Starting /dee2/code/volunteer_pipeline.sh SRR30542859
    current disk space = 1135405304
    free memory = 198419544 
SRR30542859 SRAfilesize
9160937d19c2301d2c4bac4a1c07afee  SRR30542859.sra
SRR30542859.sra file validated
SRR30542859 is single end
SRR30542859 is conventional basespace
SRR30542859 read1 length is 36 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR30542859_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	36
%GC	52
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.9305	32.0	32.0	37.0	32.0	37.0
2	34.538	37.0	32.0	37.0	32.0	37.0
3	36.038	37.0	37.0	37.0	32.0	37.0
4	36.316	37.0	37.0	37.0	37.0	37.0
5	36.378	37.0	37.0	37.0	37.0	37.0
6	36.54875	37.0	37.0	37.0	37.0	37.0
7	36.46625	37.0	37.0	37.0	37.0	37.0
8	36.59425	37.0	37.0	37.0	37.0	37.0
9	36.55575	37.0	37.0	37.0	37.0	37.0
10	36.62075	37.0	37.0	37.0	37.0	37.0
11	36.5535	37.0	37.0	37.0	37.0	37.0
12	36.50825	37.0	37.0	37.0	37.0	37.0
13	36.5265	37.0	37.0	37.0	37.0	37.0
14	36.5255	37.0	37.0	37.0	37.0	37.0
15	36.68575	37.0	37.0	37.0	37.0	37.0
16	36.5885	37.0	37.0	37.0	37.0	37.0
17	36.5835	37.0	37.0	37.0	37.0	37.0
18	36.5655	37.0	37.0	37.0	37.0	37.0
19	36.57025	37.0	37.0	37.0	37.0	37.0
20	36.55675	37.0	37.0	37.0	37.0	37.0
21	36.5935	37.0	37.0	37.0	37.0	37.0
22	36.56475	37.0	37.0	37.0	37.0	37.0
23	36.52175	37.0	37.0	37.0	37.0	37.0
24	36.5785	37.0	37.0	37.0	37.0	37.0
25	36.49125	37.0	37.0	37.0	37.0	37.0
26	36.4605	37.0	37.0	37.0	37.0	37.0
27	36.479	37.0	37.0	37.0	37.0	37.0
28	36.52175	37.0	37.0	37.0	37.0	37.0
29	36.55375	37.0	37.0	37.0	37.0	37.0
30	36.46175	37.0	37.0	37.0	37.0	37.0
31	36.28225	37.0	37.0	37.0	37.0	37.0
32	36.49725	37.0	37.0	37.0	37.0	37.0
33	36.5155	37.0	37.0	37.0	37.0	37.0
34	36.448	37.0	37.0	37.0	37.0	37.0
35	36.3055	37.0	37.0	37.0	37.0	37.0
36	36.251	37.0	37.0	37.0	37.0	37.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
11101	1	0.0
11101	2	0.0
11101	3	0.0
11101	4	0.0
11101	5	0.0
11101	6	0.0
11101	7	0.0
11101	8	0.0
11101	9	0.0
11101	10	0.0
11101	11	0.0
11101	12	0.0
11101	13	0.0
11101	14	0.0
11101	15	0.0
11101	16	0.0
11101	17	0.0
11101	18	0.0
11101	19	0.0
11101	20	0.0
11101	21	0.0
11101	22	0.0
11101	23	0.0
11101	24	0.0
11101	25	0.0
11101	26	0.0
11101	27	0.0
11101	28	0.0
11101	29	0.0
11101	30	0.0
11101	31	0.0
11101	32	0.0
11101	33	0.0
11101	34	0.0
11101	35	0.0
11101	36	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
21	2.0
22	2.0
23	2.0
24	5.0
25	4.0
26	8.0
27	10.0
28	14.0
29	19.0
30	22.0
31	33.0
32	34.0
33	51.0
34	87.0
35	166.0
36	3023.0
37	518.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	22.75	16.325	29.925	31.0
2	58.699999999999996	13.600000000000001	14.325	13.375
3	18.525	30.95	12.575	37.95
4	48.85	12.075	23.65	15.425
5	32.324999999999996	33.575	16.375	17.724999999999998
6	24.5	9.275	30.925000000000004	35.3
7	29.4	25.15	19.175	26.275
8	29.475	16.8	41.375	12.35
9	17.7	23.599999999999998	26.174999999999997	32.525
10	33.91695847923962	44.87243621810905	11.005502751375689	10.205102551275639
11	52.825	17.974999999999998	15.125	14.075
12	30.95	37.4	18.625	13.025
13	17.349999999999998	14.575	48.6	19.475
14	20.325	25.374999999999996	27.3	27.0
