Starting /dee2/code/volunteer_pipeline.sh SRR24401716
    current disk space = 1329110152
    free memory = 60216772 
SRR24401716 SRAfilesize
055a57e415b72c03a0773f2d87da8155  SRR24401716.sra
SRR24401716.sra file validated
SRR24401716 is single end
SRR24401716 is conventional basespace
SRR24401716 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR24401716_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	49
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	34.9845	37.0	37.0	37.0	25.0	37.0
2	35.2565	37.0	37.0	37.0	25.0	37.0
3	35.405	37.0	37.0	37.0	37.0	37.0
4	35.3145	37.0	37.0	37.0	25.0	37.0
5	35.358	37.0	37.0	37.0	25.0	37.0
6	34.6135	37.0	37.0	37.0	25.0	37.0
7	35.092	37.0	37.0	37.0	25.0	37.0
8	34.998	37.0	37.0	37.0	25.0	37.0
9	35.753	37.0	37.0	37.0	37.0	37.0
10	35.766	37.0	37.0	37.0	37.0	37.0
11	35.552	37.0	37.0	37.0	37.0	37.0
12	35.674	37.0	37.0	37.0	37.0	37.0
13	35.6675	37.0	37.0	37.0	37.0	37.0
14	35.542	37.0	37.0	37.0	37.0	37.0
15	35.6755	37.0	37.0	37.0	37.0	37.0
16	35.6805	37.0	37.0	37.0	37.0	37.0
17	35.6685	37.0	37.0	37.0	37.0	37.0
18	35.73	37.0	37.0	37.0	37.0	37.0
19	35.715	37.0	37.0	37.0	37.0	37.0
20	35.3875	37.0	37.0	37.0	37.0	37.0
21	35.6335	37.0	37.0	37.0	37.0	37.0
22	35.5315	37.0	37.0	37.0	37.0	37.0
23	35.669	37.0	37.0	37.0	37.0	37.0
24	35.7375	37.0	37.0	37.0	37.0	37.0
25	35.517	37.0	37.0	37.0	37.0	37.0
26	35.181	37.0	37.0	37.0	25.0	37.0
27	35.5685	37.0	37.0	37.0	37.0	37.0
28	35.6665	37.0	37.0	37.0	37.0	37.0
29	35.7935	37.0	37.0	37.0	37.0	37.0
30	35.6165	37.0	37.0	37.0	37.0	37.0
31	35.7345	37.0	37.0	37.0	37.0	37.0
32	35.7475	37.0	37.0	37.0	37.0	37.0
33	35.3095	37.0	37.0	37.0	25.0	37.0
34	35.4695	37.0	37.0	37.0	37.0	37.0
35	35.573	37.0	37.0	37.0	37.0	37.0
36	35.686	37.0	37.0	37.0	37.0	37.0
37	35.8475	37.0	37.0	37.0	37.0	37.0
38	35.732	37.0	37.0	37.0	37.0	37.0
39	35.812	37.0	37.0	37.0	37.0	37.0
40	35.632	37.0	37.0	37.0	37.0	37.0
41	35.535	37.0	37.0	37.0	37.0	37.0
42	35.386	37.0	37.0	37.0	37.0	37.0
43	35.6235	37.0	37.0	37.0	37.0	37.0
44	35.6525	37.0	37.0	37.0	37.0	37.0
45	35.498	37.0	37.0	37.0	37.0	37.0
46	35.2845	37.0	37.0	37.0	25.0	37.0
47	35.535	37.0	37.0	37.0	37.0	37.0
48	35.358	37.0	37.0	37.0	37.0	37.0
49	35.432	37.0	37.0	37.0	37.0	37.0
50	35.328	37.0	37.0	37.0	37.0	37.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
22	1.0
23	0.0
24	2.0
25	6.0
26	5.0
27	20.0
28	34.0
29	55.0
30	77.0
31	100.0
32	128.0
33	198.0
34	308.0
35	538.0
36	1907.0
37	621.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	21.375	31.4	29.175	18.05
2	25.739348370927317	24.085213032581454	24.260651629072683	25.914786967418546
3	34.275	24.075	21.525	20.125
4	31.3	27.950000000000003	25.275	15.475
5	20.825	35.875	19.625	23.674999999999997
6	23.05	21.2	33.074999999999996	22.675
7	34.875	25.8	25.05	14.274999999999999
8	19.75	31.25	32.9	16.1
9	21.725	34.575	23.95	19.75
10	37.7	16.325	27.875	18.099999999999998
11	21.775	22.55	35.949999999999996	19.725
12	22.35	19.1	29.625	28.925
13	24.224999999999998	25.3	20.549999999999997	29.925
14	23.65	36.15	24.2	16.0
15	32.625	29.325000000000003	21.575	16.475
16	18.325	35.55	23.799999999999997	22.325
17	26.924999999999997	30.475	28.349999999999998	14.249999999999998
