#Starting miRDeep2
/Home/ii/phongphakk/mirdeep2_0_0_8/bin/miRDeep2.pl dmel.fa /Home/ii/phongphakk/test/genome/Drosophila_melanogaster.BDGP6.dna.toplevel.fa dmel_vs_genome.arf /Home/ii/phongphakk/test/data/mature_miRNAs_dmel.fa /Home/ii/phongphakk/test/data/mature_miRNAs_dsim.fa /Home/ii/phongphakk/test/data/precursors_miRNAs_dmel.fa -t d.melanogaster

miRDeep2 started at 16:31:45


mkdir mirdeep_runs/run_31_10_2016_t_16_31_45

#testing input files
started: 16:32:10
sanity_check_mature_ref.pl /Home/ii/phongphakk/test/data/mature_miRNAs_dmel.fa


ended: 16:32:10
total:0h:0m:0s

started: 16:32:10
sanity_check_mature_ref.pl /Home/ii/phongphakk/test/data/mature_miRNAs_dsim.fa


ended: 16:32:10
total:0h:0m:0s

sanity_check_reads_ready_file.pl dmel.fa

started: 16:32:10

ended: 16:32:59
total:0h:0m:49s

started: 16:32:59
sanity_check_genome.pl /Home/ii/phongphakk/test/genome/Drosophila_melanogaster.BDGP6.dna.toplevel.fa


ended: 16:33:03
total:0h:0m:4s

started: 16:33:03
sanity_check_mapping_file.pl dmel_vs_genome.arf


ended: 16:33:09
total:0h:0m:6s

started: 16:33:09
sanity_check_mature_ref.pl /Home/ii/phongphakk/test/data/precursors_miRNAs_dmel.fa


ended: 16:33:09
total:0h:0m:0s

started: 16:33:09
Quantitation of expressed miRNAs in data


quantifier.pl -p /Home/ii/phongphakk/test/data/precursors_miRNAs_dmel.fa -m /Home/ii/phongphakk/test/data/mature_miRNAs_dmel.fa  -r dmel.fa  -t d.melanogaster -y 31_10_2016_t_16_31_45 -k  
getting samples and corresponding read numbers

Converting input files
building bowtie index
mapping mature sequences against index
mapping read sequences against index
Mapping statistics

#desc	total	mapped	unmapped	%mapped	%unmapped
total: 8606723	1091632	7515091	0.127	0.873
seq: 8606723	1091632	7515091	0.127	0.873
analyzing data
Expressed miRNAs are written to expression_analyses/expression_analyses_31_10_2016_t_16_31_45/miRNA_expressed.csv
not expressed miRNAs are written to expression_analyses/expression_analyses_31_10_2016_t_16_31_45/miRNA_not_expressed.csv

Creating miRBase.mrd file

make_html2.pl -q expression_analyses/expression_analyses_31_10_2016_t_16_31_45/miRBase.mrd -k mature_miRNAs_dmel.fa -t d.melanogaster -y 31_10_2016_t_16_31_45  -o -i expression_analyses/expression_analyses_31_10_2016_t_16_31_45/mature_miRNAs_dmel.fa_mapped.arf   -m dme -M miRNAs_expressed_all_samples_31_10_2016_t_16_31_45.csv  
miRNAs_expressed_all_samples_31_10_2016_t_16_31_45.csv file with miRNA expression values
parsing miRBase.mrd file finished
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ended: 16:49:24
total:0h:16m:15s

started: 16:49:24
rna2dna.pl /Home/ii/phongphakk/test/data/mature_miRNAs_dmel.fa > mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/mature_miRNAs_dmel.fa

rna2dna.pl /Home/ii/phongphakk/test/data/mature_miRNAs_dsim.fa > mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/mature_miRNAs_dsim.fa


ended: 16:49:24
total:0h:0m:0s

rna2dna.pl /Home/ii/phongphakk/test/data/precursors_miRNAs_dmel.fa > mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors_miRNAs_dmel.fa


ended: 16:49:24
total:0h:0m:0s

#parsing genome mappings
parse_mappings.pl dmel_vs_genome.arf -a 0 -b 18 -c 25 -i 5 > mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/dmel_vs_genome.arf_parsed.arf

