I have some questions about the the DB. I have downloaded the allDB from metAmos website. Are the sequence files in the DB/refseq used by bowtie/bowtie2? Does metAmos need to build the indexes for all the reference genomes in DB/refseq? The reference genomes that are used in mapping and annotation are same?
The following code is a part of COMMAND.log. I use MIRA to do assembling work, I am confused that why the bowtie builds an index for the mira.31.asm.contig? There are many reference genomes in DB, how metAmos choose these genomes?
Dear metAmos team,
I have some questions about the the DB. I have downloaded the allDB from metAmos website. Are the sequence files in the DB/refseq used by bowtie/bowtie2? Does metAmos need to build the indexes for all the reference genomes in DB/refseq? The reference genomes that are used in mapping and annotation are same?
The following code is a part of COMMAND.log. I use MIRA to do assembling work, I am confused that why the bowtie builds an index for the mira.31.asm.contig? There are many reference genomes in DB, how metAmos choose these genomes?
|2017-05-28 16:58:26|# [ASSEMBLE] |2017-05-28 16:58:26| touch /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.run |2017-05-28 16:58:28| head -n 4 /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Preprocess/out/lib1.fastq > /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Preprocess/out/tmp.fastq |2017-05-28 16:58:28| rm -f /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Preprocess/out/tmp.fastq |2017-05-28 16:58:28| /bin/rm -rf mira_assembly |2017-05-28 17:00:13| /scratch/tmp/wc/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/mira/bin/mira /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.config |2017-05-28 17:00:13| unlink /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.asm.contig |2017-05-28 17:00:13| ln -L /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira_assembly/mira_d_results/mira_out.unpadded.fasta /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.asm.contig |2017-05-28 17:00:14| mv /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.asm.contig /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.asm.contigWIUPAC.fa |2017-05-28 17:00:15| java -cp /scratch/tmp/wc/metAMOS-1.5rc3/Utilities/java:. RemoveIUPAC /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.asm.contigWIUPAC.fa >/scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.asm.contig |2017-05-28 17:00:15| rm /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.run |2017-05-28 17:00:15| touch /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/assemble.success |2017-05-28 17:00:16|# [MAPREADS] |2017-05-28 17:00:16| /scratch/tmp/wc/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.asm.contig /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.IDX |2017-05-28 17:00:20| /scratch/tmp/wc/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/bowtie -p 14 -f -l 25 -e 140 --best --strata -m 10 -k 1 --un /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.lib1.unaligned.fasta /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.IDX /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Preprocess/out/lib1.seq > /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/lib1.bout |2017-05-28 17:00:20| cat /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.lib1.mappedmates >> /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.lib1.hdr |2017-05-28 17:00:20| cp /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.lib1.hdr /scratch/tmp/wc/metAMOS-1.5rc3/chen/classifier_test/51GHLH/Assemble/out/mira.31.lib1.mappedmates