Starting /dee2/code/volunteer_pipeline.sh SRR30542863
    current disk space = 1144748376
    free memory = 201685540 
SRR30542863 SRAfilesize
1127b07e9c1ec91fe202ea902bd4bde4  SRR30542863.sra
SRR30542863.sra file validated
SRR30542863 is single end
SRR30542863 is conventional basespace
SRR30542863 read1 length is 36 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR30542863_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	53
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	33.435	32.0	32.0	37.0	32.0	37.0
2	34.58575	37.0	32.0	37.0	32.0	37.0
3	36.06425	37.0	37.0	37.0	32.0	37.0
4	36.2235	37.0	37.0	37.0	32.0	37.0
5	36.455	37.0	37.0	37.0	37.0	37.0
6	36.5745	37.0	37.0	37.0	37.0	37.0
7	36.571	37.0	37.0	37.0	37.0	37.0
8	36.67025	37.0	37.0	37.0	37.0	37.0
9	36.71025	37.0	37.0	37.0	37.0	37.0
10	36.69375	37.0	37.0	37.0	37.0	37.0
11	36.69325	37.0	37.0	37.0	37.0	37.0
12	36.655	37.0	37.0	37.0	37.0	37.0
13	36.59375	37.0	37.0	37.0	37.0	37.0
14	36.692	37.0	37.0	37.0	37.0	37.0
15	36.648	37.0	37.0	37.0	37.0	37.0
16	36.67075	37.0	37.0	37.0	37.0	37.0
17	36.5995	37.0	37.0	37.0	37.0	37.0
18	36.58725	37.0	37.0	37.0	37.0	37.0
19	36.69825	37.0	37.0	37.0	37.0	37.0
20	36.679	37.0	37.0	37.0	37.0	37.0
21	36.64775	37.0	37.0	37.0	37.0	37.0
22	36.59425	37.0	37.0	37.0	37.0	37.0
23	36.628	37.0	37.0	37.0	37.0	37.0
24	36.58875	37.0	37.0	37.0	37.0	37.0
25	36.52925	37.0	37.0	37.0	37.0	37.0
26	36.568	37.0	37.0	37.0	37.0	37.0
27	36.57975	37.0	37.0	37.0	37.0	37.0
28	36.609	37.0	37.0	37.0	37.0	37.0
29	36.69925	37.0	37.0	37.0	37.0	37.0
30	36.563	37.0	37.0	37.0	37.0	37.0
31	36.4865	37.0	37.0	37.0	37.0	37.0
32	36.5855	37.0	37.0	37.0	37.0	37.0
33	36.578	37.0	37.0	37.0	37.0	37.0
34	36.568	37.0	37.0	37.0	37.0	37.0
35	36.5005	37.0	37.0	37.0	37.0	37.0
36	36.34125	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	2.0
23	3.0
24	4.0
25	7.0
26	6.0
27	9.0
28	15.0
29	11.0
30	17.0
31	25.0
32	23.0
33	35.0
34	67.0
35	152.0
36	2712.0
37	911.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	17.875	26.875	23.425	31.825
2	67.27499999999999	10.475	9.725	12.525
3	14.399999999999999	38.275	8.475000000000001	38.85
4	44.2	10.7	31.225	13.875000000000002
5	26.025	33.575	13.775	26.625
6	36.95	8.7	21.825	32.525
7	38.95	17.025000000000002	15.325	28.7
8	21.7	27.575	38.3	12.425
9	15.225	33.0	19.25	32.525
10	40.175	40.2	8.1	11.525
11	45.275	31.125000000000004	11.175	12.425
12	39.0	34.325	13.975000000000001	12.7
13	16.35	12.15	42.375	29.125
14	15.925	33.025	22.25	28.799999999999997
15	30.4	30.349999999999998	11.525	27.725
16	31.900000000000002	32.9	26.724999999999998	8.475000000000001
17	26.575	36.775000000000006	11.35	25.3
18	35.525	11.700000000000001	22.1	30.675
19	40.675	15.85	34.425	9.049999999999999
20	21.75	16.675	35.675000000000004	25.900000000000002
21	38.1	15.125	38.074999999999996	8.7
22	52.025	16.950000000000003	21.05	9.975000000000001
23	15.9	43.8	11.025	29.275000000000002
24	39.324999999999996	40.550000000000004	10.4	9.725
25	18.2	40.425	15.1	26.275
26	14.374999999999998	14.475	36.825	34.325
27	16.575	12.25	13.65	57.525000000000006
28	26.625	15.875	6.175	51.324999999999996
29	45.425	35.699999999999996	5.675	13.200000000000001
30	36.775000000000006	28.925	5.625	28.675
31	19.42985746436609	28.632158039509875	41.585396349087276	10.352588147036759
