Starting /dee2/code/volunteer_pipeline.sh SRR24401726
    current disk space = 1324435016
    free memory = 60142436 
SRR24401726 SRAfilesize
9546fca8926ee66e18f90c0fc3940304  SRR24401726.sra
SRR24401726.sra file validated
SRR24401726 is single end
SRR24401726 is conventional basespace
SRR24401726 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR24401726_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	35.1275	37.0	37.0	37.0	25.0	37.0
2	35.2615	37.0	37.0	37.0	37.0	37.0
3	35.5505	37.0	37.0	37.0	37.0	37.0
4	35.302	37.0	37.0	37.0	37.0	37.0
5	35.4965	37.0	37.0	37.0	37.0	37.0
6	34.448	37.0	37.0	37.0	25.0	37.0
7	35.4025	37.0	37.0	37.0	37.0	37.0
8	35.2565	37.0	37.0	37.0	25.0	37.0
9	35.714	37.0	37.0	37.0	37.0	37.0
10	35.733	37.0	37.0	37.0	37.0	37.0
11	35.617	37.0	37.0	37.0	37.0	37.0
12	35.6745	37.0	37.0	37.0	37.0	37.0
13	35.7025	37.0	37.0	37.0	37.0	37.0
14	35.354	37.0	37.0	37.0	37.0	37.0
15	35.673	37.0	37.0	37.0	37.0	37.0
16	35.582	37.0	37.0	37.0	37.0	37.0
17	35.5595	37.0	37.0	37.0	37.0	37.0
18	35.6535	37.0	37.0	37.0	37.0	37.0
19	35.661	37.0	37.0	37.0	37.0	37.0
20	35.522	37.0	37.0	37.0	37.0	37.0
21	35.629	37.0	37.0	37.0	37.0	37.0
22	35.445	37.0	37.0	37.0	37.0	37.0
23	35.272	37.0	37.0	37.0	25.0	37.0
24	35.5785	37.0	37.0	37.0	37.0	37.0
25	35.366	37.0	37.0	37.0	37.0	37.0
26	35.332	37.0	37.0	37.0	37.0	37.0
27	35.5255	37.0	37.0	37.0	37.0	37.0
28	35.6475	37.0	37.0	37.0	37.0	37.0
29	35.4965	37.0	37.0	37.0	37.0	37.0
30	35.5625	37.0	37.0	37.0	37.0	37.0
31	35.62	37.0	37.0	37.0	37.0	37.0
32	35.626	37.0	37.0	37.0	37.0	37.0
33	35.266	37.0	37.0	37.0	25.0	37.0
34	35.64	37.0	37.0	37.0	37.0	37.0
35	35.3885	37.0	37.0	37.0	37.0	37.0
36	35.4785	37.0	37.0	37.0	37.0	37.0
37	35.253	37.0	37.0	37.0	25.0	37.0
38	35.6405	37.0	37.0	37.0	37.0	37.0
39	35.5805	37.0	37.0	37.0	37.0	37.0
40	35.057	37.0	37.0	37.0	25.0	37.0
41	34.8475	37.0	37.0	37.0	25.0	37.0
42	34.6045	37.0	37.0	37.0	25.0	37.0
43	34.92	37.0	37.0	37.0	25.0	37.0
44	33.8595	37.0	37.0	37.0	25.0	37.0
45	33.779	37.0	37.0	37.0	25.0	37.0
46	35.2855	37.0	37.0	37.0	37.0	37.0
47	33.9095	37.0	37.0	37.0	25.0	37.0
48	33.5815	37.0	37.0	37.0	11.0	37.0
49	34.456	37.0	37.0	37.0	25.0	37.0
50	34.2025	37.0	37.0	37.0	25.0	37.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
22	1.0
23	1.0
24	6.0
25	7.0
26	16.0
27	22.0
28	44.0
29	44.0
30	87.0
31	125.0
32	183.0
33	276.0
34	345.0
35	600.0
36	1761.0
37	482.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	21.375	32.625	29.9	16.1
2	30.341023069207623	18.906720160481445	23.1444332998997	27.607823470411237
3	27.85	25.1	22.075	24.975
4	31.025000000000002	23.425	30.25	15.299999999999999
5	18.875	27.875	18.099999999999998	35.15
6	27.35	21.85	30.3	20.5
7	43.025000000000006	18.625	24.6	13.750000000000002
8	19.225	33.275	32.85	14.649999999999999
9	19.575	41.375	22.775000000000002	16.275000000000002
10	42.75	15.25	23.474999999999998	18.525
11	22.6	27.474999999999998	28.225	21.7
12	26.5	23.849999999999998	24.725	24.925
13	20.025000000000002	23.35	16.85	39.775
14	24.325	38.85	22.45	14.374999999999998
15	29.599999999999998	25.674999999999997	20.525	24.2
16	19.5	39.574999999999996	17.875	23.05
17	23.425	32.550000000000004	24.925	19.1
18	41.575	20.525	17.125	20.775
19	21.925	31.900000000000002	31.75	14.424999999999999
