Starting /dee2/code/volunteer_pipeline.sh SRR11699257
    current disk space = 2478720180224
    free memory = 1579940520 
SRR11699257 SRAfilesize
a7ac510dd7714131db7c414b5614f02d  SRR11699257.sra
SRR11699257.sra file validated
SRR11699257 is single end
SRR11699257 is conventional basespace
SRR11699257 read1 length is 76 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR11699257_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	52
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.16075	32.0	32.0	32.0	32.0	32.0
2	31.3785	32.0	32.0	32.0	32.0	32.0
3	31.43125	32.0	32.0	32.0	32.0	32.0
4	31.52825	32.0	32.0	32.0	32.0	32.0
5	31.4425	32.0	32.0	32.0	32.0	32.0
6	34.944	36.0	36.0	36.0	36.0	36.0
7	35.04	36.0	36.0	36.0	36.0	36.0
8	34.9515	36.0	36.0	36.0	36.0	36.0
9	34.81525	36.0	36.0	36.0	32.0	36.0
10-11	35.00775	36.0	36.0	36.0	36.0	36.0
12-13	35.0325	36.0	36.0	36.0	36.0	36.0
14-15	34.97425	36.0	36.0	36.0	36.0	36.0
16-17	35.000249999999994	36.0	36.0	36.0	36.0	36.0
18-19	35.05175	36.0	36.0	36.0	36.0	36.0
20-21	34.959500000000006	36.0	36.0	36.0	36.0	36.0
22-23	34.809749999999994	36.0	36.0	36.0	36.0	36.0
24-25	34.90825	36.0	36.0	36.0	36.0	36.0
26-27	34.800749999999994	36.0	36.0	36.0	34.0	36.0
28-29	34.8345	36.0	36.0	36.0	34.0	36.0
30-31	34.785625	36.0	36.0	36.0	34.0	36.0
32-33	34.704625	36.0	36.0	36.0	34.0	36.0
34-35	34.819125	36.0	36.0	36.0	34.0	36.0
36-37	34.814	36.0	36.0	36.0	36.0	36.0
38-39	34.74	36.0	36.0	36.0	32.0	36.0
40-41	34.658125	36.0	36.0	36.0	32.0	36.0
42-43	34.4725	36.0	36.0	36.0	32.0	36.0
44-45	34.24425	36.0	36.0	36.0	32.0	36.0
46-47	34.331625	36.0	36.0	36.0	32.0	36.0
48-49	34.029125	36.0	36.0	36.0	32.0	36.0
50-51	33.526125	36.0	36.0	36.0	24.0	36.0
52-53	33.304875	36.0	36.0	36.0	20.5	36.0
54-55	32.953	36.0	36.0	36.0	14.0	36.0
56-57	32.443375	36.0	32.0	36.0	14.0	36.0
58-59	32.085875	36.0	32.0	36.0	14.0	36.0
60-61	32.221000000000004	36.0	32.0	36.0	14.0	36.0
62-63	31.983625	36.0	32.0	36.0	14.0	36.0
64-65	32.192875	36.0	32.0	36.0	14.0	36.0
66-67	31.8585	36.0	32.0	36.0	14.0	36.0
68-69	32.031875	36.0	32.0	36.0	14.0	36.0
70-71	32.687875	36.0	32.0	36.0	14.0	36.0
72-73	32.477875	36.0	32.0	36.0	14.0	36.0
74-75	32.61125	36.0	32.0	36.0	14.0	36.0
76	29.49125	32.0	27.0	36.0	14.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
20	2.0
21	2.0
22	5.0
23	14.0
24	12.0
25	25.0
26	44.0
27	56.0
28	87.0
29	105.0
30	149.0
31	195.0
32	286.0
33	451.0
34	1032.0
35	1535.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	21.6	33.825	24.349999999999998	20.225
2	19.925	30.175	27.875	22.025
3	25.15	31.75	23.825	19.275000000000002
4	28.875	29.5	23.0	18.625
5	22.6	28.999999999999996	22.95	25.45
6	26.450000000000003	27.250000000000004	26.875	19.425
7	30.15	30.575000000000003	20.875	18.4
8	25.224999999999998	27.075	26.325	21.375
9	26.125	29.9	21.925	22.05
10-11	31.162499999999998	26.650000000000002	23.175	19.0125
12-13	25.474999999999998	25.8125	22.2125	26.5
14-15	28.037499999999998	34.862500000000004	19.2625	17.837500000000002
16-17	26.6625	26.775	26.0	20.5625
18-19	32.875	27.150000000000002	20.7	19.275000000000002
20-21	26.625	34.575	20.7125	18.087500000000002
22-23	32.0375	35.25	15.187500000000002	17.525
24-25	29.925	34.7625	15.537500000000001	19.775000000000002
26-27	29.475	32.9125	15.2375	22.375
28-29	29.362500000000004	31.8625	14.5375	24.2375
30-31	30.0375	34.075	12.675	23.2125
