Starting /dee2/code/volunteer_pipeline.sh SRR24401715
    current disk space = 252104836
    free memory = 128289468 
SRR24401715 SRAfilesize
93832fbb2de523836f0c3566f8f2179e  SRR24401715.sra
SRR24401715.sra file validated
SRR24401715 is single end
SRR24401715 is conventional basespace
SRR24401715 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR24401715_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	50
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	35.076	37.0	37.0	37.0	25.0	37.0
2	35.4005	37.0	37.0	37.0	37.0	37.0
3	35.5025	37.0	37.0	37.0	37.0	37.0
4	35.304	37.0	37.0	37.0	25.0	37.0
5	35.503	37.0	37.0	37.0	37.0	37.0
6	34.7605	37.0	37.0	37.0	25.0	37.0
7	35.4415	37.0	37.0	37.0	37.0	37.0
8	35.209	37.0	37.0	37.0	25.0	37.0
9	35.7965	37.0	37.0	37.0	37.0	37.0
10	35.8385	37.0	37.0	37.0	37.0	37.0
11	35.4885	37.0	37.0	37.0	37.0	37.0
12	35.6395	37.0	37.0	37.0	37.0	37.0
13	35.673	37.0	37.0	37.0	37.0	37.0
14	35.477	37.0	37.0	37.0	37.0	37.0
15	35.9455	37.0	37.0	37.0	37.0	37.0
16	35.676	37.0	37.0	37.0	37.0	37.0
17	35.589	37.0	37.0	37.0	37.0	37.0
18	35.6845	37.0	37.0	37.0	37.0	37.0
19	35.6215	37.0	37.0	37.0	37.0	37.0
20	35.4655	37.0	37.0	37.0	37.0	37.0
21	35.6185	37.0	37.0	37.0	37.0	37.0
22	35.5415	37.0	37.0	37.0	37.0	37.0
23	35.577	37.0	37.0	37.0	37.0	37.0
24	35.577	37.0	37.0	37.0	37.0	37.0
25	35.438	37.0	37.0	37.0	37.0	37.0
26	35.11	37.0	37.0	37.0	25.0	37.0
27	35.482	37.0	37.0	37.0	37.0	37.0
28	35.8385	37.0	37.0	37.0	37.0	37.0
29	35.7565	37.0	37.0	37.0	37.0	37.0
30	35.536	37.0	37.0	37.0	37.0	37.0
31	35.564	37.0	37.0	37.0	37.0	37.0
32	35.648	37.0	37.0	37.0	37.0	37.0
33	35.4715	37.0	37.0	37.0	37.0	37.0
34	35.39	37.0	37.0	37.0	37.0	37.0
35	35.52	37.0	37.0	37.0	37.0	37.0
36	35.535	37.0	37.0	37.0	37.0	37.0
37	35.604	37.0	37.0	37.0	37.0	37.0
38	35.5405	37.0	37.0	37.0	37.0	37.0
39	35.573	37.0	37.0	37.0	37.0	37.0
40	35.3565	37.0	37.0	37.0	37.0	37.0
41	35.4595	37.0	37.0	37.0	37.0	37.0
42	35.1965	37.0	37.0	37.0	25.0	37.0
43	35.4135	37.0	37.0	37.0	37.0	37.0
44	35.2305	37.0	37.0	37.0	25.0	37.0
45	35.4795	37.0	37.0	37.0	37.0	37.0
46	35.291	37.0	37.0	37.0	25.0	37.0
47	35.1125	37.0	37.0	37.0	25.0	37.0
48	35.3875	37.0	37.0	37.0	37.0	37.0
49	35.349	37.0	37.0	37.0	37.0	37.0
50	35.3415	37.0	37.0	37.0	37.0	37.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	1.0
22	0.0
23	1.0
24	4.0
25	6.0
26	13.0
27	25.0
28	35.0
29	53.0
30	72.0
31	107.0
32	137.0
33	182.0
34	290.0
35	552.0
36	1873.0
37	649.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	23.875	31.05	25.124999999999996	19.950000000000003
2	25.100200400801604	26.027054108216436	23.271543086172343	25.60120240480962
3	30.9	23.799999999999997	23.275000000000002	22.025
4	32.824999999999996	25.924999999999997	23.45	17.8
5	23.150000000000002	33.825	20.9	22.125
6	25.25	23.150000000000002	27.450000000000003	24.15
7	32.25	24.2	26.35	17.2
8	24.45	25.924999999999997	28.975	20.65
9	25.775	29.375	24.875	19.975
10	35.975	17.4	25.7	20.925
11	26.825	22.0	30.275000000000002	20.9
12	26.075	20.724999999999998	26.025	27.175
13	26.424999999999997	23.525	19.975	30.075000000000003
14	27.1	33.15	21.575	18.175
15	30.575000000000003	30.15	21.45	17.825
16	24.925	30.625000000000004	21.0	23.45
17	27.85	30.425	25.674999999999997	16.05
18	32.550000000000004	25.650000000000002	20.9	20.9
19	27.474999999999998	29.9	24.8	17.825
20	31.3	28.775000000000002	23.974999999999998	15.950000000000001
21	26.85	33.925	20.45	18.775
22	28.249999999999996	33.525	20.599999999999998	17.625
23	32.800000000000004	32.875	18.5	15.825
24	29.575000000000003	34.9	21.05	14.475
25	28.675	34.050000000000004	20.4	16.875
26	31.55	31.574999999999996	19.6	17.275
27	30.225	34.25	16.400000000000002	19.125
28	33.1	30.7	16.925	19.275000000000002
29	30.85	32.975	13.875000000000002	22.3
30	33.4	33.800000000000004	11.65	21.15
31	31.175000000000004	33.5	13.600000000000001	21.725
32	28.499999999999996	37.35	14.000000000000002	20.150000000000002
33	30.65	33.625	12.225	23.5
34	30.175	31.825	13.850000000000001	24.15
35	27.650000000000002	31.55	13.525	27.275
