Question: Error occuring in CleanSam after alignment with Bowtie2
gravatar for Becci2104
10 months ago by
Becci21040 wrote:


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.

bowtie sam bam chip-seq • 233 views
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