32	40.949999999999996	24.6	8.200000000000001	26.25
33	17.575	61.0	8.15	13.275
34	26.075	36.975	5.425	31.525
35	15.1	19.425	25.575	39.900000000000006
36	29.925	30.575000000000003	19.650000000000002	19.85
>>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	1.5
14	2.0
15	1.5
16	1.0
17	1.0
18	1.5
19	2.0
20	2.0
21	2.5
22	3.0
23	3.0
24	3.5
25	4.0
26	3.5
27	3.0
28	3.0
29	4.5
30	6.0
31	6.0
32	10.0
33	14.0
34	14.0
35	15.5
36	17.0
37	17.0
38	40.0
39	63.0
40	86.0
41	109.0
42	109.0
43	249.5
44	390.0
45	390.0
46	386.0
47	382.0
48	382.0
49	317.5
50	253.0
51	327.0
52	401.0
53	401.0
54	728.5
55	1056.0
56	1056.0
57	698.0
58	340.0
59	340.0
60	503.0
61	666.0
62	666.0
63	451.0
64	236.0
65	131.5
66	27.0
67	27.0
68	19.5
69	12.0
70	12.0
71	10.0
72	8.0
73	8.0
74	5.0
75	2.0
76	1.5
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	0.0
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	0.025
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	fail
#Total Deduplicated Percentage	38.175
#Duplication Level	Percentage of deduplicated	Percentage of total
1	84.67583497053045	32.324999999999996
2	7.269155206286837	5.55
3	2.4230517354289454	2.775
4	1.1132940406024885	1.7000000000000002
5	0.8513425016371972	1.625
6	0.7858546168958742	1.7999999999999998
7	0.26195153896529144	0.7000000000000001
8	0.19646365422396855	0.6
9	0.19646365422396855	0.675
>10	1.768172888015717	15.1
>50	0.3274394237066143	8.95
>100	0.06548788474132286	11.825
>500	0.06548788474132286	16.375
>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
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCG	655	16.375	TruSeq Adapter, Index 2 (100% over 35bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATT	473	11.825	No Hit
TGAGGTAGTAGGTTGTATGGTTAGATCGGAAGAGCA	90	2.25	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATA	73	1.825	No Hit
TGAGGTAGTAGTTTGTGCTGTTAGATCGGAAGAGCA	66	1.6500000000000001	No Hit
GGAAGAGCACACGTCTGAACTCCAGTCACCGATGTA	65	1.625	TruSeq Adapter, Index 2 (100% over 36bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAAG	64	1.6	No Hit
CGCGACCTCAGATCAGACGTAGATCGGAAGAGCACA	50	1.25	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTAGAT	49	1.225	No Hit
GTTTCCGTAGTGTAGTGGTTATCAGATCGGAAGAGC	45	1.125	No Hit
TGGAATGTAAGGAAGTGTGTGGAGATCGGAAGAGCA	36	0.8999999999999999	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATAGATC	36	0.8999999999999999	No Hit
TGAGGTAGTAGGTTGTGTGGTTAGATCGGAAGAGCA	33	0.8250000000000001	No Hit
TGAGGTAGTAGATTGTATAGTTAGATCGGAAGAGCA	29	0.7250000000000001	No Hit
GGGGATGTAGCTCAGTGGTAGATCGGAAGAGCACAC	29	0.7250000000000001	No Hit
GTCTACGGCCATACCACCCTGAACGCGCCCGATCTC	28	0.7000000000000001	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTC	24	0.6	No Hit
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGAAT	23	0.575	No Hit
TGAGGTAGTAGGTTGTATAGTTAGATCGGAAGAGCA	21	0.525	No Hit
CGCGACCTCAGATCGGAAGAGCACACGTCTGAACTC	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGC	20	0.5	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAGA	17	0.42500000000000004	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACA	15	0.375	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCAGATCGGA	15	0.375	No Hit
CTAGACTGAGGCTCCTTGAGGAGATCGGAAGAGCAC	14	0.35000000000000003	No Hit