18	35.55	23.525	18.7	22.225
19	24.5	29.175	30.225	16.1
20	33.725	26.950000000000003	26.424999999999997	12.9
21	27.0	37.125	17.1	18.775
22	25.624999999999996	37.275000000000006	20.849999999999998	16.25
23	32.300000000000004	35.425000000000004	17.125	15.15
24	27.474999999999998	36.85	21.875	13.8
25	27.700000000000003	35.449999999999996	21.025	15.825
26	32.4	28.725	21.224999999999998	17.65
27	25.8	36.65	17.299999999999997	20.25
28	31.7	27.825	20.200000000000003	20.275000000000002
29	30.7	31.525	14.224999999999998	23.549999999999997
30	35.05	34.599999999999994	10.4	19.950000000000003
31	34.475	34.449999999999996	11.899999999999999	19.175
32	28.975	39.525	13.25	18.25
33	30.15	36.55	10.100000000000001	23.200000000000003
34	31.6	30.325000000000003	15.375	22.7
35	24.4	33.775	12.325	29.5
36	26.924999999999997	35.9	9.025	28.15
37	24.224999999999998	36.4	10.7	28.675
38	29.575000000000003	34.300000000000004	11.325000000000001	24.8
39	24.3	27.650000000000002	16.75	31.3
40	23.825	34.075	15.1	27.0
41	23.974999999999998	27.650000000000002	16.275000000000002	32.1
42	23.525	31.175000000000004	16.05	29.25
43	24.474999999999998	24.7	23.724999999999998	27.1
44	25.575	25.2	16.925	32.300000000000004
45	19.45	33.975	20.1	26.474999999999998
46	23.5	29.875	16.425	30.2
47	18.0	31.65	16.55	33.800000000000004
48	15.5	30.25	20.025000000000002	34.225
49	20.65	27.400000000000002	13.900000000000002	38.05
50	14.025000000000002	28.7	22.775000000000002	34.5
>>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	0.5
6	1.0
7	0.5
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	0.5
18	1.0
19	0.5
20	0.0
21	0.5
22	1.0
23	0.5
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.5
30	1.0
31	1.0
32	1.0
33	2.5
34	4.0
35	17.5
36	31.0
37	43.5
38	56.0
39	80.0
40	104.0
41	157.5
42	211.0
43	317.0
44	423.0
45	443.0
46	463.0
47	506.0
48	549.0
49	558.5
50	568.0
51	582.5
52	597.0
53	569.5
54	542.0
55	416.0
56	290.0
57	198.0
58	106.0
59	68.5
60	31.0
61	24.0
62	17.0
63	10.0
64	3.0
65	1.5
66	0.0
67	0.0
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	0.25
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	62.949999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	77.99841143764893	49.1
2	14.058776806989675	17.7
3	3.8125496425734715	7.199999999999999
4	1.7077045274027005	4.3
5	0.47656870532168394	1.5
6	0.3574265289912629	1.35
7	0.4368546465448769	1.925
8	0.11914217633042098	0.6
9	0.11914217633042098	0.675
>10	0.7942811755361397	8.325000000000001
>50	0.07942811755361398	4.275
>100	0.03971405877680699	3.05
>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	122	3.05	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TTGACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTAT	95	2.375	TruSeq Adapter, Index 2 (100% over 41bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAGATCGGAAGA	76	1.9	No Hit
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGA	38	0.95	TruSeq Adapter, Index 2 (100% over 36bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGA	31	0.775	TruSeq Adapter, Index 2 (100% over 36bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	26	0.65	No Hit