36	27.025	33.975	12.125	26.875
37	25.15	35.15	13.8	25.900000000000002
38	28.7	32.375	13.725000000000001	25.2
39	26.05	31.275	15.25	27.425
40	24.45	33.6	15.5	26.450000000000003
41	24.85	29.675	15.575	29.9
42	24.45	30.75	17.175	27.625
43	24.349999999999998	27.625	21.75	26.275
44	21.45	28.65	18.8	31.1
45	22.025	31.924999999999997	17.125	28.925
46	25.75	29.175	15.075	30.0
47	20.925	31.525	18.15	29.4
48	17.25	30.525000000000002	18.9	33.324999999999996
49	18.8	29.075	18.3	33.825
50	16.725	29.5	21.349999999999998	32.425
>>END_MODULE
>>Per sequence GC content	warn
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.5
28	1.0
29	2.0
30	3.0
31	3.0
32	3.0
33	4.0
34	5.0
35	9.5
36	14.0
37	30.0
38	46.0
39	61.0
40	76.0
41	131.5
42	187.0
43	250.5
44	314.0
45	338.0
46	362.0
47	413.5
48	465.0
49	526.0
50	587.0
51	629.5
52	672.0
53	627.5
54	583.0
55	481.5
56	380.0
57	292.0
58	204.0
59	133.5
60	63.0
61	43.0
62	23.0
63	16.5
64	10.0
65	6.0
66	2.0
67	1.0
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	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
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	0.2
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	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	pass
#Total Deduplicated Percentage	73.225
#Duplication Level	Percentage of deduplicated	Percentage of total
1	82.10993513144417	60.12499999999999
2	12.01775349948788	17.599999999999998
3	3.072721065209969	6.75
4	1.0583817002389895	3.1
5	0.40969614202799587	1.5
6	0.5462615227039945	2.4
7	0.20484807101399793	1.05
8	0.06828269033799932	0.4
9	0.06828269033799932	0.44999999999999996
>10	0.40969614202799587	5.325
>50	0.03414134516899966	1.3
>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
AGTTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCC	52	1.3	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAGATCGGAAGA	46	1.15	No Hit
TTGACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCAT	38	0.95	TruSeq Adapter, Index 3 (100% over 41bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTA	19	0.475	TruSeq Adapter, Index 3 (100% over 36bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTA	15	0.375	TruSeq Adapter, Index 3 (100% over 36bp)
AGTTACTAATTCATGATCTGGCATAGATCGGAAGAGCACACGTCTGAACT	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GCGTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	12	0.3	No Hit
TTCATGGACGTTGATAAGATCTTTCAGATCGGAAGAGCACACGTCTGAAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
AACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCCGCTGTAGCACATCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCCAAATGTAGACAAAGCAGATCGGAAGAGCACACGTCTGAACTCCAGT	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CTCGTGTTGCATCCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CTTCGTGATTGATTTGCCATATTTTCTGATCAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAAGATCGGAAG	8	0.2	No Hit
TAAAACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CCAAGATGAGTGCTCTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TCCGTTGTAGTCTAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CACCCCAAGATGAGTGCTCTCCTAGATCGGAAGAGCACACGTCTGAACTC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TAAAACGACTCTCGGCAACAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AAAACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TGAAAGTGACTACATCGGGGTAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCGGCGACGTGGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTA	6	0.15	TruSeq Adapter, Index 3 (100% over 36bp)
CACGTCTGCCTGGGTGTCACAAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CCTTTGTCGCTAAGATTCGAAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGATGGGTCGGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTA	6	0.15	TruSeq Adapter, Index 3 (100% over 36bp)
GCCCTTTGTCGCTAAGATTCGAAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCAAACGAGGAAAGGCTTACGGTGGATACCTAAGATCGGAAGAGCACACG	6	0.15	No Hit
CCTCGTGTTGCATCCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGGGATATGGCGGAATTGGTAGACGCTACGGACTTAGATCGGAAGAGCAC	6	0.15	No Hit
