make.contigs how to ignore empty files?

Commands in mothur
1

Hi there,

after giving the command
make.contigs(file=filelist.files)

It stopped at a point en sent an error:
[ERROR]: …/sample_R1_001.fastq is blank Please correct
Segmentation fault

Is there a a way to add into the command something so it ignores empty file and continues?..but that it does keep track of the empty files ignored?

Thanks

2

Hi,

It normally does ignore blank fastq files. Is that the actual error message or have you edited it? It seems weird that it would have 3 ‘.’ characters. Can you also post the first several lines of filelist.files?

Pat