Starting /dee2/code/volunteer_pipeline.sh SRR11699301
    current disk space = 2467938377728
    free memory = 1043531776 
SRR11699301 SRAfilesize
cb5ba4e06e47b275669ee1556d6122a2  SRR11699301.sra
SRR11699301.sra file validated
SRR11699301 is single end
SRR11699301 is conventional basespace
SRR11699301 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699301_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	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.435	32.0	32.0	32.0	32.0	32.0
2	31.42025	32.0	32.0	32.0	32.0	32.0
3	31.552	32.0	32.0	32.0	32.0	32.0
4	31.50625	32.0	32.0	32.0	32.0	32.0
5	31.59325	32.0	32.0	32.0	32.0	32.0
6	35.067	36.0	36.0	36.0	36.0	36.0
7	35.12025	36.0	36.0	36.0	36.0	36.0
8	35.21625	36.0	36.0	36.0	36.0	36.0
9	35.16025	36.0	36.0	36.0	36.0	36.0
10-11	35.2085	36.0	36.0	36.0	36.0	36.0
12-13	35.208875	36.0	36.0	36.0	36.0	36.0
14-15	35.162125	36.0	36.0	36.0	36.0	36.0
16-17	35.23625	36.0	36.0	36.0	36.0	36.0
18-19	35.31975	36.0	36.0	36.0	36.0	36.0
20-21	35.145624999999995	36.0	36.0	36.0	36.0	36.0
22-23	35.11	36.0	36.0	36.0	36.0	36.0
24-25	35.14125	36.0	36.0	36.0	36.0	36.0
26-27	34.9765	36.0	36.0	36.0	36.0	36.0
28-29	35.052	36.0	36.0	36.0	36.0	36.0
30-31	35.028125	36.0	36.0	36.0	36.0	36.0
32-33	35.044125	36.0	36.0	36.0	36.0	36.0
34-35	35.051249999999996	36.0	36.0	36.0	36.0	36.0
36-37	35.039375	36.0	36.0	36.0	36.0	36.0
38-39	34.957750000000004	36.0	36.0	36.0	36.0	36.0
40-41	34.993125	36.0	36.0	36.0	36.0	36.0
42-43	34.983000000000004	36.0	36.0	36.0	36.0	36.0
44-45	34.877624999999995	36.0	36.0	36.0	36.0	36.0
46-47	34.901250000000005	36.0	36.0	36.0	36.0	36.0
48-49	34.733125	36.0	36.0	36.0	34.0	36.0
50-51	34.39875	36.0	36.0	36.0	32.0	36.0
52-53	34.287499999999994	36.0	36.0	36.0	32.0	36.0
54-55	33.881249999999994	36.0	36.0	36.0	29.5	36.0
56-57	33.0635	36.0	36.0	36.0	21.0	36.0
58-59	32.452125	36.0	32.0	36.0	14.0	36.0
60-61	32.0135	36.0	32.0	36.0	14.0	36.0
62-63	31.599125	36.0	32.0	36.0	14.0	36.0
64-65	31.05925	36.0	32.0	36.0	14.0	36.0
66-67	29.967875	36.0	27.0	36.0	14.0	36.0
68-69	29.6755	36.0	27.0	36.0	14.0	36.0
70-71	29.796875	36.0	27.0	36.0	14.0	36.0
72-73	29.936625	36.0	27.0	36.0	14.0	36.0
74-75	29.908375	36.0	24.0	36.0	14.0	36.0
76	25.7495	32.0	14.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	2.0
22	2.0
23	5.0
24	11.0
25	21.0
26	47.0
27	42.0
28	83.0
29	103.0
30	185.0
31	274.0
32	390.0
33	499.0
34	1118.0
35	1218.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	24.025	28.499999999999996	24.75	22.725
2	23.525	28.000000000000004	25.05	23.425
3	26.025	32.05	18.025	23.9
4	26.325	33.35	18.3	22.025
5	22.425	25.8	25.575	26.200000000000003
6	25.474999999999998	28.449999999999996	25.374999999999996	20.7
7	32.95	31.424999999999997	18.175	17.45
8	23.599999999999998	24.8	29.25	22.35
9	24.875	31.6	20.424999999999997	23.1
10-11	30.337500000000002	27.05	24.5375	18.075
12-13	23.4875	22.3375	24.9125	29.262500000000003
14-15	29.3875	35.4125	18.725	16.475
16-17	22.8625	24.9875	30.7875	21.3625
18-19	35.225	24.4875	22.75	17.5375
20-21	24.587500000000002	32.175	24.5125	18.725
22-23	31.324999999999996	36.925000000000004	15.2375	16.5125
24-25	28.000000000000004	38.4	16.3125	17.2875
26-27	28.225	31.7625	17.6125	22.400000000000002
28-29	30.75	27.6875	16.5875	24.975
30-31	33.887499999999996	34.5375	10.7125	20.8625
32-33	28.487499999999997	38.574999999999996	11.737499999999999	21.2
34-35	30.312499999999996	30.2	14.575	24.9125
36-37	27.175	33.6625	11.35	27.8125
38-39	23.2125	34.9625	13.175	28.65
40-41	25.5625	29.775000000000002	15.925	28.7375
42-43	27.625	25.85	20.225	26.3
44-45	21.275	33.95	16.0	28.775000000000002
46-47	21.25	32.9125	14.4875	31.35
48-49	15.0875	29.2875	15.8875	39.7375
50-51	15.037500000000001	28.812500000000004	16.7375	39.4125
52-53	17.349999999999998	26.875	17.05	38.725
54-55	13.450000000000001	29.6875	17.7875	39.074999999999996
56-57	9.9	27.975	16.375	45.75
58-59	9.0125	30.65	14.099999999999998	46.2375
60-61	9.65	27.3125	18.1875	44.85
62-63	9.049999999999999	28.475	19.675	42.8
64-65	9.325	23.875	23.3625	43.4375
66-67	11.837499999999999	19.0	27.375	41.7875
68-69	12.687499999999998	20.674999999999997	27.55	39.0875
70-71	15.85	20.5375	29.15	34.4625
72-73	14.1125	18.55	28.262500000000003	39.074999999999996
74-75	18.0625	12.5125	28.9125	40.5125
76	12.325	14.149999999999999	34.325	39.2
