Starting /dee2/code/volunteer_pipeline.sh SRR1759868
    current disk space = 402733700
    free memory = 127283496 
SRR1759868 SRAfilesize
0298ded93147d7ffd50d4f9ea3e03dd9  SRR1759868.sra
SRR1759868.sra file validated
SRR1759868 is single end
SRR1759868 is conventional basespace
SRR1759868 read1 length is 36 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR1759868_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	47
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.412	33.0	32.0	33.0	29.0	34.0
2	32.276	33.0	32.0	33.0	32.0	34.0
3	32.43575	33.0	32.0	33.0	32.0	34.0
4	32.54925	33.0	32.0	33.0	32.0	34.0
5	32.4545	33.0	32.0	33.0	32.0	34.0
6	35.52125	37.0	35.0	37.0	33.0	37.0
7	35.433	37.0	34.0	37.0	33.0	37.0
8	35.3755	37.0	34.0	37.0	33.0	37.0
9	35.17525	37.0	34.0	37.0	32.0	37.0
10	35.174	37.0	33.0	37.0	32.0	37.0
11	34.2235	37.0	33.0	37.0	32.0	37.0
12	34.37625	37.0	33.0	37.0	31.0	37.0
13	35.626	38.0	37.0	38.0	32.0	38.0
14	35.37375	38.0	36.0	38.0	32.0	38.0
15	35.341	38.0	36.0	38.0	32.0	38.0
16	36.3765	38.0	37.0	38.0	33.0	38.0
17	36.28725	38.0	37.0	38.0	33.0	38.0
18	36.4765	38.0	37.0	38.0	34.0	38.0
19	36.12375	38.0	37.0	38.0	33.0	38.0
20	36.43475	38.0	37.0	38.0	34.0	38.0
21	35.9215	38.0	37.0	38.0	32.0	38.0
22	36.49925	38.0	37.0	38.0	34.0	38.0
23	37.3045	39.0	38.0	39.0	36.0	39.0
24	37.27375	39.0	38.0	39.0	35.0	39.0
25	36.62525	38.0	37.0	39.0	33.0	39.0
26	36.35175	38.0	37.0	39.0	32.0	39.0
27	36.67275	38.0	37.0	39.0	33.0	39.0
28	36.9855	38.0	37.0	39.0	34.0	39.0
29	36.35075	38.0	37.0	39.0	32.0	39.0
30	36.81825	38.0	37.0	39.0	34.0	39.0
31	36.45325	38.0	37.0	39.0	33.0	39.0
32	36.913	38.0	37.0	39.0	34.0	39.0
33	37.0225	39.0	37.0	39.0	34.0	39.0
34	36.875	38.0	38.0	39.0	34.0	39.0
35	36.98275	39.0	37.0	39.0	34.0	39.0
36	36.66	39.0	37.0	39.0	33.0	39.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
23	1.0
24	3.0
25	8.0
26	10.0
27	34.0
28	48.0
29	64.0
30	79.0
31	96.0
32	149.0
33	201.0
34	329.0
35	531.0
36	1098.0
37	1349.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	26.333080616628756	16.224412433661865	46.07025524387162	11.372251705837757
2	20.674999999999997	30.4	24.6	24.325
3	23.9	32.175	23.825	20.1
4	36.025	17.299999999999997	21.025	25.650000000000002
5	28.925	29.225	26.775	15.075
6	37.425000000000004	21.2	28.549999999999997	12.825000000000001
7	25.874999999999996	24.6	31.974999999999998	17.549999999999997
8	25.1	17.575	41.275	16.05
9	27.625	18.175	38.875	15.325
10	33.85	16.0	35.65	14.499999999999998
11	23.05	24.725	35.725	16.5
12	21.224999999999998	28.675	37.25	12.85
13	27.900000000000002	30.85	28.025	13.225000000000001
14	31.374999999999996	24.175	26.875	17.575
15	21.05	34.175	29.2	15.575
16	25.424999999999997	23.825	34.1	16.650000000000002
17	26.775	21.925	30.65	20.65
18	40.949999999999996	18.099999999999998	21.125	19.825
19	30.8	27.05	21.975	20.175
20	26.775	40.025	21.125	12.075
21	27.275	38.475	18.375	15.875
22	35.6	32.225	22.05	10.125
