Stuck on Pilon polishing

[homeveg]

Hi! I am trying to performe a hybrid assembly with MinION and Illumina reads of a bacterial genome of ~8Mbs. The pipeline stuck on a pilon poilshing step:

• Unicycler generates 5 gfa files, including 005_final_clean.gfa.
• In Bandage 005_final_clean.gfa looks pretty good - 3 circular plasmids of expected size.
• inside the pilon_polish folder is the 0_insert_size_check.fasta file (only 8.1 MB in size) and 4 *.bt2 files generated by bowtie2-bild
• The last entry to the log file is the following:

Polishing assembly with Pilon (2019-03-21 20:15:13)

Unicycler now conducts multiple rounds of Pilon in an attempt to repair any remaining small-scale errors with the assembly.

Aligning reads to find appropriate insert size range... bowtie2-build 0_insert_size_check.fasta 0_insert_size_check.fasta

• the htop command on my Fedora Linux workstation shows that the only active process initiated by unicycler is a bowtie2-build-s, which runs already for at least 7 hours.

• the latest change to output files either in assembly output directory or in pilon_polish folder was done at 20:15, so exactly when the pilon polishing started according to the log file.

Is there any suggestions how to proceed? Can I just kill a Unicycler process and restart it from where it stopped? Thanks in advance!

[homeveg]

I should say, I found the reason why the Unicycler stuck, but it does not really help to solve the issue: when constructing the index bowtie2-build can't handle fasta files with very long lines - my assembly contains only 3 contigs, with the total sequence length of 8 megabases. And 2 contigs is about 4 millions bases long each therefore corresponding lines in the fasta file are about 4 millions letters long! After splitting such a long line to a standard for fasta 80 letters long lines, the bowtie2 finished immediately! I killed the bowite2 in the memory and Unicycler pipeline finished successfully without any further problem, but unfortunately skipping the pilon polishing step.

So, is there the way to restart Unicycler from a particular step, without loosing the progress?

[saranienke]

Hi! I am also performing a hybrid assembly, but after 12 hours running the process stopped due to a connection error with the server I am working on. It stopped at the polishing step too, so I would like to know if there is a way to restart the process from this step to avoid having to do the assembly and alingment all over again. Thank you!

[dswan]

@saranienke If you had an interactive shell running, and it dropped, I seriously recommend the use of "screen" to avoid this happening again...

https://www.gnu.org/software/screen/