simulator.py genome FileNotFoundError: [Errno 2] No such file or directory: 'training_model_profile'

[MAXINELSX]

https://github.com/bcgsc/NanoSim/issues/11#issue-204760214 This bug happened again: (nanosim_env) lishuxian@tong1:/mnt/md0/LSX/lishuxian/lishuxian/mag/LSX-isolates/Kleb-for-lsx/bin-file$ cat list.fasta.txt | while read line; do /mnt/md0/LSX/lishuxian/lishuxian/mag/LSX-isolates/Kleb-for-lsx/bin-file/NanoSim/src/simulator.py genome --fastq -rg filtered_${line}.fasta -b guppy -n 100000 -t 40 -s 1 ; done

running the code with following parameters:

ref_g filtered_manhole-barcode47-bin.fasta model_prefix training out simulated number [100000] perfect False kmer_bias None basecaller guppy dna_type linear strandness 1.0 sd_len None median_len None max_len inf min_len 50 fastq True chimeric False num_threads 40 2023-08-14 23:17:28: /mnt/md0/LSX/lishuxian/lishuxian/mag/LSX-isolates/Kleb-for-lsx/bin-file/NanoSim/src/simulator.py genome --fastq -rg filtered_manhole-barcode47-bin.fasta -b guppy -n 100000 -t 40 -s 1 2023-08-14 23:17:28: Read in reference 2023-08-14 23:17:28: Read error profile Traceback (most recent call last): File "/mnt/md0/LSX/lishuxian/lishuxian/mag/LSX-isolates/Kleb-for-lsx/bin-file/NanoSim/src/simulator.py", line 2433, in main() File "/mnt/md0/LSX/lishuxian/lishuxian/mag/LSX-isolates/Kleb-for-lsx/bin-file/NanoSim/src/simulator.py", line 2194, in main read_profile(ref_g, number, model_prefix, perfect, args.mode, strandness, dna_type=dna_type, chimeric=chimeric) File "/mnt/md0/LSX/lishuxian/lishuxian/mag/LSX-isolates/Kleb-for-lsx/bin-file/NanoSim/src/simulator.py", line 474, in read_profile with open(model_profile, 'r') as mod_profile: FileNotFoundError: [Errno 2] No such file or directory: 'training_model_profile'

[saberhq]

Hey @MAXINELSX

I am so sorry for this late reply. I have no idea why I missed your comment/issue.

First, make sure you are using the latest committed version. The error you posted is a FileNotFoundError meaning that NanoSim couldn't find the location of the model profiles. Are you using the pre-trained models? If so, clearly state the directory of the pre-trained models to be used in the simulation stage. You could also train your own model using the read_analysis.py script. Refer to the readme file for comprehensive information.