Error in creating similarity matrix
Hello,
I am trying to create the database for my 457 reference bacterial sequences, but it is showing an error:
ditasic_matrix.py -l 100 -o output/similarity_matrix100_E.meliloti.npy reference_paths
Done simulating reads.
Joining temporary files ... OK Executing: mason_simulator -n 250000 --illumina-read-length 100 --illumina-prob-mismatch 0.004000 --illumina-prob-mismatch-begin 0.002000 --illumina-prob-mismatch-end 0.012000 -ir 'Ensifer_meliloti/GCA_030505315.1/GCA_030505315.1_ASM3050531v1_genomic.fna' -o './temp/GCA_030505315.1_ASM3050531v1_genomic.fna.fastq' MASON SIMULATOR
INITIALIZING__________________________________________________________
Opening reference and variants file ... OK Initializing fragment-to-contig distribution ... OK Initializing simulation threads ... OK Opening output file ./temp/GCA_030505315.1_ASM3050531v1_genomic.fna.fastq ... OK
READ SIMULATION_______________________________________________________
Distributing fragments to 3 contigs (1 haplotypes each) ... OK
Simulating Reads: CP130057.1 (allele 1) .... (136006 fragments) OK CP130055.1 (allele 1) .. (53161 fragments) OK CP130056.1 (allele 1) .. (60833 fragments) OK Done simulating reads.
Joining temporary files ... OK Executing: mason_simulator -n 250000 --illumina-read-length 100 --illumina-prob-mismatch 0.004000 --illumina-prob-mismatch-begin 0.002000 --illumina-prob-mismatch-end 0.012000 -ir 'Ensifer_meliloti/GCA_028888255.1/GCA_028888255.1_ASM2888825v1_genomic.fna' -o './temp/GCA_028888255.1_ASM2888825v1_genomic.fna.fastq' MASON SIMULATOR
INITIALIZING__________________________________________________________
Opening reference and variants file ... OK Initializing fragment-to-contig distribution ... OK Initializing simulation threads ... OK Opening output file ./temp/GCA_028888255.1_ASM2888825v1_genomic.fna.fastq ... OK
READ SIMULATION_______________________________________________________
Distributing fragments to 5 contigs (1 haplotypes each) ... OK
Simulating Reads: JADZOH010000001.1 (allele 1) .... (133548 fragments) OK JADZOH010000002.1 (allele 1) .. (46365 fragments) OK JADZOH010000005.1 (allele 1) .. (59435 fragments) OK JADZOH010000003.1 (allele 1) .. (6077 fragments) OK JADZOH010000004.1 (allele 1) .. (4575 fragments) OK Done simulating reads.
Joining temporary files ... OK multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/rishav/anaconda3/lib/python3.10/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/home/rishav/anaconda3/lib/python3.10/multiprocessing/pool.py", line 48, in mapstar return list(map(*args)) File "/home/rishav/anaconda3/bin/ditasic_matrix.py", line 17, in parallelSimulate ditasic_utils.run_simulator"mason_illumina" File "/home/rishav/anaconda3/opt/ditasic/core/ditasic_utils.py", line 95, in run_mason_illumina subprocess.check_call(command, stderr=subprocess.STDOUT, shell=True) File "/home/rishav/anaconda3/lib/python3.10/subprocess.py", line 369, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'mason_simulator -n 250000 --illumina-read-length 100 --illumina-prob-mismatch 0.004000 --illumina-prob-mismatch-begin 0.002000 --illumina-prob-mismatch-end 0.012000 -ir 'Ensifer_meliloti/GCA_004003815.1/GCA_004003815.1_ASM400381v1_genomic.fna' -o './temp/GCA_004003815.1_ASM400381v1_genomic.fna.fastq'' returned non-zero exit status 134. """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/rishav/anaconda3/bin/ditasic_matrix.py", line 128, in p.map_async(parallelSimulate, arglist).get(9999999) File "/home/rishav/anaconda3/lib/python3.10/multiprocessing/pool.py", line 774, in get raise self._value subprocess.CalledProcessError: Command 'mason_simulator -n 250000 --illumina-read-length 100 --illumina-prob-mismatch 0.004000 --illumina-prob-mismatch-begin 0.002000 --illumina-prob-mismatch-end 0.012000 -ir 'Ensifer_meliloti/GCA_004003815.1/GCA_004003815.1_ASM400381v1_genomic.fna' -o './temp/GCA_004003815.1_ASM400381v1_genomic.fna.fastq'' returned non-zero exit status 134.
Kindly help me out