Open clairemerot opened 3 years ago
Are you using delta file from nucmer or nucmer -maxmatch?
On Fri, Jul 23, 2021, 07:17 Claire Mérot @.***> wrote:
Hello, I'm encountering an issue that several people have raised here but I can't find how they fixed it I am not able to run lastZ because the genomes are too big. so I am running the svmu with an empty file for it. Yet, it starts running and after a while do " Segmentation fault (core dumped) svmu". any idea how I can do? thanks for your help Claire
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hi Mahul, thanks for your answer. These are the lines of codes I used (so no -maxmatch, should I?)
nucmer -t $NB_CPU \ "$INPUT_FOLDER"/"$REFERENCE" "$INPUT_FOLDER"/"$QUERY" \ -p "$OUTPUT_FOLDER"/sam2ref
lastz "$INPUT_FOLDER"/"$REFERENCE"[multiple] "$INPUT_FOLDER"/"$QUERY"[multiple] --chain \ --format=general:name1,strand1,start1,end1,name2,strand2,start2,end2 > "$OUTPUT_FOLDER"/sam_lastz.txt
svmu "$OUTPUT_FOLDER"/sam2ref.delta "$INPUT_FOLDER"/"$REFERENCE" "$INPUT_FOLDER"/"$QUERY" l "$OUTPUT_FOLDER"/sam_lastz.txt "$OUTPUT_FOLDER"/sam2ref_svmu
thanks for your help! Claire
Hello, I'm encountering an issue that several people have raised here but I can't find how they fixed it I am not able to run lastZ because the genomes are too big. so I am running the svmu with an empty file for it. Yet, it starts running and after a while do " Segmentation fault (core dumped) svmu". any idea how I can do? thanks for your help Claire