Starting /dee2/code/volunteer_pipeline.sh SRR1759865
    current disk space = 868704300
    free memory = 119394276 
SRR1759865 SRAfilesize
2ec6cb49a9950ae4184eaefc8523c069  SRR1759865.sra
SRR1759865.sra file validated
SRR1759865 is single end
SRR1759865 is conventional basespace
SRR1759865 read1 length is 36 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR1759865_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	46
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.69025	33.0	32.0	34.0	32.0	34.0
2	32.44	33.0	32.0	34.0	32.0	34.0
3	32.658	33.0	32.0	34.0	32.0	34.0
4	32.58275	33.0	32.0	34.0	32.0	34.0
5	32.57225	33.0	32.0	34.0	32.0	34.0
6	35.59025	37.0	35.0	37.0	33.0	37.0
7	35.472	37.0	34.0	37.0	33.0	37.0
8	35.2345	37.0	34.0	37.0	33.0	37.0
9	34.809	37.0	33.0	37.0	32.0	37.0
10	34.8655	37.0	33.0	37.0	32.0	37.0
11	34.7265	37.0	33.0	37.0	32.0	37.0
12	35.34175	37.0	34.0	37.0	33.0	37.0
13	36.85375	38.0	38.0	38.0	35.0	38.0
14	36.75375	38.0	38.0	38.0	35.0	38.0
15	36.47325	38.0	37.0	38.0	34.0	38.0
16	36.77175	38.0	38.0	38.0	35.0	38.0
17	36.54325	38.0	37.0	38.0	34.0	38.0
18	36.48475	38.0	37.0	38.0	34.0	38.0
19	36.74275	38.0	37.0	38.0	35.0	38.0
20	36.77425	38.0	38.0	38.0	34.0	38.0
21	36.45875	38.0	37.0	38.0	34.0	38.0
22	36.55	38.0	37.0	38.0	34.0	38.0
23	36.9545	39.0	37.0	39.0	34.0	39.0
24	37.11975	39.0	37.0	39.0	34.0	39.0
25	36.9845	39.0	37.0	39.0	34.0	39.0
26	37.04275	39.0	37.0	39.0	34.0	39.0
27	36.7925	39.0	37.0	39.0	34.0	39.0
28	37.16875	39.0	38.0	39.0	35.0	39.0
29	36.86475	39.0	37.0	39.0	34.0	39.0
30	36.889	38.0	37.0	39.0	34.0	39.0
31	37.113	38.0	37.0	39.0	34.0	39.0
32	37.02075	39.0	37.0	39.0	34.0	39.0
33	36.693	39.0	37.0	39.0	33.0	39.0
34	36.47475	38.0	37.0	39.0	33.0	39.0
35	36.89125	39.0	37.0	39.0	33.0	39.0
36	35.69525	38.0	37.0	39.0	32.0	39.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
23	2.0
24	2.0
25	8.0
26	14.0
27	17.0
28	38.0
29	50.0
30	77.0
31	109.0
32	132.0
33	168.0
34	260.0
35	383.0
36	1070.0
37	1670.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	15.049999999999999	14.35	59.25	11.35
2	23.07306050715541	25.759477780567412	21.466231483806176	29.701230228471005
3	26.3	36.65	19.5	17.549999999999997
4	37.30932733183296	14.028507126781694	15.153788447111777	33.50837709427357
5	33.5	30.9	23.425	12.174999999999999
6	41.225	22.875	26.025	9.875
7	27.575	20.5	36.6	15.325
8	27.650000000000002	17.05	43.45	11.85
9	32.0	26.1	31.900000000000002	10.0
10	29.099999999999998	14.399999999999999	42.05	14.45
11	26.875	25.924999999999997	33.7	13.5
12	18.875	31.25	40.075	9.8
13	21.075	39.65	25.724999999999998	13.55
14	35.125	29.349999999999998	19.325	16.2
15	18.35	42.475	25.6	13.575000000000001
16	24.45	27.175	36.525	11.85
17	27.175	16.900000000000002	28.875	27.05
18	36.025	20.175	22.525000000000002	21.275
19	36.35	29.799999999999997	16.75	17.1
20	25.775	35.65	20.599999999999998	17.974999999999998
21	21.224999999999998	40.825	25.05	12.9
22	38.65	23.474999999999998	23.225	14.649999999999999
23	24.45	39.525	18.175	17.849999999999998
24	42.05	25.45	13.750000000000002	18.75
25	24.75	26.275	22.725	26.25
26	16.075	41.275	21.175	21.475
27	18.425	29.525000000000002	14.475	37.574999999999996
28	31.525	30.349999999999998	12.125	26.0
29	26.075	27.500000000000004	16.1	30.325000000000003
