Hi Ryan,
Things continue to work exceptionally well with Unicycler - thank you for such an easy yet powerful program. I'm getting hung up trying to complete one last sample (which is both pretty good luck yet incredibly frustrating to be so close to the finish!). I'm wondering if you've ever seen this phenomenon before?

• Running a hybrid assembly on a single sample (Illumina + Nanopore reads) which fully completes spades assembly (001_best_spades_graph.gfa), as well as the overlapping (002_overlaps_removed.gfa) and long read assembly (003_long_read_assembly.gfa) sections.
• The process begins for the fourth graph - Creating miniasm/Racon bridges - but gets no where. No new information is written into the log file, and no newer files are ever created (ie. no 004_final_clean.gfa or 005 or assembly.gfa/fasta).

Here's the really strange part. This only happens for one specific sample.

• I ran a script on 10 samples and it kept stalling at this one sample (which was somewhere in the middle of the loop with full sample set). After removing that one sample and re-running the script, the remaining 9 samples all finished properly.
• I ran a script on that 1 troubled sample using the short reads only and the assembly finished completely without error
• I ran a script on that 1 troubled sample using the long reads only and the assembly finished completely without error
• I reinstalled Unicycler to the most recent version (0.4.6) and updated Racon (v1.3.1), yet the hybrid issue persists.

Here's the tail of the log file for the hybrid assembly, which I've reproduced a number of times now and always looks exactly the same:

    30   not found                                       
    31   not found                                       
    32   not found                                       
    33   not found                                       
    34   not found                                       
    35   not found                                       
    36   not found                                       

Saving /mnt/lustre/macmaneslab/devon/nanoPore/VpProject/unicycler/run2/hybrid/fixed5171/miniasm_assembly/15_contigs_placed.gfa


Creating miniasm/Racon bridges (2018-06-21 19:28:08)
----------------------------------------------------
    Now that the miniasm/Racon string graph is complete, Unicycler will use it to build bridges between anchor segments.

     Start → end     Best path                                 Quality

Thanks for any advice you can offer.