Starting /dee2/code/volunteer_pipeline.sh SRR24450944
    current disk space = 401058624512
    free memory = 384050576 
SRR24450944 SRAfilesize
45bb160538af19c7ad9921229c599eb5  SRR24450944.sra
SRR24450944.sra file validated
SRR24450944 is single end
SRR24450944 is conventional basespace
SRR24450944 read1 length is 51 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR24450944_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	51
%GC	49
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	30.3225	32.0	32.0	32.0	27.0	32.0
2	30.48	32.0	32.0	32.0	22.0	32.0
3	30.84125	27.0	27.0	37.0	27.0	37.0
4	32.43125	37.0	27.0	37.0	22.0	37.0
5	34.33625	37.0	37.0	37.0	27.0	37.0
6	36.6455	41.0	37.0	41.0	27.0	41.0
7	36.442	41.0	37.0	41.0	27.0	41.0
8	37.8135	41.0	37.0	41.0	32.0	41.0
9	37.89175	41.0	37.0	41.0	32.0	41.0
10	38.10075	41.0	37.0	41.0	32.0	41.0
11	37.9475	41.0	37.0	41.0	32.0	41.0
12	35.75475	41.0	32.0	41.0	22.0	41.0
13	37.56975	41.0	37.0	41.0	27.0	41.0
14	37.33725	41.0	37.0	41.0	27.0	41.0
15	38.14775	41.0	37.0	41.0	32.0	41.0
16	38.28275	41.0	37.0	41.0	32.0	41.0
17	37.25775	41.0	37.0	41.0	27.0	41.0
18	37.7875	41.0	37.0	41.0	32.0	41.0
19	36.66875	41.0	37.0	41.0	27.0	41.0
20	37.94575	41.0	37.0	41.0	32.0	41.0
21	36.88875	41.0	37.0	41.0	27.0	41.0
22	37.449	41.0	37.0	41.0	32.0	41.0
23	36.98325	41.0	37.0	41.0	27.0	41.0
24	37.5755	41.0	37.0	41.0	27.0	41.0
25	38.052	41.0	37.0	41.0	32.0	41.0
26	38.043	41.0	37.0	41.0	32.0	41.0
27	36.10125	41.0	37.0	41.0	22.0	41.0
28	36.80525	41.0	37.0	41.0	27.0	41.0
29	35.63625	41.0	32.0	41.0	22.0	41.0
30	36.9845	41.0	37.0	41.0	27.0	41.0
31	36.6305	41.0	37.0	41.0	27.0	41.0
32	36.47875	41.0	37.0	41.0	27.0	41.0
33	36.8805	41.0	37.0	41.0	27.0	41.0
34	38.31125	41.0	37.0	41.0	32.0	41.0
35	38.0365	41.0	37.0	41.0	32.0	41.0
36	37.3585	41.0	37.0	41.0	27.0	41.0
37	37.54825	41.0	37.0	41.0	27.0	41.0
38	37.34325	41.0	37.0	41.0	27.0	41.0
39	37.2305	41.0	37.0	41.0	27.0	41.0
40	37.9345	41.0	37.0	41.0	32.0	41.0
41	36.38275	41.0	37.0	41.0	27.0	41.0
42	36.06225	41.0	37.0	41.0	22.0	41.0
43	35.97575	41.0	32.0	41.0	22.0	41.0
44	35.60175	41.0	32.0	41.0	22.0	41.0
45	35.18075	41.0	32.0	41.0	22.0	41.0
46	36.07275	41.0	32.0	41.0	22.0	41.0
47	36.26475	41.0	37.0	41.0	22.0	41.0
48	36.02375	41.0	37.0	41.0	22.0	41.0
49	36.15975	41.0	37.0	41.0	22.0	41.0
50	36.20775	41.0	37.0	41.0	22.0	41.0
51	34.7045	37.0	32.0	41.0	22.0	41.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
22	2.0
23	2.0
24	5.0
25	13.0
26	26.0
27	43.0
28	64.0
29	89.0
30	101.0
31	154.0
32	145.0
33	203.0
34	244.0
35	283.0
36	382.0
37	518.0
38	679.0
39	853.0
40	194.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	22.325	21.0	22.675	34.0
2	35.5	21.95	17.974999999999998	24.575
3	30.425	19.8	17.825	31.95
4	37.15	21.0	16.1	25.75
5	29.675	30.575000000000003	15.575	24.175
6	25.45	24.975	16.75	32.824999999999996
7	23.575	20.349999999999998	16.950000000000003	39.125
8	19.975	18.05	27.075	34.9
9	20.599999999999998	17.775	20.575	41.05
10	20.8	28.95	18.9	31.35
11	30.8	26.325	18.475	24.4
12	29.9	33.45	18.35	18.3
13	24.175	28.075	29.925	17.825
14	21.375	26.875	24.575	27.175
15	22.575	32.300000000000004	22.575	22.55
16	30.825000000000003	28.875	18.725	21.575
17	27.625	34.699999999999996	17.424999999999997	20.25
18	25.3	29.175	17.424999999999997	28.1
19	32.1	24.425	20.9	22.575
20	28.475	21.224999999999998	29.25	21.05
21	35.0	18.475	26.325	20.200000000000003
22	38.775	19.1	23.525	18.6
23	33.95	19.3	18.875	27.875
24	37.125	21.95	16.375	24.55
25	27.6	32.550000000000004	16.3	23.549999999999997
