error: `@HD VN:1.5 SO:unknown': No such file or directory about arcs HOT 2 CLOSED

Hello @shtist,

It looks like you are providing the direct BAM file in the -a option, instead of a text file listing the input SAM/BAM filenames. Try making a text file with draft.reads.sortbx.bam in it, then specifying this file for the -a option.

Also, your file names indicate that you are using the same alignment file for ARCS as you used for tigmint? You do need to re-run the alignments after running Tigmint (now using the Tigmint broken assembly as the reference), and those alignments must be sorted by name for ARCS (not by BX tag, as is required for tigmint). Check out the arcs-make Makefile (in the Examples folder), which will run all the neccessary steps for Tigmint + ARCS (or ARCS alone).

Hope that helps!
Lauren

from arcs.

I'm closing this issue for now -- feel free to re-open if you have additional questions!

from arcs.