soedinglab
Input and output files
I want to predict the phage-host using the SPacePHARER a tool developed by your team. I have metatranscriptome data and want to screen the bacteriophages. My question is what will be the .fas file (spacepharer easy-predict examples/*.fas targetSetDB predictions.tsv tmpFolder). Also which databases are accurately helpful for this identification. Can I predict phage and host using this tool?
Look forward to your help and suggestions. I have raw .gz files from the metatranscriptomics as input.
How to make Spacers file? Can I use the same .fas file (JNGQ01000029.fas and CP003088.fas) given in tutorial or I need to make new one. Please help me how to mke these files.
My predictmatch is showing failed ; Query database size: 305 type: Aminoacid Estimated memory consumption: 19G Target database size: 25366234 type: Aminoacid Index table k-mer threshold: 112 at k-mer size 6 Index table: counting k-mers [=================================================================] 100.00% 25.37M 10m 22s 736ms Index table: Masked residues: 17104442 Index table: fill tmpFolder/8143349053704083950/predict/16566698282892545376/search/8965319943649311865/blastp.sh: line 99: 36 198 Bus error $RUNNER "$MMSEQS" prefilter "$INPUT" "$TARGET" "$TMP_PATH/pref_$STEP" $PREFILTER _PAR -s "$SENS" Error: Prefilter died Error: search failed Error: predictmatch failed