Starting /dee2/code/volunteer_pipeline.sh SRR30542867
    current disk space = 1161339156
    free memory = 198871136 
SRR30542867 SRAfilesize
97ec8f22c9228789d6cb43f0f1ba207f  SRR30542867.sra
SRR30542867.sra file validated
SRR30542867 is single end
SRR30542867 is conventional basespace
SRR30542867 read1 length is 36 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR30542867_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	34.09125	32.0	32.0	37.0	32.0	37.0
2	34.784	37.0	32.0	37.0	32.0	37.0
3	36.15775	37.0	37.0	37.0	32.0	37.0
4	36.31025	37.0	37.0	37.0	32.0	37.0
5	36.5295	37.0	37.0	37.0	37.0	37.0
6	36.522	37.0	37.0	37.0	37.0	37.0
7	36.36575	37.0	37.0	37.0	37.0	37.0
8	36.6725	37.0	37.0	37.0	37.0	37.0
9	36.71875	37.0	37.0	37.0	37.0	37.0
10	36.62175	37.0	37.0	37.0	37.0	37.0
11	36.71325	37.0	37.0	37.0	37.0	37.0
12	36.62325	37.0	37.0	37.0	37.0	37.0
13	36.49525	37.0	37.0	37.0	37.0	37.0
14	36.6055	37.0	37.0	37.0	37.0	37.0
15	36.66125	37.0	37.0	37.0	37.0	37.0
16	36.56825	37.0	37.0	37.0	37.0	37.0
17	36.60475	37.0	37.0	37.0	37.0	37.0
18	36.51975	37.0	37.0	37.0	37.0	37.0
19	36.70375	37.0	37.0	37.0	37.0	37.0
20	36.5645	37.0	37.0	37.0	37.0	37.0
21	36.6475	37.0	37.0	37.0	37.0	37.0
22	36.6235	37.0	37.0	37.0	37.0	37.0
23	36.50625	37.0	37.0	37.0	37.0	37.0
24	36.49975	37.0	37.0	37.0	37.0	37.0
25	36.46875	37.0	37.0	37.0	37.0	37.0
26	36.5045	37.0	37.0	37.0	37.0	37.0
27	36.556	37.0	37.0	37.0	37.0	37.0
28	36.64675	37.0	37.0	37.0	37.0	37.0
29	36.64725	37.0	37.0	37.0	37.0	37.0
30	36.54425	37.0	37.0	37.0	37.0	37.0
31	36.5025	37.0	37.0	37.0	37.0	37.0
32	36.62275	37.0	37.0	37.0	37.0	37.0
33	36.514	37.0	37.0	37.0	37.0	37.0
34	36.596	37.0	37.0	37.0	37.0	37.0
35	36.619	37.0	37.0	37.0	37.0	37.0
36	36.31125	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	5.0
23	2.0
24	3.0
25	4.0
26	9.0
27	17.0
28	15.0
29	15.0
30	19.0
31	20.0
32	24.0
33	34.0
34	55.0
35	152.0
36	2372.0
37	1253.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.2	41.0	21.5	25.3
2	75.2	7.3999999999999995	6.65	10.75
3	11.125	52.925	5.425	30.525000000000002
4	38.875	7.124999999999999	43.35	10.65
5	24.725	26.025	8.875	40.375
6	48.825	6.425	19.2	25.55
7	47.949999999999996	17.925	11.3	22.825
8	20.485242621310658	41.32066033016508	28.139069534767387	10.055027513756878
9	12.6	43.05	18.475	25.874999999999996
10	48.94947473736869	36.39319659829915	6.328164082041019	8.329164582291146
11	39.375	44.625	7.85	8.15
12	53.425	26.75	9.4	10.424999999999999
13	12.025	10.225	36.425000000000004	41.325
14	12.4	43.824999999999996	20.025000000000002	23.75
15	24.95	25.724999999999998	8.725	40.6
16	25.15	45.45	22.075	7.324999999999999
17	22.900000000000002	30.625000000000004	8.3	38.175
18	45.1	9.425	20.575	24.9
19	36.625	10.85	44.9	7.625