32-33	27.6	33.725	14.149999999999999	24.525
34-35	26.4625	33.137499999999996	13.900000000000002	26.5
36-37	24.325	31.612499999999997	14.5875	29.475
38-39	24.85	29.9	14.95	30.3
40-41	22.45	29.8375	16.662499999999998	31.05
42-43	23.9375	28.375	18.462500000000002	29.225
44-45	20.674999999999997	31.2	16.0875	32.0375
46-47	20.1	27.762500000000003	16.2625	35.875
48-49	17.45	27.900000000000002	15.25	39.4
50-51	19.175	25.974999999999998	16.5125	38.337500000000006
52-53	16.7125	24.4375	17.95	40.9
54-55	17.3125	25.0625	17.424999999999997	40.2
56-57	16.650000000000002	22.650000000000002	18.087500000000002	42.6125
58-59	14.575	22.7125	19.787499999999998	42.925000000000004
60-61	14.5625	20.95	20.5375	43.95
62-63	14.95	20.1	24.099999999999998	40.849999999999994
64-65	15.049999999999999	17.65	26.724999999999998	40.575
66-67	17.712500000000002	16.275000000000002	26.724999999999998	39.287499999999994
68-69	17.05	18.05	29.362500000000004	35.5375
70-71	17.875	16.0	30.775000000000002	35.35
72-73	17.2	16.85	28.8625	37.0875
74-75	18.5375	15.712499999999999	32.25	33.5
76	14.499999999999998	16.25	34.925	34.325
>>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	0.5
31	0.5
32	0.5
33	1.0
34	0.5
35	0.0
36	0.0
37	0.0
38	0.0
39	3.0
40	4.5
41	7.0
42	11.0
43	12.5
44	29.5
45	67.0
46	89.0
47	132.5
48	231.5
49	356.5
50	426.0
51	663.5
52	727.5
53	559.5
54	565.0
55	465.0
56	293.5
57	167.0
58	112.0
59	100.0
60	78.0
61	46.0
62	24.0
63	17.5
64	9.5
65	9.0
66	5.5
67	1.0
68	0.5
69	0.5
70	1.0
71	1.0
72	0.5
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	1.0
91	1.5
92	1.0
93	1.0
94	1.5
95	1.0
96	0.0
97	0.0
98	0.5
99	1.5
100	2.0
>>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	pass
#Total Deduplicated Percentage	72.25
#Duplication Level	Percentage of deduplicated	Percentage of total
1	89.27335640138409	64.5
2	5.3633217993079585	7.75
3	2.006920415224913	4.35
4	1.0380622837370241	3.0
5	0.31141868512110726	1.125
6	0.3806228373702422	1.6500000000000001
7	0.06920415224913494	0.35000000000000003
8	0.2422145328719723	1.4000000000000001
9	0.4498269896193772	2.9250000000000003
>10	0.795847750865052	8.774999999999999
>50	0.06920415224913494	4.175
>100	0.0	0.0
>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	88	2.1999999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA	79	1.975	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCCAT	30	0.75	TruSeq Adapter, Index 23 (97% over 37bp)
AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCAC	26	0.65	TruSeq Adapter, Index 23 (97% over 37bp)
GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCCATCTCGTAT	17	0.42500000000000004	TruSeq Adapter, Index 23 (97% over 37bp)
ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCA	14	0.35000000000000003	TruSeq Adapter, Index 5 (97% over 36bp)
AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCAGATCGGAAGAGCACAC	13	0.325	No Hit
GGGGATGTAGCTCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGC	13	0.325	TruSeq Adapter, Index 5 (97% over 35bp)
ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GATGAAGAACGTAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACAAGATCGGAAGAGCACACG	11	0.27499999999999997	No Hit
GCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCCA	10	0.25	TruSeq Adapter, Index 23 (97% over 37bp)
AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
ATACTGTAGGGGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATC	9	0.22499999999999998	No Hit
AGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACC	9	0.22499999999999998	TruSeq Adapter, Index 23 (97% over 37bp)
ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACC	9	0.22499999999999998	TruSeq Adapter, Index 23 (97% over 37bp)
TATTCTGGTGTCCTAGGCGTAGAGGAGATCGGAAGAGCACACGTCTGAAC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GGAGGTCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCAC	9	0.22499999999999998	No Hit
TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AAGGATCATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACC	9	0.22499999999999998	TruSeq Adapter, Index 23 (97% over 37bp)
TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCCATCTCGTA	9	0.22499999999999998	TruSeq Adapter, Index 23 (97% over 37bp)
GATGAAGAACGTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCA	9	0.22499999999999998	TruSeq Adapter, Index 5 (97% over 36bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAATCAGATCGGAAGAG	8	0.2	No Hit
AAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GATGAAGAACGTAGCAAAATGCGAGATCGGAAGAGCACACGTCTGAACTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCCATCTCGTATG	8	0.2	TruSeq Adapter, Index 23 (97% over 37bp)
GAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCA	8	0.2	TruSeq Adapter, Index 5 (97% over 36bp)
AGGATCATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCC	8	0.2	TruSeq Adapter, Index 23 (97% over 37bp)
TCCGTTGTAGTCTAGCTGGTCAGGATAAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCCTGCGGCAAAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTC	7	0.17500000000000002	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	6	0.15	No Hit
TTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCCATC	6	0.15	TruSeq Adapter, Index 23 (97% over 37bp)
AAATAGCTCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGCATTTGGTCTAGTGGTATGATTCTCAGATCGGAAGAGCACACGTCTG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
CGACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCC	6	0.15	TruSeq Adapter, Index 23 (97% over 37bp)
CTAACGAACGAACGATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAG	6	0.15	No Hit
TGATGGTACGTGCTACTCGGATAACCGTAGTAGATCGGAAGAGCACACGT	6	0.15	No Hit
CACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCAC	6	0.15	TruSeq Adapter, Index 23 (97% over 37bp)
ATCCCCGCGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGTTGTAGTCTAGCTGGTCAGGATATTCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGC	5	0.125	No Hit
TTCTGGCGGAGGGCACGTCTGCCTGGGCGTCACGCAGATCGGAAGAGCAC	5	0.125	No Hit
CCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCCATCTCGTA	5	0.125	TruSeq Adapter, Index 23 (97% over 37bp)
TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAAGATCGGAAGAGCAC	5	0.125	No Hit
ACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCC	5	0.125	TruSeq Adapter, Index 23 (97% over 37bp)
ATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCCATCTCGTA	5	0.125	TruSeq Adapter, Index 23 (97% over 37bp)
>>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	0.25	0.0	0.0	0.0	0.0
2	1.2	0.0	0.0	0.0	0.0
3	1.925	0.0	0.0	0.0	0.0
4	2.35	0.0	0.0	0.0	0.0
5	2.8	0.0	0.0	0.0	0.0
6	3.525	0.0	0.0	0.0	0.0
7	4.025	0.0	0.0	0.0	0.0
8	4.725	0.0	0.0	0.0	0.0
9	6.2	0.0	0.0	0.0	0.0
10	7.15	0.0	0.0	0.0	0.0
11	8.575	0.0	0.0	0.0	0.0
12	10.55	0.0	0.0	0.0	0.0
13	13.125	0.0	0.0	0.0	0.0
