Update README.md

Author: inumanag

README.md

@@ -77,19 +77,16 @@ for j in `seq 1 22` X Y; do
 	fi
 done
 done | time parallel --will-cite -j 80 --eta
-# Running time in our case: 10m 11s
 
 # Now make sure that all runs completed successfully 
 grep Total out/log/*.log | wc -l
 # You should see here 600 (or n(n+1) if you have n chromosomes in your file)
 
 # Get the single-core running time
 grep Wall out/log/*.log | tr -d '(' | awk '{s+=$4}END{print s}'
-# In our case we get 43414.7 (12.06 h)
 
 # Get the maximum meory usage as well
 grep Memory out/log/*.log | awk '{if($3>m)m=$3}END{print m}'
-# We got 4889.0
 ```
 
 Then use `sedef-align` to bucket the files for the optimal parallel alignment, and
@@ -99,26 +96,22 @@ afterwards run the whole alignment:
 mkdir -p out/bins
 mkdir -p out/log/bins
 time sedef align bucket out out/bins 1000
-# Takes 36s (uses 5.2G of memory)
 
 # Now run the alignment
 for j in out/bins/bucket_???? ; do
 	k=$(basename $j);
 	echo "sedef align generate hg19.fa $j 11 >${j}.bed 2>out/log/bins/${k}.log"
 done | time parallel --will-cite -j 80 --eta
-# It took 5m 06s
 
 # Make sure that all runs finished nicely
 grep Finished out/log/bins/*.log | wc -l
 # Should be number of bins (in our case, 1000)
 
 # Get again the total running time
 grep Wall out/log/bins/*.log | tr -d '(' | awk '{s+=$4}END{print s}'
-# We have 17086 (4.74h)
 
 # And the memory
 grep Memory out/log/bins/*.log | awk '{if($3>m)m=$3}END{print m}'
-# We got 5017.5
 ```
 
 Finally, run `sedef-stats` to produce the final output:
@@ -130,21 +123,10 @@ cat out/bins/*.bed > out.final.bed # final chains
 
 # Count the number of SDs in each stage
 wc -l out.*bed
-#  1656305 out/out.bed
-#  1558896 out/out.init.bed
-#   231472 out/out.final.bed
 
 # Now get the final calls
 sedef stats generate hg19.fa out.final.bed > out.hg19.bed
-# Took 0m 58s (7.5G)
 ```
 
 Final calls will be in `out.hg19.bed`.
 
-## Notes ... 
-
-```# VPC
-#echo "qsub -cwd -V -b y -N \"S_${i}_${j}_${m}\" -l h_vmem=10G -l h_rt=24:00:00 -l h_stack=8M " \
-#	"python2.7 mesa sedef/sedef search single fasta/hg19.fa chr$i chr$j $m"
-```
-