20	20.925	12.55	27.175	39.35
21	31.374999999999996	10.75	52.5	5.375
22	60.550000000000004	14.45	17.625	7.375
23	13.075000000000001	56.625	8.05	22.25
24	34.925	51.2	6.425	7.449999999999999
25	14.075	34.849999999999994	11.875	39.2
26	9.577394348587147	11.927981995498875	49.91247811952989	28.582145536384097
27	12.225	9.275	9.2	69.3
28	23.275000000000002	11.95	3.6249999999999996	61.150000000000006
29	38.800000000000004	47.875	3.95	9.375
30	46.625	26.3	3.875	23.200000000000003
31	14.367959949937422	24.005006257822277	53.04130162703379	8.585732165206508
32	35.525	17.325	7.124999999999999	40.025
33	14.05	70.22500000000001	6.4	9.325
34	20.375	30.925000000000004	4.324999999999999	44.375
35	11.275	47.825	19.575	21.325
36	41.7813360020015	25.068801601200903	19.239429572179134	13.910432824618463
>>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	0.5
8	1.0
9	1.0
10	0.5
11	0.0
12	0.0
13	0.5
14	1.0
15	1.5
16	2.0
17	2.0
18	1.5
19	1.0
20	1.0
21	1.5
22	2.0
23	2.0
24	3.0
25	4.0
26	4.5
27	5.0
28	5.0
29	5.0
30	5.0
31	5.0
32	6.5
33	8.0
34	8.0
35	7.0
36	6.0
37	6.0
38	21.0
39	36.0
40	53.0
41	70.0
42	70.0
43	195.0
44	320.0
45	320.0
46	350.0
47	380.0
48	380.0
49	330.0
50	280.0
51	901.5
52	1523.0
53	1523.0
54	925.0
55	327.0
56	327.0
57	270.0
58	213.0
59	213.0
60	401.0
61	589.0
62	589.0
63	387.5
64	186.0
65	107.0
66	28.0
67	28.0
68	17.0
69	6.0
70	6.0
71	3.5
72	1.0
73	1.0
74	3.0
75	5.0
76	3.0
77	1.0
78	1.0
79	0.5
80	0.0
81	0.0
82	0.0
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	0.05
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	0.025
27	0.0
28	0.0
29	0.0
30	0.0
31	0.125
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	31.025000000000002
#Duplication Level	Percentage of deduplicated	Percentage of total
1	84.60918614020952	26.25
2	7.17163577759871	4.45
3	2.09508460918614	1.95
4	1.7727639000805804	2.1999999999999997
5	0.4834810636583401	0.75
6	0.40290088638195	0.75
7	0.5640612409347301	1.225
8	0.24174053182917005	0.6
9	0.16116035455278002	0.44999999999999996
>10	2.09508460918614	13.325000000000001
>50	0.16116035455278002	2.9250000000000003
>100	0.16116035455278002	14.025000000000002
>500	0.0	0.0
>1k	0.08058017727639001	31.1
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAG	1244	31.1	TruSeq Adapter, Index 2 (97% over 35bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATT	454	11.35	No Hit
TGAGGTAGTAGGTTGTATGGTTAGATCGGAAGAGCA	107	2.675	No Hit
TGAGGTAGTAGTTTGTGCTGTTAGATCGGAAGAGCA	64	1.6	No Hit
TGAGGTAGTAGGTTGTGTGGTTAGATCGGAAGAGCA	53	1.325	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAAG	42	1.05	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATAGATC	40	1.0	No Hit
GGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCA	39	0.975	TruSeq Adapter, Index 14 (97% over 35bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTAGAT	32	0.8	No Hit
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGAAT	30	0.75	No Hit
CGCGACCTCAGATCAGACGTAGATCGGAAGAGCACA	29	0.7250000000000001	No Hit
TGAGGTAGTAGGTTGTATGGTCAGATCGGAAGAGCA	29	0.7250000000000001	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATA	29	0.7250000000000001	No Hit
GTCTACGGCCATACCACCCTGAACGCGCCCGATCTC	27	0.675	No Hit
TGGAATGTAAGGAAGTGTGTGGAGATCGGAAGAGCA	22	0.5499999999999999	No Hit
GTTTCCGTAGTGTAGTGGTTATCAGATCGGAAGAGC	22	0.5499999999999999	No Hit
TGAGGTAGTAGGTTGTATAGTTAGATCGGAAGAGCA	20	0.5	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTAGA	18	0.44999999999999996	No Hit
TGAGGTAGTAGGTTGTGTGGTAGATCGGAAGAGCAC	17	0.42500000000000004	No Hit
GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGT	15	0.375	TruSeq Adapter, Index 8 (97% over 36bp)
TGAGGTAGTAGGTTGTGTGGTCAGATCGGAAGAGCA	15	0.375	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACA	13	0.325	No Hit
TGAGGTAGTAGATTGTATAGTTAGATCGGAAGAGCA	13	0.325	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAACAGATC	11	0.27499999999999997	No Hit
TGAGGTAGTAGGTTGTGTGGTTTAGATCGGAAGAGC	10	0.25	No Hit
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGC	10	0.25	No Hit
CGCGACCTCAGATCAGACGTGGCAGATCGGAAGAGC	10	0.25	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCAGATCGGA	10	0.25	No Hit
AACCCGTAGATCCGATCTTGTAGATCGGAAGAGCAC	10	0.25	No Hit
TGAGGTAGTAGTTTGTGCTGTCAGATCGGAAGAGCA	10	0.25	No Hit
TGAGATGAAGCACTGTAGCTCAGATCGGAAGAGCAC	10	0.25	No Hit
CGCGACCTCAGATCAGACGTGGTAGATCGGAAGAGC	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTATGGTAAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
GTAGTCGTGGCCGAGTGGTTAGATCGGAAGAGCACA	8	0.2	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAAGA	8	0.2	No Hit
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCA	8	0.2	No Hit
TGAGGTAGTAGGTTGTATGGTAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
TGAGGTAGTAGGTTGTATGGTTTAGATCGGAAGAGC	7	0.17500000000000002	No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTCA	7	0.17500000000000002	No Hit
GGGGATGTAGCTCAGTGGTAGATCGGAAGAGCACAC	7	0.17500000000000002	No Hit
TCCGGTCTTGAGCTAGATCGGAAGAGCACACGTCTG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TGAGGGGCAGAGAGCGAGACTTTAGATCGGAAGAGC	7	0.17500000000000002	No Hit
CGCGACCTCAGATCAGACAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
CGCGACCTCAGATCAGATCGGAAGAGCACACGTCTG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TGAGGTAGTAGGTTGTGTGGTAAGATCGGAAGAGCA	6	0.15	No Hit
CGCGACCTCAGATCAGACGCAGATCGGAAGAGCACA	6	0.15	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTC	6	0.15	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTA	6	0.15	No Hit