15	42.375	30.349999999999998	13.600000000000001	13.675
16	30.725	25.0	34.225	10.05
17	30.775000000000002	39.900000000000006	15.975	13.350000000000001
18	27.85	14.2	28.4	29.549999999999997
19	39.675	21.975	27.0	11.35
20	32.324999999999996	19.925	35.025	12.725
21	39.175	19.5	30.525000000000002	10.8
22	34.8	24.275	30.95	9.975000000000001
23	19.0	37.875	13.775	29.349999999999998
24	44.275	34.575	11.25	9.9
25	26.05	44.125	15.85	13.975000000000001
26	17.8	23.400000000000002	27.525	31.275
27	19.175	17.05	20.225	43.55
28	35.0	19.2	6.075	39.725
29	53.425	28.299999999999997	5.825	12.45
30	31.525	40.525	5.7250000000000005	22.225
31	21.807711567351028	41.3870806209314	23.785678517776667	13.019529293940913
32	44.175	31.95	8.225	15.65
33	26.8	51.225	8.1	13.875000000000002
34	31.85	39.900000000000006	5.8999999999999995	22.35
35	25.55	23.549999999999997	20.9	30.0
36	20.715536652489366	34.60095071303478	17.588191143357516	27.09532149111834
>>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	1.0
11	2.0
12	2.0
13	2.0
14	2.0
15	2.5
16	3.0
17	3.0
18	4.0
19	5.0
20	5.0
21	4.0
22	3.0
23	3.0
24	3.5
25	4.0
26	5.0
27	6.0
28	6.0
29	7.0
30	8.0
31	8.0
32	9.5
33	11.0
34	11.0
35	17.5
36	24.0
37	24.0
38	86.5
39	149.0
40	164.0
41	179.0
42	179.0
43	367.5
44	556.0
45	556.0
46	559.0
47	562.0
48	562.0
49	451.5
50	341.0
51	327.5
52	314.0
53	314.0
54	490.0
55	666.0
56	666.0
57	524.0
58	382.0
59	382.0
60	462.0
61	542.0
62	542.0
63	359.0
64	176.0
65	108.0
66	40.0
67	40.0
68	29.5
69	19.0
70	19.0
71	11.5
72	4.0
73	4.0
74	2.0
75	0.0
76	0.5
77	1.0
78	1.0
79	1.0
80	1.0
81	1.0
82	0.5
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	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.05
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	0.15
32	0.0
33	0.0
34	0.0
35	0.0
36	0.075
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
36	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	44.800000000000004
#Duplication Level	Percentage of deduplicated	Percentage of total
1	84.375	37.8
2	6.584821428571429	5.8999999999999995
3	2.6785714285714284	3.5999999999999996
4	1.6741071428571428	3.0
5	0.7254464285714286	1.625
6	0.6696428571428571	1.7999999999999998
7	0.5580357142857143	1.7500000000000002
8	0.390625	1.4000000000000001
9	0.16741071428571427	0.675
>10	1.7299107142857144	17.45
>50	0.27901785714285715	10.025
>100	0.16741071428571427	14.975
>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
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATT	322	8.05	No Hit
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGG	147	3.675	TruSeq Adapter, Index 2 (97% over 35bp)
GTTTCCGTAGTGTAGTGGTTATCAGATCGGAAGAGC	130	3.25	No Hit
TGAGGTAGTAGGTTGTATGGTTAGATCGGAAGAGCA	97	2.4250000000000003	No Hit
TGAGGTAGTAGATTGTATAGTTAGATCGGAAGAGCA	88	2.1999999999999997	No Hit
TGAGGTAGTAGTTTGTGCTGTTAGATCGGAAGAGCA	85	2.125	No Hit
CGCGACCTCAGATCAGACGTAGATCGGAAGAGCACA	66	1.6500000000000001	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTAGAT	65	1.625	No Hit
GGGGATGTAGCTCAGTGGTAGATCGGAAGAGCACAC	50	1.25	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATA	45	1.125	No Hit
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGC	44	1.0999999999999999	No Hit