CGCGACCTCAGATCAGATCGGAAGAGCACACGTCTG	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCA	13	0.325	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTAGA	12	0.3	No Hit
TGAGATGAAGCACTGTAGCTCAGATCGGAAGAGCAC	12	0.3	No Hit
CGCGACCTCAGATCAGACGTGGCAGATCGGAAGAGC	10	0.25	No Hit
TGAGGTAGTAGGTTGTATGGTCAGATCGGAAGAGCA	10	0.25	No Hit
CACCCGTAGAACCGACCTTGCGAGATCGGAAGAGCA	10	0.25	No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTAGAT	10	0.25	No Hit
CGCGACCTCAGATCAGACAGATCGGAAGAGCACACG	10	0.25	No Hit
TGAGGTAGTAGGTTGTATGGTAGATCGGAAGAGCAC	9	0.22499999999999998	No Hit
GTAGTCGTGGCCGAGTGGTTAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAAGATCGG	9	0.22499999999999998	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCAGATCGGAA	8	0.2	No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTCA	8	0.2	No Hit
ACTGGACTTGGAGTCAGAAGGCAGATCGGAAGAGCA	8	0.2	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAACA	7	0.17500000000000002	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGA	7	0.17500000000000002	No Hit
AGAGGTAGTAGGTTGCATAGTTAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATCAGAT	7	0.17500000000000002	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCAG	6	0.15	No Hit
TCGATGTGGTGCTGCCGCGTTCTCTTCGGGCCGGGG	6	0.15	No Hit
TGAGGTAGTAGGTTGTGTGGTAGATCGGAAGAGCAC	6	0.15	No Hit
TGAGGTAGTAGATTGTATAGTCAGATCGGAAGAGCA	6	0.15	No Hit
GGGGATGTAGCTCAGTGGCAGATCGGAAGAGCACAC	6	0.15	No Hit
CCGCGACCTCAGATCAGACGTAGATCGGAAGAGCAC	6	0.15	No Hit
AGCTACATCTGGCTACTGGGTCTCTAGATCGGAAGA	6	0.15	No Hit
AACCCGTAGATCCGATCTTGTAGATCGGAAGAGCAC	6	0.15	No Hit
TGAGGTAGTAGATTGTATAGTAGATCGGAAGAGCAC	6	0.15	No Hit
GCCGGTACAGTGAAACTAGATCGGAAGAGCACACGT	6	0.15	No Hit
GTAGTCGTGGCCGAGTAGATCGGAAGAGCACACGTC	6	0.15	No Hit
TAGCTTATCAGACTGATGTTGACTAGATCGGAAGAG	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCAGATCGGA	5	0.125	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCAGATC	5	0.125	No Hit
GGGGATGTAGCTCAGTGGAGATCGGAAGAGCACACG	5	0.125	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCG	5	0.125	No Hit
CCGCGACCTCAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TAGCTTATCAGACTGATGTTGACAAGATCGGAAGAG	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTAAGATCGGAAGAGCA	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATC	5	0.125	No Hit
TGAGGTAGTAGTTTGTGCTGTCAGATCGGAAGAGCA	5	0.125	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGAGATC	5	0.125	No Hit
TGTAAACATCCCCGACTGGAAGCAGATCGGAAGAGC	5	0.125	No Hit
CGCGACCTTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
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	17.525	0.0	0.0	0.0	0.0
2	17.65	0.0	0.0	0.0	0.0
3	17.65	0.0	0.0	0.0	0.0
4	17.675	0.0	0.0	0.0	0.0
5	17.725	0.0	0.0	0.0	0.0
6	17.8	0.0	0.0	0.0	0.0
7	17.8	0.0	0.0	0.0	0.0
8	17.85	0.0	0.0	0.0	0.0
9	17.975	0.0	0.0	0.0	0.0
10	18.825	0.0	0.0	0.0	0.0
11	19.075	0.0	0.0	0.0	0.0
12	19.475	0.0	0.0	0.0	0.0
13	19.825	0.0	0.0	0.0	0.0
14	20.225	0.0	0.0	0.0	0.0
15	21.15	0.0	0.0	0.0	0.0
16	21.6	0.0	0.0	0.0	0.0
17	23.225	0.0	0.0	0.0	0.0
18	24.25	0.0	0.0	0.0	0.0
19	25.8	0.0	0.0	0.0	0.0
20	27.95	0.0	0.0	0.0	0.0
21	31.525	0.0	0.0	0.0	0.0
22	35.45	0.0	0.0	0.0	0.0
23	47.425	0.0	0.0	0.0	0.0
24	52.275	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GGTAGTA	25	3.5274107E-4	30.0	4
TGAGGTA	25	3.5274107E-4	30.0	1