23	28.075	42.675000000000004	13.700000000000001	15.55
24	42.825	32.074999999999996	11.200000000000001	13.900000000000002
25	27.925	37.275000000000006	17.1	17.7
26	21.425	36.475	22.35	19.75
27	23.799999999999997	29.775000000000002	13.575000000000001	32.85
28	41.875	30.225	9.35	18.55
29	40.175	28.675	7.175	23.974999999999998
30	36.35	42.975	7.6	13.075000000000001
31	28.175	36.475	16.425	18.925
32	29.25	37.425000000000004	8.55	24.775
33	29.675	36.6	15.45	18.275
34	39.875	29.775000000000002	6.4750000000000005	23.875
35	19.225	41.4	8.575000000000001	30.8
36	18.4	39.475	7.7	34.425
>>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	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	1.5
22	3.0
23	3.0
24	2.5
25	2.0
26	1.5
27	1.0
28	1.0
29	7.0
30	13.0
31	13.0
32	22.5
33	32.0
34	32.0
35	44.0
36	56.0
37	56.0
38	119.5
39	183.0
40	209.0
41	235.0
42	235.0
43	402.5
44	570.0
45	570.0
46	925.5
47	1281.0
48	1281.0
49	1062.5
50	844.0
51	641.0
52	438.0
53	438.0
54	323.0
55	208.0
56	208.0
57	151.5
58	95.0
59	95.0
60	62.0
61	29.0
62	29.0
63	17.5
64	6.0
65	3.5
66	1.0
67	1.0
68	2.0
69	3.0
70	3.0
71	1.5
72	0.0
73	0.0
74	0.0
75	0.0
76	0.0
77	0.0
78	0.0
79	0.0
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	1.075
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	0.0
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	60.475
#Duplication Level	Percentage of deduplicated	Percentage of total
1	89.16907813145927	53.925
2	5.084745762711865	6.15
3	1.694915254237288	3.075
4	0.8267879288962381	2.0
5	0.37205456800330716	1.125
6	0.49607275733774286	1.7999999999999998
7	0.4547333608929309	1.925
8	0.37205456800330716	1.7999999999999998
9	0.0826787928896238	0.44999999999999996
>10	1.2401818933443571	13.350000000000001
>50	0.1653575857792476	6.875000000000001
>100	0.0413393964448119	7.5249999999999995
>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
TCAGGGTTGTTTAGATCGGAAGAGCACACGTCTGAA	301	7.5249999999999995	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TACCTGATTGATTCTGTCAGATCGGAAGAGCACACG	95	2.375	No Hit
TGAGATCGTTCAGTACGGCAATAGATCGGAAGAGCA	77	1.925	No Hit
TGGGAATCCTGGATGTTGTAAGCTAGATCGGAAGAG	52	1.3	No Hit
ATCCTGGATGTTGTAAGCTAGATCGGAAGAGCACAC	51	1.275	No Hit
GAGTTTTTTGTAGATCGGAAGAGCACACGTCTGAAC	47	1.175	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
CTGGATGTTGTAAGCTAGATCGGAAGAGCACACGTC	37	0.9249999999999999	No Hit
CTGGGAATCCTGGATGTTGTAAGCTAGATCGGAAGA	34	0.8500000000000001	No Hit
TGGAATGTAAAGAAGTATGTAAGATCGGAAGAGCAC	32	0.8	No Hit
AATCCTGGATGTTGTAAGCTAGATCGGAAGAGCACA	26	0.65	No Hit
TACCTGATTGATTCTGTCAAGATCGGAAGAGCACAC	26	0.65	No Hit
TTTTGTAGATCGGAAGAGCACACGTCTGAACTCCAG	25	0.625	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACGTCTGGTTCAGGGTTGTTTAGATCGGAAGAGCAC	23	0.575	No Hit
TCAGGGTTGTTCAGATCGGAAGAGCACACGTCTGAA	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCCTGGGAATCCTGGATGTTGTAAGCTAGATCGGAA	20	0.5	No Hit
GGAGACGGCCTGGGAATCCTGGATGTTGTAAGCTAG	17	0.42500000000000004	No Hit
