I ran HECIL on a ONT dataset with 100bps reads with the following commands:
chmod +x bwa chmod +x samtools chmod +x Align_Corr.sh
python HECIL.py -l q_combine.fasta -s test.forward.fastq -len 100 -o ONTmyseCorr
The task was given 12 hours, 100 gb, and 28 cores. Samtools and bowtie were loaded in the cluster, everything was working well until writing the output, were I got an error message:
The log is:
chmod: cannot access ‘chmod’: No such file or directory
chmod: cannot access ‘+x’: No such file or directory
chmod: cannot access ‘chmod’: No such file or directory
chmod: cannot access ‘+x’: No such file or directory
Started running alignment
[bwt_gen] Finished constructing BWT in 3807 iterations.
[samopen] SAM header is present: 18373025 sequences.
Finished running alignment
Started running correction
File "Correction.py", line 600
print ref
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(ref)?
Finished running correction
Generating output file with all (corrected and uncorrected) reads
Finished running HECIL
I checked the folder and the output has zero bits. My short-read data is about 50GB and the ONT data is about 20GB.
Appreciate any help to solving this issue, very disappointed that everything went very well until the generation of the output file.
Hi,
I ran HECIL on a ONT dataset with 100bps reads with the following commands: chmod +x bwa chmod +x samtools chmod +x Align_Corr.sh python HECIL.py -l q_combine.fasta -s test.forward.fastq -len 100 -o ONTmyseCorr
The task was given 12 hours, 100 gb, and 28 cores. Samtools and bowtie were loaded in the cluster, everything was working well until writing the output, were I got an error message: The log is: chmod: cannot access ‘chmod’: No such file or directory chmod: cannot access ‘+x’: No such file or directory chmod: cannot access ‘chmod’: No such file or directory chmod: cannot access ‘+x’: No such file or directory Started running alignment [bwt_gen] Finished constructing BWT in 3807 iterations. [samopen] SAM header is present: 18373025 sequences. Finished running alignment Started running correction File "Correction.py", line 600 print ref ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(ref)? Finished running correction Generating output file with all (corrected and uncorrected) reads Finished running HECIL
I checked the folder and the output has zero bits. My short-read data is about 50GB and the ONT data is about 20GB.
Appreciate any help to solving this issue, very disappointed that everything went very well until the generation of the output file.
Thanks;