20	32.725	21.7	25.525	20.05
21	25.924999999999997	26.900000000000002	22.675	24.5
22	35.949999999999996	30.9	15.85	17.299999999999997
23	33.625	36.825	13.125	16.425
24	24.275	46.075	16.8	12.85
25	24.15	37.8	15.125	22.925
26	38.2	25.4	22.325	14.075
27	21.425	38.1	17.875	22.6
28	30.025000000000002	24.975	17.45	27.55
29	25.575	31.175000000000004	15.8	27.450000000000003
30	40.8	33.800000000000004	9.025	16.375
31	29.2	32.05	15.35	23.400000000000002
32	22.625	43.45	11.35	22.575
33	24.075	38.05	10.549999999999999	27.325
34	34.425	24.775	16.0	24.8
35	23.599999999999998	29.7	23.549999999999997	23.150000000000002
36	31.55	28.7	10.05	29.7
37	20.325	37.625	16.5	25.55
38	30.025000000000002	31.924999999999997	10.549999999999999	27.500000000000004
39	19.6	30.75	15.75	33.900000000000006
40	19.525000000000002	41.725	11.625	27.125
41	20.525	31.374999999999996	13.25	34.849999999999994
42	23.474999999999998	24.175	25.474999999999998	26.875
43	19.525000000000002	22.625	24.025	33.825
44	25.974999999999998	23.175	16.675	34.175
45	18.45	35.05	17.775	28.725
46	33.900000000000006	25.1	12.325	28.675
47	19.55	29.45	20.175	30.825000000000003
48	14.649999999999999	31.1	20.724999999999998	33.525
49	15.225	30.9	20.599999999999998	33.275
50	19.025	22.15	24.775	34.050000000000004
>>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	1.0
24	2.0
25	1.0
26	0.0
27	1.5
28	3.0
29	2.0
30	1.0
31	3.0
32	5.0
33	8.5
34	12.0
35	15.0
36	18.0
37	31.0
38	44.0
39	62.5
40	81.0
41	176.0
42	271.0
43	262.0
44	253.0
45	286.0
46	319.0
47	404.0
48	489.0
49	474.0
50	459.0
51	516.0
52	573.0
53	674.0
54	775.0
55	561.0
56	347.0
57	270.5
58	194.0
59	155.0
60	116.0
61	71.0
62	26.0
63	17.5
64	9.0
65	6.0
66	3.0
67	1.5
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	0.3
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	warn
#Total Deduplicated Percentage	62.64999999999999
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.36711891460496	50.349999999999994
2	12.49002394253791	15.65
3	3.6711891460494814	6.9
4	1.077414205905826	2.7
5	0.5586592178770949	1.7500000000000002
6	0.4389465283320032	1.6500000000000001
7	0.1596169193934557	0.7000000000000001
8	0.11971268954509177	0.6
9	0.1596169193934557	0.8999999999999999
>10	0.7581803671189146	7.6499999999999995
>50	0.11971268954509177	4.925
>100	0.07980845969672785	6.225
>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
TTGACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAAT	133	3.325	TruSeq Adapter, Index 4 (100% over 41bp)
TCCGCTGTAGCACATCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	116	2.9000000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCGCGGTTG	94	2.35	TruSeq Adapter, Index 4 (97% over 45bp)
AGTTACTAATTCATGATCTGGCATAGATCGGAAGAGCACACGTCTGAACT	52	1.3	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AGTTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCC	51	1.275	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TCCGCTGTAGCACACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	44	1.0999999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGTTACTAATTCATGATCTGGCAAAGATCGGAAGAGCACACGTCTGAACT	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGGTTG	25	0.625	TruSeq Adapter, Index 4 (97% over 45bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	25	0.625	No Hit