CTAGACTGAGGCTCCTTGAGGAGATCGGAAGAGCAC	5	0.125	No Hit
CACCCGTAGAACCGACCTTGCGAGATCGGAAGAGCA	5	0.125	No Hit
TGTAAACATCCCCGACTGGAAGCAGATCGGAAGAGC	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTAGATCGGAAGAGCAC	5	0.125	No Hit
CCGGTCTTGAGCTAGATCGGAAGAGCACACGTCTGA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATCAGAT	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	32.575	0.0	0.0	0.0	0.0
2	32.7	0.0	0.0	0.0	0.0
3	32.7	0.0	0.0	0.0	0.0
4	32.7	0.0	0.0	0.0	0.0
5	32.7	0.0	0.0	0.0	0.0
6	32.7	0.0	0.0	0.0	0.0
7	32.725	0.0	0.0	0.0	0.0
8	32.875	0.0	0.0	0.0	0.0
9	32.975	0.0	0.0	0.0	0.0
10	33.35	0.0	0.0	0.0	0.0
11	33.775	0.0	0.0	0.0	0.0
12	34.175	0.0	0.0	0.0	0.0
13	34.825	0.0	0.0	0.0	0.0
14	35.625	0.0	0.0	0.0	0.0
15	36.75	0.0	0.0	0.0	0.0
16	37.6	0.0	0.0	0.0	0.0
17	38.35	0.0	0.0	0.0	0.0
18	39.25	0.0	0.0	0.0	0.0
19	40.45	0.0	0.0	0.0	0.0
20	41.95	0.0	0.0	0.0	0.0
21	44.35	0.0	0.0	0.0	0.0
22	47.85	0.0	0.0	0.0	0.0
23	59.9	0.0	0.0	0.0	0.0
24	63.375	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AGTAGGT	30	2.707939E-5	30.000002	7
TAGTAGG	30	2.707939E-5	30.000002	6
AGGTTGT	30	2.707939E-5	30.000002	10
GTAGGTT	30	2.707939E-5	30.000002	8
TAGGTTG	30	2.707939E-5	30.000002	9
GAGGTAG	35	2.0637017E-6	30.0	2
CAGTCAC	145	0.0	30.0	28
GTCACAG	145	0.0	30.0	30
CCAGTCA	145	0.0	30.0	27
CTCCAGT	145	0.0	30.0	25
ACTCCAG	145	0.0	30.0	24
GTCTGAA	145	0.0	30.0	18
TCCAGTC	145	0.0	30.0	26
AACTCCA	145	0.0	30.0	23
CTGAACT	145	0.0	30.0	20
GAACTCC	145	0.0	30.0	22
TCTGAAC	145	0.0	30.0	19
GGTAGTA	35	2.0637017E-6	30.0	4
TGAGGTA	35	2.0637017E-6	30.0	1
TGAACTC	145	0.0	30.0	21
>>END_MODULE
Read 44240 spots for SRR30542867.sra
Written 44240 spots for SRR30542867.sra
Read 44238 spots for SRR30542867.sra
Written 44238 spots for SRR30542867.sra
Read 44238 spots for SRR30542867.sra
Written 44238 spots for SRR30542867.sra
Read 44238 spots for SRR30542867.sra
Written 44238 spots for SRR30542867.sra
Read 44238 spots for SRR30542867.sra
Written 44238 spots for SRR30542867.sra
Read 44238 spots for SRR30542867.sra
Written 44238 spots for SRR30542867.sra
Read 44238 spots for SRR30542867.sra
Written 44238 spots for SRR30542867.sra
Read 44238 spots for SRR30542867.sra
Written 44238 spots for SRR30542867.sra
SRR ids: ['SRR30542867.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ix8v2h_3
SRR30542867.sra spots: 353906
blocks: [[1, 44238], [44239, 88476], [88477, 132714], [132715, 176952], [176953, 221190], [221191, 265428], [265429, 309666], [309667, 353906]]
SRR30542867 file size 50420
SRR30542867 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 SRR30542867 SRR30542867_1.fastq
Input file:	SRR30542867_1.fastq
trimmed:	SRR30542867-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 05:50:32 2025 >> started