TGAGGTAGTAGGTTGTATAGTTAGATCGGAAGAGCA	44	1.0999999999999999	No Hit
CGCGACCTCAGATCAGACGTGGCAGATCGGAAGAGC	40	1.0	No Hit
CGCGACCTCAGATCAGATCGGAAGAGCACACGTCTG	37	0.9249999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TGAGGTAGTAGGTTGTGTGGTTAGATCGGAAGAGCA	37	0.9249999999999999	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAAG	36	0.8999999999999999	No Hit
TGGAATGTAAGGAAGTGTGTGGAGATCGGAAGAGCA	34	0.8500000000000001	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATAGATC	33	0.8250000000000001	No Hit
CTAGACTGAGGCTCCTTGAGGAGATCGGAAGAGCAC	30	0.75	No Hit
GGAAGAGCACACGTCTGAACTCCAGTCACGGCTACA	20	0.5	TruSeq Adapter, Index 11 (100% over 36bp)
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCA	20	0.5	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGAGATC	18	0.44999999999999996	No Hit
TGAGATGAAGCACTGTAGCTCAGATCGGAAGAGCAC	17	0.42500000000000004	No Hit
CGCGACCTCAGATCGGAAGAGCACACGTCTGAACTC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CGCGACCTCAGATCAGACAGATCGGAAGAGCACACG	14	0.35000000000000003	No Hit
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGAAT	14	0.35000000000000003	No Hit
GGCTTTTTAAGTCGGATGTGAGATCGGAAGAGCACA	14	0.35000000000000003	No Hit
AGAGGTAGTAGGTTGCATAGTTAGATCGGAAGAGCA	14	0.35000000000000003	No Hit
GTCTACGGCCATACCACCCTGAACGCGCCCGATCTC	13	0.325	No Hit
TGAGGTAGTAGATTGTATAGTAGATCGGAAGAGCAC	13	0.325	No Hit
CGCGACCTCAGATCAGAAGATCGGAAGAGCACACGT	12	0.3	No Hit
TGAGGTAGTAGTTTGTACAGTTAGATCGGAAGAGCA	12	0.3	No Hit
TAGCTTATCAGACTGATGTTGACTAGATCGGAAGAG	12	0.3	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACA	10	0.25	No Hit
AACCCGTAGATCCGATCTTGTAGATCGGAAGAGCAC	10	0.25	No Hit
TCTCTGTGCTGATTGTCATGTTCTGATCAGATCGGA	10	0.25	No Hit
TGAGGTAGTAGGTTGTATGGTAGATCGGAAGAGCAC	10	0.25	No Hit
TTCACAGTGGCTAAGTTCTGCAGATCGGAAGAGCAC	10	0.25	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGA	10	0.25	No Hit
TACCTGGTTGATCCTGCCAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
TGGAAGACTAGTGATTTTGTTGTTAGATCGGAAGAG	9	0.22499999999999998	No Hit
GGCCGGTACAGTGAAACTAGATCGGAAGAGCACACG	9	0.22499999999999998	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCAGATC	8	0.2	No Hit
TGAGGTAGTAGATTGTATAGTCAGATCGGAAGAGCA	8	0.2	No Hit
ACCGGGTGCTGTAGGCTTTAGATCGGAAGAGCACAC	8	0.2	No Hit
CGCGACCTCAGATCAGACGCAGATCGGAAGAGCACA	8	0.2	No Hit
AAAAGCTGGGTTGAGAGGGCGAAGATCGGAAGAGCA	8	0.2	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGATT	8	0.2	No Hit
TGAGATGAAGCACTGTAGCTAGATCGGAAGAGCACA	8	0.2	No Hit
TCGATGTGGTGCTGCCGCGTTCTCTTCGGGCCGGGG	7	0.17500000000000002	No Hit
CAACGGAATCCCAAAAGCAGCTGAGATCGGAAGAGC	7	0.17500000000000002	No Hit
TGAGGTAGTAGTTTGTGCTGTAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCAGATCGGAA	7	0.17500000000000002	No Hit
TGAGGTAGTAGGTTGTATAGTAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
GTTTCCGTAGTGTAGTGGTTATTAGATCGGAAGAGC	7	0.17500000000000002	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGAGAT	7	0.17500000000000002	No Hit
GTCTACGGCCATACCACCCTGAACGCGCCCGATCAG	7	0.17500000000000002	No Hit
CACCCGTAGAACCGACCTTGCGAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