14	15.5	0.0	0.0	0.0	0.0
15	18.3	0.0	0.0	0.0	0.0
16	21.1	0.0	0.0	0.0	0.0
17	24.45	0.0	0.0	0.0	0.0
18	27.625	0.0	0.0	0.0	0.0
19	30.825	0.0	0.0	0.0	0.0
20	34.375	0.0	0.0	0.0	0.0
21	38.425	0.0	0.0	0.0	0.0
22	44.1	0.0	0.0	0.0	0.0
23	49.65	0.0	0.0	0.0	0.0
24	52.625	0.0	0.0	0.0	0.0
25	57.35	0.0	0.0	0.0	0.0
26	60.275	0.0	0.0	0.0	0.0
27	63.175	0.0	0.0	0.0	0.0
28	65.575	0.0	0.0	0.0	0.0
29	67.875	0.0	0.0	0.0	0.0
30	70.175	0.0	0.0	0.0	0.0
31	72.225	0.0	0.0	0.0	0.0
32	74.9	0.0	0.0	0.0	0.0
33	77.85	0.0	0.0	0.0	0.0
34	80.175	0.0	0.0	0.0	0.0
35	82.15	0.0	0.0	0.0	0.0
36	84.325	0.0	0.0	0.0	0.0
37	85.95	0.0	0.0	0.0	0.0
38	87.425	0.0	0.0	0.0	0.0
39	88.875	0.0	0.0	0.0	0.0
40	90.075	0.0	0.0	0.0	0.0
41	91.125	0.0	0.0	0.0	0.0
42	91.925	0.0	0.0	0.0	0.0
43	92.75	0.0	0.0	0.0	0.0
44	93.3	0.0	0.0	0.0	0.0
45	94.125	0.0	0.0	0.0	0.0
46	94.65	0.0	0.0	0.0	0.0
47	95.0	0.0	0.0	0.0	0.0
48	95.3	0.0	0.0	0.0	0.0
49	95.65	0.0	0.0	0.0	0.0
50	95.85	0.0	0.0	0.0	0.0
51	96.0	0.0	0.0	0.0	0.0
52	96.275	0.0	0.0	0.0	0.0
53	96.35	0.0	0.0	0.0	0.0
54	96.375	0.0	0.0	0.0	0.0
55	96.4	0.0	0.0	0.0	0.0
56	96.425	0.0	0.0	0.0	0.0
57	96.45	0.0	0.0	0.0	0.0
58	96.55	0.0	0.0	0.0	0.0
59	96.55	0.0	0.0	0.0	0.0
60	96.55	0.0	0.0	0.0	0.0
61	96.55	0.0	0.0	0.0	0.0
62	96.55	0.0	0.0	0.0	0.0
63	96.55	0.0	0.0	0.0	0.0
64	96.55	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CGACACG	15	0.0020658788	70.00001	1
ACACGAC	20	0.0064587677	52.5	3
GACACGA	20	0.0064587677	52.5	2
CTAACGA	55	1.4588295E-9	50.90909	1
TAACGAA	60	3.1559466E-9	46.666668	2
GAACGAA	70	1.2352757E-8	40.000004	6
TTGAACA	55	5.1802162E-6	38.181816	17
AACGATT	75	2.2724635E-8	37.333332	11
GAACGAT	75	2.2724635E-8	37.333332	10
TTTGAAC	60	9.417061E-6	35.000004	16
TGAACAG	60	9.417061E-6	35.000004	18
ACGATTT	80	4.0159648E-8	35.0	12
CGATTTG	80	4.0159648E-8	35.0	13
GATTTGA	85	6.8515874E-8	32.941174	14
ATTTGAA	85	6.8515874E-8	32.941174	15
GAACAGA	65	1.6304151E-5	32.307693	19
AACAGAT	65	1.6304151E-5	32.307693	20
ACAGATC	70	2.707939E-5	30.000002	21
TTCTGCT	80	0.0022346217	21.875	70
AACGAAC	135	3.930252E-6	20.74074	3
>>END_MODULE
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Written 361530 spots for SRR11699257.sra
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
Rejected 361540 READS because READLEN < 1
Read 361540 spots for SRR11699257.sra
Written 361540 spots for SRR11699257.sra
Rejected 361530 READS because READLEN < 1
Read 361530 spots for SRR11699257.sra
Written 361530 spots for SRR11699257.sra
SRR ids: ['SRR11699257.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_s97b9ia_
SRR11699257.sra spots: 7230610
blocks: [[1, 361530], [361531, 723060], [723061, 1084590], [1084591, 1446120], [1446121, 1807650], [1807651, 2169180], [2169181, 2530710], [2530711, 2892240], [2892241, 3253770], [3253771, 3615300], [3615301, 3976830], [3976831, 4338360], [4338361, 4699890], [4699891, 5061420], [5061421, 5422950], [5422951, 5784480], [5784481, 6146010], [6146011, 6507540], [6507541, 6869070], [6869071, 7230610]]
SRR11699257 file size 1374753
SRR11699257 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 SRR11699257 SRR11699257_1.fastq
Input file:	SRR11699257_1.fastq
trimmed:	SRR11699257-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 03:10:49 2025 >> started

Wed Jun 18 03:10:52 2025 >> done (2.961s)
7230610 reads processed; of these:
2117891 (29.29%) short reads filtered out after trimming by size control
