Using empty placeholder bam files to process a large number of files

[ontalin]

In order to jointly call SVs from a large number of samples, I followed the pipeline in #354 to create empty placeholder bam files and preprocessed them for batch assembly. However, when preprocessing the empty bam files, which have only the headers, gridss unsurprisingly failed to produce the EMPTY_BAM.insert_size_metrics and gave the following error message:

Wed Nov 25 16:50:47 CST 2020   CollectGridssMetricsAndExtractSVReads|samtools	EMPTY_BAM
rm: cannot remove './EMPTY_BAM.bam.gridss.working/tmp.empty_AF04.bam.insert_size_metrics': No such file or directory
rm: cannot remove './EMPTY_BAM.bam.gridss.working/tmp.empty_AF04.bam.insert_size_histogram.pdf': No such file or directory

Three files required for following assembly: EMPTY_BAM.insert_size_metrics, EMPTY_BAM.sv.bam, and EMPTY_BAM.sv.bam.bai are absent as well.

Is there a solution to this pipeline?

Thank you in advance.

[d-cameron]

Work-around no longer required :)