Bam indexing error-the samtools index command for just 1 chromosome is also not working in this case, the following error is showing [E::hts_idx_push] Region 536871288..536871299 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6 samtools index...
The problem is that bowtie and Galaxy (can) use a different samtools version. Galaxy needs samtools to create metadata for BAM files, so this process is actually running ofter bowtie has finished. You need a samtools version globally accessible for Galaxy. Make sure you have smatools in your...