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGGGTG	20	0.5	TruSeq Adapter, Index 4 (97% over 45bp)
AACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
GCGGCGACGTGGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGA	14	0.35000000000000003	TruSeq Adapter, Index 2 (97% over 36bp)
GCGTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCGCTGTAGCACACCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGA	12	0.3	TruSeq Adapter, Index 2 (97% over 36bp)
AACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCCGCTGTAGCACTTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGTTACTAATTCATGATCTGGCAAGATCGGAAGAGCACACGTCTGAACTC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGTCTGTAGTCCAACGGTAGGATAATTGCAGATCGGAAGAGCACACGTC	10	0.25	No Hit
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCGCGGGTG	10	0.25	TruSeq Adapter, Index 4 (97% over 45bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCGCGGTTT	10	0.25	TruSeq Adapter, Index 4 (97% over 45bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTTTG	10	0.25	TruSeq Adapter, Index 4 (97% over 49bp)
TGACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATC	10	0.25	TruSeq Adapter, Index 4 (100% over 42bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
CCGCTGTAGCACATCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGCTTTTATGTTAGTTCGTACTATAGATCGGAAGAGCACACGTCTGAA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TGCGGAAGGATCATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAGATCGGAAGA	8	0.2	No Hit
TAAAACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TAAAACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CTTCGTGATTGATTTGCCATATTTTCTGATCAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
TCCCAAATGTAGACAAAGCAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AGTTACTAATTCATGATCTGGTAGATCGGAAGAGCACACGTCTGAACTCC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
AACTACGATCTTTGGCTCTGGAACTGAATCATTTCCAGATCGGAAGAGCA	6	0.15	No Hit
GGGATGGGTCGGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTG	6	0.15	TruSeq Adapter, Index 2 (97% over 35bp)
GGATGGGTCGGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGA	6	0.15	TruSeq Adapter, Index 2 (97% over 36bp)
TCCGTTGTAGTCTAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AAAACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCGCTGTAGCACACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CCACTTCTGACACCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
CAACTGTGACGATAGCAAGTGCCGTCTGAGCTAGATCGGAAGAGCACACG	6	0.15	No Hit
TTCATGGACGTTGATAAGATCTTTCAGATCGGAAGAGCACACGTCTGAAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCCGCTTTTATGTTAGTTCGTACTATAAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TAAAACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCGCGTTTG	5	0.125	TruSeq Adapter, Index 4 (97% over 46bp)
GCTGCCGTGATCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGA	5	0.125	TruSeq Adapter, Index 2 (97% over 36bp)
GCCCTTTGTCGCTAAGATTCGAAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGGACGGACTGGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATG	5	0.125	TruSeq Adapter, Index 4 (100% over 49bp)
TAACATTGATGATACTTCTGCAATTCTGAGGCAGATCGGAAGAGCACACG	5	0.125	No Hit