26	23.974999999999998	28.575	16.375	31.075000000000003
27	19.7	26.650000000000002	17.25	36.4
28	20.25	22.400000000000002	16.5	40.849999999999994
29	28.000000000000004	22.35	18.075	31.574999999999996
30	22.75	21.2	19.650000000000002	36.4
31	23.225	21.7	29.025000000000002	26.05
32	29.475	23.3	24.95	22.275
33	23.375	34.575	23.1	18.95
34	24.0	40.300000000000004	21.325	14.374999999999998
35	17.875	33.45	33.550000000000004	15.125
36	15.775	28.125	40.925	15.174999999999999
37	16.45	24.45	43.3	15.8
38	15.425	34.699999999999996	33.575	16.3
39	18.85	38.324999999999996	25.624999999999996	17.2
40	29.599999999999998	32.4	20.775	17.224999999999998
41	24.125	29.45	20.0	26.424999999999997
42	22.7	33.35	21.65	22.3
43	20.075000000000003	27.725	31.474999999999998	20.724999999999998
44	19.125	34.849999999999994	28.349999999999998	17.675
45	17.9	27.700000000000003	37.65	16.75
46	18.099999999999998	27.200000000000003	39.125	15.575
47	19.400000000000002	33.775	30.925000000000004	15.9
48	27.675	28.425	26.625	17.275
49	26.3	24.625	31.5	17.575
50	24.75	23.175	25.45	26.625
51	23.075000000000003	31.724999999999998	22.875	22.325
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	2.0
14	4.0
15	2.5
16	1.0
17	1.0
18	1.0
19	4.5
20	8.0
21	11.0
22	14.0
23	19.0
24	24.0
25	23.0
26	39.0
27	56.0
28	62.0
29	68.0
30	75.0
31	82.0
32	88.0
33	94.0
34	105.0
35	116.0
36	115.0
37	114.0
38	123.5
39	133.0
40	126.5
41	120.0
42	126.0
43	132.0
44	139.5
45	147.0
46	197.0
47	247.0
48	333.5
49	420.0
50	613.0
51	806.0
52	571.0
53	336.0
54	249.5
55	163.0
56	154.0
57	145.0
58	159.0
59	173.0
60	168.0
61	163.0
62	136.5
63	110.0
64	114.0
65	118.0
66	95.0
67	72.0
68	61.0
69	50.0
70	43.0
71	36.0
72	24.5
73	13.0
74	10.0
75	5.0
76	3.0
77	1.5
78	0.0
79	0.5
80	1.0
81	1.0
82	1.0
83	0.5
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	0.0
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	0.0
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
51	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
51	4000.0
>>END_MODULE
>>Sequence Duplication Levels	pass
#Total Deduplicated Percentage	75.125
#Duplication Level	Percentage of deduplicated	Percentage of total
1	89.45091514143095	67.2
2	6.655574043261231	10.0
3	1.6638935108153077	3.75
4	0.7653910149750416	2.3
5	0.5657237936772047	2.125
6	0.19966722129783696	0.8999999999999999
7	0.13311148086522462	0.7000000000000001
8	0.06655574043261231	0.4
9	0.033277870216306155	0.22499999999999998
>10	0.4326123128119801	6.550000000000001
>50	0.0	0.0
>100	0.033277870216306155	5.8500000000000005
>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
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCA	234	5.8500000000000005	No Hit
TCGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	37	0.9249999999999999	No Hit
GCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCAG	34	0.8500000000000001	No Hit
AGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCA	26	0.65	No Hit
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	24	0.6	No Hit
TGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCA	21	0.525	No Hit
CGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGG	18	0.44999999999999996	No Hit
CGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCAGC	18	0.44999999999999996	No Hit
AAGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	17	0.42500000000000004	No Hit
ACGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	16	0.4	No Hit
CGTGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCA	16	0.4	No Hit
CGCGGCCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCA	12	0.3	No Hit
CCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCAG	12	0.3	No Hit
CGGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	11	0.27499999999999997	No Hit
CTCGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGT	9	0.22499999999999998	No Hit
CGCGTCCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCA	8	0.2	No Hit
ACCGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGT	8	0.2	No Hit
GGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCA	7	0.17500000000000002	No Hit
CCCGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGT	7	0.17500000000000002	No Hit
TACGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGT	7	0.17500000000000002	No Hit
ACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAG	7	0.17500000000000002	No Hit
CCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGG	6	0.15	No Hit
CGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTT	6	0.15	No Hit
CGCCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	6	0.15	No Hit
GGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTTG	6	0.15	No Hit
AACGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGT	6	0.15	No Hit
AGCGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGT	6	0.15	No Hit
GACGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGT	5	0.125	No Hit
CGCTACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCA	5	0.125	No Hit
ACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGTTCCGACCAT	5	0.125	No Hit
GAGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	5	0.125	No Hit
CGCACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCAG	5	0.125	No Hit
CCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGG	5	0.125	No Hit
GGGTTGGGGATTTAGCTCAGTGGTAGAGCGCTTGCCTAGCAAGCGCAAGGC	5	0.125	No Hit
CACGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGT	5	0.125	No Hit
CGCGCACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	5	0.125	No Hit
CGCGGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	5	0.125	No Hit
AGCCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	5	0.125	No Hit
TAGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	5	0.125	No Hit
GGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAAC	5	0.125	No Hit
CATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGG	5	0.125	No Hit
GCGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	5	0.125	No Hit
CTGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTC	5	0.125	No Hit
AATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGTT	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	pass
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.0	0.0	0.0	0.0
2	0.05	0.0	0.0	0.0	0.0
3	0.05	0.0	0.0	0.0	0.0
4	0.075	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	0.1	0.0	0.0	0.0	0.0
9	0.1	0.0	0.0	0.0	0.0
10	0.175	0.0	0.0	0.0	0.0
11	0.25	0.0	0.0	0.0	0.0
12	0.25	0.0	0.0	0.0	0.0
13	0.325	0.0	0.0	0.0	0.0
14	0.325	0.0	0.0	0.0	0.0
15	0.325	0.0	0.0	0.0	0.0
16	0.35	0.0	0.0	0.0	0.0
17	0.375	0.0	0.0	0.0	0.0
18	0.375	0.0	0.0	0.0	0.0
19	0.5	0.0	0.0	0.0	0.0
20	0.525	0.0	0.0	0.0	0.0
21	0.55	0.0	0.0	0.0	0.0
22	0.575	0.0	0.0	0.0	0.0
23	0.6	0.0	0.0	0.0	0.0
24	0.65	0.0	0.0	0.0	0.0
25	0.7	0.0	0.0	0.0	0.0
26	0.725	0.0	0.0	0.0	0.0
27	0.775	0.0	0.0	0.0	0.0
28	0.8	0.0	0.0	0.0	0.0
29	0.85	0.0	0.0	0.0	0.0
30	0.9	0.0	0.0	0.0	0.0
31	0.925	0.0	0.0	0.0	0.0
32	1.025	0.0	0.0	0.0	0.0
33	1.15	0.0	0.0	0.0	0.0
34	1.2	0.0	0.0	0.0	0.0
35	1.225	0.0	0.0	0.0	0.0
36	1.25	0.0	0.0	0.0	0.0
37	1.25	0.0	0.0	0.0	0.0
