Some questions about the DB

[chen496]

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