30	52.825	23.65	10.375	13.15
31	18.55	30.049999999999997	30.675	20.724999999999998
32	17.349999999999998	33.85	18.175	30.625000000000004
33	22.925	29.125	29.4	18.55
34	40.975	29.45	10.299999999999999	19.275000000000002
35	21.925	43.824999999999996	11.600000000000001	22.650000000000002
36	18.224999999999998	37.35	18.475	25.95
>>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	0.5
14	0.0
15	0.5
16	1.0
17	1.0
18	0.5
19	0.0
20	0.0
21	1.5
22	3.0
23	3.0
24	2.0
25	1.0
26	2.0
27	3.0
28	3.0
29	4.5
30	6.0
31	6.0
32	18.5
33	31.0
34	31.0
35	92.0
36	153.0
37	153.0
38	298.0
39	443.0
40	304.5
41	166.0
42	166.0
43	320.0
44	474.0
45	474.0
46	887.5
47	1301.0
48	1301.0
49	1057.5
50	814.0
51	600.5
52	387.0
53	387.0
54	261.5
55	136.0
56	136.0
57	100.5
58	65.0
59	65.0
60	37.0
61	9.0
62	9.0
63	7.5
64	6.0
65	3.0
66	0.0
67	0.0
68	0.0
69	0.0
70	0.0
71	0.0
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	0.0
2	0.42500000000000004
3	0.0
4	0.025
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	fail
#Total Deduplicated Percentage	37.724999999999994
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.649436713055	30.425
2	8.482438701126574	6.4
3	3.3797216699801194	3.8249999999999997
4	1.656726308813784	2.5
5	0.5301524188204109	1.0
6	0.8614976805831678	1.95
7	0.06626905235255136	0.17500000000000002
8	0.46388336646785955	1.4000000000000001
9	0.5301524188204109	1.7999999999999998
>10	2.9158383035122597	20.875
>50	0.26507620941020543	7.35
>100	0.13253810470510272	9.25
>500	0.06626905235255136	13.05
>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	522	13.05	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GTGCAAGGATGAAAAAGAACTCTCTCACTGATAGAT	197	4.925	No Hit
TACCTGATTGATTCTGTCAGATCGGAAGAGCACACG	173	4.324999999999999	No Hit
TAGCTTCAGCGATGGATCGGTTGCATCGAGTATCGA	88	2.1999999999999997	No Hit
TGGAATGTAAAGAAGTATGTAAGATCGGAAGAGCAC	78	1.95	No Hit
TGAGATCGTTCAGTACGGCAATAGATCGGAAGAGCA	76	1.9	No Hit
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAC	52	1.3	TruSeq Adapter, Index 5 (100% over 35bp)
AGTCAATGATGTTTTTTCAAGACGGGACCGACTGGT	47	1.175	No Hit
TCTCAACCTGAACTCAGTCGTGATTACCCGCTGAAC	38	0.95	No Hit
TCAGGGTTGTTTAACAGATCGGAAGAGCACACGTCT	38	0.95	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
CGATGATGATGAAGAATTTTTGATATGGTGTCAGGA	37	0.9249999999999999	No Hit
TCAGGGTTGTTCAGATCGGAAGAGCACACGTCTGAA	36	0.8999999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TACCTGATTGATTCTGTTAGATCGGAAGAGCACACG	35	0.8750000000000001	No Hit
TAATACGTCGTTGGTGTTTCCATAGATCGGAAGAGC	33	0.8250000000000001	No Hit
CAGGGTTGTTTAGATCGGAAGAGCACACGTCTGAAC	30	0.75	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TACCTGATTGATTCTGTCAGCGCGATATGCTCAAGT	28	0.7000000000000001	No Hit
TGACTAGAGACACATTCAGCTAGATCGGAAGAGCAC	22	0.5499999999999999	No Hit
CCTTTTATACTGCGATCTGTTGAGACTATCCTTTGA	22	0.5499999999999999	No Hit
CTAGCTTCAGCGATGGATCGGTTGCATCGAGTATCG	21	0.525	No Hit
TGAGATCATCGTGAAAGCCAGTAGATCGGAAGAGCA	20	0.5	No Hit
TACCTGATTGATTCTGTCAAGATCGGAAGAGCACAC	19	0.475	No Hit
TGTGTATGACGACAACGTGTTAGGGACATCTGCACC	19	0.475	No Hit
GTTTGTGATGACTGCATACGGATCACTGGGCTCTGA	18	0.44999999999999996	No Hit
GTGCGATGAATGACTTGGATAAGTTTCGGCTGAAAC	18	0.44999999999999996	No Hit
TAACAGTGATCGAGAGTCGGGTGCTAGACTGTAAGT	18	0.44999999999999996	No Hit
