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
