completed HPC section

Author: eead-csic-compbio

Diff for: pangenes/README.md

@@ -1182,6 +1182,8 @@ As get_pangenes.pl includes 3 other scripts, logs are split in independent files
 
 The main log of get_pangenes.pl might contain error messages such as:
 
+* INFO: no cluster config file; see section [Runmodes and HPC configuration](#runmodes-and-hpc-configuration)
+
 * EXIT, folder_pangenes/_oryza_sativa_arc.oryza_sativa_chaomeo.algMmap.overlap0.5.patch.tsv does not exist, WGA might have failed or hard drive is still writing it (please re-run). This can happen in HPC cluster jobs due to drive latency issues. The fix is to open the relevant specific log (_collinear_genes.pl in this case) and look for the failing command, which in this example looks like:
 
     plant-scripts/pangenes/_collinear_genes.pl -sp1 oryza_sativa_arc -fa1 folder_pangenes/_oryza_sativa_arc.fna -gf1 folder_pangenes/_oryza_sativa_arc.patched.gff -sp2 oryza_sativa_chaomeo -fa2 folder_pangenes/_oryza_sativa_chaomeo.fna -gf2 folder_pangenes/_oryza_sativa_chaomeo.patched.gff -out folder_pangenes/_oryza_sativa_arc.oryza_sativa_chaomeo.algMmap.overlap0.5.patch.tsv -p 1 -a 1 -ovl 0.5 -q 50 -wf 0 -gs 0 -A  -c 0 -s '' -M plant-scripts/pangenes/../lib/minimap2/minimap2 -W plant-scripts/pangenes/bin/wfmash/build/bin/wfmash -G ./ -B bedtools -T folder_pangenes/tmp/ -t 4 -i 0 -r 1 -H 0