Starting /dee2/code/volunteer_pipeline.sh SRR24401724
    current disk space = 1324085112
    free memory = 60099048 
SRR24401724 SRAfilesize
ceb4279d0aa343eb3297a9bcfecc5cfd  SRR24401724.sra
SRR24401724.sra file validated
SRR24401724 is single end
SRR24401724 is conventional basespace
SRR24401724 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR24401724_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	47
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	36.511	37.0	37.0	37.0	37.0	37.0
2	36.1205	37.0	37.0	37.0	37.0	37.0
3	36.503	37.0	37.0	37.0	37.0	37.0
4	36.611	37.0	37.0	37.0	37.0	37.0
5	36.518	37.0	37.0	37.0	37.0	37.0
6	36.5345	37.0	37.0	37.0	37.0	37.0
7	36.539	37.0	37.0	37.0	37.0	37.0
8	36.4935	37.0	37.0	37.0	37.0	37.0
9	36.5845	37.0	37.0	37.0	37.0	37.0
10	36.4445	37.0	37.0	37.0	37.0	37.0
11	36.562	37.0	37.0	37.0	37.0	37.0
12	36.617	37.0	37.0	37.0	37.0	37.0
13	36.649	37.0	37.0	37.0	37.0	37.0
14	36.581	37.0	37.0	37.0	37.0	37.0
15	36.451	37.0	37.0	37.0	37.0	37.0
16	36.63	37.0	37.0	37.0	37.0	37.0
17	36.492	37.0	37.0	37.0	37.0	37.0
18	36.3245	37.0	37.0	37.0	37.0	37.0
19	36.549	37.0	37.0	37.0	37.0	37.0
20	36.5685	37.0	37.0	37.0	37.0	37.0
21	36.6285	37.0	37.0	37.0	37.0	37.0
22	36.546	37.0	37.0	37.0	37.0	37.0
23	36.555	37.0	37.0	37.0	37.0	37.0
24	36.4845	37.0	37.0	37.0	37.0	37.0
25	36.4885	37.0	37.0	37.0	37.0	37.0
26	36.582	37.0	37.0	37.0	37.0	37.0
27	36.433	37.0	37.0	37.0	37.0	37.0
28	36.376	37.0	37.0	37.0	37.0	37.0
29	36.6045	37.0	37.0	37.0	37.0	37.0
30	36.5935	37.0	37.0	37.0	37.0	37.0
31	36.6535	37.0	37.0	37.0	37.0	37.0
32	36.5385	37.0	37.0	37.0	37.0	37.0
33	36.5235	37.0	37.0	37.0	37.0	37.0
34	36.4615	37.0	37.0	37.0	37.0	37.0
35	36.36975	37.0	37.0	37.0	37.0	37.0
36	36.4635	37.0	37.0	37.0	37.0	37.0
37	36.4335	37.0	37.0	37.0	37.0	37.0
38	36.5075	37.0	37.0	37.0	37.0	37.0
39	36.4655	37.0	37.0	37.0	37.0	37.0
40	36.4995	37.0	37.0	37.0	37.0	37.0
41	36.361	37.0	37.0	37.0	37.0	37.0
42	36.453	37.0	37.0	37.0	37.0	37.0
43	36.2435	37.0	37.0	37.0	37.0	37.0
44	36.1895	37.0	37.0	37.0	37.0	37.0
45	36.178	37.0	37.0	37.0	37.0	37.0
46	36.223	37.0	37.0	37.0	37.0	37.0
47	36.1235	37.0	37.0	37.0	37.0	37.0
48	36.2165	37.0	37.0	37.0	37.0	37.0
49	36.277	37.0	37.0	37.0	37.0	37.0
50	36.3305	37.0	37.0	37.0	37.0	37.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
23	1.0
24	0.0
25	3.0
26	2.0
27	5.0
28	9.0
29	14.0
30	20.0
31	37.0
32	31.0
33	47.0
34	83.0
35	216.0
36	1637.0
37	1895.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	18.35	33.975	39.275	8.4
2	23.604060913705585	17.00507614213198	31.472081218274113	27.918781725888326
3	29.349999999999998	16.825000000000003	27.0	26.825
4	29.004004004004003	24.34934934934935	32.45745745745746	14.18918918918919
5	16.425	31.2	20.125	32.25
6	15.975	26.400000000000002	37.125	20.5
7	44.95	17.8	27.950000000000003	9.3
8	14.875	38.65	36.525	9.950000000000001
9	14.875	49.0	22.275	13.850000000000001
10	43.55	15.625	28.475	12.35
11	14.924999999999999	27.675	37.175000000000004	20.225
12	15.7	25.275	31.724999999999998	27.3
13	14.75	28.575	20.95	35.725
14	24.775	38.05	25.324999999999996	11.85
15	34.025	26.55	24.45	14.975
16	14.85	43.25	18.075	23.825
17	20.175	39.625	28.575	11.625
18	43.125	17.875	16.6	22.400000000000002
19	15.725	35.9	34.849999999999994	13.525
20	33.975	20.5	32.875	12.65
21	24.925	28.9	16.8	29.375