CAGGGTTGTTTAGATCGGAAGAGCACACGTCTGAAC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCTCAACCTGAACTCAGTCGTGATTAGATCGGAAGA	15	0.375	No Hit
CACCCGTACATATGTTTCCGTGCTAGATCGGAAGAG	14	0.35000000000000003	No Hit
TCACCGGGTGGAAACTAGCAGTAGATCGGAAGAGCA	14	0.35000000000000003	No Hit
TGGATGTTGTAAGCTAGATCGGAAGAGCACACGTCT	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TGAGATCGTTCAGTACGGCAAAGATCGGAAGAGCAC	13	0.325	No Hit
GACGGCCTGGGAATCCTGGATGTTGTAAGCTAGATC	13	0.325	No Hit
TACCTGATTGATTCTGTCAGCGCGATATGCTAGATC	12	0.3	No Hit
CCTGGATGTTGTAAGCTAGATCGGAAGAGCACACGT	12	0.3	No Hit
TCTCAACCTGAACTAGATCGGAAGAGCACACGTCTG	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
TTTGATTGAGTTTTTTGTAGATCGGAAGAGCACACG	11	0.27499999999999997	No Hit
TACCTGATTGATTCTAGATCGGAAGAGCACACGTCT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TTGATTGAGTTTTTTGTAGATCGGAAGAGCACACGT	10	0.25	No Hit
GAATAGATACGCGGTATGAGGTAGATCGGAAGAGCA	10	0.25	No Hit
CTTTGATTGAGTTTTTTGTAGATCGGAAGAGCACAC	10	0.25	No Hit
TACCTGATTGATTCTGTTAGATCGGAAGAGCACACG	10	0.25	No Hit
TGAAAGACATGGGTAGTGAGACGAGATCGGAAGAGC	10	0.25	No Hit
AATGGCACTGCATGAATTCACGGAGATCGGAAGAGC	10	0.25	No Hit
TCACCGGGTGTAAATCAGCTTGAGATCGGAAGAGCA	10	0.25	No Hit
TACGTCTGGTTCAGGGTTGTTTAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
TACCTGATTGATTCTGTAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
TACCTGATTAGATCGGAAGAGCACACGTCTGAACTC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TGGGAATCCTGGATGTTGTAAGCCAGATCGGAAGAG	8	0.2	No Hit
AGGCAAGATGTTGGCATAGCTGAAGATCGGAAGAGC	8	0.2	No Hit
TCTCAACCTGAACTCAGTAGATCGGAAGAGCACACG	8	0.2	No Hit
TAATACGTCGTTGGTGTTTCCATAGATCGGAAGAGC	8	0.2	No Hit
TACCCTGTAGATCGAGCTGTGTGTAGATCGGAAGAG	8	0.2	No Hit
CTGGATGTTGTAAGCCAGATCGGAAGAGCACACGTC	8	0.2	No Hit
GAGTTTTTTGCAGATCGGAAGAGCACACGTCTGAAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TCAGGGTTGTGTAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
ACTTGGATCGGAGACGGCCTGGGAATCCTGGATGTT	7	0.17500000000000002	No Hit
CCTGGGAATCCTGGATGTTGTAAGCTAGATCGGAAG	7	0.17500000000000002	No Hit
TGAGGTAGGCTCAGTAGATGCGAAGATCGGAAGAGC	7	0.17500000000000002	No Hit
TGACTAGAGACACATTCAGCTAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
CGTCTGGTTCAGGGTTGTTTAGATCGGAAGAGCACA	7	0.17500000000000002	No Hit
TGATATGTTGTTTGAATGCCCCTAGATCGGAAGAGC	7	0.17500000000000002	No Hit
TGGGAATCCTGGATGTTGTAAGCGAGATCGGAAGAG	7	0.17500000000000002	No Hit
GAATCCTGGATGTTGTAAGCTAGATCGGAAGAGCAC	7	0.17500000000000002	No Hit
TACCTGATTGATTCTGTAAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
TACCCGTAGCTCCTATCCATGTTAGATCGGAAGAGC	7	0.17500000000000002	No Hit
TCTCAACCTGAACTCAGTCGTGAGATCGGAAGAGCA	7	0.17500000000000002	No Hit
TGAGATCATCGTGAAAGCTAGTAGATCGGAAGAGCA	6	0.15	No Hit
AGGGTTGTTTAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TGAGATCGTTCAGTACGGCAACAGATCGGAAGAGCA	6	0.15	No Hit
TACCTGATTGATTCTGTCAGCGCGATATGCTCAGAT	6	0.15	No Hit
TCTCAACCTGAACTCAGTCAGATCGGAAGAGCACAC	6	0.15	No Hit
GCTGGATCATCGAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TGAGATCATCGTGAAAGCCAGTAGATCGGAAGAGCA	6	0.15	No Hit
ATCCTGGATGTTGTAAGCCAGATCGGAAGAGCACAC	6	0.15	No Hit
CGGCCTGGGAATCCTGGATGTTGTAAGCTAGATCGG	6	0.15	No Hit
TGAGATCATTAGTTGAAAGCCGAAGATCGGAAGAGC	6	0.15	No Hit
TCTCAACCTGAACTCAGTCGTGATTACCCGCTAGAT	6	0.15	No Hit
TACCCGTAATGTTTCCGCTGAGAGATCGGAAGAGCA	6	0.15	No Hit
TGGATCATCGAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TTTAGCCGCACGAGATTGAGCAGATCGGAAGAGCAC	5	0.125	No Hit
GAGACGGCCTGGGAATCCTGGATGTTGTAAGCTAGA	5	0.125	No Hit
TTGTAAGCTAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
CATGACACTGATTAGGGATGTGAAGATCGGAAGAGC	5	0.125	No Hit
GAGACTATCCTTTGATTAGATCGGAAGAGCACACGT	5	0.125	No Hit
TGGTTCAGGGTTGTTTAGATCGGAAGAGCACACGTC	5	0.125	No Hit
TACCTGATTGATTCTGAGATCGGAAGAGCACACGTC	5	0.125	No Hit
TGATTGAGTTTTTTGTAGATCGGAAGAGCACACGTC	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	0.125	0.0	0.0	0.0	0.0
2	0.175	0.0	0.0	0.0	0.0
3	0.325	0.0	0.0	0.0	0.0
4	0.375	0.0	0.0	0.0	0.0
5	0.425	0.0	0.0	0.0	0.0
6	0.55	0.0	0.0	0.0	0.0
7	1.725	0.0	0.0	0.0	0.0
8	2.025	0.0	0.0	0.0	0.0
9	2.575	0.0	0.0	0.0	0.0
10	3.6	0.0	0.0	0.0	0.0
11	4.675	0.0	0.0	0.0	0.0
12	7.95	0.0	0.0	0.0	0.0
13	18.6	0.0	0.0	0.0	0.0
14	20.4	0.0	0.0	0.0	0.0
15	22.25	0.0	0.0	0.0	0.0
16	24.625	0.0	0.0	0.0	0.0
17	28.0	0.0	0.0	0.0	0.0
18	30.375	0.0	0.0	0.0	0.0
19	35.85	0.0	0.0	0.0	0.0
20	41.1	0.0	0.0	0.0	0.0
21	44.1	0.0	0.0	0.0	0.0
22	53.725	0.0	0.0	0.0	0.0
23	69.5	0.0	0.0	0.0	0.0
24	77.625	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TACCTGA	40	1.10703695E-7	31.12987	1
TGATTCT	30	2.7312073E-5	29.9625	9
CTGATTG	30	2.7312073E-5	29.9625	4
GATTGAT	30	2.7312073E-5	29.9625	6
TTGATTC	30	2.7312073E-5	29.9625	8
GATTCTG	25	3.5533935E-4	29.9625	10
ATTGATT	30	2.7312073E-5	29.9625	7
ATTCTGT	25	3.5533935E-4	29.9625	11
ACCTGAT	40	1.5771002E-7	29.962498	2
CCTGATT	45	4.4324406E-7	26.633333	3
TCAGGGT	65	2.8194336E-10	26.340658	1
TTGTTTA	65	4.5474735E-10	25.352884	7
GGTTGTT	65	4.5474735E-10	25.352884	5
GGGTTGT	65	4.5474735E-10	25.352884	4
TGTTTAG	65	4.5474735E-10	25.352884	8
GTTTAGA	65	4.5474735E-10	25.352884	9
CAGGGTT	65	4.5474735E-10	25.352884	2
GTTGTTT	65	4.5474735E-10	25.352884	6
AGGGTTG	70	1.0768417E-9	23.541965	3
TTTAGAT	70	1.0768417E-9	23.541965	10
>>END_MODULE
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
Rejected 160346 READS because READLEN < 1
Read 160346 spots for SRR1759868.sra
Written 160346 spots for SRR1759868.sra
SRR ids: ['SRR1759868.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_7yam2jwe
SRR1759868.sra spots: 5131072
blocks: [[1, 160346], [160347, 320692], [320693, 481038], [481039, 641384], [641385, 801730], [801731, 962076], [962077, 1122422], [1122423, 1282768], [1282769, 1443114], [1443115, 1603460], [1603461, 1763806], [1763807, 1924152], [1924153, 2084498], [2084499, 2244844], [2244845, 2405190], [2405191, 2565536], [2565537, 2725882], [2725883, 2886228], [2886229, 3046574], [3046575, 3206920], [3206921, 3367266], [3367267, 3527612], [3527613, 3687958], [3687959, 3848304], [3848305, 4008650], [4008651, 4168996], [4168997, 4329342], [4329343, 4489688], [4489689, 4650034], [4650035, 4810380], [4810381, 4970726], [4970727, 5131072]]