GCGTCCATTGTCTAATGGATAGGACATAGGTCTTCTAAACAGATCGGAAG	6	0.15	No Hit
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCTAGATCGGAAGAGCACAC	6	0.15	No Hit
AAAACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
AACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
CAAGATGAGTGCTCTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
AGACCGGTAGACTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GGTCGGCTTGTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTA	5	0.125	TruSeq Adapter, Index 3 (100% over 36bp)
AAGATGAGTGCTCTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TAAAAAAGCGATAGATAAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GGGATGGGTCGGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTT	5	0.125	TruSeq Adapter, Index 1 (97% over 35bp)
TAAAACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGGATATAGCTCAGTTGGTAGAGCTCCGCTCTTGCAAAGATCGGAAGAG	5	0.125	No Hit
AAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGAGATCGGAAG	5	0.125	No Hit
AACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGAGATCGGAAGA	5	0.125	No Hit
AAAATGGATCCGTAACTTCGGGAAAAGGATTGGCTCTGAGGAAGATCGGA	5	0.125	No Hit
TAAAACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
>>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	0.125	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	0.125	0.0	0.0	0.0	0.0
5	0.125	0.0	0.0	0.0	0.0
6	0.125	0.0	0.0	0.0	0.0
7	0.15	0.0	0.0	0.0	0.0
8	0.15	0.0	0.0	0.0	0.0
9	1.225	0.0	0.0	0.0	0.0
10	1.225	0.0	0.0	0.0	0.0
11	1.4	0.0	0.0	0.0	0.0
12	1.8	0.0	0.0	0.0	0.0
13	2.775	0.0	0.0	0.0	0.0
14	5.05	0.0	0.0	0.0	0.0
15	7.05	0.0	0.0	0.0	0.0
16	9.475	0.0	0.0	0.0	0.0
17	13.025	0.0	0.0	0.0	0.0
18	16.525	0.0	0.0	0.0	0.0
19	20.325	0.0	0.0	0.0	0.0
20	24.1	0.0	0.0	0.0	0.0
21	27.95	0.0	0.0	0.0	0.0
22	33.275	0.0	0.0	0.0	0.0
23	39.05	0.0	0.0	0.0	0.0
24	43.325	0.0	0.0	0.0	0.0
25	49.225	0.0	0.0	0.0	0.0
26	52.975	0.0	0.0	0.0	0.0
27	56.275	0.0	0.0	0.0	0.0
28	58.975	0.0	0.0	0.0	0.0
29	62.0	0.0	0.0	0.0	0.0
30	64.6	0.0	0.0	0.0	0.0
31	66.825	0.0	0.0	0.0	0.0
32	70.05	0.0	0.0	0.0	0.0
33	72.4	0.0	0.0	0.0	0.0
34	74.8	0.0	0.0	0.0	0.0
35	76.875	0.0	0.0	0.0	0.0
36	79.45	0.0	0.0	0.0	0.0
37	81.975	0.0	0.0	0.0	0.0
38	83.9	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGTAGTC	20	6.952051E-4	44.000004	6
CTCCAGT	125	0.0019514224	12.32	44
ACTCCAG	130	0.0026225161	11.846154	43
AACTCCA	150	0.007661297	10.266666	42
>>END_MODULE
Rejected 3259066 READS because READLEN < 1
Read 3259066 spots for SRR24401715.sra
Written 3259066 spots for SRR24401715.sra
Rejected 3259061 READS because READLEN < 1
Read 3259061 spots for SRR24401715.sra
Written 3259061 spots for SRR24401715.sra
Rejected 3259061 READS because READLEN < 1
Read 3259061 spots for SRR24401715.sra
Written 3259061 spots for SRR24401715.sra
Rejected 3259061 READS because READLEN < 1
Read 3259061 spots for SRR24401715.sra
Written 3259061 spots for SRR24401715.sra
Rejected 3259061 READS because READLEN < 1
Read 3259061 spots for SRR24401715.sra
Written 3259061 spots for SRR24401715.sra
Rejected 3259061 READS because READLEN < 1
Read 3259061 spots for SRR24401715.sra
Written 3259061 spots for SRR24401715.sra
Rejected 3259061 READS because READLEN < 1
Read 3259061 spots for SRR24401715.sra
Written 3259061 spots for SRR24401715.sra
Rejected 3259061 READS because READLEN < 1
Read 3259061 spots for SRR24401715.sra
Written 3259061 spots for SRR24401715.sra
SRR ids: ['SRR24401715.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_q48e_0nm
SRR24401715.sra spots: 26072493
blocks: [[1, 3259061], [3259062, 6518122], [6518123, 9777183], [9777184, 13036244], [13036245, 16295305], [16295306, 19554366], [19554367, 22813427], [22813428, 26072493]]
SRR24401715 file size 3670212
SRR24401715 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	/usr/local/bin/skewer -f sanger -l 18 -q 10 -k inf -t 8 -o SRR24401715 SRR24401715_1.fastq
Input file:	SRR24401715_1.fastq
trimmed:	SRR24401715-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):	8
Tue Jan 13 11:08:41 2026 >> started