TGAGATCATCGTGAAAGCTAGTAGATCGGAAGAGCA	16	0.4	No Hit
TACCCTGTAGATCGAGCTGTGTGTAGATCGGAAGAG	16	0.4	No Hit
TACCTGATTGATTCTGAGATCGGAAGAGCACACGTC	15	0.375	No Hit
GATGATGATGAAGAATTTTTGATATGGTGTCAGGAC	15	0.375	No Hit
TACCCGTAGCTCCTATCCATGTTAGATCGGAAGAGC	15	0.375	No Hit
TTTTGTAGATCGGAAGAGCACACGTCTGAACTCCAG	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACTTGGATCGGAGACGGCCTGGGAATCCTGGATGTT	14	0.35000000000000003	No Hit
TTATACTGCGATCTGTTGAGACTATCCTTTGATTGA	14	0.35000000000000003	No Hit
ACGTCTGGTTCAGGGTTGTTTAGATCGGAAGAGCAC	14	0.35000000000000003	No Hit
CTGCGGTGACGATCAACTCTTACCTACTATGACAAA	14	0.35000000000000003	No Hit
TGTGCAAGGATGAAAAAGAACTCTCTCACTGATAGA	13	0.325	No Hit
TTTATACTGCGATCTGTTGAGACTATCCTTTGATTG	13	0.325	No Hit
TCTCAACCTGAACTAGATCGGAAGAGCACACGTCTG	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 22bp)
AGGCAAGATGTTGGCATAGCTGAAGATCGGAAGAGC	13	0.325	No Hit
CGTCTGGTTCAGGGTTGTTTAGATCGGAAGAGCACA	13	0.325	No Hit
GCGCGATGAACTCTTTACCATCTTTCGGGGCATAAC	13	0.325	No Hit
TGACTAGAACCGTTACTCATCAGATCGGAAGAGCAC	12	0.3	No Hit
AATGGCACTGCATGAATTCACGGAGATCGGAAGAGC	12	0.3	No Hit
GTGGGGCACAGAGTTGCAGTTGATTGAAACTAAATC	12	0.3	No Hit
TGAAAGACATGGGTAGTGAGACGAGATCGGAAGAGC	11	0.27499999999999997	No Hit
AGGGTTGTTTAGATCGGAAGAGCACACGTCTGAACT	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CGTACTAGCTTCAGCGATGGATCGGTTGCATCGAGT	11	0.27499999999999997	No Hit
TCAGGGTTGTGTAGATCGGAAGAGCACACGTCTGAA	11	0.27499999999999997	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
ACTAGCTTCAGCGATGGATCGGTTGCATCGAGTATC	11	0.27499999999999997	No Hit
TGGAATGTAAAGAAGTATGTAGATCGGAAGAGCACA	10	0.25	No Hit
TTTTATACTGCGATCTGTTGAGACTATCCTTTGATT	10	0.25	No Hit
AACAGTGATCGAGAGTCGGGTGCTAGACTGTAAGTG	9	0.22499999999999998	No Hit
CACCCGTACATATGTTTCCGTGCTAGATCGGAAGAG	9	0.22499999999999998	No Hit
TATACTGCGATCTGTTGAGACTATCCTTTGATTGAG	9	0.22499999999999998	No Hit
TCACCGGGTGGAAACTAGCAGTAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
TACCTGATTGATTCTGTCAGCGCGATATGCTAGATC	9	0.22499999999999998	No Hit
TCTCAACCTGAACTCAGTCGTGAGATCGGAAGAGCA	9	0.22499999999999998	No Hit
GACAATGATAGGATAACCTAGAGTCTCTGAACCATT	9	0.22499999999999998	No Hit
TACCTGATTGATTCTGTAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
CGACAATGATAGGATAACCTAGAGTCTCTGAACCAT	8	0.2	No Hit
ACGTACTAGCTTCAGCGATGGATCGGTTGCATCGAG	8	0.2	No Hit
TGAGGTAGGCTCAGTAGATGCGAAGATCGGAAGAGC	8	0.2	No Hit
GCGGATTGAAGATGAAATCAACGACGCTGACCGGTA	8	0.2	No Hit
TACGTCTGGTTCAGGGTTGTTTAGATCGGAAGAGCA	8	0.2	No Hit
TGAGATCGTTCAGTACGGCAAAGATCGGAAGAGCAC	8	0.2	No Hit
GAGTTTTTTGTAGATCGGAAGAGCACACGTCTGAAC	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
ATACTGCGATCTGTTGAGACTATCCTTTGATTGAGT	7	0.17500000000000002	No Hit
TCAGGGTTGTTAGATCGGAAGAGCACACGTCTGAAC	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TACTAGCTTCAGCGATGGATCGGTTGCATCGAGTAT	6	0.15	No Hit
TATGACACTGAAGCGTTACCGAAAGATCGGAAGAGC	6	0.15	No Hit
ACGCATAGCACCAACTGGGCCTCCAGTTGGTACGTC	6	0.15	No Hit
CTTTTATACTGCGATCTGTTGAGACTATCCTTTGAT	6	0.15	No Hit
TCAGGGTTGTTTAACTAGATCGGAAGAGCACACGTC	6	0.15	No Hit
TGGCAAGATGTAGGCAGTTCAGTAGATCGGAAGAGC	6	0.15	No Hit
TAGAGTGGTGAAATTTCGAACGCATAGCACCAACTG	6	0.15	No Hit
TCGAACGCATAGCACCAACTGGGCCTCCAGTTGGTA	6	0.15	No Hit
TTAGAGTGGTGAAATTTCGAACGCATAGCACCAACT	6	0.15	No Hit
TTTGTACTCCGATGCCATTCAGAAGATCGGAAGAGC	6	0.15	No Hit