SRR1759868 file size 569064
SRR1759868 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 32 -o SRR1759868 SRR1759868_1.fastq
Input file:	SRR1759868_1.fastq
trimmed:	SRR1759868-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 (auto detected)
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	32
Sat Feb  8 08:28:04 2020 >> started

Sat Feb  8 08:28:09 2020 >> done (5.680s)
5131072 reads processed; of these:
  20104 ( 0.39%) short reads filtered out after trimming by size control
   3496 ( 0.07%) empty reads filtered out after trimming by size control
5107472 (99.54%) reads available; of these:
     16 ( 0.00%) trimmed reads available after processing
5107456 (100.00%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 29	      3	  0.00%
 30	      1	  0.00%
 31	      0	  0.00%
 32	      0	  0.00%
 33	      1	  0.00%
 34	      1	  0.00%
 35	     10	  0.00%
 36	5107456	100.00%
5107472 reads passed initial QC


criterion=sequence-density
sequence-density=50.07
sequence-density-rank=1
fanout-score=13.44
fanout-score-rank=8
prefix-density=54.67
prefix-fanout=12.3
sequence=TAGATCGGAAGAGCACACGTCTGAACTCCAGTC


criterion=fanout-score
sequence-density=8.60
sequence-density-rank=4
fanout-score=38.75
fanout-score-rank=1
prefix-density=9.19
prefix-fanout=36.2
sequence=GAGATCGGAAGA
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:	skewer -l 18 -t 32 -x TAGATCGGAAGAGCACACGTCTGAACTCCAGTC -o SRR1759868 -
Input file:	STDIN
trimmed:	SRR1759868-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TAGATCGGAAGAGCACACGTCTGAACTCCAGTC
-- 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):		Unknown format (auto detected)
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	32
Sat Feb  8 08:28:30 2020 >> started

Sat Feb  8 08:28:39 2020 >> done (8.486s)
4907179 reads processed; of these:
1885201 (38.42%) short reads filtered out after trimming by size control
      0 ( 0.00%) empty reads filtered out after trimming by size control
3021978 (61.58%) reads available; of these:
1800109 (59.57%) trimmed reads available after processing
1221869 (40.43%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 214001	  7.08%
 19	 122046	  4.04%
 20	 230229	  7.62%
 21	 437620	 14.48%
 22	 191456	  6.34%
 23	 198204	  6.56%
 24	 101760	  3.37%
 25	  52341	  1.73%
 26	  53754	  1.78%
 27	  20886	  0.69%
 28	  31028	  1.03%
 29	  20457	  0.68%
 30	  49798	  1.65%
 31	  32312	  1.07%
 32	  13972	  0.46%
 33	  30246	  1.00%
 34	      0	  0.00%
 35	      4	  0.00%
 36	1221864	 40.43%


criterion=sequence-density
sequence-density=25.32
sequence-density-rank=1
fanout-score=45.24
fanout-score-rank=1
prefix-density=30.84
prefix-fanout=37.1
