Starting /dee2/code/volunteer_pipeline.sh SRR30542862
    current disk space = 1222796472
    free memory = 198263164 
SRR30542862 SRAfilesize
ec0a6597a0684b496a664c98f9220bd7  SRR30542862.sra
SRR30542862.sra file validated
SRR30542862 is single end
SRR30542862 is conventional basespace
SRR30542862 read1 length is 36 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR30542862_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	33.09625	32.0	32.0	37.0	32.0	37.0
2	34.70975	37.0	32.0	37.0	32.0	37.0
3	36.07	37.0	37.0	37.0	32.0	37.0
4	36.332	37.0	37.0	37.0	37.0	37.0
5	36.49575	37.0	37.0	37.0	37.0	37.0
6	36.59325	37.0	37.0	37.0	37.0	37.0
7	36.51175	37.0	37.0	37.0	37.0	37.0
8	36.62375	37.0	37.0	37.0	37.0	37.0
9	36.689	37.0	37.0	37.0	37.0	37.0
10	36.60625	37.0	37.0	37.0	37.0	37.0
11	36.704	37.0	37.0	37.0	37.0	37.0
12	36.61225	37.0	37.0	37.0	37.0	37.0
13	36.577	37.0	37.0	37.0	37.0	37.0
14	36.6375	37.0	37.0	37.0	37.0	37.0
15	36.66725	37.0	37.0	37.0	37.0	37.0
16	36.69125	37.0	37.0	37.0	37.0	37.0
17	36.62225	37.0	37.0	37.0	37.0	37.0
18	36.64675	37.0	37.0	37.0	37.0	37.0
19	36.68775	37.0	37.0	37.0	37.0	37.0
20	36.63775	37.0	37.0	37.0	37.0	37.0
21	36.64475	37.0	37.0	37.0	37.0	37.0
22	36.71775	37.0	37.0	37.0	37.0	37.0
23	36.59	37.0	37.0	37.0	37.0	37.0
24	36.6065	37.0	37.0	37.0	37.0	37.0
25	36.5185	37.0	37.0	37.0	37.0	37.0
26	36.528	37.0	37.0	37.0	37.0	37.0
27	36.56775	37.0	37.0	37.0	37.0	37.0
28	36.53575	37.0	37.0	37.0	37.0	37.0
29	36.7175	37.0	37.0	37.0	37.0	37.0
30	36.64125	37.0	37.0	37.0	37.0	37.0
31	36.59975	37.0	37.0	37.0	37.0	37.0
32	36.45075	37.0	37.0	37.0	37.0	37.0
33	36.4825	37.0	37.0	37.0	37.0	37.0
34	36.53625	37.0	37.0	37.0	37.0	37.0
35	36.4595	37.0	37.0	37.0	37.0	37.0
36	36.47025	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	1.0
22	1.0
23	3.0
24	2.0
25	2.0
26	9.0
27	12.0
28	7.0
29	12.0
30	17.0
31	28.0
32	39.0
33	35.0
34	65.0
35	153.0
36	2962.0
37	652.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	20.225	19.400000000000002	30.85	29.525000000000002
2	48.575	17.2	17.175	17.05
3	19.375	27.725	13.600000000000001	39.300000000000004
4	44.175	15.049999999999999	22.650000000000002	18.125
5	31.374999999999996	32.4	20.125	16.1
6	28.825	13.075000000000001	28.375	29.725
7	27.975	24.5	20.200000000000003	27.325
8	28.875	19.5	36.725	14.899999999999999
9	22.35	20.25	26.25	31.15
10	29.35733933483371	40.56014003500875	15.178794698674668	14.90372593148287
11	45.4	20.974999999999998	16.35	17.275
12	29.625	35.75	19.925	14.7
13	20.9	17.275	43.075	18.75
14	22.875	24.9	26.25	25.974999999999998
15	39.300000000000004	30.125	16.8	13.775
16	32.25	26.85	29.975	10.925
17	29.95	37.574999999999996	19.25	13.225000000000001
18	25.575	16.5	27.3	30.625000000000004
19	39.525	21.375	25.85	13.25
20	29.425	21.85	33.175	15.55
21	39.025	20.45	28.749999999999996	11.774999999999999
22	37.85	24.474999999999998	26.5	11.175
23	23.474999999999998	35.775	14.725	26.025