Tue Jan 13 11:09:03 2026 >> done (21.810s)
26072493 reads processed; of these:
 4347096 (16.67%) short reads filtered out after trimming by size control
   47229 ( 0.18%) empty reads filtered out after trimming by size control
21678168 (83.15%) reads available; of these:
  930462 ( 4.29%) trimmed reads available after processing
20747706 (95.71%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  930454	  4.29%
 19	       0	  0.00%
 20	       0	  0.00%
 21	       0	  0.00%
 22	       0	  0.00%
 23	       0	  0.00%
 24	       0	  0.00%
 25	       0	  0.00%
 26	       0	  0.00%
 27	       0	  0.00%
 28	       0	  0.00%
 29	       0	  0.00%
 30	       0	  0.00%
 31	       0	  0.00%
 32	       0	  0.00%
 33	       0	  0.00%
 34	       0	  0.00%
 35	       0	  0.00%
 36	       0	  0.00%
 37	       0	  0.00%
 38	       0	  0.00%
 39	       2	  0.00%
 40	       0	  0.00%
 41	       0	  0.00%
 42	       0	  0.00%
 43	       0	  0.00%
 44	       0	  0.00%
 45	       0	  0.00%
 46	       0	  0.00%
 47	       0	  0.00%
 48	       6	  0.00%
 49	       0	  0.00%
 50	20747706	 95.71%
21678168 reads passed initial QC


