Starting /dee2/code/volunteer_pipeline.sh SRR30542857
    current disk space = 1193668244
    free memory = 196249584 
SRR30542857 SRAfilesize
3f5c72ac0363225d937b98c0eeb90e57  SRR30542857.sra
SRR30542857.sra file validated
SRR30542857 is single end
SRR30542857 is conventional basespace
SRR30542857 read1 length is 36 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR30542857_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	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	33.18275	32.0	32.0	37.0	32.0	37.0
2	34.7585	37.0	32.0	37.0	32.0	37.0
3	36.151	37.0	37.0	37.0	32.0	37.0
4	36.4135	37.0	37.0	37.0	37.0	37.0
5	36.45125	37.0	37.0	37.0	37.0	37.0
6	36.56025	37.0	37.0	37.0	37.0	37.0
7	36.51975	37.0	37.0	37.0	37.0	37.0
8	36.70475	37.0	37.0	37.0	37.0	37.0
9	36.623	37.0	37.0	37.0	37.0	37.0
10	36.66275	37.0	37.0	37.0	37.0	37.0
11	36.76375	37.0	37.0	37.0	37.0	37.0
12	36.632	37.0	37.0	37.0	37.0	37.0
13	36.55975	37.0	37.0	37.0	37.0	37.0
14	36.6565	37.0	37.0	37.0	37.0	37.0
15	36.739	37.0	37.0	37.0	37.0	37.0
16	36.721	37.0	37.0	37.0	37.0	37.0
17	36.6905	37.0	37.0	37.0	37.0	37.0
18	36.7065	37.0	37.0	37.0	37.0	37.0
19	36.72175	37.0	37.0	37.0	37.0	37.0
20	36.678	37.0	37.0	37.0	37.0	37.0
21	36.68275	37.0	37.0	37.0	37.0	37.0
22	36.62575	37.0	37.0	37.0	37.0	37.0
23	36.63575	37.0	37.0	37.0	37.0	37.0
24	36.74325	37.0	37.0	37.0	37.0	37.0
25	36.609	37.0	37.0	37.0	37.0	37.0
26	36.61275	37.0	37.0	37.0	37.0	37.0
27	36.61625	37.0	37.0	37.0	37.0	37.0
28	36.64375	37.0	37.0	37.0	37.0	37.0
29	36.77325	37.0	37.0	37.0	37.0	37.0
30	36.6105	37.0	37.0	37.0	37.0	37.0
31	36.4975	37.0	37.0	37.0	37.0	37.0
32	36.68125	37.0	37.0	37.0	37.0	37.0
33	36.56075	37.0	37.0	37.0	37.0	37.0
34	36.5665	37.0	37.0	37.0	37.0	37.0
35	36.55125	37.0	37.0	37.0	37.0	37.0
36	36.364	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
18	1.0
19	0.0
20	0.0
21	0.0
22	3.0
23	1.0
24	0.0
25	5.0
26	7.0
27	8.0
28	7.0
29	15.0
30	16.0
31	18.0
32	25.0
33	42.0
34	71.0
35	154.0
36	2907.0
37	720.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	23.25	19.950000000000003	32.25	24.55
2	53.300000000000004	14.7	15.299999999999999	16.7
3	22.6	34.449999999999996	13.975000000000001	28.975
4	44.6	17.150000000000002	22.650000000000002	15.6
5	33.050000000000004	31.225	18.55	17.175
6	28.249999999999996	14.05	33.1	24.6
7	37.375	24.75	18.9	18.975
8	30.25	21.625	34.25	13.875000000000002
9	20.125	30.175	27.250000000000004	22.45
10	37.3	35.75	14.475	12.475
11	43.925	21.525	15.2	19.35
12	28.475	32.775	22.325	16.425
13	20.175	16.375	37.125	26.325
14	20.424999999999997	29.175	29.65	20.75
15	43.525000000000006	23.875	13.5	19.1
16	23.849999999999998	24.9	38.574999999999996	12.675
17	32.1	34.575	18.6	14.725
18	33.324999999999996	18.025	26.474999999999998	22.175
19	31.175000000000004	25.650000000000002	29.025000000000002	14.149999999999999
20	31.4	22.45	30.375000000000004	15.775
21	34.125	21.275	31.1	13.5
22	30.23255813953488	29.707426856714182	25.581395348837212	14.47861965491373
23	22.15	40.375	16.225	21.25
24	36.95	35.175	13.450000000000001	14.424999999999999
25	27.400000000000002	39.35	17.175	16.075