24	42.5	32.9	13.475000000000001	11.125
25	23.875	41.85	20.474999999999998	13.8
26	20.825	22.675	25.074999999999996	31.424999999999997
27	24.05	18.85	16.825000000000003	40.275
28	35.199999999999996	20.025000000000002	8.975	35.8
29	48.725	28.625	8.125	14.524999999999999
30	29.875	35.275	7.75	27.1
31	23.317488116087066	37.478108581436075	23.867900925694272	15.336502376782587
32	41.4	31.95	10.45	16.2
33	24.75	47.349999999999994	10.2	17.7
34	30.025000000000002	38.175	8.125	23.674999999999997
35	22.25	25.35	21.675	30.725
36	19.004751187796952	35.23380845211303	19.629907476869217	26.131532883220803
>>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	0.5
11	1.0
12	1.0
13	1.0
14	1.0
15	0.5
16	0.0
17	0.0
18	0.5
19	1.0
20	1.0
21	2.5
22	4.0
23	4.0
24	5.5
25	7.0
26	5.0
27	3.0
28	3.0
29	5.0
30	7.0
31	7.0
32	7.5
33	8.0
34	8.0
35	20.0
36	32.0
37	32.0
38	84.0
39	136.0
40	172.0
41	208.0
42	208.0
43	363.0
44	518.0
45	518.0
46	536.0
47	554.0
48	554.0
49	513.5
50	473.0
51	461.0
52	449.0
53	449.0
54	467.0
55	485.0
56	485.0
57	423.0
58	361.0
59	361.0
60	430.5
61	500.0
62	500.0
63	347.5
64	195.0
65	116.0
66	37.0
67	37.0
68	22.5
69	8.0
70	8.0
71	7.5
72	7.0
73	7.0
74	5.0
75	3.0
76	2.0
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	0.025
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	0.075
32	0.0
33	0.0
34	0.0
35	0.0
36	0.025
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
36	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	59.425
#Duplication Level	Percentage of deduplicated	Percentage of total
1	89.60875052587295	53.25
2	4.9221708035338665	5.8500000000000005
3	1.6827934371055953	3.0
4	0.9255363904080774	2.1999999999999997
5	0.4627681952040387	1.375
6	0.5048380311316786	1.7999999999999998
7	0.2524190155658393	1.05
8	0.12620950778291964	0.6
9	0.2524190155658393	1.35
>10	1.093815734118637	15.4
>50	0.12620950778291964	5.800000000000001
>100	0.04206983592763988	8.325000000000001
>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	333	8.325000000000001	No Hit
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCC	89	2.225	TruSeq Adapter, Index 5 (97% over 35bp)
TGAGGTAGTAGGTTGTATGGTTAGATCGGAAGAGCA	80	2.0	No Hit
TGAGGTAGTAGTTTGTGCTGTTAGATCGGAAGAGCA	63	1.575	No Hit
GACTTTGATCCGGAGATCTCTGAATGGGGGAACCCA	48	1.2	No Hit
GTTTCCGTAGTGTAGTGGTTATCAGATCGGAAGAGC	46	1.15	No Hit
TGAGGTAGTAGATTGTATAGTTAGATCGGAAGAGCA	42	1.05	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTAGAT	40	1.0	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATAGATC	38	0.95	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAAG	33	0.8250000000000001	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATA	28	0.7000000000000001	No Hit
GTCTACGGCCATACCACCCTGAACGCGCCCGATCTC	28	0.7000000000000001	No Hit
TGAGGTAGTAGGTTGTGTGGTTAGATCGGAAGAGCA	28	0.7000000000000001	No Hit
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGC	25	0.625	No Hit
CGCGACCTCAGATCAGACGTGGCAGATCGGAAGAGC	23	0.575	No Hit
