Hello,
I am using GNU parallel 20140222 and have noticed a problem when piping to parallel from cat.
It appears that the output from the commands within the file I am cat'ing from is incorrect where a few lines are missing or lines are written out in an incorrect format that causes downstream processing to fail.
An example of the commands within the file (flashParallel.txt) I am cat'ing is:
flash kc148_S1_L001_R1_001.fastq kc148_S1_L001_R2_001.fastq -o kc148
flash kc1_S6_L001_R1_001.fastq kc1_S6_L001_R2_001.fastq -o kc1
flash is a program in my path used to merge DNA sequence data that requires two files and -o specifies the output prefix.
I have been running parallel with the following command:
cat flashParallel.txt | parallel
The files are rather large so not sure how best to provide data to reproduce the problem.
Any suggestions/solutions would be greatly appreciated and thanks for developing the software.
-james