26	22.900000000000002	21.95	29.299999999999997	25.85
27	24.45	21.125	16.1	38.324999999999996
28	37.574999999999996	25.85	7.9750000000000005	28.599999999999998
29	46.675	31.974999999999998	6.6000000000000005	14.75
30	31.5	43.275000000000006	7.9750000000000005	17.25
31	26.26970227670753	42.2817112834626	17.212909682261696	14.235676757568177
32	37.65	32.525	10.95	18.875
33	26.724999999999998	46.2	8.0	19.075
34	32.025	33.475	7.625	26.875
35	26.325	27.750000000000004	15.275	30.65
36	16.85	41.625	11.875	29.65
>>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	1.0
14	2.0
15	2.0
16	2.0
17	2.0
18	2.5
19	3.0
20	3.0
21	2.5
22	2.0
23	2.0
24	5.0
25	8.0
26	5.0
27	2.0
28	2.0
29	5.0
30	8.0
31	8.0
32	11.5
33	15.0
34	15.0
35	17.0
36	19.0
37	19.0
38	101.0
39	183.0
40	177.0
41	171.0
42	171.0
43	339.5
44	508.0
45	508.0
46	557.5
47	607.0
48	607.0
49	536.0
50	465.0
51	560.0
52	655.0
53	655.0
54	606.0
55	557.0
56	557.0
57	441.5
58	326.0
59	326.0
60	317.0
61	308.0
62	308.0
63	210.0
64	112.0
65	67.0
66	22.0
67	22.0
68	20.0
69	18.0
70	18.0
71	11.5
72	5.0
73	5.0
74	3.0
75	1.0
76	0.5
77	0.0
78	0.0
79	0.5
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	0.0
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	0.025
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	0.075
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
36	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	55.375
#Duplication Level	Percentage of deduplicated	Percentage of total
1	86.59142212189617	47.949999999999996
2	7.133182844243792	7.9
3	2.076749435665914	3.45
4	0.6320541760722348	1.4000000000000001
5	0.8577878103837472	2.375
6	0.40632054176072235	1.35
7	0.27088036117381487	1.05
8	0.2257336343115124	1.0
9	0.09029345372460496	0.44999999999999996
>10	1.3544018058690745	14.299999999999999
>50	0.27088036117381487	12.049999999999999
>100	0.09029345372460496	6.7250000000000005
>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
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGA	149	3.7249999999999996	TruSeq Adapter, Index 7 (97% over 35bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATT	120	3.0	No Hit
GGGGATGTAGCTCAGTGGTAGATCGGAAGAGCACAC	95	2.375	No Hit
TGAGGTAGTAGATTGTATAGTTAGATCGGAAGAGCA	94	2.35	No Hit
GGAAGAGCACACGTCTGAACTCCAGTCACGATCAGA	83	2.075	TruSeq Adapter, Index 9 (100% over 36bp)
TGAGGTAGTAGTTTGTGCTGTTAGATCGGAAGAGCA	76	1.9	No Hit
TGAGGTAGTAGGTTGTATGGTTAGATCGGAAGAGCA	71	1.775	No Hit
GTTTCCGTAGTGTAGTGGTTATCAGATCGGAAGAGC	63	1.575	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATA	44	1.0999999999999999	No Hit
TGAGATGAAGCACTGTAGCTCAGATCGGAAGAGCAC	35	0.8750000000000001	No Hit
CGCGACCTCAGATCAGACGTAGATCGGAAGAGCACA	35	0.8750000000000001	No Hit
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGC	32	0.8	No Hit
TGGAATGTAAGGAAGTGTGTGGAGATCGGAAGAGCA	32	0.8	No Hit
CTAGACTGAGGCTCCTTGAGGAGATCGGAAGAGCAC	28	0.7000000000000001	No Hit
TGAGATGAAGCACTGTAGCTCTAGATCGGAAGAGCA	26	0.65	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTAGAT	26	0.65	No Hit
TGAGGTAGTAGGTTGTATAGTTAGATCGGAAGAGCA	25	0.625	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATAGATC	25	0.625	No Hit