>>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	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.5
37	1.0
38	1.0
39	1.5
40	5.0
41	9.5
42	11.0
43	21.0
44	55.0
45	109.0
46	139.0
47	177.0
48	339.5
49	642.0
50	820.0
51	673.5
52	527.5
53	498.5
54	469.0
55	380.0
56	229.0
57	130.5
58	94.0
59	92.5
60	62.5
61	21.5
62	9.0
63	6.5
64	4.0
65	4.0
66	3.5
67	3.0
68	2.0
69	1.0
70	0.5
71	0.0
72	0.0
73	0.0
74	0.0
75	0.0
76	0.0
77	0.0
78	0.0
79	0.0
80	0.0
81	0.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.5
92	1.0
93	1.0
94	0.5
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	67.27499999999999
#Duplication Level	Percentage of deduplicated	Percentage of total
1	89.00037160906726	59.875
2	5.2396878483835	7.049999999999999
3	1.932367149758454	3.9
4	0.966183574879227	2.6
5	0.8547008547008548	2.875
6	0.33444816053511706	1.35
7	0.29728725380899296	1.4000000000000001
8	0.11148272017837235	0.6
9	0.11148272017837235	0.675
>10	1.0405053883314752	12.875
>50	0.07432181345224824	3.3000000000000003
>100	0.03716090672612412	3.5000000000000004
>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	140	3.5000000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC	77	1.925	No Hit
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	55	1.375	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	49	1.225	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	30	0.75	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	30	0.75	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAC	26	0.65	TruSeq Adapter, Index 7 (97% over 35bp)
TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	25	0.625	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	23	0.575	No Hit
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGTTGTAGTCTAGCTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	22	0.5499999999999999	No Hit
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAC	15	0.375	TruSeq Adapter, Index 7 (97% over 35bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACA	14	0.35000000000000003	TruSeq Adapter, Index 7 (97% over 37bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACACCAT	14	0.35000000000000003	TruSeq Adapter, Index 7 (97% over 37bp)
GCGAGCGTAGTTCAGTGGTAAAACATCTCCTTGCCAAGGAGAGATCGGAA	12	0.3	No Hit
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT	11	0.27499999999999997	No Hit
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACACC	11	0.27499999999999997	TruSeq Adapter, Index 7 (97% over 37bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	11	0.27499999999999997	No Hit
GCGACCCCAGGTCAGTCGGGACTAGATCGGAAGAGCACACGTCTGAACTC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCAC	11	0.27499999999999997	No Hit
ATCCTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGA	9	0.22499999999999998	No Hit
GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC	9	0.22499999999999998	No Hit
CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACACCATC	8	0.2	TruSeq Adapter, Index 7 (97% over 37bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACACCA	8	0.2	TruSeq Adapter, Index 7 (97% over 37bp)
CGACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GCCGCCATGGTGAAATTGGTAGACACGCTGCTCTTAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGAAGATCGG	7	0.17500000000000002	No Hit
CGACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCAGATCGGAAG	7	0.17500000000000002	No Hit
GCGACCCCAGGTCAGTCGGGACTACCCGCTAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
TCCGTTGTAGTCTAGTTGGTCAGGATACTCAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	6	0.15	No Hit
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAAAAGGCTGACGCGGGCTCTAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTAGATCGGAAGAGCA	6	0.15	No Hit
GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACAC	6	0.15	TruSeq Adapter, Index 7 (97% over 37bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GCGACCCCAGGTCAGTCGGGAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	6	0.15	No Hit
GCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACAC	5	0.125	No Hit
CTGCACTGCCTCTTCCCTGGCAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGTTGTAGTCTAGTTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAATCAGATCGGAAGAG	5	0.125	No Hit
TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	5	0.125	TruSeq Adapter, Index 7 (100% over 35bp)
TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA	5	0.125	No Hit
GCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAG	5	0.125	No Hit
CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA	5	0.125	TruSeq Adapter, Index 7 (100% over 35bp)
GATCCAGCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACAC	5	0.125	TruSeq Adapter, Index 7 (97% over 37bp)
AGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACA	5	0.125	No Hit
TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
TCCACAGGCTTTCTTGAACTGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CTAACGAACGAACGATTTGAATAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTAGATCGGAAGAGC	5	0.125	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA	5	0.125	No Hit
GACACGACTCTCGGCAACGGATATCTCAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTAGATCGGAAGAGCACAC	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	0.125	0.0	0.0	0.0	0.0
3	0.125	0.0	0.0	0.0	0.0
4	0.15	0.0	0.0	0.0	0.0
5	0.25	0.0	0.0	0.0	0.0
6	0.325	0.0	0.0	0.0	0.0
7	0.375	0.0	0.0	0.0	0.0
8	0.675	0.0	0.0	0.0	0.0
9	1.2	0.0	0.0	0.0	0.0
10	1.625	0.0	0.0	0.0	0.0
11	2.075	0.0	0.0	0.0	0.0
12	2.725	0.0	0.0	0.0	0.0
13	3.5	0.0	0.0	0.0	0.0
14	5.65	0.0	0.0	0.0	0.0
15	7.1	0.0	0.0	0.0	0.0
16	8.5	0.0	0.0	0.0	0.0
17	11.425	0.0	0.0	0.0	0.0
18	14.075	0.0	0.0	0.0	0.0
19	16.35	0.0	0.0	0.0	0.0
20	19.0	0.0	0.0	0.0	0.0
21	22.025	0.0	0.0	0.0	0.0
22	28.75	0.0	0.0	0.0	0.0
23	36.875	0.0	0.0	0.0	0.0
24	40.55	0.0	0.0	0.0	0.0
25	48.9	0.0	0.0	0.0	0.0
26	52.75	0.0	0.0	0.0	0.0
27	55.1	0.0	0.0	0.0	0.0
28	57.625	0.0	0.0	0.0	0.0
29	60.225	0.0	0.0	0.0	0.0
30	62.475	0.0	0.0	0.0	0.0
31	67.0	0.0	0.0	0.0	0.0
32	69.9	0.0	0.0	0.0	0.0
33	72.075	0.0	0.0	0.0	0.0
34	74.75	0.0	0.0	0.0	0.0
35	77.175	0.0	0.0	0.0	0.0
36	81.925	0.0	0.0	0.0	0.0
37	83.975	0.0	0.0	0.0	0.0
38	85.8	0.0	0.0	0.0	0.0
39	87.35	0.0	0.0	0.0	0.0
40	88.7	0.0	0.0	0.0	0.0
41	90.1	0.0	0.0	0.0	0.0
42	91.525	0.0	0.0	0.0	0.0
43	92.325	0.0	0.0	0.0	0.0
44	93.2	0.0	0.0	0.0	0.0
45	93.675	0.0	0.0	0.0	0.0
46	94.075	0.0	0.0	0.0	0.0
47	94.4	0.0	0.0	0.0	0.0
48	94.55	0.0	0.0	0.0	0.0
49	94.9	0.0	0.0	0.0	0.0
50	95.0	0.0	0.0	0.0	0.0
51	95.175	0.0	0.0	0.0	0.0
52	95.225	0.0	0.0	0.0	0.0
53	95.275	0.0	0.0	0.0	0.0
54	95.3	0.0	0.0	0.0	0.0
55	95.4	0.0	0.0	0.0	0.0
56	95.475	0.0	0.0	0.0	0.0
57	95.5	0.0	0.0	0.0	0.0
58	95.5	0.0	0.0	0.0	0.0
59	95.525	0.0	0.0	0.0	0.0
60	95.525	0.0	0.0	0.0	0.0
61	95.525	0.0	0.0	0.0	0.0
62	95.55	0.0	0.0	0.0	0.0
63	95.55	0.0	0.0	0.0	0.0
64	95.55	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CGCCCTG	15	0.0020658788	70.00001	29
TTCAATT	15	0.0020658788	70.00001	11
CCGCCCT	15	0.0020658788	70.00001	28
CACCGCC	15	0.0020658788	70.00001	26
ACCGCCC	15	0.0020658788	70.00001	27
CAATTGG	15	0.0020658788	70.00001	13
TCAATTG	15	0.0020658788	70.00001	12
GTTCAAT	15	0.0020658788	70.00001	10
AGCACCG	15	0.0020658788	70.00001	24
GCACCGC	15	0.0020658788	70.00001	25
AGTTCAA	15	0.0020658788	70.00001	9
AATTGGT	15	0.0020658788	70.00001	14
TGGTCAG	25	2.3570374E-6	70.0	17
TTGTAGT	25	2.3570374E-6	70.0	5
ATTGGTC	20	7.003785E-5	70.0	15
GGTCAGA	20	7.003785E-5	70.0	18
GATTGTA	20	7.003785E-5	70.0	3
TAGTTCA	20	7.003785E-5	70.0	8
CAGAGCA	20	7.003785E-5	70.0	21
ATTGTAG	20	7.003785E-5	70.0	4
>>END_MODULE
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287273 READS because READLEN < 1
Read 287273 spots for SRR11699301.sra
Written 287273 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
Rejected 287254 READS because READLEN < 1
Read 287254 spots for SRR11699301.sra
Written 287254 spots for SRR11699301.sra
SRR ids: ['SRR11699301.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_n7muws5a
SRR11699301.sra spots: 5745099
blocks: [[1, 287254], [287255, 574508], [574509, 861762], [861763, 1149016], [1149017, 1436270], [1436271, 1723524], [1723525, 2010778], [2010779, 2298032], [2298033, 2585286], [2585287, 2872540], [2872541, 3159794], [3159795, 3447048], [3447049, 3734302], [3734303, 4021556], [4021557, 4308810], [4308811, 4596064], [4596065, 4883318], [4883319, 5170572], [5170573, 5457826], [5457827, 5745099]]
SRR11699301 file size 1091868
SRR11699301 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 SRR11699301 SRR11699301_1.fastq
Input file:	SRR11699301_1.fastq
trimmed:	SRR11699301-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 10:05:34 2025 >> started

