find_genes_in_sim.py generates empty ground_truth

[mahmudhera]

This probably happens when the header of the simulated metagenome using bbmap changes.

two examples headers:

@SYN_0_1949_2098_0_-123923734_1._NZ_MVAG01000141.1$Chryseobacterium$mucoviscidosis$strain$VT16-26$NODE_39_length_2559_cov_7378.13_ID_77,$whole$genome$shotgun$sequence 1:

@SYN_0_4459478_4459627_0_-21276121_1._$AP012030.1$Escherichia$coli$DH1$(ME8569)$DNA,$complete$genome 1:

Notice the extra $ in the second header. This did not originate by a different bbmap version, rather by an extra space in the fasta file.

[mahmudhera]

@dkoslicki I almost solved this locally — just making sure that you do not spend time on this.