.0	0.0	0.0
60	95.1	0.0	0.0	0.0	0.0
61	95.1	0.0	0.0	0.0	0.0
62	95.1	0.0	0.0	0.0	0.0
63	95.1	0.0	0.0	0.0	0.0
64	95.1	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TTGTAGT	30	7.878043E-8	70.00001	5
GACACGA	15	0.0020658788	70.00001	1
TGTAGTC	30	7.878043E-8	70.00001	6
GTCTAGC	15	0.0020658788	70.00001	10
CGTTGTA	30	7.878043E-8	70.00001	3
GTTGTAG	30	7.878043E-8	70.00001	4
TGGTCAG	20	7.003785E-5	70.0	17
TCAGGAT	20	7.003785E-5	70.0	20
TAACGAA	25	2.3570374E-6	70.0	2
CCGTTGT	25	2.3570374E-6	70.0	2
TAGTCTA	25	2.3570374E-6	70.0	8
GGTCAGG	20	7.003785E-5	70.0	18
CTAACGA	25	2.3570374E-6	70.0	1
TCCGTTG	25	2.3570374E-6	70.0	1
AGTCTAG	25	2.3570374E-6	70.0	9
CAGGATA	20	7.003785E-5	70.0	21
GTCAGGA	20	7.003785E-5	70.0	19
GTAGTCT	25	2.3570374E-6	70.0	7
ACACGAC	20	0.0064587677	52.5	2
GAACGAA	50	1.4254966E-4	35.0	6
>>END_MODULE
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342069 READS because READLEN < 1
Read 342069 spots for SRR11699278.sra
Written 342069 spots for SRR11699278.sra
Rejected 342078 READS because READLEN < 1
Read 342078 spots for SRR11699278.sra
Written 342078 spots for SRR11699278.sra
SRR ids: ['SRR11699278.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_i2b4u87b
SRR11699278.sra spots: 6841389
blocks: [[1, 342069], [342070, 684138], [684139, 1026207], [1026208, 1368276], [1368277, 1710345], [1710346, 2052414], [2052415, 2394483], [2394484, 2736552], [2736553, 3078621], [3078622, 3420690], [3420691, 3762759], [3762760, 4104828], [4104829, 4446897], [4446898, 4788966], [4788967, 5131035], [5131036, 5473104], [5473105, 5815173], [5815174, 6157242], [6157243, 6499311], [6499312, 6841389]]
SRR11699278 file size 1300634
SRR11699278 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 SRR11699278 SRR11699278_1.fastq
Input file:	SRR11699278_1.fastq
trimmed:	SRR11699278-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 08:06:35 2025 >> started

Wed Jun 18 08:06:38 2025 >> done (2.894s)
6841389 reads processed; of these:
2967458 (43.38%) short reads filtered out after trimming by size control
  10280 ( 0.15%) empty reads filtered out after trimming by size control
3863651 (56.47%) reads available; of these:
3839940 (99.39%) trimmed reads available after processing
  23711 ( 0.61%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 250532	  6.48%
 19	 331925	  8.59%
 20	 316492	  8.19%
 21	 400090	 10.36%
 22	 661494	 17.12%
 23	 234043	  6.06%
 24	 534941	 13.85%
 25	 212472	  5.50%
 26	 127413	  3.30%
 27	 160944	  4.17%
 28	  81571	  2.11%
 29	  75679	  1.96%
 30	 118271	  3.06%
 31	  61842	  1.60%
 32	  56762	  1.47%
 33	  42288	  1.09%
 34	  39908	  1.03%
 35	  51405	  1.33%
 36	  36977	  0.96%
 37	  14995	  0.39%
 38	   8655	  0.22%
 39	   7127	  0.18%
 40	   4610	  0.12%
 41	   4216	  0.11%
 42	   2465	  0.06%
 43	   1745	  0.05%
 44	   1078	  0.03%
 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	  23711	  0.61%
3863651 reads passed initial QC


criterion=sequence-density
sequence-density=3.89
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=13
prefix-density=0.02
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATA


criterion=fanout-score
sequence-density=0.24
sequence-density-rank=14
fanout-score=14.31
fanout-score-rank=1
prefix-density=3.37
prefix-fanout=1.0
sequence=GTCTAGCTGGTTAGGATA
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 18 08:07:01
                             Started mapping on |	Jun 18 08:07:01
                                    Finished on |	Jun 18 08:07:21
       Mapping speed, Million of reads per hour |	695.46

                          Number of input reads |	3863651
                      Average input read length |	23
                                    UNIQUE READS:
                   Uniquely mapped reads number |	474651
                        Uniquely mapped reads % |	12.29%
                          Average mapped length |	22.11
                       Number of splices: Total |	10283
            Number of splices: Annotated (sjdb) |	4790
                       Number of splices: GT/AG |	9749
                       Number of splices: GC/AG |	452
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	81
                      Mismatch rate per base, % |	1.09%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.40
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.30
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	551573
             % of reads mapped to multiple loci |	14.28%
        Number of reads mapped to too many loci |	680594
             % of reads mapped to too many loci |	17.62%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	3.09%
                     % of reads unmapped: other |	52.73%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2837427	2837427	2837427
N_multimapping	551573	551573	551573
N_noFeature	376966	393640	454525
N_ambiguous	3508	38	28
UnstrandedReadsAssigned:94177 PositiveStrandReadsAssigned:80973 NegativeStrandReadsAssigned:20098
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=20 echo kmer=19
SRR11699278 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: SRR11699278-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,863,651 reads, 791,463 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 862 rounds

  72540 SRR11699278.ke.tsv
  44303 SRR11699278.se.tsv
 116843 total
==> SRR11699278.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	5	2.02562
Zm00001eb323640_T001	3273	3174	0	0
Zm00001eb314140_T001	893	794	0	0
Zm00001eb080260_T001	3529	3430	0	0
Zm00001eb026490_T001	2433	2334	1	0.575923
Zm00001eb026490_T002	2229	2130	0	0
Zm00001eb026490_T003	2220	2121	0	0
Zm00001eb281360_T001	2412	2313	1	0.581152

==> SRR11699278.se.tsv <==
Zm00001eb015280	2
Zm00001eb000610	0
Zm00001eb033210	1
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699278 completed mapping pipeline successfully