GGCTTTTTAAGTCGGATGTGAGATCGGAAGAGCACA	21	0.525	No Hit
CGCGACCTCAGATCGGAAGAGCACACGTCTGAACTC	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTAGATCGGAAGAGCAC	17	0.42500000000000004	No Hit
CTCTGTGCTGATTGTCATGTTCTGATCAGATCGGAA	16	0.4	No Hit
CGCGACCTCAGATCAGACGTGGCAGATCGGAAGAGC	15	0.375	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAAG	15	0.375	No Hit
TTCACAGTGGCTAAGTTCTGCAGATCGGAAGAGCAC	15	0.375	No Hit
CGCGACCTCAGATCAGATCGGAAGAGCACACGTCTG	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
GTCTACGGCCATACCACCCTGAACGCGCCCGATCTC	14	0.35000000000000003	No Hit
TCTCTGTGCTGATTGTCATGTTCTGATCAGATCGGA	12	0.3	No Hit
TGAGATGAAGCACTGTAGCTAGATCGGAAGAGCACA	12	0.3	No Hit
TGAGATGAAGCACTGTAGCTTAGATCGGAAGAGCAC	11	0.27499999999999997	No Hit
TGAGGTAGTAGATTGTATAGTCAGATCGGAAGAGCA	11	0.27499999999999997	No Hit
TGAGGTAGTAGGTTGTGTGGTTAGATCGGAAGAGCA	11	0.27499999999999997	No Hit
TCGATGTGGTGCTGCCGCGTTCTCTTCGGGCCGGGG	10	0.25	No Hit
GGGGATGTAGCTCAGTGGCAGATCGGAAGAGCACAC	10	0.25	No Hit
TGCACTGATGAAACTAGAAATAGGAAGTGCCGTCCG	10	0.25	No Hit
TGAGGTAGTAGTTTGTGCTGTCAGATCGGAAGAGCA	10	0.25	No Hit
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCA	10	0.25	No Hit
ACTGGACTTGGAGTCAGAAGGCAGATCGGAAGAGCA	10	0.25	No Hit
ACCGGGTGCTGTAGGCTTTAGATCGGAAGAGCACAC	9	0.22499999999999998	No Hit
CGCGACCTTAGATCGGAAGAGCACACGTCTGAACTC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTCAGATCGGAAGAGCA	8	0.2	No Hit
TGAGGTAGTAGGTTGTATGGTAGATCGGAAGAGCAC	8	0.2	No Hit
TGAGGTAGTAGTTTGTACAGTTAGATCGGAAGAGCA	8	0.2	No Hit
GCCGGTACAGTGAAACTAGATCGGAAGAGCACACGT	8	0.2	No Hit
TGTAAACATCCCCGACTGGAAGCTAGATCGGAAGAG	8	0.2	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCAGATCGGA	7	0.17500000000000002	No Hit
TGAGGTAGTAGTTTGTGCTGTAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCTAGATC	7	0.17500000000000002	No Hit
TAGCTTATCAGACTGATGTTGAAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
TGGAAGACTAGTGATTTTGTTGTTAGATCGGAAGAG	7	0.17500000000000002	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTC	7	0.17500000000000002	No Hit
AGAGGTAGTAGGTTGCATAGTAGATCGGAAGAGCAC	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCA	6	0.15	No Hit
CGCGACCTCAGATCAGACAGATCGGAAGAGCACACG	6	0.15	No Hit
CTTCGGTGATGACACGATGACGAGATCGGAAGAGCA	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATCAGAT	6	0.15	No Hit
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGAAT	6	0.15	No Hit
TCAGTGCACTACAGAACTTTGTAGATCGGAAGAGCA	6	0.15	No Hit
AGCTACATCTGGCTACTGGGTCTCTAGATCGGAAGA	6	0.15	No Hit
TAGCTTATCAGACTGATGTTGACTAGATCGGAAGAG	6	0.15	No Hit
TGAGGTAGTAGATTGTATAGCAGATCGGAAGAGCAC	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGTAGATCGGAAGAGC	5	0.125	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCAGATCG	5	0.125	No Hit
GTAGTCGTGGCCGAGTGGTTAGATCGGAAGAGCACA	5	0.125	No Hit
TGAGGTAGTAGATTGTATAGTAAGATCGGAAGAGCA	5	0.125	No Hit
TGGAATGTAAGGAAGTGTGTGAAGATCGGAAGAGCA	5	0.125	No Hit
AACCCGTAGATCCGATCTTGTAGATCGGAAGAGCAC	5	0.125	No Hit
CGCGACCTCAGATCAGACGCAGATCGGAAGAGCACA	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTAAGATCGGAAGAGCAC	5	0.125	No Hit
