Flye tool error in galaxy

I would appreciate help by someone regarding ‘flye’ tool in galaxy to perform assembly of Pacbio data in bam format, step by step guide will be better. i tried it, using SRA accession number from NCBI but it gives error.
thank you!


Assembly tutorials and workflows are available here.

The training site can be navigated by topic or searched with keywords like the datatype or tool name. This is probably your best match.

Input Datatype

  • Flye requires input reads in a fastq or fasta format.
  • Start up a new empty history, then load up a tool’s form to review what the exact supported input datatypes are (file content/format + “datatype” metadata).


  • Get the reads from SRA using a tool like Faster Download and Extract Reads in FASTQ.
  • Avoid attempting to retrieve reads in BAM format with the tool Download and Extract Reads in BAM. From my experiences, that one rarely works correctly due to time/data limits set at NCBI. The query can either error (red) or output truncated results (putatively “successful”, but not actually usable). Confusing, and better to skip using it anyway since very few tools accept read inputs in that format.

Read data in BAM format already?

  • A tool like SamToFastq can be used to extract the reads.
  • If the BAM was a mapping job result, keep in mind that some reads might be output more than once.

Hope that helps!

I have data of which flye always ends with an error. I am using fastq files as input but its not working.

@Ghazal_Aziz – Please follow up in our current topic. plasmid spades: fatal error exit code 255