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATA


criterion=fanout-score
sequence-density=25.32
sequence-density-rank=1
fanout-score=45.24
fanout-score-rank=1
prefix-density=30.84
prefix-fanout=37.1
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATA
                                 Started job on |	Feb 08 08:29:40
                             Started mapping on |	Feb 08 08:29:40
                                    Finished on |	Feb 08 08:30:53
       Mapping speed, Million of reads per hour |	158.91

                          Number of input reads |	3222271
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1227730
                        Uniquely mapped reads % |	38.10%
                          Average mapped length |	22.96
                       Number of splices: Total |	35021
            Number of splices: Annotated (sjdb) |	24078
                       Number of splices: GT/AG |	30618
                       Number of splices: GC/AG |	279
                       Number of splices: AT/AC |	147
               Number of splices: Non-canonical |	3977
                      Mismatch rate per base, % |	0.53%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.10
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	561447
             % of reads mapped to multiple loci |	17.42%
        Number of reads mapped to too many loci |	480253
             % of reads mapped to too many loci |	14.90%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	29.50%
                     % of reads unmapped: other |	0.07%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	1433094	1433094	1433094
N_multimapping	561447	561447	561447
N_noFeature	84898	432475	775042
N_ambiguous	119347	12854	2628
UnstrandedReadsAssigned:1023485 PositiveStrandReadsAssigned:782401 NegativeStrandReadsAssigned:450060
Dataset is classified unstranded
MeadianReadLen=25 20thPercentileLength=21 echo kmer=19
SRR1759868 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: 33,746
[index] number of k-mers: 28,835,158
[index] number of equivalence classes: 89,260
[quant] running in single-end mode
[quant] will process file 1: SRR1759868-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,222,271 reads, 643,893 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,141 rounds

  33747 SRR1759868.ke.tsv
  46739 SRR1759868.se.tsv
  80486 total
==> SRR1759868.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Y110A7A.10	1787	1688	12	9.43004
F27C8.1	1940	1841	1	0.720528
F07C3.7	1728	1629	2	1.6286
F52H2.2a	1739	1640	0	0
F52H2.2b	1840	1741	3	2.28574
T13A10.10a	1734	1635	0	0
T13A10.10b	1598	1499	0	0
C55C2.5a	1840	1741	0	0
C55C2.5b	1606	1507	0	0

==> SRR1759868.se.tsv <==
WBGene00197333	0
WBGene00198386	0
WBGene00015153	19
WBGene00002061	14
WBGene00255704	2
WBGene00235314	0
WBGene00001177	41
WBGene00169236	0
WBGene00219784	0
WBGene00015152	0
SRR1759868 completed mapping pipeline successfully
