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

[pipecedeno]

Hello,
I recently installed sibeliaz in the cluster were im working using conda as it's shown instalation part. But when im trying to align 2 genomes, like the 2 genomes of the example of the github y get the following output:
`sibeliaz genome1.fa genome2.fa
Constructing the graph...
Threads = 8
Vertex length = 25
Hash functions = 5
Filter size = 17179869184
Capacity = 1
Files:
genome1.fa
genome2.fa

Round 0, 0:17179869184
Pass Filling Filtering
1 25 3
2 0 0
True junctions count = 79040
False junctions count = 0
Hash table size = 79040
Candidate marks count = 500858

Reallocating bifurcations time: 0
True marks count: 500858
Edges construction time: 1

Distinct junctions = 79040

Loading the graph...
Analyzing the graph...
[...................................................]
Generating the output...
Blocks found: 1350
Coverage: 1.00
Performing global alignment..
bash: line 11: : No such file or directory
bash: line 12: : No such file or directory
bash: line 11: : No such file or directory
bash: line 12: : No such file or directory
bash: line 13: : No such file or directory
bash: line 13: : No such file or directory
bash: line 11: : No such file or directory
bash: line 12: : No such file or directory`
And more of the same error.
I tried reinstaling sibeliaz again as i thought it may be that it wasn't installed correctly but the same error keeps appearing, so im not sure what i may be doing wrong or why this problem appears, because it doesnt matter which genomes.
Thanks for the help.

[ghost]

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

[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.