bwa mem - failure to execute
Hello all,
I am VERY new to both working in Linux and manually performing alignments. I work in a lab that has always used Miseq Reporter, but I've found it is not at all optimized for the next gen assay I'm developing, that is: targeted (~360 amplicons), reads about 200 bp in length, PE, human genome reference.
After trimming my adapters using trimmomatic, I have attempted to use BWA-0.7.9a (specifically bwa mem) to generate .sam files from .fastq. Below are the commands I've entered into terminal:
bwa index -a bwtsw /home/.../genome.fa
bwa mem -t 8 /home/.../genome.fa read1.fastq read2.fastq > output.sam
After pressing enter following the bwa mem command, I get a line like the one below:
[M::main_mem] read 823456 sequences (170495870 bp)...
And then literally NOTHING happens. I gave it a few hours, and that is still the last line displayed in the terminal.
I apologize for not being able to trouble shoot this myself. I made sure to perform make, and it was successful from what I can tell. It also looks like the indexing was successful, with all the files that are typically generated.
Regarding the genome.fa indexing though, the computer I'm using already had the .fa file and several other files with different extensions in the same folder, perhaps because the .fa file was already indexed? Is it possible that this is causing the problem?
Any help would be greatly appreciated.
Thank you.
Lindsay
I am VERY new to both working in Linux and manually performing alignments. I work in a lab that has always used Miseq Reporter, but I've found it is not at all optimized for the next gen assay I'm developing, that is: targeted (~360 amplicons), reads about 200 bp in length, PE, human genome reference.
After trimming my adapters using trimmomatic, I have attempted to use BWA-0.7.9a (specifically bwa mem) to generate .sam files from .fastq. Below are the commands I've entered into terminal:
bwa index -a bwtsw /home/.../genome.fa
bwa mem -t 8 /home/.../genome.fa read1.fastq read2.fastq > output.sam
After pressing enter following the bwa mem command, I get a line like the one below:
[M::main_mem] read 823456 sequences (170495870 bp)...
And then literally NOTHING happens. I gave it a few hours, and that is still the last line displayed in the terminal.
I apologize for not being able to trouble shoot this myself. I made sure to perform make, and it was successful from what I can tell. It also looks like the indexing was successful, with all the files that are typically generated.
Regarding the genome.fa indexing though, the computer I'm using already had the .fa file and several other files with different extensions in the same folder, perhaps because the .fa file was already indexed? Is it possible that this is causing the problem?
Any help would be greatly appreciated.
Thank you.
Lindsay
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