CGCGACCTCAGATCAGATCGGAAGAGCACACGTCTG	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
CGCGACCTCAGATCAGACGTAGATCGGAAGAGCACA	23	0.575	No Hit
TGAGGTAGTAGGTTGTATAGTTAGATCGGAAGAGCA	22	0.5499999999999999	No Hit
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGAAT	22	0.5499999999999999	No Hit
TGGAATGTAAGGAAGTGTGTGGAGATCGGAAGAGCA	21	0.525	No Hit
TGAGATGAAGCACTGTAGCTCAGATCGGAAGAGCAC	17	0.42500000000000004	No Hit
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCA	16	0.4	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTC	16	0.4	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTAGA	14	0.35000000000000003	No Hit
AACCCGTAGATCCGATCTTGTAGATCGGAAGAGCAC	13	0.325	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACA	10	0.25	No Hit
GGGGATGTAGCTCAGTGGTAGATCGGAAGAGCACAC	10	0.25	No Hit
TGAGGTAGTAGTTTGTGCTGTCAGATCGGAAGAGCA	10	0.25	No Hit
CGCGACCTCAGATCAGACAGATCGGAAGAGCACACG	10	0.25	No Hit
TTAGATCTCAAATCAGATAGGATTACCCGCTGAACT	10	0.25	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCAGATCGGA	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTGTGGTAGATCGGAAGAGCAC	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTGTGGTTTAGATCGGAAGAGC	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTATGGTCAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCAGATCGGA	9	0.22499999999999998	No Hit
TAGCTTATCAGACTGATGTTGACTAGATCGGAAGAG	9	0.22499999999999998	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGAGATC	8	0.2	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAGA	8	0.2	No Hit
AGAGGTAGTAGGTTGCATAGTTAGATCGGAAGAGCA	8	0.2	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGAGATCGGA	7	0.17500000000000002	No Hit
TACCTGGTTGATCCTGCCAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
GGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCA	7	0.17500000000000002	TruSeq Adapter, Index 16 (97% over 35bp)
TTCACAGTGGCTAAGTTCTGCAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTAGAT	7	0.17500000000000002	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGA	7	0.17500000000000002	No Hit
TGAGATGAAGCACTGTAGCTTAGATCGGAAGAGCAC	6	0.15	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCAG	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCAGATC	6	0.15	No Hit
CGGCGGTAACAGGGGTTCGAGTCCCCTAGGGGACAG	6	0.15	No Hit
TGTAAACATCCCCGACTGGAAGCAGATCGGAAGAGC	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATCAGAT	6	0.15	No Hit
AGGCTAAGCTCTTGTTCAACAGATTTGTAGATCGGA	6	0.15	No Hit
TGGAAGACTAGTGATTTTGTTGTTAGATCGGAAGAG	6	0.15	No Hit
CGCGACCTCAGATCAGAAGATCGGAAGAGCACACGT	6	0.15	No Hit
AACTTTCAACAACGGATCTCTTGGCTCTCGCATCGA	6	0.15	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTAGATCGGAAG	6	0.15	No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTCA	6	0.15	No Hit
CGCGACCTCAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ACCGGGTGCTGTAGGCTTTAGATCGGAAGAGCACAC	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAAGATCGG	5	0.125	No Hit