38	1.275	0.0	0.0	0.0	0.0
39	1.325	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TTAGTCA	70	9.094947E-12	35.357143	45
CGCGACC	55	2.9676485E-6	28.636364	1
ATTAGTC	110	1.8244464E-9	22.5	44
GCGACCT	85	3.2802945E-6	21.17647	2
CGACCTC	95	8.614274E-6	18.947369	3
ACCTCAG	120	1.3009594E-7	18.749998	5
GACCTCA	110	1.3276876E-6	18.40909	4
CTGAATT	145	4.440335E-8	17.068964	30
GCTGAAT	145	4.440335E-8	17.068964	29
TGAATTT	145	4.440335E-8	17.068964	31
CGCTGAA	150	6.553819E-8	16.5	28
GCGACCC	150	6.553819E-8	16.5	22
AATTTAA	150	6.553819E-8	16.5	33
TAAGCAT	150	6.553819E-8	16.5	37
CCGCTGA	150	6.553819E-8	16.5	27
GGCGACC	150	6.553819E-8	16.5	21
ACCCGCT	150	6.553819E-8	16.5	25
CGTGGCG	150	6.553819E-8	16.5	18
TTAAGCA	150	6.553819E-8	16.5	36
GAATTTA	150	6.553819E-8	16.5	32
>>END_MODULE
Rejected 745066 READS because READLEN < 1
Read 745066 spots for SRR24450944.sra
Written 745066 spots for SRR24450944.sra
Rejected 745066 READS because READLEN < 1
Read 745066 spots for SRR24450944.sra
Written 745066 spots for SRR24450944.sra
Rejected 745066 READS because READLEN < 1
Read 745066 spots for SRR24450944.sra
Written 745066 spots for SRR24450944.sra
Rejected 745066 READS because READLEN < 1
Read 745066 spots for SRR24450944.sra
Written 745066 spots for SRR24450944.sra
Rejected 745066 READS because READLEN < 1
Read 745066 spots for SRR24450944.sra
Written 745066 spots for SRR24450944.sra
Rejected 745066 READS because READLEN < 1
Read 745066 spots for SRR24450944.sra
Written 745066 spots for SRR24450944.sra
Rejected 745066 READS because READLEN < 1
Read 745066 spots for SRR24450944.sra
Written 745066 spots for SRR24450944.sra
Rejected 745066 READS because READLEN < 1
Read 745066 spots for SRR24450944.sra
Written 745066 spots for SRR24450944.sra
Rejected 745066 READS because READLEN < 1
Read 745066 spots for SRR24450944.sra
Written 745066 spots for SRR24450944.sra
Rejected 745075 READS because READLEN < 1
Read 745075 spots for SRR24450944.sra
Written 745075 spots for SRR24450944.sra
Rejected 745066 READS because READLEN < 1
Read 745066 spots for SRR24450944.sra
Written 745066 spots for SRR24450944.sra
Rejected 745066 READS because READLEN < 1
Read 745066 spots for SRR24450944.sra
Written 745066 spots for SRR24450944.sra
Rejected 745066 READS because READLEN < 1
Read 745066 spots for SRR24450944.sra
Written 745066 spots for SRR24450944.sra
Rejected 745066 READS because READLEN < 1
Read 745066 spots for SRR24450944.sra
Written 745066 spots for SRR24450944.sra
Rejected 745066 READS because READLEN < 1
Read 745066 spots for SRR24450944.sra
Written 745066 spots for SRR24450944.sra
Rejected 745066 READS because READLEN < 1
Read 745066 spots for SRR24450944.sra
Written 745066 spots for SRR24450944.sra
SRR ids: ['SRR24450944.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_8su2nbs3
SRR24450944.sra spots: 11921065
blocks: [[1, 745066], [745067, 1490132], [1490133, 2235198], [2235199, 2980264], [2980265, 3725330], [3725331, 4470396], [4470397, 5215462], [5215463, 5960528], [5960529, 6705594], [6705595, 7450660], [7450661, 8195726], [8195727, 8940792], [8940793, 9685858], [9685859, 10430924], [10430925, 11175990], [11175991, 11921065]]
SRR24450944 file size 322797
SRR24450944 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 16 -o SRR24450944 SRR24450944_1.fastq
Input file:	SRR24450944_1.fastq
trimmed:	SRR24450944-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):	16
Thu Jul 16 19:22:48 2026 >> started

Thu Jul 16 19:22:53 2026 >> done (5.708s)