GTAGTAG	25	3.5274107E-4	30.0	5
TGGTCCG	20	0.00456452	29.999998	4
ATCTCAA	20	0.00456452	29.999998	24
TAGTGAG	20	0.00456452	29.999998	15
GGTCCGA	20	0.00456452	29.999998	5
TTATCTC	20	0.00456452	29.999998	22
GCTGGTC	20	0.00456452	29.999998	2
GTCCGAA	20	0.00456452	29.999998	6
CGAAGGT	20	0.00456452	29.999998	9
GGCTGGT	20	0.00456452	29.999998	1
GTGAGTT	20	0.00456452	29.999998	17
GAGTTAT	20	0.00456452	29.999998	19
CTGGTCC	20	0.00456452	29.999998	3
TATCTCA	20	0.00456452	29.999998	23
GGTAGTG	20	0.00456452	29.999998	13
AAGGTAG	20	0.00456452	29.999998	11
AGTGAGT	20	0.00456452	29.999998	16
TGGTGGT	20	0.00456452	29.999998	5
>>END_MODULE
Read 27945 spots for SRR30542863.sra
Written 27945 spots for SRR30542863.sra
Read 27945 spots for SRR30542863.sra
Written 27945 spots for SRR30542863.sra
Read 27945 spots for SRR30542863.sra
Written 27945 spots for SRR30542863.sra
Read 27945 spots for SRR30542863.sra
Written 27945 spots for SRR30542863.sra
Read 27945 spots for SRR30542863.sra
Written 27945 spots for SRR30542863.sra
Read 27945 spots for SRR30542863.sra
Written 27945 spots for SRR30542863.sra
Read 27945 spots for SRR30542863.sra
Written 27945 spots for SRR30542863.sra
Read 27952 spots for SRR30542863.sra
Written 27952 spots for SRR30542863.sra
SRR ids: ['SRR30542863.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_jrjchp85
SRR30542863.sra spots: 223567
blocks: [[1, 27945], [27946, 55890], [55891, 83835], [83836, 111780], [111781, 139725], [139726, 167670], [167671, 195615], [195616, 223567]]
SRR30542863 file size 31816
SRR30542863 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 SRR30542863 SRR30542863_1.fastq
Input file:	SRR30542863_1.fastq
trimmed:	SRR30542863-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 05:48:20 2025 >> started

Thu Nov  6 05:48:20 2025 >> done (0.136s)
223567 reads processed; of these:
   345 ( 0.15%) short reads filtered out after trimming by size control
 38952 (17.42%) empty reads filtered out after trimming by size control
184270 (82.42%) reads available; of these:
    20 ( 0.01%) trimmed reads available after processing
184250 (99.99%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 35	    20	  0.01%
 36	184250	 99.99%
184270 reads passed initial QC


criterion=sequence-density
sequence-density=41.28
sequence-density-rank=1
fanout-score=19.79
fanout-score-rank=1
prefix-density=46.76
prefix-fanout=17.5
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTAT


criterion=fanout-score
sequence-density=41.28
sequence-density-rank=1
fanout-score=19.79
fanout-score-rank=1
prefix-density=46.76
prefix-fanout=17.5
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTAT
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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTAT -o SRR30542863 -
Input file:	STDIN
trimmed:	SRR30542863-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTAT
-- 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 05:48:22 2025 >> started

Thu Nov  6 05:48:22 2025 >> done (0.054s)
175495 reads processed; of these:
 14292 ( 8.14%) short reads filtered out after trimming by size control
   174 ( 0.10%) empty reads filtered out after trimming by size control
161029 (91.76%) reads available; of these:
 95975 (59.60%) trimmed reads available after processing
