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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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./bin/SatsumaSynteny2/satsuma_run.sh: Not a directory #58

Open hannahdevens opened 1 year ago

hannahdevens commented 1 year ago

Hi, when I run the test command, I keep getting the notification "sh: ./bin/SatsumaSynteny2/satsuma_run.sh: Not a directory" . The command never finishes successfully, so I'm assuming there is an issue with satsuma_run.sh not being a directory. Below is the read out I get. Any idea what is going wrong?

SATSUMA: Welcome to SatsumaSynteny! Current date and time: 2022/12/04 18:58:25 Path for Satsuma2: './bin/SatsumaSynteny2' Creating directory xcorr_sample_synt Executing bin/SatsumaSynteny2 Setting up grid. Preparing... select=0 chunks=261 chunks: 261 select=0 chunks=245 chunks: 245 size x=11 y=11 size=121 Initializing multimatches... Done. SATSUMA: Acquiring seeds, date and time: 2022/12/04 18:58:26 Running seed pre-filter: ./bin/SatsumaSynteny2/KMatch samples/human.X.part.fasta samples/dog.X.part.fasta 11 xcorr_sample_synt/kmatch_results.k11 11 10 1; touch xcorr_sample_synt/kmatch_results.k11.finished sh: ./bin/SatsumaSynteny2/satsuma_run.sh: Not a directory Running seed pre-filter: ./bin/SatsumaSynteny2/KMatch samples/human.X.part.fasta samples/dog.X.part.fasta 13 xcorr_sample_synt/kmatch_results.k13 13 12 1; touch xcorr_sample_synt/kmatch_results.k13.finished sh: ./bin/SatsumaSynteny2/satsuma_run.sh: Not a directory Running seed pre-filter: ./bin/SatsumaSynteny2/KMatch samples/human.X.part.fasta samples/dog.X.part.fasta 15 xcorr_sample_synt/kmatch_results.k15 15 14 1; touch xcorr_sample_synt/kmatch_results.k15.finished sh: ./bin/SatsumaSynteny2/satsuma_run.sh: Not a directory Running seed pre-filter: ./bin/SatsumaSynteny2/KMatch samples/human.X.part.fasta samples/dog.X.part.fasta 17 xcorr_sample_synt/kmatch_results.k17 17 16 1; touch xcorr_sample_synt/kmatch_results.k17.finished sh: ./bin/SatsumaSynteny2/satsuma_run.sh: Not a directory Running seed pre-filter: ./bin/SatsumaSynteny2/KMatch samples/human.X.part.fasta samples/dog.X.part.fasta 19 xcorr_sample_synt/kmatch_results.k19 19 18 1; touch xcorr_sample_synt/kmatch_results.k19.finished sh: ./bin/SatsumaSynteny2/satsuma_run.sh: Not a directory Running seed pre-filter: ./bin/SatsumaSynteny2/KMatch samples/human.X.part.fasta samples/dog.X.part.fasta 21 xcorr_sample_synt/kmatch_results.k21 21 20 1; touch xcorr_sample_synt/kmatch_results.k21.finished sh: ./bin/SatsumaSynteny2/satsuma_run.sh: Not a directory Running seed pre-filter: ./bin/SatsumaSynteny2/KMatch samples/human.X.part.fasta samples/dog.X.part.fasta 23 xcorr_sample_synt/kmatch_results.k23 23 22 1; touch xcorr_sample_synt/kmatch_results.k23.finished sh: ./bin/SatsumaSynteny2/satsuma_run.sh: Not a directory Running seed pre-filter: ./bin/SatsumaSynteny2/KMatch samples/human.X.part.fasta samples/dog.X.part.fasta 25 xcorr_sample_synt/kmatch_results.k25 25 24 1; touch xcorr_sample_synt/kmatch_results.k25.finished sh: ./bin/SatsumaSynteny2/satsuma_run.sh: Not a directory Running seed pre-filter: ./bin/SatsumaSynteny2/KMatch samples/human.X.part.fasta samples/dog.X.part.fasta 27 xcorr_sample_synt/kmatch_results.k27 27 26 1; touch xcorr_sample_synt/kmatch_results.k27.finished sh: ./bin/SatsumaSynteny2/satsuma_run.sh: Not a directory Running seed pre-filter: ./bin/SatsumaSynteny2/KMatch samples/human.X.part.fasta samples/dog.X.part.fasta 29 xcorr_sample_synt/kmatch_results.k29 29 28 1; touch xcorr_sample_synt/kmatch_results.k29.finished sh: ./bin/SatsumaSynteny2/satsuma_run.sh: Not a directory Running seed pre-filter: ./bin/SatsumaSynteny2/KMatch samples/human.X.part.fasta samples/dog.X.part.fasta 31 xcorr_sample_synt/kmatch_results.k31 31 30 1; touch xcorr_sample_synt/kmatch_results.k31.finished sh: ./bin/SatsumaSynteny2/satsuma_run.sh: Not a directory Waiting for seed pre-filters...