22	30.8	34.8	18.224999999999998	16.175
23	33.85	34.5	14.2	17.45
24	20.05	48.475	18.375	13.100000000000001
25	17.775	46.5	17.599999999999998	18.125
26	47.025	23.125	18.575	11.275
27	14.825	43.775	24.099999999999998	17.299999999999997
28	30.525000000000002	17.125	27.325	25.025
29	24.675	20.25	20.4	34.675
30	47.775	33.1	6.2	12.925
31	34.150000000000006	38.175	6.825	20.849999999999998
32	21.224999999999998	57.35	8.924999999999999	12.5
33	22.625	40.9	9.225	27.250000000000004
34	43.2	24.2	18.6	14.000000000000002
35	18.714035526644984	33.80035026269702	18.463847885914436	29.02176632474356
36	27.625	25.7	7.225	39.45
37	17.825	30.325000000000003	15.5	36.35
38	32.6	38.775	7.825	20.8
39	14.625	32.550000000000004	17.05	35.775
40	19.35	41.6	11.275	27.775
41	20.150000000000002	24.9	15.25	39.7
42	29.75	18.975	23.825	27.450000000000003
43	26.275	16.525000000000002	29.25	27.950000000000003
44	18.75	19.0	14.374999999999998	47.875
45	16.400000000000002	35.55	22.6	25.45
46	33.525	36.55	8.9	21.025
47	8.375	45.525	19.5	26.6
48	9.4	33.050000000000004	20.95	36.6
49	12.25	30.65	14.374999999999998	42.725
50	10.65	13.825000000000001	33.650000000000006	41.875
>>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	0.5
20	1.0
21	1.0
22	1.0
23	1.0
24	1.0
25	1.5
26	2.0
27	2.0
28	2.0
29	2.5
30	3.0
31	3.0
32	3.0
33	7.0
34	11.0
35	29.5
36	48.0
37	76.0
38	104.0
39	123.0
40	142.0
41	293.0
42	444.0
43	466.0
44	488.0
45	503.5
46	519.0
47	631.0
48	743.0
49	588.0
50	433.0
51	405.0
52	377.0
53	423.5
54	470.0
55	301.5
56	133.0
57	93.5
58	54.0
59	36.0
60	18.0
61	10.5
62	3.0
63	1.5
64	0.0
65	0.0
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	1.5
3	0.0
4	0.1
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	0.075
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	56.725
#Duplication Level	Percentage of deduplicated	Percentage of total
1	86.1172322609079	48.85
2	9.167033935654473	10.4
3	1.4984574702512121	2.55
4	0.6610841780520054	1.5
5	0.3966505068312032	1.125
6	0.22036139268400176	0.75
7	0.3085059497576025	1.225
8	0.22036139268400176	1.0
9	0.08814455707360071	0.44999999999999996
>10	1.0577346848832083	12.174999999999999
>50	0.13221683561040104	4.35
>100	0.13221683561040104	15.625
>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
TTGACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATAT	309	7.725	TruSeq Adapter, Index 6 (100% over 41bp)
TCCGCTGTAGCACATCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	194	4.8500000000000005	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGTTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCC	122	3.05	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	64	1.6	No Hit
AGTTACTAATTCATGATCTGGCATAGATCGGAAGAGCACACGTCTGAACT	59	1.4749999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AGTTACTAATTCATGATCTGGCAAAGATCGGAAGAGCACACGTCTGAACT	51	1.275	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TCCGCTGTAGCACACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	35	0.8750000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCC	35	0.8750000000000001	TruSeq Adapter, Index 6 (100% over 36bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATG	34	0.8500000000000001	TruSeq Adapter, Index 6 (100% over 49bp)
CTTCGTGATTGATTTGCCATATTTTCTGATCAGATCGGAAGAGCACACGT	32	0.8	No Hit
TCCGTTGTAGTCTAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	29	0.7250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TTCATGGACGTTGATAAGATCTTTCAGATCGGAAGAGCACACGTCTGAAC	29	0.7250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GCGTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	28	0.7000000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGTCTGTAGTCCAACGGTAGGATAATTGCAGATCGGAAGAGCACACGTC	26	0.65	No Hit
TCCCAAATGTAGACAAAGCAGATCGGAAGAGCACACGTCTGAACTCCAGT	26	0.65	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCGCGTATG	19	0.475	TruSeq Adapter, Index 6 (97% over 49bp)
TCCCAAATGTAGACAAAGCAAGATCGGAAGAGCACACGTCTGAACTCCAG	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TGACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATC	17	0.42500000000000004	TruSeq Adapter, Index 6 (100% over 42bp)
TCCGTTATCGTCCAGCGGTTAGGATATCTGGAGATCGGAAGAGCACACGT	16	0.4	No Hit
AACTACGATCTTTGGCTCTGGAACTGAATCATTTAGATCGGAAGAGCACA	16	0.4	No Hit
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAGATCGGAAGA	15	0.375	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	14	0.35000000000000003	No Hit
AACTACGATCTTTGGCTCTGGAACTGAATCATTAGATCGGAAGAGCACAC	14	0.35000000000000003	No Hit
AACTACGATCTTTGGCTCTGGAACTGAATCATTTCAGATCGGAAGAGCAC	14	0.35000000000000003	No Hit
GTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGC	13	0.325	TruSeq Adapter, Index 5 (97% over 35bp)
AGTTACTAATTCATGATCTGGCAAGATCGGAAGAGCACACGTCTGAACTC	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCTAGATCGGAAGAGCACAC	12	0.3	No Hit
TCCGCTGTAGCACACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AGTTACTAATTCATGATCTGGTAGATCGGAAGAGCACACGTCTGAACTCC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
ATTTATTTCTACATCTAGGATCCGATTTGTATCAGATCGGAAGAGCACAC	10	0.25	No Hit
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCC	9	0.22499999999999998	TruSeq Adapter, Index 6 (100% over 36bp)
TAACATTGATGATACTTCTGCAATTCTGAGGCAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
CCGCTGTAGCACATCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACG	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
AACTACGATCTTTGGCTCTGGAACTGAATCATAGATCGGAAGAGCACACG	8	0.2	No Hit
GGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTAGATCGGAAGAGCACA	8	0.2	No Hit
AGTTACTAATTCATGATCTGGCACAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
ATTCTTTGACGAGAAAAACGCTGGCTTACTGAGGTAAGATCGGAAGAGCA	8	0.2	No Hit
GGGGATGTAGCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGCTGTAGCACTTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TNCGCTGTAGCACATCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TTCATGGACGTTGATAAGATCTTTCCAGATCGGAAGAGCACACGTCTGAA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TGTGGCTGCTTAAAAAACTGATTCAACGAGATAAGATCGGAAGAGCACAC	7	0.17500000000000002	No Hit
TCCGCTTTTATGTTAGTTCGTACTATAAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
AACTACGATCTTTGGCTCTGGAACTGAATCATTTAAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
GGGGGTGTAGCTCATAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCGCTGTAGCACACCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TTTGGATTGAAGGGAGCTCTAAGATCGGAAGAGCACACGTCTGAACTCCA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
ANTTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TTTGGATTGAAGGGAGCTCTAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AACTACGATCTTTGGCTCTGGAACTGAATCATTTCCAGATCGGAAGAGCA	5	0.125	No Hit