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCTAGATCGGAAGAGCACAC	5	0.125	No Hit
TCCGCTGTAGCACATCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCTGTGATTCTCTGTGTAAGCAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ACGACTTAAATACGCGACGGAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AAAACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
CGTCCTGGTCGGATGCGGAACGGAGCAATCCAGATCGGAAGAGCACACGT	5	0.125	No Hit
AACTACGATCTTTGGCTCTGGAACTGAATCATTTCAGATCGGAAGAGCAC	5	0.125	No Hit
GGTCGGCTTGTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTG	5	0.125	TruSeq Adapter, Index 2 (97% over 35bp)
>>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	6.6	0.0	0.0	0.0	0.0
2	6.675	0.0	0.0	0.0	0.0
3	6.7	0.0	0.0	0.0	0.0
4	6.725	0.0	0.0	0.0	0.0
5	6.775	0.0	0.0	0.0	0.0
6	6.8	0.0	0.0	0.0	0.0
7	6.9	0.0	0.0	0.0	0.0
8	7.3	0.0	0.0	0.0	0.0
9	11.475	0.0	0.0	0.0	0.0
10	11.65	0.0	0.0	0.0	0.0
11	11.8	0.0	0.0	0.0	0.0
12	12.2	0.0	0.0	0.0	0.0
13	13.15	0.0	0.0	0.0	0.0
14	15.575	0.0	0.0	0.0	0.0
15	17.675	0.0	0.0	0.0	0.0
16	20.075	0.0	0.0	0.0	0.0
17	28.725	0.0	0.0	0.0	0.0
18	31.325	0.0	0.0	0.0	0.0
19	34.0	0.0	0.0	0.0	0.0
20	36.675	0.0	0.0	0.0	0.0
21	39.425	0.0	0.0	0.0	0.0
22	42.85	0.0	0.0	0.0	0.0
23	48.15	0.0	0.0	0.0	0.0
24	52.425	0.0	0.0	0.0	0.0
25	61.125	0.0	0.0	0.0	0.0
26	63.75	0.0	0.0	0.0	0.0
27	66.4	0.0	0.0	0.0	0.0
28	68.7	0.0	0.0	0.0	0.0
29	71.025	0.0	0.0	0.0	0.0
30	73.6	0.0	0.0	0.0	0.0
31	75.425	0.0	0.0	0.0	0.0
32	78.375	0.0	0.0	0.0	0.0
33	80.6	0.0	0.0	0.0	0.0
34	82.875	0.0	0.0	0.0	0.0
35	84.975	0.0	0.0	0.0	0.0
36	87.4	0.0	0.0	0.0	0.0
37	89.55	0.0	0.0	0.0	0.0
38	90.675	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CACATCA	20	6.952051E-4	44.000004	11
ACTAATT	30	1.9515464E-6	44.0	5
CATGATC	30	1.9515464E-6	44.0	12
TTCATGA	30	1.9515464E-6	44.0	10
TTACTAA	30	1.9515464E-6	44.0	3
AATTCAT	30	1.9515464E-6	44.0	8
ATGATCT	30	1.9515464E-6	44.0	13
TCTGGCA	30	1.9515464E-6	44.0	17
CCGCTGT	30	1.9515464E-6	44.0	2
TAGCACA	30	1.9515464E-6	44.0	8
GCTGTAG	30	1.9515464E-6	44.0	4
CTAATTC	30	1.9515464E-6	44.0	6
TCATGAT	30	1.9515464E-6	44.0	11
TAATTCA	30	1.9515464E-6	44.0	7
TGTAGCA	30	1.9515464E-6	44.0	6
GTTACTA	30	1.9515464E-6	44.0	2
ATTCATG	30	1.9515464E-6	44.0	9
ATCTGGC	30	1.9515464E-6	44.0	16
CTGTAGC	30	1.9515464E-6	44.0	5
GTAGCAC	30	1.9515464E-6	44.0	7
>>END_MODULE
Rejected 6401347 READS because READLEN < 1
Read 6401347 spots for SRR24401726.sra
Written 6401347 spots for SRR24401726.sra
Rejected 6401347 READS because READLEN < 1
Read 6401347 spots for SRR24401726.sra
Written 6401347 spots for SRR24401726.sra
Rejected 6401347 READS because READLEN < 1
Read 6401347 spots for SRR24401726.sra
Written 6401347 spots for SRR24401726.sra
Rejected 6401347 READS because READLEN < 1
Read 6401347 spots for SRR24401726.sra
Written 6401347 spots for SRR24401726.sra
SRR ids: ['SRR24401726.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_l__tfvxl
SRR24401726.sra spots: 25605388
blocks: [[1, 6401347], [6401348, 12802694], [12802695, 19204041], [19204042, 25605388]]
SRR24401726 file size 3604064
SRR24401726 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 4 -o SRR24401726 SRR24401726_1.fastq
Input file:	SRR24401726_1.fastq
trimmed:	SRR24401726-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):	4
Tue Jan 13 11:25:35 2026 >> started

