I am just starting to get familiar with Galaxy and bumped into a problem of which I don’t know how to handle. I generated a collection of dataset pairs and run Bowtie2 on that collection. Now, I am trying to run CleanSam on the generated bam files but an error occurs:
Error occurred during initialization of VM Could not reserve enough space for 4194304KB object heap [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_index_
I visualized the bam files with IGV and was not able to see any alignments. Does that mean that something with Bowtie2 went wrong? What can I do to solve this problem? Unfortunately, I don’t have any background in bioinformatics.
Thanks a lot.