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

pipecedeno commented 3 years ago

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 commented 3 years ago

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

sapoudel commented 3 years ago

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 commented 3 years ago

Hi all,

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

matt-shenton commented 3 years ago

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

markopetek commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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

iminkin commented 3 years ago

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.

medvedevgroup / SibeliaZ