I have mapped RNA seq reads with Bowtie2 against my viral reference genome to filter viral sequences. Now I want to assemble the aligned reads from the output (aligned forward fastq and aligned reverse fastq) with the genome-guided trinity. For orientation I used the Bowtie2 BAM file coordinated with samtool sort as it is written in the manual. Unfortunately I only get an error message, no matter what I try. The job is green on the display, but when I click on it the following error message appears:
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