CAMISIM: NanoSim - KeyError: sequence_id not found in mapping

Hi,

Thanks for developing CAMISIM! I am currently trying to simulate data with Illumina and Nanopore reads using the de novo community design. I am using the CAMISIM master branch. With the provided test data (CAMISIM/defaults/genomes/) and the provided mapping files I got it running using art and nanosim(from the https://github.com/abremgesfork).

Then I tried to use the 2nd CAMI Toy Mouse Gut Dataset genomes/, metadata.tsv and genome_to_id.tsv data as a basis to generate new data. For Illumina data this worked smoothly. However, for Nanopore data I get the following errors after simulating the reads and in the final anonymization step:

...
2021-07-09 16:17:40 DEBUG: [GenomePreparation 89018136530] 270448.0     22
2021-07-09 16:17:40 DEBUG: [GenomePreparation 89018136530] SysCmd: '/home-link/qeakr01/development/NanoSim/src/simulator.py linear -n 22 -r /sfs/7/workspace/ws/qeakr01-camisim-0/toy_mouse_gut_time_series/output_nanopore_test2/source_genomes/GCF_000403395.2_Anae_bact_G3_V1.fa -o /sfs/7/workspace/ws/qeakr01-camisim-0/toy_mouse_gut_time_series/tmp/tmp4bpxOM/2021.07.09_15.59.47_sample_0/reads/270448.0 -c tools/nanosim_profile/ecoli --seed 2998104995'
2021-07-09 16:17:40 INFO: [GenomePreparation 89018136530] Simulating reads from 270448.0: '/sfs/7/workspace/ws/qeakr01-camisim-0/toy_mouse_gut_time_series/output_nanopore_test2/source_genomes/GCF_000403395.2_Anae_bact_G3_V1.fa'
2021-07-09 16:31:15 INFO: [GenomePreparation 89018136530] Simulating reads finished
[W::sam_parse1] urecognized reference name; treated as unmapped
[W::sam_parse1] urecognized reference name; treated as unmapped
[W::sam_parse1] urecognized reference name; treated as unmapped
...

and

...
2021-07-09 16:44:30 INFO: [MetagenomeSimulationPipeline] Anonymize Data
2021-07-09 16:44:30 DEBUG: [MetagenomeSimulationPipeline] /sfs/7/workspace/ws/qeakr01-camisim-0/toy_mouse_gut_time_series/tmp/tmp4bpxOM/tmpgY5Fcq
2021-07-09 16:44:30 INFO: [FastaAnonymizer] Shuffle and anonymize '/sfs/7/workspace/ws/qeakr01-camisim-0/toy_mouse_gut_time_series/tmp/tmp4bpxOM/2021.07.09_15.59.47_sample_0/reads'
2021-07-09 16:44:30 DEBUG: [FastaAnonymizer] get_seeded_random() { seed="$1"; openssl enc -aes-256-ctr -pass pass:"$seed" -nosalt < /dev/zero 2>/dev/null; }; python '/nfsmounts/home/qeakr01/development/CAMISIM/fastastreamer.py' -input '/sfs/7/workspace/ws/qeakr01-camisim-0/toy_mouse_gut_time_series/tmp/tmp4bpxOM/2021.07.09_15.59.47_sample_0/reads' -format 'fastq' -ext 'fq' -s | shuf -z --random-source=<(get_seeded_random 2944938622045856594) | tr -d '\000' | python '/nfsmounts/home/qeakr01/development/CAMISIM/anonymizer.py' -prefix 'S0R' -format 'fastq' -map '/sfs/7/workspace/ws/qeakr01-camisim-0/toy_mouse_gut_time_series/tmp/tmp4bpxOM/tmpoArF7B' -out '/sfs/7/workspace/ws/qeakr01-camisim-0/toy_mouse_gut_time_series/tmp/tmp4bpxOM/tmpLJDFBS' -s
2021-07-09 16:48:06 INFO: [MetadataReader 1434768039] Reading file: '/sfs/7/workspace/ws/qeakr01-camisim-0/toy_mouse_gut_time_series/output_nanopore_test2/internal/genome_locations.tsv'
2021-07-09 16:48:08 INFO: [MetadataReader 31538633047] Reading file: '/sfs/7/workspace/ws/qeakr01-camisim-0/toy_mouse_gut_time_series/output_nanopore_test2/internal/meta_data.tsv'
2021-07-09 16:48:08 INFO: [MetadataReader 14979527976] Reading file: '/sfs/7/workspace/ws/qeakr01-camisim-0/toy_mouse_gut_time_series/tmp/tmp4bpxOM/tmpoArF7B'
2021-07-09 16:48:08 ERROR: [Validator 31115876351] sequence_id 'NZ-JH590862.1' not found in mapping

2021-07-09 16:48:08 DEBUG: [MetagenomeSimulationPipeline]
Traceback (most recent call last):
  File "/home-link/qeakr01/development/CAMISIM/metagenomesimulation.py", line 117, in run_pipeline
    self._anonymize_data(list_of_output_gsa, file_path_output_gsa_pooled)
  File "/home-link/qeakr01/development/CAMISIM/metagenomesimulation.py", line 639, in _anonymize_data
    file_path_genome_locations, file_path_metadata, file_path_anonymous_mapping_tmp, stream_output
  File "/nfsmounts/home/qeakr01/development/CAMISIM/scripts/GoldStandardFileFormat/goldstandardfileformat.py", line 370, in gs_read_mapping
    stream_output, dict_anonymous_to_read_id, dict_sequence_to_genome_id, dict_genome_id_to_tax_id)
  File "/nfsmounts/home/qeakr01/development/CAMISIM/scripts/GoldStandardFileFormat/goldstandardfileformat.py", line 244, in write_gs_read_mapping
    raise KeyError(msg)
KeyError: "sequence_id 'NZ-JH590862.1' not found in mapping\n"


2021-07-09 16:48:08 ERROR: [MetagenomeSimulationPipeline] "sequence_id 'NZ-JH590862.1' not found in mapping\n" in line 117
2021-07-09 16:48:08 INFO: [MetagenomeSimulationPipeline] Metagenome simulation aborted
2021-07-09 16:48:08 INFO: [MetagenomeSimulationPipeline] Temporary data stored at:
/sfs/7/workspace/ws/qeakr01-camisim-0/toy_mouse_gut_time_series/tmp/tmp4bpxOM

Do you have any idea what could cause this issue or how I could proceed to fix this?

sim_nanosim.test2.log sim_config.nanosim.test2.ini.txt