GCCGGTACAGTGAAACTAGATCGGAAGAGCACACGT	7	0.17500000000000002	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAAAGATCG	6	0.15	No Hit
TAGCTTATCAGACTGATGTTGATAGATCGGAAGAGC	6	0.15	No Hit
CTCTGTGCTGATTGTCATGTTCTGATCAGATCGGAA	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTCAGATCGGAAGAGCA	6	0.15	No Hit
TGAGGTAGTAGTTTGTGCTGTCAGATCGGAAGAGCA	6	0.15	No Hit
CGACTCTTAGCGGTGGATCACTCGGCAGATCGGAAG	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAAGATCGG	6	0.15	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTAGATC	6	0.15	No Hit
CGCGACCTCAGATCAGACGTGAGATCGGAAGAGCAC	6	0.15	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGAGATCG	6	0.15	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTAGA	6	0.15	No Hit
CCGCGACCTCAGATCAGACGTAGATCGGAAGAGCAC	6	0.15	No Hit
TGAGGTAGTAGGTTGTGTGGTAGATCGGAAGAGCAC	5	0.125	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCAGATCG	5	0.125	No Hit
CCGGTACAGTGAAACTGCGAATGGCTCATTAGATCG	5	0.125	No Hit
GTGGACGGTGTGAGGCAGATCGGAAGAGCACACGTC	5	0.125	No Hit
TGTAAACATCCCCGACTGGAAGCAGATCGGAAGAGC	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATCAGAT	5	0.125	No Hit
TTCACAGTGGCTAAGTTCTAGATCGGAAGAGCACAC	5	0.125	No Hit
TAGCTTATCAGACTGATGTTGAAGATCGGAAGAGCA	5	0.125	No Hit
GTTTCCGTAGTGTAGTGGTTATAAGATCGGAAGAGC	5	0.125	No Hit
AGCTACATTGTCTGCTGGGTTTCAGATCGGAAGAGC	5	0.125	No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTAGAT	5	0.125	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTC	5	0.125	No Hit
TGGCTCAGTTCAGCAGGAACAGAGATCGGAAGAGCA	5	0.125	No Hit
>>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	3.925	0.0	0.0	0.0	0.0
2	3.95	0.0	0.0	0.0	0.0
3	4.0	0.0	0.0	0.0	0.0
4	4.025	0.0	0.0	0.0	0.0
5	4.025	0.0	0.0	0.0	0.0
6	4.025	0.0	0.0	0.0	0.0
7	4.075	0.0	0.0	0.0	0.0
8	4.075	0.0	0.0	0.0	0.0
9	4.15	0.0	0.0	0.0	0.0
10	4.75	0.0	0.0	0.0	0.0
11	5.0	0.0	0.0	0.0	0.0
12	5.375	0.0	0.0	0.0	0.0
13	5.875	0.0	0.0	0.0	0.0
14	6.8	0.0	0.0	0.0	0.0
15	9.025	0.0	0.0	0.0	0.0
16	10.025	0.0	0.0	0.0	0.0
17	11.725	0.0	0.0	0.0	0.0
18	13.55	0.0	0.0	0.0	0.0
19	16.25	0.0	0.0	0.0	0.0
20	19.5	0.0	0.0	0.0	0.0
21	23.425	0.0	0.0	0.0	0.0
22	29.125	0.0	0.0	0.0	0.0
23	46.25	0.0	0.0	0.0	0.0
24	56.4	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CGCGACC	90	0.0	30.000002	1
CGCTGAA	60	5.456968E-12	30.000002	28
GAGGTAG	60	5.456968E-12	30.000002	2
TTGTATA	30	2.707939E-5	30.000002	13
AGTAGGT	30	2.707939E-5	30.000002	7
GCGACCT	90	0.0	30.000002	2
GCGACCC	60	5.456968E-12	30.000002	22
CCGCTGA	60	5.456968E-12	30.000002	27
GGCGACC	60	5.456968E-12	30.000002	21
ACCCGCT	60	5.456968E-12	30.000002	25
GTATAGT	30	2.707939E-5	30.000002	15
CCCGCTG	60	5.456968E-12	30.000002	26
CGTGGCG	60	5.456968E-12	30.000002	18
CTGAATT	55	6.366463E-11	30.000002	30
TAGTAGG	30	2.707939E-5	30.000002	6
GGTAGTA	60	5.456968E-12	30.000002	4
GCTGAAT	60	5.456968E-12	30.000002	29
TGAGGTA	55	6.366463E-11	30.000002	1
AGGTTGT	30	2.707939E-5	30.000002	10
GTAGGTT	30	2.707939E-5	30.000002	8
>>END_MODULE
Read 43048 spots for SRR30542859.sra
Written 43048 spots for SRR30542859.sra
Read 43048 spots for SRR30542859.sra
Written 43048 spots for SRR30542859.sra
Read 43048 spots for SRR30542859.sra
Written 43048 spots for SRR30542859.sra
Read 43048 spots for SRR30542859.sra
Written 43048 spots for SRR30542859.sra
