Hi there,
I am trying to run a lastz to perform a whole genome alignment between a turtle and the chicken genomes. I have split the fasta filenames of the target (turtle) into 24 files (one per CPU that I have in my server), and run 24 commands like this:
for i in `cat ps1/x00.txt`; do for j in gg4/*.fa; do lastz ps1/$i $j B=0 C=0 E=30 H=0 K=3000 L=3000 M=50 O=400 T=1 Y=9400 > lav/`basename $i .fa`-`basename $j .fa`.lav; done; done;
where x00.txt is the list with 1/24 of all fasta files for the turtle genome. Next is x01.txt, and so on to x23.txt.
Now my problem is that even when the 24 threads finish doing all possible alignments (I get the correct number of output files given all the possible combinations), the lastz processes continue, starting again, i.e., they don't stop when the last combination is reached. So, I guess something's wrong with my command. Then, I try like in the "how-to" tutorial
for i in `cat ps1/x00.txt`; do echo 'for j in gg4/*.fa; do lastz ps1/'$i' $j B=0 C=0 E=30 H=0 K=3000 L=3000 M=50 O=400 T=1 Y=9400 > lav/`basename '$i' .fa`-`basename $j .fa`.lav; done'; done;
But that just echoes the commands....
Where am I wrong?
Cheers,
champi
I am trying to run a lastz to perform a whole genome alignment between a turtle and the chicken genomes. I have split the fasta filenames of the target (turtle) into 24 files (one per CPU that I have in my server), and run 24 commands like this:
for i in `cat ps1/x00.txt`; do for j in gg4/*.fa; do lastz ps1/$i $j B=0 C=0 E=30 H=0 K=3000 L=3000 M=50 O=400 T=1 Y=9400 > lav/`basename $i .fa`-`basename $j .fa`.lav; done; done;
where x00.txt is the list with 1/24 of all fasta files for the turtle genome. Next is x01.txt, and so on to x23.txt.
Now my problem is that even when the 24 threads finish doing all possible alignments (I get the correct number of output files given all the possible combinations), the lastz processes continue, starting again, i.e., they don't stop when the last combination is reached. So, I guess something's wrong with my command. Then, I try like in the "how-to" tutorial
for i in `cat ps1/x00.txt`; do echo 'for j in gg4/*.fa; do lastz ps1/'$i' $j B=0 C=0 E=30 H=0 K=3000 L=3000 M=50 O=400 T=1 Y=9400 > lav/`basename '$i' .fa`-`basename $j .fa`.lav; done'; done;
But that just echoes the commands....
Where am I wrong?
Cheers,
champi
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