Thu Nov  6 05:50:32 2025 >> done (0.156s)
353906 reads processed; of these:
   975 ( 0.28%) short reads filtered out after trimming by size control
120877 (34.16%) empty reads filtered out after trimming by size control
232054 (65.57%) reads available; of these:
    28 ( 0.01%) trimmed reads available after processing
232026 (99.99%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 35	    28	  0.01%
 36	232026	 99.99%
232054 reads passed initial QC


criterion=sequence-density
sequence-density=46.57
sequence-density-rank=1
fanout-score=16.92
fanout-score-rank=2
prefix-density=51.60
prefix-fanout=15.3
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCA


criterion=fanout-score
sequence-density=1.29
sequence-density-rank=9
fanout-score=18.18
fanout-score-rank=1
prefix-density=23.38
prefix-fanout=1.0
sequence=GACCCGCTGAAAG
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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCA -o SRR30542867 -
Input file:	STDIN
trimmed:	SRR30542867-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCA
-- 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 05:50:33 2025 >> started

Thu Nov  6 05:50:34 2025 >> done (0.080s)
222179 reads processed; of these:
 23222 (10.45%) short reads filtered out after trimming by size control
   254 ( 0.11%) empty reads filtered out after trimming by size control
198703 (89.43%) reads available; of these:
121479 (61.14%) trimmed reads available after processing
 77224 (38.86%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  5175	  2.60%
 19	  4673	  2.35%
 20	  8017	  4.03%
 21	 10359	  5.21%
 22	 39858	 20.06%
 23	 12444	  6.26%
 24	  5089	  2.56%
 25	  3530	  1.78%
 26	  2506	  1.26%
 27	  2981	  1.50%
 28	  3708	  1.87%
 29	  2554	  1.29%
 30	  2854	  1.44%
 31	  6747	  3.40%
 32	  7088	  3.57%
 33	  3896	  1.96%
 34	     0	  0.00%
 35	    11	  0.01%
 36	 77213	 38.86%


criterion=sequence-density
sequence-density=12.59
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=7
prefix-density=0.00
prefix-fanout=1.0
sequence=TGAGGTAGTAGGTTGTATGGTTAGATCGGAAG


criterion=fanout-score
sequence-density=0.25
sequence-density-rank=30
fanout-score=52.42
fanout-score-rank=1
prefix-density=13.05
prefix-fanout=1.0
sequence=GTAGTAGGTTGCATAGTT
                                 Started job on |	Nov 06 05:50:41
                             Started mapping on |	Nov 06 05:50:41
                                    Finished on |	Nov 06 05:50:47
       Mapping speed, Million of reads per hour |	125.15

                          Number of input reads |	208578
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	45202
                        Uniquely mapped reads % |	21.67%
                          Average mapped length |	22.88
                       Number of splices: Total |	458
            Number of splices: Annotated (sjdb) |	88
                       Number of splices: GT/AG |	433
                       Number of splices: GC/AG |	9
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	16
                      Mismatch rate per base, % |	0.38%
                         Deletion rate per base |	0.00%
                        Deletion average length |	2.29
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	73403
             % of reads mapped to multiple loci |	35.19%
        Number of reads mapped to too many loci |	68396
             % of reads mapped to too many loci |	32.79%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.83%
                     % of reads unmapped: other |	0.51%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	89973	89973	89973
N_multimapping	73403	73403	73403
N_noFeature	7689	9789	43066
N_ambiguous	461	425	0
UnstrandedReadsAssigned:37052 PositiveStrandReadsAssigned:34988 NegativeStrandReadsAssigned:2136
Dataset is classified positive stranded
MeadianReadLen=31 20thPercentileLength=22 echo kmer=19
SRR30542867 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: SRR30542867-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 208,578 reads, 3,436 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 620 rounds

  31716 SRR30542867.ke.tsv
  32883 SRR30542867.se.tsv
  64599 total
==> SRR30542867.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSRNOT00000047550.4	955	856	3	996.666
ENSRNOT00000040993.4	1039	940	0	0
ENSRNOT00000050156.3	1545	1446	43	8456.72
ENSRNOT00000043693.3	684	585	16	7777.97
ENSRNOT00000046201.3	204	105	0	0
ENSRNOT00000046108.3	681	582	5	2443.14
ENSRNOT00000049683.3	784	685	11	4566.72
ENSRNOT00000041241.3	348	249	1	1142.1
ENSRNOT00000044582.3	297	198	8	11490.2

==> SRR30542867.se.tsv <==
ENSRNOG00000046319	0
ENSRNOG00000047964	0
ENSRNOG00000050370	0
ENSRNOG00000032365	0
ENSRNOG00000040300	0
ENSRNOG00000058808	0
ENSRNOG00000061316	0
ENSRNOG00000050129	0
ENSRNOG00000040316	0
ENSRNOG00000023659	0
SRR30542867 completed mapping pipeline successfully