TTCAGGGTTGTTTAGATCGGAAGAGCACACGTCTGA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
GCGCGATGAGGATTGATAACACATACACACACTCTG	6	0.15	No Hit
GAGCGGTGATGAATGCACGTATTGCTCTGACACCTC	5	0.125	No Hit
TGAGATCGTTCAGTACGGCAACAGATCGGAAGAGCA	5	0.125	No Hit
CATAGCACCAACTGGGCCTCCAGTTGGTACGTCTGG	5	0.125	No Hit
TCAGGGTTGTTTAGATCGGAAGAGCACACGTCTAAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (95% over 24bp)
TGAGATCATTAGTTGAAAGCCGAAGATCGGAAGAGC	5	0.125	No Hit
TACGTACTAGCTTCAGCGATGGATCGGTTGCATCGA	5	0.125	No Hit
AATCGGTGATGTGATATCCAGTTCTGCTACTGAGTT	5	0.125	No Hit
GGTGAAATTTCGAACGCATAGCACCAACTGGGCCTC	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	1.35	0.0	0.0	0.0	0.0
2	1.475	0.0	0.0	0.0	0.0
3	1.575	0.0	0.0	0.0	0.0
4	1.65	0.0	0.0	0.0	0.0
5	1.85	0.0	0.0	0.0	0.0
6	2.0	0.0	0.0	0.0	0.0
7	2.575	0.0	0.0	0.0	0.0
8	2.825	0.0	0.0	0.0	0.0
9	3.025	0.0	0.0	0.0	0.0
10	3.525	0.0	0.0	0.0	0.0
11	4.375	0.0	0.0	0.0	0.0
12	6.5	0.0	0.0	0.0	0.0
13	22.7	0.0	0.0	0.0	0.0
14	23.75	0.0	0.0	0.0	0.0
15	25.15	0.0	0.0	0.0	0.0
16	26.9	0.0	0.0	0.0	0.0
17	28.65	0.0	0.0	0.0	0.0
18	29.95	0.0	0.0	0.0	0.0
19	36.825	0.0	0.0	0.0	0.0
20	38.125	0.0	0.0	0.0	0.0
21	39.75	0.0	0.0	0.0	0.0
22	45.125	0.0	0.0	0.0	0.0
23	51.25	0.0	0.0	0.0	0.0
24	56.925	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TCAGGGT	110	0.0	30.000002	1
TTCTGTC	35	2.0637017E-6	30.0	12
TCTGTCA	35	2.0637017E-6	30.0	13
CTGTCAG	35	2.0637017E-6	30.0	14
CGATATG	20	0.00456452	29.999998	23
ACTGATA	20	0.00456452	29.999998	27
GATATGC	20	0.00456452	29.999998	24
TGCAAGG	20	0.00456452	29.999998	2
GCGATAT	20	0.00456452	29.999998	22
CTCTCTC	20	0.00456452	29.999998	20
TGATTGA	40	1.5598562E-7	29.999998	5
TGATTCT	40	1.5598562E-7	29.999998	9
CTCTCAC	20	0.00456452	29.999998	22
GAAAAAG	20	0.00456452	29.999998	11
CCTGATT	40	1.5598562E-7	29.999998	3
TGTCAGC	20	0.00456452	29.999998	15
GCGCGAT	20	0.00456452	29.999998	20
CTGATTG	40	1.5598562E-7	29.999998	4
ACTCTCT	20	0.00456452	29.999998	19
CACTGAT	20	0.00456452	29.999998	26
>>END_MODULE
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
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Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
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Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
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Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
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Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
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Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
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Written 82132 spots for SRR1759865.sra
Rejected 82162 READS because READLEN < 1
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Written 82162 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
Rejected 82132 READS because READLEN < 1
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Written 82132 spots for SRR1759865.sra
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Read 82132 spots for SRR1759865.sra
Written 82132 spots for SRR1759865.sra
SRR ids: ['SRR1759865.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_2j2ixy24
SRR1759865.sra spots: 5256478
