careful and unicycler assembly error

[aslangabriel99]

Hi, when I tried to run with careful or unicycler model the error occurred as follows"Execution cancelled -- Finishing pending tasks before exit -[nf-core/rad] Pipeline completed with errors- ERROR ~ Error executing process > 'RAD:GENBANK_TO_FASTA'

Caused by: Process RAD:GENBANK_TO_FASTA terminated with an error exit status (127)

Command executed:

python3 configure_reference.py OR666647DHAV3.gb biopython.convert OR666647DHAV3.gb genbank OR666647DHAV3.gff gff3

cat <<-END_VERSIONS > versions.yml "RAD:GENBANK_TO_FASTA": biopython verswion 1.81 END_VERSIONS

Command exit status: 127

Command output: (empty)

Command error: .command.sh: line 3: biopython.convert: command not found

Work dir: /home/aslangabriel/anpingwangtest/work/a1/0eb61d0ade4bc1f294f799010e8653

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line ". But I have installed the bipython editon. would you like to fix this problem?

[jfurlong]

I think you may need to use: --genbank_ref /path/to/reference.gb

Eg. --genbank_ref ./NC_001798.gb

[aslangabriel]

Thanks for your help. The command I ran was "nextflow run greninger-lab/rad_assembler \ --input ./2_3Rsamplesheet.csv \ --outdir ./2_3Routput \ --bowtie2_host_index /home/aslangabriel/duckrefgenome/gooseref \ --spades_flag careful --genbank_ref ./OM264914_1GASVI.gb \ -profile docker \ -r main \", I also tested with unicycler, the error was uploaded as mentioned above. It always said that "Command error: .command.sh: line 3: biopython.convert: command not found"

[jfurlong]

It looks like you are running the pipeline locally, not in the cloud. I just ran the pipeline successfully on my Intel Mac - can you let me know the specs of the system or cluster that you are running on? Also, can you provide OM264914_1GASVI.gb? That way I can test with your genbank file.

[aslangabriel99]

Thanks for your help. I ran the pipeline successfully with default settings using meta. Would you like to explian the output files? I found two consesus files. I don't know which is useful and the difference between them.

[jfurlong]

The files in the mugsy output directory are intermediary files. 06YR_new_ref_consensus.fasta is a consensus sequence/scaffold that is created by aligning de novo assembled contigs to the supplied reference with mugsy, and then any gaps between contigs are filled with the reference sequence based on the alignment. Once this "new_ref_consensus" is generated, the reads are then re-mapped to it. The resulting final consensus is then generated using iVar, and can be found in the final_consensus directory - 06YR_new_ref_consensus.fasta.