bash: line 11, 12 and 13: No such file or directory

[medvedevgroup]

bash: line 11, 12 and 13: No such file or directory

[dpryan79]

This is caused by https://github.com/medvedevgroup/SibeliaZ/blob/master/SibeliaZ-LCB/sibeliaz#L129

$DIR is set to "", which ends up causing problems due to https://github.com/medvedevgroup/SibeliaZ/blob/master/SibeliaZ-LCB/sibeliaz#L77 , since $4 is actually now in $3. Since spoa is somewhere in the path, there's no reason $DIR should be passed around. An easy solution is to adjust line 129 to:

find $outdir -name "*.tmp" -printf "%p\n" | xargs -I @ -P $threads bash -c "block_align @ '$outfile' '\"$DIR\"'"

[sapoudel]

@dpryan79 suggestion works if you installed it with bioconda. Thanks!

[iminkin]

Hi all,

Sorry for messing this up. I removed the patch setting DIR to '', should be fixed in 1.2.4. Special thanks to @dpryan79 for pointing out the root cause.

I also get the same error after multiple re-installs. Sibeliaz runs but with an empty maf file. I installed sibeliaz via conda.

[sapoudel]

Same. All the .tmp files are there and populated. So are block* files. Alignment file is also there but it only contains path to the input file e.g.
/path/to/file1.fna /path/to/file2.fna ... etc.

[iminkin]

Hi all,

Thank you for the reports. I will take a look soon.

[matt-shenton]

Getting the same error here too. Looking forward to trying out the tool!

[markopetek]

Same error for me. Installed using conda. It did however generate the maf and gff files and did not leave any tmp or block* files.

The maf file is empty.

[dpryan79]

Same here, on the command line it's trying to run the following:

bash -c "block_align outdir/229.tmp 'outdir/alignment.maf' ''"

It seems likely that this is the source of the error