 65054 (40.40%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  3621	  2.25%
 19	  4482	  2.78%
 20	  6156	  3.82%
 21	  8113	  5.04%
 22	 25421	 15.79%
 23	 10417	  6.47%
 24	  4082	  2.53%
 25	  3095	  1.92%
 26	  2397	  1.49%
 27	  3196	  1.98%
 28	  3820	  2.37%
 29	  2778	  1.73%
 30	  3164	  1.96%
 31	  5415	  3.36%
 32	  6129	  3.81%
 33	  3689	  2.29%
 34	     0	  0.00%
 35	    10	  0.01%
 36	 65044	 40.39%


criterion=sequence-density
sequence-density=7.34
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=0.28
sequence-density-rank=27
fanout-score=87.24
fanout-score-rank=1
prefix-density=24.55
prefix-fanout=1.0
sequence=GACCCGCTGAACA
                                 Started job on |	Nov 06 05:48:29
                             Started mapping on |	Nov 06 05:48:29
                                    Finished on |	Nov 06 05:48:33
       Mapping speed, Million of reads per hour |	152.82

                          Number of input reads |	169804
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	39850
                        Uniquely mapped reads % |	23.47%
                          Average mapped length |	24.63
                       Number of splices: Total |	342
            Number of splices: Annotated (sjdb) |	92
                       Number of splices: GT/AG |	327
                       Number of splices: GC/AG |	6
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	9
                      Mismatch rate per base, % |	0.37%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.35
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	56976
             % of reads mapped to multiple loci |	33.55%
        Number of reads mapped to too many loci |	54747
             % of reads mapped to too many loci |	32.24%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.19%
                     % of reads unmapped: other |	1.55%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	72978	72978	72978
N_multimapping	56976	56976	56976
N_noFeature	12631	14880	37557
N_ambiguous	669	625	0
UnstrandedReadsAssigned:26550 PositiveStrandReadsAssigned:24345 NegativeStrandReadsAssigned:2293
Dataset is classified positive stranded
MeadianReadLen=31 20thPercentileLength=22 echo kmer=19
SRR30542863 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: SRR30542863-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 169,804 reads, 3,851 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 511 rounds

  31716 SRR30542863.ke.tsv
  32883 SRR30542863.se.tsv
  64599 total
==> SRR30542863.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSRNOT00000047550.4	955	856	8	2254.18
ENSRNOT00000040993.4	1039	940	6	1539.56
ENSRNOT00000050156.3	1545	1446	45	7506.15
ENSRNOT00000043693.3	684	585	6	2473.82
ENSRNOT00000046201.3	204	105	2	4594.24
ENSRNOT00000046108.3	681	582	4	1657.72
ENSRNOT00000049683.3	784	685	7	2464.79
ENSRNOT00000041241.3	348	249	0	0
ENSRNOT00000044582.3	297	198	3	3654.51

==> SRR30542863.se.tsv <==
ENSRNOG00000046319	0
ENSRNOG00000047964	0
ENSRNOG00000050370	0
ENSRNOG00000032365	0
ENSRNOG00000040300	0
ENSRNOG00000058808	0
ENSRNOG00000061316	0
ENSRNOG00000050129	0
ENSRNOG00000040316	0
ENSRNOG00000023659	0
SRR30542863 completed mapping pipeline successfully