GTAGTCGTGGCCGAGTAGATCGGAAGAGCACACGTC	5	0.125	No Hit
TCTCTGTGCTGATTGTCATGTTCTGATCAGATCGGA	5	0.125	No Hit
TGAGGTAGTAGGTTGTATAGTAGATCGGAAGAGCAC	5	0.125	No Hit
TGAGGTAGTAGTTTGTACAGTTAGATCGGAAGAGCA	5	0.125	No Hit
AGCTACATTGTCTGCTGGGTTTCAGATCGGAAGAGC	5	0.125	No Hit
AGCTACATCTGGCTACTGGGTCTCTAGATCGGAAGA	5	0.125	No Hit
TGAGGTAGTAGATTGTATAGTAGATCGGAAGAGCAC	5	0.125	No Hit
TGGCTCAGTTCAGCAGGAACAGATCGGAAGAGCACA	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	2.425	0.0	0.0	0.0	0.0
2	2.425	0.0	0.0	0.0	0.0
3	2.425	0.0	0.0	0.0	0.0
4	2.45	0.0	0.0	0.0	0.0
5	2.45	0.0	0.0	0.0	0.0
6	2.475	0.0	0.0	0.0	0.0
7	2.5	0.0	0.0	0.0	0.0
8	2.55	0.0	0.0	0.0	0.0
9	2.725	0.0	0.0	0.0	0.0
10	3.275	0.0	0.0	0.0	0.0
11	3.575	0.0	0.0	0.0	0.0
12	4.0	0.0	0.0	0.0	0.0
13	4.7	0.0	0.0	0.0	0.0
14	5.9	0.0	0.0	0.0	0.0
15	7.8	0.0	0.0	0.0	0.0
16	9.5	0.0	0.0	0.0	0.0
17	11.475	0.0	0.0	0.0	0.0
18	13.675	0.0	0.0	0.0	0.0
19	16.525	0.0	0.0	0.0	0.0
20	19.325	0.0	0.0	0.0	0.0
21	22.6	0.0	0.0	0.0	0.0
22	27.625	0.0	0.0	0.0	0.0
23	40.65	0.0	0.0	0.0	0.0
24	46.95	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AGTAGGT	25	3.5274107E-4	30.0	7
TAGTAGG	25	3.5274107E-4	30.0	6
GGTAGTA	35	2.0637017E-6	30.0	4
TGAGGTA	35	2.0637017E-6	30.0	1
GTTAGAT	25	3.5274107E-4	30.0	20
AGGTTGT	25	3.5274107E-4	30.0	10
GTAGGTT	25	3.5274107E-4	30.0	8
GTAGTAG	35	2.0637017E-6	30.0	5
TAGGTTG	25	3.5274107E-4	30.0	9
TAGTGGT	20	0.00456452	29.999998	13
AGTGGTT	20	0.00456452	29.999998	14
GTGGTTA	20	0.00456452	29.999998	15
CGCGACC	60	1.7644197E-10	27.500002	1
GCGACCT	60	1.7644197E-10	27.500002	2
CCTCAGA	60	1.7644197E-10	27.500002	6
GATCAGA	60	1.7644197E-10	27.500002	11
CAGATCA	60	1.7644197E-10	27.500002	9
ACCTCAG	60	1.7644197E-10	27.500002	5
GACCTCA	60	1.7644197E-10	27.500002	4
AGATCAG	60	1.7644197E-10	27.500002	10
>>END_MODULE
Read 44594 spots for SRR30542862.sra
Written 44594 spots for SRR30542862.sra
Read 44593 spots for SRR30542862.sra
Written 44593 spots for SRR30542862.sra
Read 44593 spots for SRR30542862.sra
Written 44593 spots for SRR30542862.sra
Read 44593 spots for SRR30542862.sra
Written 44593 spots for SRR30542862.sra
Read 44593 spots for SRR30542862.sra
Written 44593 spots for SRR30542862.sra
Read 44593 spots for SRR30542862.sra
Written 44593 spots for SRR30542862.sra
Read 44593 spots for SRR30542862.sra
Written 44593 spots for SRR30542862.sra
Read 44593 spots for SRR30542862.sra
Written 44593 spots for SRR30542862.sra
SRR ids: ['SRR30542862.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_97yomo0o
SRR30542862.sra spots: 356745
blocks: [[1, 44593], [44594, 89186], [89187, 133779], [133780, 178372], [178373, 222965], [222966, 267558], [267559, 312151], [312152, 356745]]
SRR30542862 file size 50824
SRR30542862 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 SRR30542862 SRR30542862_1.fastq
Input file:	SRR30542862_1.fastq
trimmed:	SRR30542862-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 06:58:11 2025 >> started