  15539 ( 0.21%) empty reads filtered out after trimming by size control
5097180 (70.49%) reads available; of these:
4894288 (96.02%) trimmed reads available after processing
 202892 ( 3.98%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 205557	  4.03%
 19	 259995	  5.10%
 20	 288239	  5.65%
 21	 412468	  8.09%
 22	 432369	  8.48%
 23	 224913	  4.41%
 24	 335572	  6.58%
 25	 227694	  4.47%
 26	 215273	  4.22%
 27	 193439	  3.80%
 28	 175469	  3.44%
 29	 182754	  3.59%
 30	 212918	  4.18%
 31	 187700	  3.68%
 32	 194915	  3.82%
 33	 164607	  3.23%
 34	 158548	  3.11%
 35	 137565	  2.70%
 36	 109456	  2.15%
 37	 103578	  2.03%
 38	 104264	  2.05%
 39	  89872	  1.76%
 40	  67519	  1.32%
 41	  61472	  1.21%
 42	  56312	  1.10%
 43	  50660	  0.99%
 44	  41150	  0.81%
 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	      1	  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	      9	  0.00%
 76	 202892	  3.98%
5097180 reads passed initial QC


criterion=sequence-density
sequence-density=3.39
sequence-density-rank=1
fanout-score=29.46
fanout-score-rank=1
prefix-density=3.45
prefix-fanout=28.9
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCCATCTCGTATGCCGTCTTCTGCTTGAA


criterion=fanout-score
sequence-density=3.39
sequence-density-rank=1
fanout-score=29.46
fanout-score-rank=1
prefix-density=3.45
prefix-fanout=28.9
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCCATCTCGTATGCCGTCTTCTGCTTGAA
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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCCATCTCGTATGCCGTCTTCTGCTTGAA -o SRR11699257 -
Input file:	STDIN
trimmed:	SRR11699257-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCCATCTCGTATGCCGTCTTCTGCTTG
-- 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 03:10:59 2025 >> started

Wed Jun 18 03:11:01 2025 >> done (1.820s)
2548590 reads processed; of these:
   6929 ( 0.27%) short reads filtered out after trimming by size control
     10 ( 0.00%) empty reads filtered out after trimming by size control
2541651 (99.73%) reads available; of these:
 130662 ( 5.14%) trimmed reads available after processing
2410989 (94.86%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 102871	  4.05%
 19	 131289	  5.17%
 20	 147742	  5.81%
 21	 208888	  8.22%
 22	 214821	  8.45%
 23	 109128	  4.29%
 24	 165619	  6.52%
 25	 113790	  4.48%
 26	 107090	  4.21%
 27	  95457	  3.76%
 28	  87213	  3.43%
 29	  91566	  3.60%
 30	 106832	  4.20%
 31	  93471	  3.68%
 32	  97341	  3.83%
 33	  81757	  3.22%
 34	  78557	  3.09%
 35	  68680	  2.70%
 36	  54514	  2.14%
 37	  51727	  2.04%
 38	  52070	  2.05%
 39	  45143	  1.78%
 40	  36958	  1.45%
 41	  31502	  1.24%
 42	  27366	  1.08%
 43	  22179	  0.87%
 44	  19619	  0.77%
 45	  23679	  0.93%
 46	  14706	  0.58%
 47	  11647	  0.46%
 48	  11641	  0.46%
 49	   8161	  0.32%
 50	   4971	  0.20%
 51	   3618	  0.14%
 52	   2621	  0.10%
 53	   1823	  0.07%
 54	   1473	  0.06%
 55	    694	  0.03%
 56	    559	  0.02%
 57	    531	  0.02%
 58	    349	  0.01%
 59	    153	  0.01%
 60	    152	  0.01%
 61	    369	  0.01%
 62	    188	  0.01%
 63	     50	  0.00%
 64	     30	  0.00%
 65	     17	  0.00%
 66	     13	  0.00%
 67	     11	  0.00%
 68	      7	  0.00%
 69	     11	  0.00%
 70	      6	  0.00%
 71	      4	  0.00%
 72	      3	  0.00%
 73	     24	  0.00%
 74	      0	  0.00%