blocks: [[1, 82132], [82133, 164264], [164265, 246396], [246397, 328528], [328529, 410660], [410661, 492792], [492793, 574924], [574925, 657056], [657057, 739188], [739189, 821320], [821321, 903452], [903453, 985584], [985585, 1067716], [1067717, 1149848], [1149849, 1231980], [1231981, 1314112], [1314113, 1396244], [1396245, 1478376], [1478377, 1560508], [1560509, 1642640], [1642641, 1724772], [1724773, 1806904], [1806905, 1889036], [1889037, 1971168], [1971169, 2053300], [2053301, 2135432], [2135433, 2217564], [2217565, 2299696], [2299697, 2381828], [2381829, 2463960], [2463961, 2546092], [2546093, 2628224], [2628225, 2710356], [2710357, 2792488], [2792489, 2874620], [2874621, 2956752], [2956753, 3038884], [3038885, 3121016], [3121017, 3203148], [3203149, 3285280], [3285281, 3367412], [3367413, 3449544], [3449545, 3531676], [3531677, 3613808], [3613809, 3695940], [3695941, 3778072], [3778073, 3860204], [3860205, 3942336], [3942337, 4024468], [4024469, 4106600], [4106601, 4188732], [4188733, 4270864], [4270865, 4352996], [4352997, 4435128], [4435129, 4517260], [4517261, 4599392], [4599393, 4681524], [4681525, 4763656], [4763657, 4845788], [4845789, 4927920], [4927921, 5010052], [5010053, 5092184], [5092185, 5174316], [5174317, 5256478]]
SRR1759865 file size 583024
SRR1759865 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 64 -o SRR1759865 SRR1759865_1.fastq
Input file:	SRR1759865_1.fastq
trimmed:	SRR1759865-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 08:26:42 2020 >> started

Sat Feb  8 08:26:47 2020 >> done (4.880s)
5256478 reads processed; of these:
  25672 ( 0.49%) short reads filtered out after trimming by size control
  59318 ( 1.13%) empty reads filtered out after trimming by size control
5171488 (98.38%) reads available; of these:
    406 ( 0.01%) trimmed reads available after processing
5171082 (99.99%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 24	     22	  0.00%
 25	     33	  0.00%
 26	     58	  0.00%
 27	     23	  0.00%
 28	      0	  0.00%
 29	      3	  0.00%
 30	      9	  0.00%
 31	      5	  0.00%
 32	     42	  0.00%
 33	    109	  0.00%
 34	     74	  0.00%
 35	     28	  0.00%
 36	5171082	 99.99%
5171488 reads passed initial QC


criterion=sequence-density
sequence-density=56.86
sequence-density-rank=1
fanout-score=10.48
fanout-score-rank=5
prefix-density=60.95
prefix-fanout=9.8
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAA


criterion=fanout-score
sequence-density=1.48
sequence-density-rank=7
fanout-score=21.65
fanout-score-rank=1
prefix-density=1.53
prefix-fanout=21.0
sequence=GCAGATCGGAAG
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 64 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAA -o SRR1759865 -
Input file:	STDIN
trimmed:	SRR1759865-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAA
-- 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 08:27:00 2020 >> started

Sat Feb  8 08:27:07 2020 >> done (7.238s)
4990032 reads processed; of these:
1483246 (29.72%) short reads filtered out after trimming by size control
     76 ( 0.00%) empty reads filtered out after trimming by size control
3506710 (70.27%) reads available; of these:
2030474 (57.90%) trimmed reads available after processing
1476236 (42.10%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	 335805	  9.58%