CTAGACTGAGGCTCCTTGAGAAGATCGGAAGAGCAC	5	0.125	No Hit
GTAGTCGTGGCCGAGTAGATCGGAAGAGCACACGTC	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTAGATC	5	0.125	No Hit
TGAGGTAGTAGTTTGTGCTGTTAAGATCGGAAGAGC	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAACA	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTAAGATCGGAAGAGCA	5	0.125	No Hit
TGAGGTAGTAGATTGTATAGTTAAGATCGGAAGAGC	5	0.125	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGA	5	0.125	No Hit
TGAGGTAGTAGTTTGTGCTGTAAGATCGGAAGAGCA	5	0.125	No Hit
ACAGTAGTCTGCACATTGGTTAGATCGGAAGAGCAC	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	4.375	0.0	0.0	0.0	0.0
2	4.425	0.0	0.0	0.0	0.0
3	4.55	0.0	0.0	0.0	0.0
4	4.575	0.0	0.0	0.0	0.0
5	4.575	0.0	0.0	0.0	0.0
6	4.575	0.0	0.0	0.0	0.0
7	4.675	0.0	0.0	0.0	0.0
8	4.8	0.0	0.0	0.0	0.0
9	4.975	0.0	0.0	0.0	0.0
10	6.15	0.0	0.0	0.0	0.0
11	6.55	0.0	0.0	0.0	0.0
12	7.15	0.0	0.0	0.0	0.0
13	7.75	0.0	0.0	0.0	0.0
14	9.025	0.0	0.0	0.0	0.0
15	10.775	0.0	0.0	0.0	0.0
16	12.1	0.0	0.0	0.0	0.0
17	14.425	0.0	0.0	0.0	0.0
18	16.325	0.0	0.0	0.0	0.0
19	18.95	0.0	0.0	0.0	0.0
20	24.45	0.0	0.0	0.0	0.0
21	29.475	0.0	0.0	0.0	0.0
22	36.75	0.0	0.0	0.0	0.0
23	52.9	0.0	0.0	0.0	0.0
24	59.95	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TTGTATA	30	2.707939E-5	30.000002	13
GACCTCA	30	2.707939E-5	30.000002	4
TGTATAG	30	2.707939E-5	30.000002	14
CGACCTC	30	2.707939E-5	30.000002	3
GTAGTAG	45	1.1683369E-8	30.000002	5
CGCGACC	35	2.0637017E-6	30.0	1
GAGGTAG	50	8.6583896E-10	30.0	2
GGTTGTA	25	3.5274107E-4	30.0	11
AGTAGGT	25	3.5274107E-4	30.0	7
GCGACCT	35	2.0637017E-6	30.0	2
GTATAGT	25	3.5274107E-4	30.0	15
TAGTAGG	25	3.5274107E-4	30.0	6
TGAGGTA	50	8.6583896E-10	30.0	1
AGGTTGT	25	3.5274107E-4	30.0	10
GTAGGTT	25	3.5274107E-4	30.0	8
GTTGTAT	25	3.5274107E-4	30.0	12
TAGGTTG	25	3.5274107E-4	30.0	9
CGCTGAA	20	0.00456452	29.999998	28
GCGACCC	20	0.00456452	29.999998	22
CCGCTGA	20	0.00456452	29.999998	27
>>END_MODULE
Read 31800 spots for SRR30542857.sra
Written 31800 spots for SRR30542857.sra
Read 31800 spots for SRR30542857.sra
Written 31800 spots for SRR30542857.sra
Read 31800 spots for SRR30542857.sra
Written 31800 spots for SRR30542857.sra
Read 31800 spots for SRR30542857.sra
Written 31800 spots for SRR30542857.sra
Read 31800 spots for SRR30542857.sra
Written 31800 spots for SRR30542857.sra
Read 31800 spots for SRR30542857.sra
Written 31800 spots for SRR30542857.sra
Read 31801 spots for SRR30542857.sra
Written 31801 spots for SRR30542857.sra
Read 31800 spots for SRR30542857.sra
Written 31800 spots for SRR30542857.sra
SRR ids: ['SRR30542857.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_b2a2dz0u
SRR30542857.sra spots: 254401
blocks: [[1, 31800], [31801, 63600], [63601, 95400], [95401, 127200], [127201, 159000], [159001, 190800], [190801, 222600], [222601, 254401]]
SRR30542857 file size 36212
SRR30542857 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 SRR30542857 SRR30542857_1.fastq
Input file:	SRR30542857_1.fastq
trimmed:	SRR30542857-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 06:32:42 2025 >> started

