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bioinfologics / satsuma2

FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing
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Unable to find satsuma_run.sh #26

Closed dthorburn closed 4 years ago

dthorburn commented 4 years ago

Hi,

I am trying to run SatsumaSynteny2 on our HPC, but it appears I keep getting the same error when slaves jobs are being created.

Running the command: SatsumaSynteny2 -q $Ref_Geno1/tig00000011_pilon.fa -t $Ref_Geno2/Gac-HiC_revised_genome_assembly.fasta -o $OUT_DIR/

I then get the following error: sh: :/data/home/btx316/privatemodules/satsuma2/bin/satsuma_run.sh: No such file or directory

The head of the output file is: SATSUMA: Welcome to SatsumaSynteny! Current date and time: 2020/02/27 12:57:51 Path for Satsuma2: ':/data/home/btx316/privatemodules/satsuma2/bin' Executing /data/home/btx316/privatemodules/satsuma2/bin/SatsumaSynteny2 Setting up grid. Preparing... select=0 chunks=150742 chunks: 150742 select=0 chunks=47 chunks: 47 size x=6281 y=2 size=12562 Initializing multimatches... Done. SATSUMA: Acquiring seeds, date and time: 2020/02/27 12:58:01 Running seed pre-filter: :/data/home/btx316/privatemodules/satsuma2/bin/KMatch /data/SBCS-EizaguirreLab/Miles/CompGenomics_Collab/00_Ref_Genomes/Gynogene_Genome/All_Contigs_Ind/tig00000011_pilon.fa /data/SBCS-EizaguirreLab/Miles/CompGenomics_Collab/00_Ref_Genomes/Peichel_Genome/Gac-HiC_revised_genome_assembly.fasta 11 /data/scratch/btx316/Comp_Genomics/08_Satsuma2/02_IndContigs_Satsuma2/tig00000011_pilon.fa/kmatch_results.k11 11 10 1; touch /data/scratch/btx316/Comp_Genomics/08_Satsuma2/02_IndContigs_Satsuma2/tig00000011_pilon.fa/kmatch_results.k11.finished sh: :/data/home/btx316/privatemodules/satsuma2/bin/satsuma_run.sh: No such file or directory

The contents of the binary directory is $ ls /data/home/btx316/privatemodules/satsuma2/bin/ BlockDisplaySatsuma FilterGridSeeds MatchesByFeature ReverseSatsumaOut SortSatsuma ChainMatches HomologyByXCorr MergeScaffoldsBySynteny satsuma_run.sh Chromosemble HomologyByXCorrSlave MergeXCorrMatches SatsumaSynteny2 ChromosomePaint KMatch MicroSyntenyPlot SatsumaToFASTA ColaAlignSatsuma MatchDump OrderOrientBySynteny SatsumaToGFF

And satsuma_run.sh exists and exectutes when I submit sh satsuma_run.sh.

In case it's important I used gcc/7.1.0 and cmake/3.16.0 to compile.

jonwright99 commented 4 years ago

Hi, Can you check you are exporting the SATSUMA2_PATH variable correctly before you run Satsuma2. It looks like you are setting it to :/data/home/btx316/privatemodules/satsuma2/bin/ rather than /data/home/btx316/privatemodules/satsuma2/bin/, ie. adding an extra colon to the start.

dthorburn commented 4 years ago

Hey, Thanks for the quick response. I can't believe I missed something so obvious - I had just finished building a singularity container and hadn't make the same mistake and it seemed to work there.