Read 43048 spots for SRR30542859.sra
Written 43048 spots for SRR30542859.sra
Read 43048 spots for SRR30542859.sra
Written 43048 spots for SRR30542859.sra
Read 43048 spots for SRR30542859.sra
Written 43048 spots for SRR30542859.sra
Read 43048 spots for SRR30542859.sra
Written 43048 spots for SRR30542859.sra
SRR ids: ['SRR30542859.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_udpqac7n
SRR30542859.sra spots: 344384
blocks: [[1, 43048], [43049, 86096], [86097, 129144], [129145, 172192], [172193, 215240], [215241, 258288], [258289, 301336], [301337, 344384]]
SRR30542859 file size 49064
SRR30542859 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	/usr/local/bin/skewer -f sanger -l 18 -q 10 -k inf -t 8 -o SRR30542859 SRR30542859_1.fastq
Input file:	SRR30542859_1.fastq
trimmed:	SRR30542859-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- end quality threshold (-q):		10
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ 
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	8
Thu Nov  6 06:06:06 2025 >> started

Thu Nov  6 06:06:06 2025 >> done (0.186s)
344384 reads processed; of these:
   282 ( 0.08%) short reads filtered out after trimming by size control
 13818 ( 4.01%) empty reads filtered out after trimming by size control
330284 (95.91%) reads available; of these:
    36 ( 0.01%) trimmed reads available after processing
330248 (99.99%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 35	    36	  0.01%
 36	330248	 99.99%
330284 reads passed initial QC


criterion=sequence-density
sequence-density=55.84
sequence-density-rank=1
fanout-score=18.69
fanout-score-rank=1
prefix-density=62.01
prefix-fanout=16.8
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACA


criterion=fanout-score
sequence-density=55.84
sequence-density-rank=1
fanout-score=18.69
fanout-score-rank=1
prefix-density=62.01
prefix-fanout=16.8
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACA
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	/usr/local/bin/skewer -f sanger -l 18 -t 8 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACA -o SRR30542859 -
Input file:	STDIN
trimmed:	SRR30542859-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACA
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ 
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	8
Thu Nov  6 06:06:08 2025 >> started

Thu Nov  6 06:06:08 2025 >> done (0.104s)
318488 reads processed; of these:
 32610 (10.24%) short reads filtered out after trimming by size control
    83 ( 0.03%) empty reads filtered out after trimming by size control
285795 (89.73%) reads available; of these:
213079 (74.56%) trimmed reads available after processing
 72716 (25.44%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  7954	  2.78%
 19	 11039	  3.86%
 20	 15590	  5.45%
 21	 20523	  7.18%
 22	 58957	 20.63%
 23	 31936	 11.17%
 24	  9072	  3.17%
 25	  5630	  1.97%
 26	  4325	  1.51%
 27	  5624	  1.97%
 28	  6392	  2.24%
 29	  4871	  1.70%
 30	  5942	  2.08%
 31	 10027	  3.51%
 32	 11167	  3.91%
 33	  4030	  1.41%
 34	     0	  0.00%
 35	    12	  0.00%
 36	 72704	 25.44%


criterion=sequence-density
