I downloaded Seqcleanx86_64. I want to remove contaminants from a powdery mildew DNA sequence data using databases I created using makeblast. I use Mac operating system. I tried running the following command line:
$ Vperl ~/bin/seqclean-x86_64/seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A
The terminal output recorded the following error:
Process terminated with an error!
seqclean (LA_Run18_R1.fa) encountered an error.
Working directory was /Volumes/Data_2/Sandile/raw_data
seqclean (LA_Run18_R1.fa) encountered an error.
Working directory was /Vperl ~/bin/seqclean-x86_64/seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A
* Using screening files:
/Volumes/Data_2/Sandile/raw_data/cont_db/bgh
seqclean running options:
seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A
Standard log file: seqcl_LA_Run18_R1.fa.log
Error log file: err_seqcl_LA_Run18_R1.fa.log
Using 1 CPUs for cleaning
-= Rebuilding LA_Run18_R1.fa cdb index =-
Error at cdbfasta LA_Run18_R1.fa -o LA_Run18_R1.fa.cidx
Process terminated with an error!
seqclean (LA_Run18_R1.fa) encountered an error.
Working directory was /Volumes/Data_2/Sandile/raw_data
seqclean (LA_Run18_R1.fa) encountered an error.
Working directory was /Vperl ~/bin/seqclean-x86_64/seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A
I am beginner level at bioinformatics, hence may not have phrased my question properly. Please advise on the probable cause of this error and ways to overcome it.
$ Vperl ~/bin/seqclean-x86_64/seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A
The terminal output recorded the following error:
Process terminated with an error!
seqclean (LA_Run18_R1.fa) encountered an error.
Working directory was /Volumes/Data_2/Sandile/raw_data
seqclean (LA_Run18_R1.fa) encountered an error.
Working directory was /Vperl ~/bin/seqclean-x86_64/seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A
* Using screening files:
/Volumes/Data_2/Sandile/raw_data/cont_db/bgh
seqclean running options:
seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A
Standard log file: seqcl_LA_Run18_R1.fa.log
Error log file: err_seqcl_LA_Run18_R1.fa.log
Using 1 CPUs for cleaning
-= Rebuilding LA_Run18_R1.fa cdb index =-
Error at cdbfasta LA_Run18_R1.fa -o LA_Run18_R1.fa.cidx
Process terminated with an error!
seqclean (LA_Run18_R1.fa) encountered an error.
Working directory was /Volumes/Data_2/Sandile/raw_data
seqclean (LA_Run18_R1.fa) encountered an error.
Working directory was /Vperl ~/bin/seqclean-x86_64/seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A
I am beginner level at bioinformatics, hence may not have phrased my question properly. Please advise on the probable cause of this error and ways to overcome it.
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