Open annasimonsen opened 4 years ago
I am trying to get the map function working using "Experiment 2" data downloaded from the pantools read mapping preprint. .sam files for all 10 genomes were made, but only contained the first @SQ lines.
java -server -Xmx16g -jar $PANTOOLSJAR map -dp ${dir}/genus_pangenome -1 ${dir}/MSv31.fq -2 ${dir}/MSv32.fq -gn ${dir}/numbers.txt -op ${dir}/my_files
PATH_TO_THE_PANGENOME_DATABASE = /mnt/oldscratch/sheik005/shared/readmapping_materials/Exp2/genus_pangenome PATH_TO_THE_FIRST_SRA = /mnt/oldscratch/sheik005/shared/readmapping_materials/Exp2/MSv31.fq PATH_TO_THE_SECOND_SRA = /mnt/oldscratch/sheik005/shared/readmapping_materials/Exp2/MSv32.fq PATH_TO_THE_GENOME_NUMBERS_FILE =/mnt/oldscratch/sheik005/shared/readmapping_materials/Exp2/numbers.txt OUTPUT_PATH = /mnt/oldscratch/sheik005/shared/readmapping_materials/Exp2/my_files
Mapping paired-end reads on 10 genome(s) : Reads: 243100
Genome Total Unique Unmapped 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 ........................................ 0 0 0 Number_of_hits = 0 Number_of_alignments = 0
Do you have any ideas what might be causing this?
Appreciate the help!
I am trying to get the map function working using "Experiment 2" data downloaded from the pantools read mapping preprint. .sam files for all 10 genomes were made, but only contained the first @SQ lines.
java -server -Xmx16g -jar $PANTOOLSJAR map -dp ${dir}/genus_pangenome -1 ${dir}/MSv31.fq -2 ${dir}/MSv32.fq -gn ${dir}/numbers.txt -op ${dir}/my_files
PATH_TO_THE_PANGENOME_DATABASE = /mnt/oldscratch/sheik005/shared/readmapping_materials/Exp2/genus_pangenome PATH_TO_THE_FIRST_SRA = /mnt/oldscratch/sheik005/shared/readmapping_materials/Exp2/MSv31.fq PATH_TO_THE_SECOND_SRA = /mnt/oldscratch/sheik005/shared/readmapping_materials/Exp2/MSv32.fq PATH_TO_THE_GENOME_NUMBERS_FILE =/mnt/oldscratch/sheik005/shared/readmapping_materials/Exp2/numbers.txt OUTPUT_PATH = /mnt/oldscratch/sheik005/shared/readmapping_materials/Exp2/my_files
Mapping paired-end reads on 10 genome(s) : Reads: 243100
Genome Total Unique Unmapped 1 0 0 0 2 0 0 0 3 0 0 0 4 0 0 0 5 0 0 0 6 0 0 0 7 0 0 0 8 0 0 0 9 0 0 0 10 0 0 0 ........................................ 0 0 0 Number_of_hits = 0 Number_of_alignments = 0
Total time : 8.241 seconds Peak memory : 933 MB
Do you have any ideas what might be causing this?
Appreciate the help!