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atarashansky / SAMap

SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.
MIT License
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error in runing map_genes.sh #127

Open rdf1993 opened 9 months ago

rdf1993 commented 9 months ago

bash map_genes.sh --tr1 /mnt/volume3/rdf/01_refData/GRCh38_fa/Homo_sapiens.GRCh38.dna.primary_assembly.fa --t1 nucl --n1 hs --tr2 /mnt/volume3/rdf/01_refData/GRCm38_fa/Mus_musculus.GRCm38.dna.primary_assembly.fa --t2 nucl --n2 mm --threads 8 Running tblastx in both directions map_genes.sh: line 124: 308696 Segmentation fault (core dumped) tblastx -query $tr1 -db $tr2 -outfmt 6 -out "maps/${n1}${n2}/${n1}to${n2}.txt" -num_threads ${n_threads} -max_hsps 1 -evalue 1e-6 map_genes.sh: line 124: 310032 Segmentation fault (core dumped) tblastx -query $tr2 -db $tr1 -outfmt 6 -out "maps/${n1}${n2}/${n2}to${n1}.txt" -num_threads ${n_threads} -max_hsps 1 -evalue 1e-6

jylee43 commented 7 months ago

Hi, you need to use sequences from mRNAs or proteins not chromosomes. "*.dna.primary_assembly.fa" are for genome sequences, so they are not appropriate for SAMap.