Wed Jun 18 10:05:37 2025 >> done (2.456s)
5745099 reads processed; of these:
 873535 (15.20%) short reads filtered out after trimming by size control
   2982 ( 0.05%) empty reads filtered out after trimming by size control
4868582 (84.74%) reads available; of these:
4706420 (96.67%) trimmed reads available after processing
 162162 ( 3.33%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 133251	  2.74%
 19	 200402	  4.12%
 20	 219468	  4.51%
 21	 330417	  6.79%
 22	 510609	 10.49%
 23	 212802	  4.37%
 24	 524815	 10.78%
 25	 245964	  5.05%
 26	 152290	  3.13%
 27	 161021	  3.31%
 28	 139810	  2.87%
 29	 148348	  3.05%
 30	 255189	  5.24%
 31	 147546	  3.03%
 32	 139941	  2.87%
 33	 167119	  3.43%
 34	 149834	  3.08%
 35	 249886	  5.13%
 36	 127751	  2.62%
 37	  97104	  1.99%
 38	  73187	  1.50%
 39	  72606	  1.49%
 40	  55601	  1.14%
 41	  75902	  1.56%
 42	  46596	  0.96%
 43	  39754	  0.82%
 44	  29202	  0.60%
 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	      1	  0.00%
 73	      0	  0.00%
 74	      1	  0.00%
 75	      2	  0.00%
 76	 162162	  3.33%
4868582 reads passed initial QC