started: 16:49:24

ended: 16:50:09
total:0h:0m:45s

#excising precursors
started: 16:50:09
excise_precursors_iterative_final.pl /Home/ii/phongphakk/test/genome/Drosophila_melanogaster.BDGP6.dna.toplevel.fa mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/dmel_vs_genome.arf_parsed.arf mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors.fa mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors.coords 50000
1	369988
2	84528
3	37782

ended: 16:53:44
total:0h:3m:35s

#preparing signature
prepare_signature.pl dmel.fa mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors.fa 1 -a mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/mature_miRNAs_dmel.fa -o mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/signature.arf 2>>error_31_10_2016_t_16_31_45.log

started: 16:53:44

ended: 16:59:35
total:0h:5m:51s

#folding precursors
started: 16:59:35
RNAfold < mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors.fa -noPS > mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors.str


ended: 17:9:47
total:0h:10m:12s

#computing randfold p-values
select_for_randfold.pl mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/signature.arf mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors.str > mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors_for_randfold.ids

started: 17:9:47

ended: 17:11:30
total:0h:1m:43s

started: 17:11:30
fastaselect.pl mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors.fa mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors_for_randfold.ids > mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors_for_randfold.fa


ended: 17:11:30
total:0h:0m:0s

started: 17:11:30
randfold -s mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors_for_randfold.fa 99 > mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors_for_randfold.rand


ended: 20:17:54
total:3h:6m:24s

#running miRDeep core algorithm
started: 20:17:54
miRDeep2_core_algorithm.pl mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/signature.arf mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors.str -s mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/mature_miRNAs_dsim.fa -v -50 -l 29 -y mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors_for_randfold.rand > mirdeep_runs/run_31_10_2016_t_16_31_45/output.mrd

ended: 20:19:44
total:0h:1m:50s

#running permuted controls
started: 20:19:44
echo 'miRDeep2_core_algorithm.pl mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/signature.arf mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors.str -s mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/mature_miRNAs_dsim.fa -v -50 -y mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors_for_randfold.rand > mirdeep_runs/run_31_10_2016_t_16_31_45/output.mrd' > mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/command_line

perform_controls.pl mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/command_line mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors.str 100 -a > mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/output_permuted.mrd 2>>error_31_10_2016_t_16_31_45.log


ended: 23:21:26
total:3h:1m:42s

#doing survey of accuracy
survey.pl mirdeep_runs/run_31_10_2016_t_16_31_45/output.mrd -a mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/output_permuted.mrd -b mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/mature_miRNAs_dmel.fa -c mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/signature.arf -d 3 > mirdeep_runs/run_31_10_2016_t_16_31_45/survey.csv

started: 23:21:26

ended: 23:21:37
total:0h:0m:11s

#producing graphic results
started: 23:21:37
make_html.pl -f mirdeep_runs/run_31_10_2016_t_16_31_45/output.mrd -k mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/mature_miRNAs_dmel.fa -p mirdeep_runs/run_31_10_2016_t_16_31_45/tmp/precursors.coords -s mirdeep_runs/run_31_10_2016_t_16_31_45/survey.csv -c -e -q expression_analyses/expression_analyses_31_10_2016_t_16_31_45/miRBase.mrd -x expression_analyses/expression_analyses_31_10_2016_t_16_31_45/miRNA_expressed.csv -r /Home/ii/phongphakk/mirdeep2_0_0_8/bin//../Rfam_for_miRDeep.fa -v 0 -y 31_10_2016_t_16_31_45 -o  -t d.melanogaster -V 2.0.0.8 

parsing input file finished
checking Rfam for hits to precursors
Build bowtie index of Rfam entries

Mapping mature,star and loop sequences against index
# reads processed: 1871
# reads with at least one reported alignment: 14 (0.75%)
# reads that failed to align: 1857 (99.25%)
Reported 54 alignments to 1 output stream(s)
parsing miRBase.mrd file finished
creating PDF files
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fasta and bed files have been created in subfolder mirna_results_31_10_2016_t_16_31_45


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