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