AACTGTGACGATAGCAAGTGCCGTCTGAGCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
TCGATAAACCTCTGCATCCAGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGCTTTTATGTTAGTTCGTACTATAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCGTCTGTAGTCCAACGGTAGGATAATTGCCAGATCGGAAGAGCACACGT	5	0.125	No Hit
TCCGCTGTAGCACATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TTGACAGAAGATCGGAAAGCACACGTCTGAACTCCAGTCACGCCAATATC	5	0.125	TruSeq Adapter, Index 6 (97% over 35bp)
TTCTTTGACGAGAAAAACGCTGGCTTACTGAGGTAAGATCGGAAGAGCAC	5	0.125	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
>>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	1.45	0.0	0.0	0.0	0.0
2	1.5	0.0	0.0	0.0	0.0
3	1.5	0.0	0.0	0.0	0.0
4	1.5	0.0	0.0	0.0	0.0
5	1.525	0.0	0.0	0.0	0.0
6	1.75	0.0	0.0	0.0	0.0
7	1.775	0.0	0.0	0.0	0.0
8	2.375	0.0	0.0	0.0	0.0
9	10.725	0.0	0.0	0.0	0.0
10	10.875	0.0	0.0	0.0	0.0
11	11.05	0.0	0.0	0.0	0.0
12	11.2	0.0	0.0	0.0	0.0
13	11.85	0.0	0.0	0.0	0.0
14	13.675	0.0	0.0	0.0	0.0
15	14.95	0.0	0.0	0.0	0.0
16	16.375	0.0	0.0	0.0	0.0
17	26.575	0.0	0.0	0.0	0.0
18	27.25	0.0	0.0	0.0	0.0
19	28.65	0.0	0.0	0.0	0.0
20	30.675	0.0	0.0	0.0	0.0
21	33.25	0.0	0.0	0.0	0.0
22	37.225	0.0	0.0	0.0	0.0
23	45.775	0.0	0.0	0.0	0.0
24	51.75	0.0	0.0	0.0	0.0
25	68.85	0.0	0.0	0.0	0.0
26	70.975	0.0	0.0	0.0	0.0
27	72.15	0.0	0.0	0.0	0.0
28	73.15	0.0	0.0	0.0	0.0
29	73.775	0.0	0.0	0.0	0.0
30	74.7	0.0	0.0	0.0	0.0
31	76.675	0.0	0.0	0.0	0.0
32	81.275	0.0	0.0	0.0	0.0
33	83.7	0.0	0.0	0.0	0.0
34	86.175	0.0	0.0	0.0	0.0
35	88.25	0.0	0.0	0.0	0.0
36	89.825	0.0	0.0	0.0	0.0
37	90.775	0.0	0.0	0.0	0.0
38	91.35	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CACACAG	20	6.952051E-4	44.000004	11
TTGACAG	20	6.952051E-4	44.000004	1
AACGGTT	20	6.952051E-4	44.000004	14
ACGGTTA	20	6.952051E-4	44.000004	15
GCACACA	20	6.952051E-4	44.000004	10
CCAACGG	30	1.9515464E-6	44.0	12
CCGCTGT	35	1.02281774E-7	44.0	2
TAGCACA	25	3.6958358E-5	44.0	8
GGTTAGG	25	3.6958358E-5	44.0	17
TGTAGCA	35	1.02281774E-7	44.0	6
GCGTCTG	30	1.9515464E-6	44.0	1
GTTAGGA	25	3.6958358E-5	44.0	18
TTAGGAT	25	3.6958358E-5	44.0	19
TCCGCTG	35	1.02281774E-7	44.0	1
TCCAACG	30	1.9515464E-6	44.0	11
CGGTTAG	25	3.6958358E-5	44.0	16
CTGTAGC	35	1.02281774E-7	44.0	5
CGTCTGT	30	1.9515464E-6	44.0	2
GTAGCAC	35	1.02281774E-7	44.0	7
CAACGGT	30	1.9515464E-6	44.0	13
>>END_MODULE
Rejected 2722845 READS because READLEN < 1
Read 2722845 spots for SRR24401724.sra
Written 2722845 spots for SRR24401724.sra
Rejected 2722847 READS because READLEN < 1
Read 2722847 spots for SRR24401724.sra
Written 2722847 spots for SRR24401724.sra
Rejected 2722845 READS because READLEN < 1
Read 2722845 spots for SRR24401724.sra
Written 2722845 spots for SRR24401724.sra
Rejected 2722845 READS because READLEN < 1
Read 2722845 spots for SRR24401724.sra
Written 2722845 spots for SRR24401724.sra
SRR ids: ['SRR24401724.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ca29esjm
SRR24401724.sra spots: 10891382
blocks: [[1, 2722845], [2722846, 5445690], [5445691, 8168535], [8168536, 10891382]]
SRR24401724 file size 1520536
SRR24401724 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 SRR24401724 SRR24401724_1.fastq
Input file:	SRR24401724_1.fastq
trimmed:	SRR24401724-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 11:50:49 2026 >> started

