###mixcr####
for i in `seq 42 50`
do
sample=R71090$i;
read1=R71090$i*R1*;
read2=R71090$i*R2*;
echo `date` "start do mixcr for " $sample;
mixcr align -r $sample"_log.txt" $read1 $read2 $sample"_alignments.vdjca"
mixcr assemble -r $sample"_log.txt" $sample"_alignments.vdjca" $sample"_clones.clns"
mixcr exportClones -o -t -c TRB --preset-file myFields.txt $sample"_clones.clns" $sample"_TRB.clones.txt"
mixcr exportClones -o -t -c TRA --preset-file myFields.txt $sample"_clones.clns" $sample"_TRA.clones.txt"
echo `date` "end do mixcr for " $sample;
done  
###qc_log###  
 for i in *log.txt; 
 do 
 echo $i;
 grep "Total sequencing reads" $i;
 grep "Successfully aligned reads" $i;
 grep "Reads used in clonotypes, percent of total" $i;
 grep "Final clonotype count" $i;
 done


######add1. myFields.txt####
-cloneId
-count
-fraction
-vHit
-dHit
-jHit
-aaFeature CDR3
######add2. log.txt####
Total sequencing reads
Successfully aligned reads
Alignment failed, no hits
Alignment failed because of absence of V hits
Alignment failed because of absence of J hits
Alignment failed because of low total score
Reads used in clonotypes, percent of total
Reads dropped due to the lack of a clone sequence: 82394 (8.12%)
Reads dropped due to failed mapping
Reads dropped with low quality clones
Final clonotype count
TRB chains