criterion=sequence-density
sequence-density=78.45
sequence-density-rank=1
fanout-score=60.35
fanout-score-rank=1
prefix-density=88.14
prefix-fanout=53.7
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCGCGTATGCCGTC


criterion=fanout-score
sequence-density=78.45
sequence-density-rank=1
fanout-score=60.35
fanout-score-rank=1
prefix-density=88.14
prefix-fanout=53.7
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCGCGTATGCCGTC
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:	/usr/local/bin/skewer -f sanger -l 18 -t 8 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCGCGTATGCCGTC -o SRR24401715 -
Input file:	STDIN
trimmed:	SRR24401715-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCGCGTATGCCGTC
-- 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):	8
Tue Jan 13 11:10:21 2026 >> started

Tue Jan 13 11:10:35 2026 >> done (13.494s)
21129354 reads processed; of these:
   26065 ( 0.12%) short reads filtered out after trimming by size control
     324 ( 0.00%) empty reads filtered out after trimming by size control
21102965 (99.88%) reads available; of these:
19944753 (94.51%) trimmed reads available after processing
 1158212 ( 5.49%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  921729	  4.37%
 19	  984225	  4.66%
 20	 1040260	  4.93%
 21	 1312336	  6.22%
 22	 1484781	  7.04%
 23	 1155400	  5.48%
 24	 1595205	  7.56%
 25	  919263	  4.36%
 26	  886766	  4.20%
 27	  773147	  3.66%
 28	  741543	  3.51%
 29	  727282	  3.45%
 30	  698714	  3.31%
 31	  801502	  3.80%
 32	  698476	  3.31%
 33	  675675	  3.20%
 34	  582490	  2.76%
 35	  626310	  2.97%
 36	  579973	  2.75%
 37	  536462	  2.54%
 38	  533561	  2.53%
 39	  860122	  4.08%
 40	  549991	  2.61%
 41	  441377	  2.09%
 42	  350214	  1.66%
 43	  210143	  1.00%
 44	   84530	  0.40%
 45	   32140	  0.15%
 46	   15990	  0.08%
 47	   21304	  0.10%
 48	       1	  0.00%
 49	       0	  0.00%
 50	  262053	  1.24%


criterion=sequence-density
sequence-density=2.18
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=10
prefix-density=0.00
prefix-fanout=1.0
sequence=AGTTACTAATTCATGATCTGGCAT


criterion=fanout-score
sequence-density=0.26
sequence-density-rank=10
fanout-score=49.54
fanout-score-rank=1
prefix-density=0.34
prefix-fanout=37.8
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCGCGTATGCCGTC
                                 Started job on |	Jan 13 11:11:48
                             Started mapping on |	Jan 13 11:11:48
                                    Finished on |	Jan 13 11:13:02
       Mapping speed, Million of reads per hour |	1053.33

                          Number of input reads |	21651779
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	4047395
                        Uniquely mapped reads % |	18.69%
                          Average mapped length |	28.73
                       Number of splices: Total |	95782
            Number of splices: Annotated (sjdb) |	56475
                       Number of splices: GT/AG |	87438
                       Number of splices: GC/AG |	1087
                       Number of splices: AT/AC |	721
               Number of splices: Non-canonical |	6536
                      Mismatch rate per base, % |	0.34%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.10
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	16294455
             % of reads mapped to multiple loci |	75.26%
        Number of reads mapped to too many loci |	518807
             % of reads mapped to too many loci |	2.40%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	3.05%
                     % of reads unmapped: other |	0.60%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1309929	1309929	1309929
N_multimapping	16294455	16294455	16294455
N_noFeature	1282992	1407279	3764757
N_ambiguous	239195	80368	3472
UnstrandedReadsAssigned:2525208 PositiveStrandReadsAssigned:2559748 NegativeStrandReadsAssigned:279166
Dataset is classified positive stranded
MeadianReadLen=27 20thPercentileLength=21 echo kmer=19
SRR24401715 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: 48,359
[index] number of k-mers: 44,957,248
[index] number of equivalence classes: 195,259
[quant] running in single-end mode
[quant] will process file 1: SRR24401715-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 21,651,779 reads, 1,388,434 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 956 rounds

  48360 SRR24401715.ke.tsv
  32833 SRR24401715.se.tsv
  81193 total
==> SRR24401715.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
AT1G19090.1	2509	2410	65	17.7793
AT1G18320.1	699	600	0	0
AT5G11100.1	1709	1610	0	0
AT4G35335.1	1280	1181	15	8.37259
AT1G60930.1	3876	3777	0	0
AT1G17000.1	2351	2252	0	0
AT3G55270.1	3130	3031	28	6.08962
AT4G16150.1	3181	3082	45	9.62494
AT3G18150.1	1370	1271	0	0

==> SRR24401715.se.tsv <==
AT1G01010	9
AT1G01020	3
AT1G03987	0
AT1G01030	2
AT1G01040	32
AT1G03993	0
AT1G01046	20
AT1G01050	36
AT1G03997	0
AT1G01060	58
SRR24401715 completed mapping pipeline successfully