criterion=sequence-density
sequence-density=3.93
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCG


criterion=fanout-score
sequence-density=0.25
sequence-density-rank=16
fanout-score=17.91
fanout-score-rank=1
prefix-density=0.99
prefix-fanout=4.6
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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCG -o SRR11699301 -
Input file:	STDIN
trimmed:	SRR11699301-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
Wed Jun 18 10:05:44 2025 >> started

Wed Jun 18 10:05:46 2025 >> done (2.020s)
2434291 reads processed; of these:
   7543 ( 0.31%) short reads filtered out after trimming by size control
  97331 ( 4.00%) empty reads filtered out after trimming by size control
2329417 (95.69%) reads available; of these:
  17962 ( 0.77%) trimmed reads available after processing
2311455 (99.23%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  67325	  2.89%
 19	 100959	  4.33%
 20	 107285	  4.61%
 21	 164675	  7.07%
 22	 254812	 10.94%
 23	 105914	  4.55%
 24	 259318	 11.13%
 25	 122579	  5.26%
 26	  75971	  3.26%
 27	  80312	  3.45%
 28	  69829	  3.00%
 29	  73372	  3.15%
 30	 127463	  5.47%
 31	  73486	  3.15%
 32	  68220	  2.93%
 33	  60396	  2.59%
 34	  65072	  2.79%
 35	  67983	  2.92%
 36	  61014	  2.62%
 37	  47991	  2.06%
 38	  36415	  1.56%
 39	  36379	  1.56%
 40	  27725	  1.19%
 41	  37528	  1.61%
 42	  22895	  0.98%
 43	  19409	  0.83%
 44	  14334	  0.62%
 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	      1	  0.00%
 71	      1	  0.00%
 72	      0	  0.00%
 73	   1664	  0.07%
 74	      0	  0.00%
 75	      2	  0.00%
 76	  79088	  3.40%


criterion=sequence-density
sequence-density=3.37
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=16
prefix-density=0.01
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATA


criterion=fanout-score
sequence-density=0.26
sequence-density-rank=16
fanout-score=18.08
fanout-score-rank=1
prefix-density=1.02
prefix-fanout=4.6
sequence=GTCTAGTGGTATGATTCTCGCTT
                                 Started job on |	Jun 18 10:06:21
                             Started mapping on |	Jun 18 10:06:21
                                    Finished on |	Jun 18 10:06:34
       Mapping speed, Million of reads per hour |	1319.18

                          Number of input reads |	4763708
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	458300
                        Uniquely mapped reads % |	9.62%
                          Average mapped length |	24.60
                       Number of splices: Total |	10344
            Number of splices: Annotated (sjdb) |	4436
                       Number of splices: GT/AG |	9548
                       Number of splices: GC/AG |	537
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	259
                      Mismatch rate per base, % |	1.08%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.50
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.43
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	559432
             % of reads mapped to multiple loci |	11.74%
        Number of reads mapped to too many loci |	870211
             % of reads mapped to too many loci |	18.27%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.16%
                     % of reads unmapped: other |	52.21%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	3745976	3745976	3745976
N_multimapping	559432	559432	559432
N_noFeature	382364	395963	442032
N_ambiguous	2731	37	35
UnstrandedReadsAssigned:73205 PositiveStrandReadsAssigned:62300 NegativeStrandReadsAssigned:16233
Dataset is classified unstranded
MeadianReadLen=25 20thPercentileLength=22 echo kmer=19
SRR11699301 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: SRR11699301-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,763,708 reads, 918,599 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 843 rounds

  72540 SRR11699301.ke.tsv
  44303 SRR11699301.se.tsv
 116843 total
==> SRR11699301.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	10	3.38691
Zm00001eb323640_T001	3273	3174	0	0
Zm00001eb314140_T001	893	794	0	0
Zm00001eb080260_T001	3529	3430	0	0
Zm00001eb026490_T001	2433	2334	1	0.481481
Zm00001eb026490_T002	2229	2130	0	0
Zm00001eb026490_T003	2220	2121	0	0
Zm00001eb281360_T001	2412	2313	0	0

==> SRR11699301.se.tsv <==
Zm00001eb015280	1
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699301 completed mapping pipeline successfully