Tue Jan 13 11:50:54 2026 >> done (5.269s)
10891382 reads processed; of these:
 2877696 (26.42%) short reads filtered out after trimming by size control
  142647 ( 1.31%) empty reads filtered out after trimming by size control
 7871039 (72.27%) reads available; of these:
  110702 ( 1.41%) trimmed reads available after processing
 7760337 (98.59%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 108749	  1.38%
 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	      0	  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	    878	  0.01%
 48	    351	  0.00%
 49	    724	  0.01%
 50	7760337	 98.59%
7871039 reads passed initial QC


criterion=sequence-density
sequence-density=88.96
sequence-density-rank=1
fanout-score=41.60
fanout-score-rank=1
prefix-density=92.55
prefix-fanout=40.0
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTC


criterion=fanout-score
sequence-density=88.96
sequence-density-rank=1
fanout-score=41.60
fanout-score-rank=1
prefix-density=92.55
prefix-fanout=40.0
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTC
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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTC -o SRR24401724 -
Input file:	STDIN
trimmed:	SRR24401724-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTC
-- 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 11:51:01 2026 >> started

Tue Jan 13 11:51:08 2026 >> done (6.916s)
7694162 reads processed; of these:
  13784 ( 0.18%) short reads filtered out after trimming by size control
    803 ( 0.01%) empty reads filtered out after trimming by size control
7679575 (99.81%) reads available; of these:
7421088 (96.63%) trimmed reads available after processing
 258487 ( 3.37%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 106578	  1.39%
 19	 226895	  2.95%
 20	 277620	  3.62%
 21	 501803	  6.53%
 22	 953004	 12.41%
 23	 768227	 10.00%
 24	1990444	 25.92%
 25	 236139	  3.07%
 26	 143098	  1.86%
 27	  99327	  1.29%
 28	  83998	  1.09%
 29	  93322	  1.22%
 30	 188224	  2.45%
 31	 518033	  6.75%
 32	 231522	  3.01%
 33	 231028	  3.01%
 34	 181107	  2.36%
 35	 170269	  2.22%
 36	 102448	  1.33%
 37	  55058	  0.72%
 38	  44143	  0.57%
 39	  91657	  1.19%
 40	  43503	  0.57%
 41	  37086	  0.48%
 42	  35403	  0.46%
 43	  40286	  0.52%
 44	  25051	  0.33%
 45	  21779	  0.28%
 46	  13319	  0.17%
 47	  14269	  0.19%
 48	     25	  0.00%
 49	     21	  0.00%
 50	 154889	  2.02%


criterion=sequence-density
sequence-density=10.66
sequence-density-rank=1
fanout-score=5.56
fanout-score-rank=3
prefix-density=0.12
prefix-fanout=5.6
sequence=AGTTACTAATTCATGATCTGGCA


criterion=fanout-score
sequence-density=0.27
sequence-density-rank=15
fanout-score=43.05
fanout-score-rank=1
prefix-density=0.47
prefix-fanout=25.2
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCT
                                 Started job on |	Jan 13 11:51:23
                             Started mapping on |	Jan 13 11:51:23
                                    Finished on |	Jan 13 11:52:09
       Mapping speed, Million of reads per hour |	614.85

                          Number of input reads |	7856452
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	3618183
                        Uniquely mapped reads % |	46.05%
                          Average mapped length |	25.74
                       Number of splices: Total |	36416
            Number of splices: Annotated (sjdb) |	16523
                       Number of splices: GT/AG |	33405
                       Number of splices: GC/AG |	288
                       Number of splices: AT/AC |	81
               Number of splices: Non-canonical |	2642
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.10
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.04
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	3160753
             % of reads mapped to multiple loci |	40.23%
        Number of reads mapped to too many loci |	669793
             % of reads mapped to too many loci |	8.53%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	4.74%
                     % of reads unmapped: other |	0.45%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1077516	1077516	1077516
N_multimapping	3160753	3160753	3160753
N_noFeature	1932668	2117497	3270405
N_ambiguous	267571	104018	1945
UnstrandedReadsAssigned:1417944 PositiveStrandReadsAssigned:1396668 NegativeStrandReadsAssigned:345833
Dataset is classified unstranded
MeadianReadLen=24 20thPercentileLength=22 echo kmer=19
SRR24401724 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: SRR24401724-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 7,856,452 reads, 909,742 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,125 rounds

  48360 SRR24401724.ke.tsv
  32833 SRR24401724.se.tsv
  81193 total
==> SRR24401724.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
AT1G19090.1	2509	2410	302	134.033
AT1G18320.1	699	600	0	0
AT5G11100.1	1709	1610	0	0
AT4G35335.1	1280	1181	5	4.52837
AT1G60930.1	3876	3777	1	0.283188
AT1G17000.1	2351	2252	0	0
AT3G55270.1	3130	3031	14	4.94042
AT4G16150.1	3181	3082	18	6.24686
AT3G18150.1	1370	1271	6	5.04926

==> SRR24401724.se.tsv <==
AT1G01010	3
AT1G01020	3
AT1G03987	0
AT1G01030	0
AT1G01040	24
AT1G03993	0
AT1G01046	14
AT1G01050	8
AT1G03997	0
AT1G01060	10
SRR24401724 completed mapping pipeline successfully