Tue Jan 13 11:25:48 2026 >> done (12.832s)
25605388 reads processed; of these:
 6227516 (24.32%) short reads filtered out after trimming by size control
 1587938 ( 6.20%) empty reads filtered out after trimming by size control
17789934 (69.48%) reads available; of these:
  677648 ( 3.81%) trimmed reads available after processing
17112286 (96.19%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  677635	  3.81%
 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	      11	  0.00%
 49	       0	  0.00%
 50	17112286	 96.19%
17789934 reads passed initial QC


criterion=sequence-density
sequence-density=84.30
sequence-density-rank=1
fanout-score=55.90
fanout-score-rank=1
prefix-density=90.36
prefix-fanout=52.2
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCGCG


criterion=fanout-score
sequence-density=84.30
sequence-density-rank=1
fanout-score=55.90
fanout-score-rank=1
prefix-density=90.36
prefix-fanout=52.2
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCGCG
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 4 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCGCG -o SRR24401726 -
Input file:	STDIN
trimmed:	SRR24401726-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCGCG
-- 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):	4
Tue Jan 13 11:26:02 2026 >> started

Tue Jan 13 11:26:17 2026 >> done (14.592s)
17371347 reads processed; of these:
   23801 ( 0.14%) short reads filtered out after trimming by size control
    3947 ( 0.02%) empty reads filtered out after trimming by size control
17343599 (99.84%) reads available; of these:
16419619 (94.67%) trimmed reads available after processing
  923980 ( 5.33%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  671596	  3.87%
 19	  742531	  4.28%
 20	  790453	  4.56%
 21	 1030717	  5.94%
 22	 1358017	  7.83%
 23	 1093017	  6.30%
 24	 2258207	 13.02%
 25	  704596	  4.06%
 26	  642576	  3.70%
 27	  571776	  3.30%
 28	  516418	  2.98%
 29	  520204	  3.00%
 30	  590586	  3.41%
 31	  868515	  5.01%
 32	  637724	  3.68%
 33	  657213	  3.79%
 34	  555243	  3.20%
 35	  550601	  3.17%
 36	  428911	  2.47%
 37	  342428	  1.97%
 38	  323084	  1.86%
 39	  353076	  2.04%
 40	  285016	  1.64%
 41	  230535	  1.33%
 42	  162349	  0.94%
 43	  100812	  0.58%
 44	   35373	  0.20%
 45	   20795	  0.12%
 46	   13628	  0.08%
 47	   16959	  0.10%
 48	       3	  0.00%
 49	       0	  0.00%
 50	  270640	  1.56%


criterion=sequence-density
sequence-density=6.00
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=7
prefix-density=0.01
prefix-fanout=1.0
sequence=AGTTACTAATTCATGATCTGGCATAGA


criterion=fanout-score
sequence-density=0.27
sequence-density-rank=13
fanout-score=40.54
fanout-score-rank=1
prefix-density=0.32
prefix-fanout=34.5
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCGCG
                                 Started job on |	Jan 13 11:26:41
                             Started mapping on |	Jan 13 11:26:41
                                    Finished on |	Jan 13 11:28:05
       Mapping speed, Million of reads per hour |	761.24

                          Number of input reads |	17762186
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	4444968
                        Uniquely mapped reads % |	25.02%
                          Average mapped length |	27.23
                       Number of splices: Total |	92063
            Number of splices: Annotated (sjdb) |	53921
                       Number of splices: GT/AG |	86473
                       Number of splices: GC/AG |	937
                       Number of splices: AT/AC |	235
               Number of splices: Non-canonical |	4418
                      Mismatch rate per base, % |	0.33%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.09
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.06
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	11768925
             % of reads mapped to multiple loci |	66.26%
        Number of reads mapped to too many loci |	762552
             % of reads mapped to too many loci |	4.29%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	3.81%
                     % of reads unmapped: other |	0.62%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1548293	1548293	1548293
N_multimapping	11768925	11768925	11768925
N_noFeature	1732852	1917567	4004950
N_ambiguous	391321	135982	2982
UnstrandedReadsAssigned:2320795 PositiveStrandReadsAssigned:2391419 NegativeStrandReadsAssigned:437036
Dataset is classified positive stranded
MeadianReadLen=26 20thPercentileLength=22 echo kmer=19
SRR24401726 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: SRR24401726-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 17,762,186 reads, 1,160,640 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 932 rounds

  48360 SRR24401726.ke.tsv
  32833 SRR24401726.se.tsv
  81193 total
==> SRR24401726.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
AT1G19090.1	2509	2410	85	29.038
AT1G18320.1	699	600	0	0
AT5G11100.1	1709	1610	0	0
AT4G35335.1	1280	1181	23	16.034
AT1G60930.1	3876	3777	2	0.435961
AT1G17000.1	2351	2252	0	0
AT3G55270.1	3130	3031	26	7.06239
AT4G16150.1	3181	3082	67	17.8981
AT3G18150.1	1370	1271	2	1.29553

==> SRR24401726.se.tsv <==
AT1G01010	13
AT1G01020	8
AT1G03987	0
AT1G01030	2
AT1G01040	47
AT1G03993	1
AT1G01046	29
AT1G01050	25
AT1G03997	0
AT1G01060	7
SRR24401726 completed mapping pipeline successfully