TTCATGGACGTTGATAAGATCTTTCAGATCGGAAGAGCACACGTCTGAAC	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TTAGGGAAGTACTTTAAGAAACATATGTATAAGATCGGAAGAGCACACGT	17	0.42500000000000004	No Hit
CCAAGATGAGTGCTCTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGT	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TAAAACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCC	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TAAAACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGGATATGGCGGAATTGGTAGACGCTACGGACTTAGATCGGAAGAGCAC	14	0.35000000000000003	No Hit
TGACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATC	13	0.325	TruSeq Adapter, Index 2 (100% over 42bp)
TCCCAAATGTAGACAAAGCAGATCGGAAGAGCACACGTCTGAACTCCAGT	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GCGTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGTTACTAATTCATGATCTGGTAGATCGGAAGAGCACACGTCTGAACTCC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
AACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GCGTCTGTAGTCCAACGGTAGGATAATTGCAGATCGGAAGAGCACACGTC	12	0.3	No Hit
CTTCGTGATTGATTTGCCATATTTTCTGATCAGATCGGAAGAGCACACGT	11	0.27499999999999997	No Hit
CAAGATGAGTGCTCTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTC	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TGAAAGTGACTACATCGGGGTAGATCGGAAGAGCACACGTCTGAACTCCA	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CTAACAGACCGGTAGACTTGAACAGATCGGAAGAGCACACGTCTGAACTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAAGATCGGAAG	9	0.22499999999999998	No Hit
AAAACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGAAGATCGGAAGA	8	0.2	No Hit
AACTGTGACGATAGCAAGTGCCGTCTGAGCAGATCGGAAGAGCACACGTC	8	0.2	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	8	0.2	No Hit
TCCGCTGTAGCACATCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
GACTCTAGTCCGACTTTGTGAAATGAGATCGGAAGAGCACACGTCTGAAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
ATAGCTCGACGCCAGGATGAGATCGGAAGAGCACACGTCTGAACTCCAGT	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCGATAAACCTCTGCATCCAGAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAAAACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGATGTCGTCCAGCGGTTAGGATATCTGGAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCTAGATCGGAAGAGCACAC	7	0.17500000000000002	No Hit
TCCGCTGTAGCACACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGCTTTTATGTTAGTTCGTACTATAAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TCCCAAATGTAGACAAAGCAAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCGTTATCGTCCAGCGGTTAGGATATCTGGAGATCGGAAGAGCACACGT	6	0.15	No Hit
AGCTTGACTCTAGTCCGACTTTGTGAAATGACTTGAGATCGGAAGAGCAC	6	0.15	No Hit
TTCATGGACGTTGATAAGATCTTTCCAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCAGATCGGAAGAGCACACG	6	0.15	No Hit
AGTTACTAATTCATGATCTGGCATAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AGAGATATCGATATTGTTGAACGGAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AAAACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCCTTCGGGATCGGAGTAATGATTAACAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
CTGCGGAAGGATCATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TTGACTCTAGTCCGACTTTGTGAAATGACAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CCCAAGATGAGTGCTCTCCTAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CGACTTTGTGAAATGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCTAACAGACCGGTAGACTTGAACAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TAAAACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
AAAACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGTCCGACTTTGTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
CGGAAAAATAGCTCGACGCCAGGATGAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TGACTTGAGAGGTGTAGGATAAGTGGGAGCTTCAGATCGGAAGAGCACAC	5	0.125	No Hit
AAAACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TTGTTGATCTCAATAGCATTGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AAAGGACTTTGAAAAGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
>>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	0.1	0.0	0.0	0.0	0.0
3	0.1	0.0	0.0	0.0	0.0
4	0.1	0.0	0.0	0.0	0.0
5	0.1	0.0	0.0	0.0	0.0
6	0.1	0.0	0.0	0.0	0.0
7	0.1	0.0	0.0	0.0	0.0
8	0.45	0.0	0.0	0.0	0.0
9	3.375	0.0	0.0	0.0	0.0
10	3.475	0.0	0.0	0.0	0.0
11	3.575	0.0	0.0	0.0	0.0
12	3.725	0.0	0.0	0.0	0.0
13	4.175	0.0	0.0	0.0	0.0
14	7.625	0.0	0.0	0.0	0.0
15	9.375	0.0	0.0	0.0	0.0
16	10.975	0.0	0.0	0.0	0.0
17	14.35	0.0	0.0	0.0	0.0
18	16.75	0.0	0.0	0.0	0.0
19	20.0	0.0	0.0	0.0	0.0
20	23.975	0.0	0.0	0.0	0.0
21	27.775	0.0	0.0	0.0	0.0
22	33.5	0.0	0.0	0.0	0.0
23	42.2	0.0	0.0	0.0	0.0
24	46.725	0.0	0.0	0.0	0.0
25	54.925	0.0	0.0	0.0	0.0
26	58.725	0.0	0.0	0.0	0.0
27	62.775	0.0	0.0	0.0	0.0
28	65.95	0.0	0.0	0.0	0.0
29	68.225	0.0	0.0	0.0	0.0
30	70.525	0.0	0.0	0.0	0.0
31	73.075	0.0	0.0	0.0	0.0
32	77.225	0.0	0.0	0.0	0.0
33	79.775	0.0	0.0	0.0	0.0
34	81.875	0.0	0.0	0.0	0.0
35	83.9	0.0	0.0	0.0	0.0
36	86.075	0.0	0.0	0.0	0.0
37	87.75	0.0	0.0	0.0	0.0
38	88.95	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CATGATC	20	6.952051E-4	44.000004	12
TGGCAGA	20	6.952051E-4	44.000004	19
AATTCAT	20	6.952051E-4	44.000004	8
ATGATCT	20	6.952051E-4	44.000004	13
TCTGGCA	20	6.952051E-4	44.000004	17
TGATCTG	20	6.952051E-4	44.000004	14
CTGGCAG	20	6.952051E-4	44.000004	18
GACGTTG	20	6.952051E-4	44.000004	7
GATCTGG	20	6.952051E-4	44.000004	15
ATCTGGC	20	6.952051E-4	44.000004	16
GGCAGAT	25	0.002084305	35.2	20
>>END_MODULE
Rejected 6814557 READS because READLEN < 1
Read 6814557 spots for SRR24401716.sra
Written 6814557 spots for SRR24401716.sra
Rejected 6814557 READS because READLEN < 1
Read 6814557 spots for SRR24401716.sra
Written 6814557 spots for SRR24401716.sra
Rejected 6814557 READS because READLEN < 1
Read 6814557 spots for SRR24401716.sra
Written 6814557 spots for SRR24401716.sra
Rejected 6814559 READS because READLEN < 1
Read 6814559 spots for SRR24401716.sra
Written 6814559 spots for SRR24401716.sra
SRR ids: ['SRR24401716.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_bpat0vv8
SRR24401716.sra spots: 27258230
blocks: [[1, 6814557], [6814558, 13629114], [13629115, 20443671], [20443672, 27258230]]
SRR24401716 file size 3838112
SRR24401716 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 SRR24401716 SRR24401716_1.fastq
Input file:	SRR24401716_1.fastq
trimmed:	SRR24401716-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 10:59:54 2026 >> started