11921065 reads processed; of these:
   22302 ( 0.19%) short reads filtered out after trimming by size control
    4580 ( 0.04%) empty reads filtered out after trimming by size control
11894183 (99.77%) reads available; of these:
   11162 ( 0.09%) trimmed reads available after processing
11883021 (99.91%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    5005	  0.04%
 19	    6157	  0.05%
 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	       0	  0.00%
 48	       0	  0.00%
 49	       0	  0.00%
 50	       0	  0.00%
 51	11883021	 99.91%
11894183 reads passed initial QC


criterion=sequence-density
sequence-density=12.70
sequence-density-rank=1
fanout-score=43.32
fanout-score-rank=1
prefix-density=1.52
prefix-fanout=43.3
sequence=CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCAGCGGAGGAAAAGAAACTAACCAGGATTCCCTCAGTAACGGCGAGTGAACAGGGAAGAGCCCAGCGCCGAATCCCCGCCGCGCGTCGCGGCGTGGGAAATGTGGCGTACGGAAGACCCACTCCCCGGCGCCGCTCGTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCAGCCCGTGGACGGTGTGAGGCCGGTAGCGGCCCCCGGCGCGCCGGGCTCGGGTCTTCCCGGAGTCGGGTTGCTTGGGAATGCAGCCCAAAGCGGGTGGTAAACTCCATCTAAGGCTAAATACCGGCACGAGACCGATAGTCAACAAGTACCGTAAGGGAAAGTTGAAAA


criterion=fanout-score
sequence-density=12.70
sequence-density-rank=1
fanout-score=43.32
fanout-score-rank=1
prefix-density=1.52
prefix-fanout=43.3
sequence=CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCAGCGGAGGAAAAGAAACTAACCAGGATTCCCTCAGTAACGGCGAGTGAACAGGGAAGAGCCCAGCGCCGAATCCCCGCCGCGCGTCGCGGCGTGGGAAATGTGGCGTACGGAAGACCCACTCCCCGGCGCCGCTCGTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCAGCCCGTGGACGGTGTGAGGCCGGTAGCGGCCCCCGGCGCGCCGGGCTCGGGTCTTCCCGGAGTCGGGTTGCTTGGGAATGCAGCCCAAAGCGGGTGGTAAACTCCATCTAAGGCTAAATACCGGCACGAGACCGATAGTCAACAAGTACCGTAAGGGAAAGTTGAAAA
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 16 -x CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCAGCGGAGGAAAAGAAACTAACCAGGATTCCCTCAGTAACGGCGAGTGAACAGGGAAGAGCCCAGCGCCGAATCCCCGCCGCGCGTCGCGGCGTGGGAAATGTGGCGTACGGAAGACCCACTCCCCGGCGCCGCTCGTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCAGCCCGTGGACGGTGTGAGGCCGGTAGCGGCCCCCGGCGCGCCGGGCTCGGGTCTTCCCGGAGTCGGGTTGCTTGGGAATGCAGCCCAAAGCGGGTGGTAAACTCCATCTAAGGCTAAATACCGGCACGAGACCGATAGTCAACAAGTACCGTAAGGGAAAGTTGAAAA -o SRR24450944 -
Input file:	STDIN
trimmed:	SRR24450944-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTAGTCAGCGGAGGAAAAGA
-- 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):	16
Thu Jul 16 19:23:14 2026 >> started

Thu Jul 16 19:23:23 2026 >> done (9.029s)
10064309 reads processed; of these:
 1443321 (14.34%) short reads filtered out after trimming by size control
 1562936 (15.53%) empty reads filtered out after trimming by size control
 7058052 (70.13%) reads available; of these:
   38088 ( 0.54%) trimmed reads available after processing
 7019964 (99.46%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   4289	  0.06%
 19	   5286	  0.07%
 20	    136	  0.00%
 21	     67	  0.00%
 22	      9	  0.00%
 23	      7	  0.00%
 24	     13	  0.00%
 25	     19	  0.00%
 26	     10	  0.00%
 27	      6	  0.00%
 28	      3	  0.00%
 29	     30	  0.00%
 30	      9	  0.00%
 31	     39	  0.00%
 32	      8	  0.00%
 33	      4	  0.00%
 34	     67	  0.00%
 35	     84	  0.00%
 36	     17	  0.00%
 37	    102	  0.00%
 38	    155	  0.00%
 39	     44	  0.00%
 40	     39	  0.00%
 41	     25	  0.00%
 42	     44	  0.00%
 43	     14	  0.00%
 44	     54	  0.00%
 45	    110	  0.00%
 46	    697	  0.01%
 47	   4182	  0.06%
 48	  31964	  0.45%
