Execution error using singularity exec

[UpalabdhaD]

System Configuration: OS: Debian GNU/Linux bookworm/sid x86_64 Host: HP Z6 G4 Workstation Kernel: 5.18.0-2-amd64 Uptime: 1 day, 6 hours, 21 mins Packages: 2306 (dpkg) CPU: Intel Xeon Silver 4214R (24) @ 3.500GHz GPU: NVIDIA Quadro T400 Mobile Memory: 5000MiB / 64108MiB

Command:

singularity exec mummer2circos.simg mummer2circos -r GMI1000.fasta -q SEPPX05_genomic.fna -gb SEPPX05_genomic.gbk -l fasta1 GMI1000.fasta

input_files_mummer2circos.zip

Output: nucmer -b 200 -c 65 -g 90 -l 20 -p SEPPX05_genomic GMI1000.fasta SEPPX05_genomic.fna show-coords -T -r -c -L 100 -I 30 SEPPX05_genomic.delta > SEPPX05_genomic.coords show_ticks = yes show_tick_labels = yes

tick_label_font = condensed radius = dims(ideogram,radius_outer) label_offset = 8p label_size = 4p color = black thickness = 2p show_ticks = yes skip_first_label = no multiplier = 10/1u spacing = 1u size = 5p show_label = no label_size = 5p format = %%.1d show_ticks = yes skip_first_label = no multiplier = 10/1u spacing = 10u size = 15p show_label = yes label_size = 25p format = %%.1d kb thickness = 2p

Traceback (most recent call last): File "/opt/conda/envs/mummer2circos/bin/mummer2circos", line 8, in sys.exit(main()) File "/opt/conda/envs/mummer2circos/lib/python3.7/site-packages/mummer2circos/init.py", line 67, in main blast_identity_cutoff=args.blast_identity_cutoff) File "/opt/conda/envs/mummer2circos/lib/python3.7/site-packages/mummer2circos/mummer2circos.py", line 94, in init minus, plus = self.gbk2circos_data(gbk2orf) File "/opt/conda/envs/mummer2circos/lib/python3.7/site-packages/mummer2circos/mummer2circos.py", line 1145, in gbk2circos_data start = str(feature.location.start + self.contigs_add[record.id][0]) KeyError: 'NZ_CP088237.1'

[tpillone]

Hi @UpalabdhaD

The genbank file should match the reference genome (-r) and not the query genome (-q), you have to reverse the query and the reference in your command:

singularity exec mummer2circos.simg mummer2circos -q GMI1000.fasta -r SEPPX05_genomic.fna -gb SEPPX05_genomic.gbk -l

[UpalabdhaD]

Your answer resolved the issue. thanks