 19	  86473	  2.47%
 20	  84607	  2.41%
 21	 280915	  8.01%
 22	 307835	  8.78%
 23	 287429	  8.20%
 24	 114331	  3.26%
 25	  37675	  1.07%
 26	  35830	  1.02%
 27	  24169	  0.69%
 28	  19149	  0.55%
 29	  23627	  0.67%
 30	  23127	  0.66%
 31	  39760	  1.13%
 32	 276159	  7.88%
 33	  53733	  1.53%
 34	     35	  0.00%
 35	      7	  0.00%
 36	1476044	 42.09%


criterion=sequence-density
sequence-density=10.67
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=10
prefix-density=0.00
prefix-fanout=1.0
sequence=TACCTGATTGATTCTGTCAGCGCGATATGCTCAAGTAAAAGATTA


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=39
fanout-score=296.59
fanout-score-rank=1
prefix-density=3.68
prefix-fanout=1.0
sequence=CAGTACGGCAACACCCGTACATATGTTTCCGTGCT
                                 Started job on |	Feb 08 08:27:37
                             Started mapping on |	Feb 08 08:27:37
                                    Finished on |	Feb 08 08:27:58
       Mapping speed, Million of reads per hour |	632.26

                          Number of input reads |	3688166
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2449856
                        Uniquely mapped reads % |	66.42%
                          Average mapped length |	29.46
                       Number of splices: Total |	7406
            Number of splices: Annotated (sjdb) |	3975
                       Number of splices: GT/AG |	6390
                       Number of splices: GC/AG |	73
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	941
                      Mismatch rate per base, % |	0.22%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.09
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.07
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	981725
             % of reads mapped to multiple loci |	26.62%
        Number of reads mapped to too many loci |	117642
             % of reads mapped to too many loci |	3.19%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	3.76%
                     % of reads unmapped: other |	0.01%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	256585	256585	256585
N_multimapping	981725	981725	981725
N_noFeature	17228	47083	2118202
N_ambiguous	371628	70494	353
UnstrandedReadsAssigned:2061000 PositiveStrandReadsAssigned:2332279 NegativeStrandReadsAssigned:331301
Dataset is classified positive stranded
MeadianReadLen=32 20thPercentileLength=21 echo kmer=19
SRR1759865 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: SRR1759865-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,688,166 reads, 119,094 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 928 rounds

  33747 SRR1759865.ke.tsv
  46739 SRR1759865.se.tsv
  80486 total
==> SRR1759865.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
Y110A7A.10	1787	1688	0	0
F27C8.1	1940	1841	2	8.07467
F07C3.7	1728	1629	0	0
F52H2.2a	1739	1640	4	18.1286
F52H2.2b	1840	1741	0	0
T13A10.10a	1734	1635	0	0
T13A10.10b	1598	1499	3	14.8754
C55C2.5a	1840	1741	0	0
C55C2.5b	1606	1507	0.999369	4.92903

==> SRR1759865.se.tsv <==
WBGene00197333	0
WBGene00198386	0
WBGene00015153	0
WBGene00002061	5
WBGene00255704	0
WBGene00235314	0
WBGene00001177	9
WBGene00169236	0
WBGene00219784	0
WBGene00015152	0
SRR1759865 completed mapping pipeline successfully
