Error message: Argument list too long

[Victor-fe]

Hi guys,

we are working with a relatively large number of bam files (smart-seq2). Each bam file is for one cell. When too many files are used as input at once we get the error message 'Argument list too long'. However, the documentation seems to specify no limits in this regard. Could you elaborate what are the determining factors we have to consider when deciding how many files to use as input .

Best, Victor

[hxj5]

Hi Victor,

I suppose the error is probably not a cellsnp-lite issue, but a system issue that the length of the cmdline exceeds the system limits (e.g., related to exec and ARG_MAX constant, see this page).

If you were using -s option, you may try -S option instead, to specify the bam files in a plain file (one bam file per line). Similarly, use -i instead of -I if applicable (see this manual).

Best, Xianjie