Tue Jan 13 11:00:07 2026 >> done (13.511s)
27258230 reads processed; of these:
 4579864 (16.80%) short reads filtered out after trimming by size control
   31635 ( 0.12%) empty reads filtered out after trimming by size control
22646731 (83.08%) reads available; of these:
  810979 ( 3.58%) trimmed reads available after processing
21835752 (96.42%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  810963	  3.58%
 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	       1	  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	      15	  0.00%
 49	       0	  0.00%
 50	21835752	 96.42%
22646731 reads passed initial QC


criterion=sequence-density
sequence-density=83.80
sequence-density-rank=1
fanout-score=50.06
fanout-score-rank=1
prefix-density=91.85
prefix-fanout=45.7
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCGCGTATGCCGTC


criterion=fanout-score
sequence-density=83.80
sequence-density-rank=1
fanout-score=50.06
fanout-score-rank=1
prefix-density=91.85
prefix-fanout=45.7
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCGCGTATGCCGTC
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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCGCGTATGCCGTC -o SRR24401716 -
Input file:	STDIN
trimmed:	SRR24401716-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCGCGTATGCCGTC
-- 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 11:00:26 2026 >> started

Tue Jan 13 11:00:46 2026 >> done (20.439s)
22107523 reads processed; of these:
   23165 ( 0.10%) short reads filtered out after trimming by size control
     129 ( 0.00%) empty reads filtered out after trimming by size control
22084229 (99.89%) reads available; of these:
21070602 (95.41%) trimmed reads available after processing
 1013627 ( 4.59%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  806014	  3.65%
 19	 1024760	  4.64%
 20	 1089911	  4.94%
 21	 1565717	  7.09%
 22	 2318288	 10.50%
 23	 1363367	  6.17%
 24	 2379648	 10.78%
 25	 1009811	  4.57%
 26	  889741	  4.03%
 27	  705043	  3.19%
 28	  645383	  2.92%
 29	  644766	  2.92%
 30	  714847	  3.24%
 31	 1010931	  4.58%
 32	  692313	  3.13%
 33	  731453	  3.31%
 34	  586863	  2.66%
 35	  598736	  2.71%
 36	  463506	  2.10%
 37	  391911	  1.77%
 38	  374354	  1.70%
 39	  980156	  4.44%
 40	  342332	  1.55%
 41	  222678	  1.01%
 42	  134011	  0.61%
 43	   72602	  0.33%
 44	   37665	  0.17%
 45	   21875	  0.10%
 46	   13251	  0.06%
 47	   20075	  0.09%
 48	       6	  0.00%
 49	       0	  0.00%
 50	  232215	  1.05%


criterion=sequence-density
sequence-density=5.32
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=6
prefix-density=0.01
prefix-fanout=1.0
sequence=AGTTACTAATTCATGATCTGGCAT


criterion=fanout-score
sequence-density=0.20
sequence-density-rank=16
fanout-score=17.46
fanout-score-rank=1
prefix-density=0.16
prefix-fanout=17.5
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCGCGTATGCCGTC
                                 Started job on |	Jan 13 11:00:58
                             Started mapping on |	Jan 13 11:00:58
                                    Finished on |	Jan 13 11:02:45
       Mapping speed, Million of reads per hour |	761.16

                          Number of input reads |	22623437
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	6220300
                        Uniquely mapped reads % |	27.49%
                          Average mapped length |	27.79
                       Number of splices: Total |	95770
            Number of splices: Annotated (sjdb) |	53582
                       Number of splices: GT/AG |	89512
                       Number of splices: GC/AG |	792
                       Number of splices: AT/AC |	698
               Number of splices: Non-canonical |	4768
                      Mismatch rate per base, % |	0.31%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.09
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.02
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	14797207
             % of reads mapped to multiple loci |	65.41%
        Number of reads mapped to too many loci |	791239
             % of reads mapped to too many loci |	3.50%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	3.16%
                     % of reads unmapped: other |	0.44%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1605930	1605930	1605930
N_multimapping	14797207	14797207	14797207
N_noFeature	2292609	2513408	5713767
N_ambiguous	439075	152281	4311
UnstrandedReadsAssigned:3488616 PositiveStrandReadsAssigned:3554611 NegativeStrandReadsAssigned:502222
Dataset is classified positive stranded
MeadianReadLen=25 20thPercentileLength=21 echo kmer=19
SRR24401716 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: SRR24401716-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 22,623,437 reads, 1,487,751 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 945 rounds

  48360 SRR24401716.ke.tsv
  32833 SRR24401716.se.tsv
  81193 total
==> SRR24401716.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
AT1G19090.1	2509	2410	166	45.177
AT1G18320.1	699	600	2.81254	3.07449
AT5G11100.1	1709	1610	0	0
AT4G35335.1	1280	1181	10	5.55362
AT1G60930.1	3876	3777	2	0.347304
AT1G17000.1	2351	2252	0	0
AT3G55270.1	3130	3031	40	8.65566
AT4G16150.1	3181	3082	53	11.279
AT3G18150.1	1370	1271	5	2.58018

==> SRR24401716.se.tsv <==
AT1G01010	2
AT1G01020	5
AT1G03987	0
AT1G01030	1
AT1G01040	43
AT1G03993	0
AT1G01046	26
AT1G01050	30
AT1G03997	0
AT1G01060	66
SRR24401716 completed mapping pipeline successfully
