Re: GNU Parallel Bug Reports trouble with space after filename substitution

[Rob Sargent]

On 01/06/2015 11:21 AM, Ole Tange wrote:

parallel --verbose --joblog ba.ll --jobs 6 java -cp . BillAuer {1} 9 {2} "

>>  {//}/peakdector.{2}" :::: pvalFilelist ::: 15 20 25 30 35 40

This behaves the same way.  The verbose is there just to see what parallel is up to.

parallel --verbose --jobs 6 echo BillAuer {1} 9 {2} ">"  {//}/peakdector.{2} :::: pvalFilelist1 ::: 15 20 25 30 35 40

The file arguement is a file of filename:

/raid3/TITP/CLL/sgs/dist/ped6228/chr7/d02/cumulative.pval
/raid3/TITP/CLL/sgs/dist/ped6228/chr7/para1/cumulative.pval
/raid3/TITP/CLL/sgs/dist/ped6228/chr7/d01/cumulative.pval
/raid3/TITP/CLL/sgs/dist/ped6228/chr9/para1/cumulative.pval
/raid3/TITP/CLL/sgs/dist/ped6228/chr8/d02/cumulative.pval
/raid3/TITP/CLL/sgs/dist/ped6228/chr8/para1/cumulative.pval
/raid3/TITP/CLL/sgs/dist/ped6228/chr8/d01/cumulative.pval
/raid3/TITP/CLL/sgs/dist/ped6228/chr16/para1/cumulative.pval
/raid3/TITP/CLL/sgs/dist/ped6228/chr1/d02/cumulative.pval
/raid3/TITP/CLL/sgs/dist/ped6228/chr1/d01/cumulative.pval
/raid3/TITP/CLL/sgs/dist/ped6228/chr2/d02/cumulative.pval
/raid3/TITP/CLL/sgs/dist/ped6228/chr2/para1/cumulative.pval
/raid3/TITP/CLL/sgs/dist/ped6228/chr2/d01/cumulative.pval
/raid3/TITP/CLL/sgs/dist/ped6228/chr3/d02/cumulative.pval

and since each file has the same basename I wanted to get dirname and write to <dirname>/peakdector.{2}

but the result is (thanks to --verbose)

echo BillAuer /raid3/TITP/CLL/sgs/dist/ped6228/chr7/d02/cumulative.pval 9 15 > /raid3/TITP/CLL/sgs/dist/ped6228/chr7/d02 ./peakdector.15
echo BillAuer /raid3/TITP/CLL/sgs/dist/ped6228/chr7/d02/cumulative.pval 9 20 > /raid3/TITP/CLL/sgs/dist/ped6228/chr7/d02 ./peakdector.20
echo BillAuer /raid3/TITP/CLL/sgs/dist/ped6228/chr7/d02/cumulative.pval 9 25 > /raid3/TITP/CLL/sgs/dist/ped6228/chr7/d02 ./peakdector.25
echo BillAuer /raid3/TITP/CLL/sgs/dist/ped6228/chr7/d02/cumulative.pval 9 30 > /raid3/TITP/CLL/sgs/dist/ped6228/chr7/d02 ./peakdector.30
echo BillAuer /raid3/TITP/CLL/sgs/dist/ped6228/chr7/d02/cumulative.pval 9 35 > /raid3/TITP/CLL/sgs/dist/ped6228/chr7/d02 ./peakdector.35
echo BillAuer /raid3/TITP/CLL/sgs/dist/ped6228/chr7/d02/cumulative.pval 9 40 > /raid3/TITP/CLL/sgs/dist/ped6228/chr7/d02 ./peakdector.40
/bin/bash: /raid3/TITP/CLL/sgs/dist/ped6228/chr7/d02: Is a directory
etc

Thanks,
rjs

PS: I remade the file-of-files into a table of the the necessary permutations (inputfile outputfile percentile) and just ran from there.