 75	      1	  0.00%
 76	  10949	  0.43%


criterion=sequence-density
sequence-density=1.86
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=14
prefix-density=0.03
prefix-fanout=1.0
sequence=TCCGTTGTAGTCTAGCTGGTCAGGATATTCGGCTCTCACCCGA


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=46
fanout-score=22.66
fanout-score-rank=1
prefix-density=0.11
prefix-fanout=1.1
sequence=GGGACGGACCGGGAACGGCCCCCTCGGGGGCCTTCCCCGGGCGTCGAACAACCGACTCAGAACTGGTACGGACAAGGGGAATCCGACTGTTTAATTAAAACAAAGCATTGCGACGGTCCTCGAGGATGCTGACGCAATGTGATTTCTGCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAACCAAGCGCGGGTAAACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCCAAATGCCTCGTCATCTAATTAGTGACGCGCATGAATGGATTAACGAGATTCCCACTGTCCCTGTCTACTATCCAGCGAAACC
                                 Started job on |	Jun 18 03:11:12
                             Started mapping on |	Jun 18 03:11:12
                                    Finished on |	Jun 18 03:11:26
       Mapping speed, Million of reads per hour |	1308.92

                          Number of input reads |	5090241
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	371764
                        Uniquely mapped reads % |	7.30%
                          Average mapped length |	25.65
                       Number of splices: Total |	9164
            Number of splices: Annotated (sjdb) |	4004
                       Number of splices: GT/AG |	7850
                       Number of splices: GC/AG |	448
                       Number of splices: AT/AC |	8
               Number of splices: Non-canonical |	858
                      Mismatch rate per base, % |	1.28%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.42
                        Insertion rate per base |	0.01%
                       Insertion average length |	1.26
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	439290
             % of reads mapped to multiple loci |	8.63%
        Number of reads mapped to too many loci |	1043384
             % of reads mapped to too many loci |	20.50%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.21%
                     % of reads unmapped: other |	56.36%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	4279187	4279187	4279187
N_multimapping	439290	439290	439290
N_noFeature	303343	312620	360262
N_ambiguous	2292	47	21
UnstrandedReadsAssigned:66129 PositiveStrandReadsAssigned:59097 NegativeStrandReadsAssigned:11481
Dataset is classified positive stranded
MeadianReadLen=26 20thPercentileLength=21 echo kmer=19
SRR11699257 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: SRR11699257-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 5,090,241 reads, 603,918 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 958 rounds

  72540 SRR11699257.ke.tsv
  44303 SRR11699257.se.tsv
 116843 total
==> SRR11699257.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Zm00001eb096110_T001	2067	1968	0	0
Zm00001eb321680_T001	3417	3318	3	1.43463
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	0.0169449	0.0126228
Zm00001eb026490_T003	2220	2121	0.983055	0.735417
Zm00001eb281360_T001	2412	2313	0	0

==> SRR11699257.se.tsv <==
Zm00001eb015280	0
Zm00001eb000610	0
Zm00001eb033210	0
Zm00001eb044610	0
Zm00001eb014360	0
Zm00001eb051320	0
Zm00001eb021860	0
Zm00001eb011690	0
Zm00001eb016840	0
Zm00001eb052060	0
SRR11699257 completed mapping pipeline successfully