 49	      0	  0.00%
 50	      0	  0.00%
 51	7010519	 99.33%


criterion=sequence-density
sequence-density=0.59
sequence-density-rank=1
fanout-score=14.30
fanout-score-rank=2
prefix-density=0.21
prefix-fanout=14.3
sequence=GGAAGAGCACACGTCTGAACTCCAGTCACTATGTCATCTCGTATGCCGTCTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=29
fanout-score=29.17
fanout-score-rank=1
prefix-density=0.08
prefix-fanout=5.0
sequence=GGAGAAGAAAGTGGAGGCAAAGAAGGAAGAGTCCGAGGAGTCTGAAGATGACATGGGCTTCGGTCTTTTTGACTAAACTGCTTTTGTTAAGTTGGCTAATAAAGAGCTGAACCTGTA
                                 Started job on |	Jul 16 19:23:50
                             Started mapping on |	Jul 16 19:23:51
                                    Finished on |	Jul 16 19:24:23
       Mapping speed, Million of reads per hour |	999.89

                          Number of input reads |	8887926
                      Average input read length |	50
                                    UNIQUE READS:
                   Uniquely mapped reads number |	5430505
                        Uniquely mapped reads % |	61.10%
                          Average mapped length |	49.51
                       Number of splices: Total |	260128
            Number of splices: Annotated (sjdb) |	243302
                       Number of splices: GT/AG |	246682
                       Number of splices: GC/AG |	2606
                       Number of splices: AT/AC |	125
               Number of splices: Non-canonical |	10715
                      Mismatch rate per base, % |	0.80%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.73
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.12
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	2222130
             % of reads mapped to multiple loci |	25.00%
        Number of reads mapped to too many loci |	194843
             % of reads mapped to too many loci |	2.19%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.16%
                     % of reads unmapped: other |	0.55%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1235291	1235291	1235291
N_multimapping	2222130	2222130	2222130
N_noFeature	1143852	1177953	4526068
N_ambiguous	916091	45512	713191
UnstrandedReadsAssigned:3370562 PositiveStrandReadsAssigned:4207040 NegativeStrandReadsAssigned:191246
Dataset is classified positive stranded
MeadianReadLen=51 20thPercentileLength=51 echo kmer=47
SRR24450944 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31

[quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20
[index] k-mer length: 31
[index] number of targets: 109,282
[index] number of k-mers: 95,711,799
[index] number of equivalence classes: 391,900
[quant] running in single-end mode
[quant] will process file 1: SRR24450944-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 8,887,926 reads, 3,642,366 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,128 rounds

 109283 SRR24450944.ke.tsv
  52636 SRR24450944.se.tsv
 161919 total
==> SRR24450944.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSMUST00000177564.1	16	4.59059	0	0
ENSMUST00000196221.1	9	3.70903	0	0
ENSMUST00000179664.1	11	4.02702	0	0
ENSMUST00000178537.1	12	4.16231	0	0
ENSMUST00000178862.1	14	4.39563	0	0
ENSMUST00000179520.1	11	4.02702	0	0
ENSMUST00000179883.1	16	4.59059	0	0
ENSMUST00000195858.1	10	3.87667	0	0
ENSMUST00000179932.1	12	4.16231	0	0

==> SRR24450944.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	20
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR24450944 completed mapping pipeline successfully
