ethanagb / silico Goto Github PK

Hi,

Thanks for your work, but when I run SiLiCO like this :

python SiLiCO.py -i ${path to desulfosporosinus_acidiphilus genome in fasta} -o test

or like this

python SiLiCO.py -i ~/dat/MBRAC-5/genomes/desulfosporosinus_acidiphilus.fasta -o test --fasta
python SiLiCO.py -i ~/dat/MBRAC-5/genomes/desulfosporosinus_acidiphilus.fasta -o test_ -n --fasta -m 100000000000
python3 SiLiCO.py -i ~/dat/MBRAC-5/genomes/desulfosporosinus_acidiphilus.fasta -o test_ -n --fasta -m 100000000000

The bed and fasta file is empty.

Link to my test reference genome https://www.ncbi.nlm.nih.gov/assembly/GCF_000255115.2/

Thanks

Hey,

When I run the following command:

python SiLiCO.py -i data/e.fa -f -p

The bed coordinates are not being converted to FASTA format. Also, are errors introduced into the simulated reads when using the two modes (-n or -p)? Thanks!

It terminated with following error !

➜  SiLiCO git:(master) ✗ python SiLiCO.py -i /media/urbe/ARCgenomic/toyGenome/toy.fasta -o toyGenomeONTReads -n -m 20000
Preparing the genome file.
The Scratch dir already exists. Cleaning up...
Done!
Generating a genome index file...
Done!
Generating simulated reads in Oxford Nanopore mode...
Building threshold dictionaries...
Calculating distribution parameters...
Traceback (most recent call last):
  File "SiLiCO.py", line 166, in <module>
    main(sys.argv[1:])
  File "SiLiCO.py", line 151, in main
    simulateReads(infileName,outfileName,mean,std,desired_cov,trialCount,names, SEQ_MODE)
  File "/home/urbe/Tools/SiLiCO/simulateReads.py", line 143, in simulateReads
    outfile.write(str(selected_chrom) + '\t' + str(start_pos-correctionDict[str(selected_chrom)]) + '\t' + str(end_pos-correctionDict[str(selected_chrom)]) + '\t' + 'trial_'+str(trial_counter) +'_sim_read_' + str(name_counter) + '\n')
  File "/home/urbe/anaconda3/lib/python3.6/gzip.py", line 260, in write
    data = memoryview(data)
TypeError: memoryview: a bytes-like object is required, not 'str'

Hello here are my commands

$ python /home/usr/SiLiCO-1.0.1/SiLiCO.py -i /home/usr/fasta/human_g1k_v37.fasta -n

STDOUT:

preparing the genome file.
The Scratch dir already exists. Cleaning up...
Done!
Generating a genome index file...
Done!
Generating simulated reads in Oxford Nanopore mode...
Building threshold dictionaries...
Calculating distribution parameters...
Completed trial 2 of 1. (200.0%)
Done!
Exiting...

Output:

$ ls 

SiLiCO_Scratch  simulated_read_positions_trial_1.bed.gz

$ less simulated_read_positions_trial_1.bed.gz | wc -l

0

I extract and read the file and it's empty. My python version is: Python 2.7.13 :: Anaconda 2.3.0 (64-bit)

Any help would be appreciated!

Thanks!

Python 3.5 support in in development. You may encounter an encoding error using Python 3.5, which is resolved by running SiLiCO with Python 2.7.

A bed.gz file is successfully created when I run the code:

$ python SiLiCO.py -i ../NC_002695.fasta -n

However when I pass the -f flag:

$ python SiLiCO.py -i ../NC_002695.fasta -f -n

I am getting permission denied:

Converting simulated BED files to FASTA files... Traceback (most recent call last): File "SiLiCO.py", line 166, in <module> main(sys.argv[1:]) File "SiLiCO.py", line 157, in main convertToFasta(infileName, outfileName) File "/Users/m31237/Desktop/Simulations/SiLiCO/convertToFasta.py", line 20, in convertToFasta b = a.save_seqs(str(nameRoot) + ".fa") File "/Users/m31237/miniconda3/lib/python3.6/site-packages/pybedtools/bedtool.py", line 2414, in save_seqs fout = open(fn, 'w') PermissionError: [Errno 13] Permission denied: '/simulated_read_positions_trial_0.fa'

Hi, I'm getting the following error running the simulator, any help would be great!

/data/Python-3.5.2/python /data/SiLiCO-master/SiLiCO.py -i chr1.fa -m 2000 -s 500 -c 30

Preparing the genome file.
The Scratch dir already exists. Cleaning up...
Done!
Generating a genome index file...
Done!
Generating simulated reads in PacBio mode...
Building threshold dictionaries...
Calculating distribution parameters...
Traceback (most recent call last):
File "/data/SiLiCO-master/SiLiCO.py", line 166, in
main(sys.argv[1:])
File "/data/SiLiCO-master/SiLiCO.py", line 151, in main
simulateReads(infileName,outfileName,mean,std,desired_cov,trialCount,names, SEQ_MODE)
File "/data/SiLiCO-master/simulateReads.py", line 92, in simulateReads
y=getRandomPosition(buf,genomeLength,thresholdDict,names,lengthDict)
File "/data/SiLiCO-master/getRandomPosition.py", line 23, in getRandomPosition
if t+buf <= y <= r-buf:
UnboundLocalError: local variable 'r' referenced before assignment