sequence-density=7.08
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=8
prefix-density=0.00
prefix-fanout=1.0
sequence=TGAGGTAGTAGGTTGTATGGTTAGATCGGA


criterion=fanout-score
sequence-density=0.46
sequence-density-rank=21
fanout-score=16.76
fanout-score-rank=1
prefix-density=7.69
prefix-fanout=1.0
sequence=GTAGTAGGTTGCATAGTT
                                 Started job on |	Nov 06 06:06:20
                             Started mapping on |	Nov 06 06:06:20
                                    Finished on |	Nov 06 06:06:39
       Mapping speed, Million of reads per hour |	56.39

                          Number of input reads |	297591
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	86344
                        Uniquely mapped reads % |	29.01%
                          Average mapped length |	23.84
                       Number of splices: Total |	748
            Number of splices: Annotated (sjdb) |	184
                       Number of splices: GT/AG |	697
                       Number of splices: GC/AG |	16
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	35
                      Mismatch rate per base, % |	0.41%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.43
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.42
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	104962
             % of reads mapped to multiple loci |	35.27%
        Number of reads mapped to too many loci |	77937
             % of reads mapped to too many loci |	26.19%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.49%
                     % of reads unmapped: other |	2.04%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	106285	106285	106285
N_multimapping	104962	104962	104962
N_noFeature	21569	27319	80485
N_ambiguous	2202	2093	0
UnstrandedReadsAssigned:62573 PositiveStrandReadsAssigned:56932 NegativeStrandReadsAssigned:5859
Dataset is classified positive stranded
MeadianReadLen=24 20thPercentileLength=22 echo kmer=19
SRR30542859 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: 31,715
[index] number of k-mers: 49,362,984
[index] number of equivalence classes: 166,181
[quant] running in single-end mode
[quant] will process file 1: SRR30542859-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 297,591 reads, 7,840 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 544 rounds

  31716 SRR30542859.ke.tsv
  32883 SRR30542859.se.tsv
  64599 total
==> SRR30542859.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSRNOT00000047550.4	955	856	11	1338.13
ENSRNOT00000040993.4	1039	940	17	1883.22
ENSRNOT00000050156.3	1545	1446	51	3672.67
ENSRNOT00000043693.3	684	585	16	2848.02
ENSRNOT00000046201.3	204	105	5	4958.61
ENSRNOT00000046108.3	681	582	7	1252.43
ENSRNOT00000049683.3	784	685	13	1976.21
ENSRNOT00000041241.3	348	249	2	836.393
ENSRNOT00000044582.3	297	198	9	4733.22

==> SRR30542859.se.tsv <==
ENSRNOG00000046319	0
ENSRNOG00000047964	0
ENSRNOG00000050370	0
ENSRNOG00000032365	0
ENSRNOG00000040300	0
ENSRNOG00000058808	0
ENSRNOG00000061316	2
ENSRNOG00000050129	0
ENSRNOG00000040316	0
ENSRNOG00000023659	0
SRR30542859 completed mapping pipeline successfully