Thu Nov  6 06:58:11 2025 >> done (0.126s)
356745 reads processed; of these:
   149 ( 0.04%) short reads filtered out after trimming by size control
  8767 ( 2.46%) empty reads filtered out after trimming by size control
347829 (97.50%) reads available; of these:
    39 ( 0.01%) trimmed reads available after processing
347790 (99.99%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 35	    39	  0.01%
 36	347790	 99.99%
347829 reads passed initial QC


criterion=sequence-density
sequence-density=46.29
sequence-density-rank=1
fanout-score=30.55
fanout-score-rank=1
prefix-density=54.09
prefix-fanout=26.2
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCA


criterion=fanout-score
sequence-density=46.29
sequence-density-rank=1
fanout-score=30.55
fanout-score-rank=1
prefix-density=54.09
prefix-fanout=26.2
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCA
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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCA -o SRR30542862 -
Input file:	STDIN
trimmed:	SRR30542862-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCA
-- 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 06:58:12 2025 >> started

Thu Nov  6 06:58:13 2025 >> done (0.119s)
333028 reads processed; of these:
 40492 (12.16%) short reads filtered out after trimming by size control
    29 ( 0.01%) empty reads filtered out after trimming by size control
292507 (87.83%) reads available; of these:
202146 (69.11%) trimmed reads available after processing
 90361 (30.89%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  9410	  3.22%
 19	  9868	  3.37%
 20	 13159	  4.50%
 21	 17429	  5.96%
 22	 44049	 15.06%
 23	 20732	  7.09%
 24	 10770	  3.68%
 25	  7875	  2.69%
 26	  6714	  2.30%
 27	  7651	  2.62%
 28	  9293	  3.18%
 29	  6887	  2.35%
 30	  7733	  2.64%
 31	 11678	  3.99%
 32	 11329	  3.87%
 33	  7569	  2.59%
 34	     0	  0.00%
 35	    16	  0.01%
 36	 90345	 30.89%


criterion=sequence-density
sequence-density=5.24
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=11
prefix-density=0.00
prefix-fanout=1.0
sequence=TGAGGTAGTAGGTTGTATGGTTAGATCGGA


criterion=fanout-score
sequence-density=2.34
sequence-density-rank=4
fanout-score=17.57
fanout-score-rank=1
prefix-density=2.30
prefix-fanout=17.6
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCA
                                 Started job on |	Nov 06 06:58:19
                             Started mapping on |	Nov 06 06:58:19
                                    Finished on |	Nov 06 06:58:27
       Mapping speed, Million of reads per hour |	138.29

                          Number of input reads |	307308
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	64534
                        Uniquely mapped reads % |	21.00%
                          Average mapped length |	22.90
                       Number of splices: Total |	1255
            Number of splices: Annotated (sjdb) |	156
                       Number of splices: GT/AG |	1215
                       Number of splices: GC/AG |	25
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	15
                      Mismatch rate per base, % |	0.77%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.20
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.50
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	115198
             % of reads mapped to multiple loci |	37.49%
        Number of reads mapped to too many loci |	68200
             % of reads mapped to too many loci |	22.19%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	18.78%
                     % of reads unmapped: other |	0.54%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	127576	127576	127576
N_multimapping	115198	115198	115198
N_noFeature	19859	22956	61353
N_ambiguous	996	909	3
UnstrandedReadsAssigned:43679 PositiveStrandReadsAssigned:40669 NegativeStrandReadsAssigned:3178
Dataset is classified positive stranded
MeadianReadLen=28 20thPercentileLength=22 echo kmer=19
SRR30542862 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: SRR30542862-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 307,308 reads, 5,057 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 512 rounds

  31716 SRR30542862.ke.tsv
  32883 SRR30542862.se.tsv
  64599 total
==> SRR30542862.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSRNOT00000047550.4	955	856	9	1743.22
ENSRNOT00000040993.4	1039	940	10	1763.83
ENSRNOT00000050156.3	1545	1446	50	5733.05
ENSRNOT00000043693.3	684	585	15	4251.27
ENSRNOT00000046201.3	204	105	2	3158.09
ENSRNOT00000046108.3	681	582	6	1709.28
ENSRNOT00000049683.3	784	685	4	968.173
ENSRNOT00000041241.3	348	249	0	0
ENSRNOT00000044582.3	297	198	0	0

==> SRR30542862.se.tsv <==
ENSRNOG00000046319	0
ENSRNOG00000047964	0
ENSRNOG00000050370	0
ENSRNOG00000032365	0
ENSRNOG00000040300	0
ENSRNOG00000058808	0
ENSRNOG00000061316	0
ENSRNOG00000050129	0
ENSRNOG00000040316	0
ENSRNOG00000023659	0
SRR30542862 completed mapping pipeline successfully