Thu Nov  6 06:32:42 2025 >> done (0.100s)
254401 reads processed; of these:
   436 ( 0.17%) short reads filtered out after trimming by size control
 11332 ( 4.45%) empty reads filtered out after trimming by size control
242633 (95.37%) reads available; of these:
    28 ( 0.01%) trimmed reads available after processing
242605 (99.99%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 35	    28	  0.01%
 36	242605	 99.99%
242633 reads passed initial QC


criterion=sequence-density
sequence-density=57.67
sequence-density-rank=1
fanout-score=27.99
fanout-score-rank=1
prefix-density=65.48
prefix-fanout=24.6
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGAT


criterion=fanout-score
sequence-density=57.67
sequence-density-rank=1
fanout-score=27.99
fanout-score-rank=1
prefix-density=65.48
prefix-fanout=24.6
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGAT
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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGAT -o SRR30542857 -
Input file:	STDIN
trimmed:	SRR30542857-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGAT
-- 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 06:32:43 2025 >> started

Thu Nov  6 06:32:43 2025 >> done (0.075s)
234266 reads processed; of these:
 30267 (12.92%) short reads filtered out after trimming by size control
   126 ( 0.05%) empty reads filtered out after trimming by size control
203873 (87.03%) reads available; of these:
163415 (80.16%) trimmed reads available after processing
 40458 (19.84%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  6480	  3.18%
 19	 12894	  6.32%
 20	 11778	  5.78%
 21	 16982	  8.33%
 22	 38793	 19.03%
 23	 18483	  9.07%
 24	  7799	  3.83%
 25	  4971	  2.44%
 26	  4302	  2.11%
 27	  5202	  2.55%
 28	  5836	  2.86%
 29	  4349	  2.13%
 30	  4679	  2.30%
 31	  6578	  3.23%
 32	  6392	  3.14%
 33	  7897	  3.87%
 34	     0	  0.00%
 35	     8	  0.00%
 36	 40450	 19.84%


criterion=sequence-density
sequence-density=4.42
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=7
prefix-density=0.00
prefix-fanout=1.0
sequence=TGAGGTAGTAGATTGTATAGTTAGATCGGA


criterion=fanout-score
sequence-density=2.64
sequence-density-rank=7
fanout-score=13.38
fanout-score-rank=1
prefix-density=2.58
prefix-fanout=13.4
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGA
                                 Started job on |	Nov 06 06:32:49
                             Started mapping on |	Nov 06 06:32:49
                                    Finished on |	Nov 06 06:32:57
       Mapping speed, Million of reads per hour |	95.51

                          Number of input reads |	212240
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	77106
                        Uniquely mapped reads % |	36.33%
                          Average mapped length |	24.49
                       Number of splices: Total |	630
            Number of splices: Annotated (sjdb) |	144
                       Number of splices: GT/AG |	590
                       Number of splices: GC/AG |	17
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	23
                      Mismatch rate per base, % |	0.42%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.27
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	72567
             % of reads mapped to multiple loci |	34.19%
        Number of reads mapped to too many loci |	34211
             % of reads mapped to too many loci |	16.12%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.77%
                     % of reads unmapped: other |	3.59%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	62567	62567	62567
N_multimapping	72567	72567	72567
N_noFeature	27965	32680	72284
N_ambiguous	2589	2480	2
UnstrandedReadsAssigned:46552 PositiveStrandReadsAssigned:41946 NegativeStrandReadsAssigned:4820
Dataset is classified positive stranded
MeadianReadLen=24 20thPercentileLength=21 echo kmer=19
SRR30542857 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: SRR30542857-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 212,240 reads, 8,359 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 523 rounds

  31716 SRR30542857.ke.tsv
  32883 SRR30542857.se.tsv
  64599 total
==> SRR30542857.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSRNOT00000047550.4	955	856	10	1271.02
ENSRNOT00000040993.4	1039	940	6	694.462
ENSRNOT00000050156.3	1545	1446	83	6245.03
ENSRNOT00000043693.3	684	585	22	4091.59
ENSRNOT00000046201.3	204	105	3	3108.54
ENSRNOT00000046108.3	681	582	3	560.819
ENSRNOT00000049683.3	784	685	12	1905.97
ENSRNOT00000041241.3	348	249	0	0
ENSRNOT00000044582.3	297	198	0	0

==> SRR30542857.se.tsv <==
ENSRNOG00000046319	0
ENSRNOG00000047964	0
ENSRNOG00000050370	0
ENSRNOG00000032365	0
ENSRNOG00000040300	0
ENSRNOG00000058808	0
ENSRNOG00000061316	1
ENSRNOG00000050129	0
ENSRNOG00000040316	0
ENSRNOG00000023659	0
SRR30542857 completed mapping pipeline successfully
