Closed ChristianMichelsen closed 8 months ago
When I run the same command, the name of the generated files differ between Mac and Linux (i.e. on my local laptop vs the server).
In particular, I run:
./metaDMG-cpp lca -bam raw_data/alignment.bam -outnames data/lca/tmp/alignment/alignment -names raw_data/names-mdmg.dmp -nodes raw_data/nodes-mdmg.dmp -acc2tax raw_data/acc2taxid.map.gz -fix_ncbi 0 -tempfolder data/lca/tmp/alignment/
which either generates alignment.bamalignment.bam.bin on my Mac or acc2taxid.map.gzalignment.bam.bin on the server.
alignment.bamalignment.bam.bin
acc2taxid.map.gzalignment.bam.bin
The output of my Mac is:
-> Will output lca results in file: 'data/lca/tmp/alignment/alignment.lca.gz' -> [thread1] Will read header -> Will output lca distribution in file: 'data/lca/tmp/alignment/alignment.stat' -> Will output lca weight in file: 'data/lca/tmp/alignment/alignment.wlca' -> Will output log info (problems) in file: 'data/lca/tmp/alignment/alignment.log' -> [thread1] Done reading header: 0.00 sec, header contains: 2 -> -bam raw_data/alignment.bam -> -names raw_data/names-mdmg.dmp -> -nodes raw_data/nodes-mdmg.dmp -> -acc2tax raw_data/acc2taxid.map.gz -> -simscoreLow 0.000000 -> -simscoreHigh 1.000000 -> -editdistMin 0 -> -editdistMax 10 -> -outnames data/lca/tmp/alignment/alignment -> -minmapq 0 -> -lca_rank species -> -norank2species 0 -> -howmany 5 -> -fix_ncbi 0 -> -weighttype 0 -> -tempfolder 38245184 -> Starting to extract (acc->taxid) from binary file: 'raw_data/acc2taxid.map.gz' -> Checking if exits: 'data/lca/tmp/alignment/alignment.bamalignment.bam.bin' -> Checking if bimnary file exists. dodump=1 -> opening file: 'data/lca/tmp/alignment/alignment.bamalignment.bam.bin' mode: 'wb' -> Setting threads to: 4 -> opening file: 'raw_data/acc2taxid.map.gz' mode: 'rb' -> Setting threads to: 2 -> At linenr: 200001 in 'raw_data/acc2taxid.map.gz' -> Number of entries to use from accesion to taxid: 2, time taken: 0.00 sec -> [raw_data/names-mdmg.dmp] Number of unique names (column1): 65949 with third column 'scientific name' -> Number of unique names (column1): 65949 from file: raw_data/nodes-mdmg.dmp parent.size():65949 child.size():0 -> Number of entries with level information: 46 [hts] -> editMin:0 editmMax:10 scoreLow:0.000000 scoreHigh:1.000000 minlength:-1 discard: 516 prefix: data/lca/tmp/alignment/alignment howmany: 5 skipnorank: 1 weighttype: 0 -> Will dump: 'data/lca/tmp/alignment/alignment.bdamage.gz' this contains damage patterns for: 2 items -> Setting threads to: 4 -> Number of species with reads that map uniquely: 2 -> [ALL done] walltime used = 0.00 sec
and the output on Linux is:
-> Will output lca results in file: 'data/lca/tmp/alignment/alignment.lca.gz' -> [thread1] Will read header -> [thread1] Done reading header: 0.00 sec, header contains: 2 -> Will output lca distribution in file: 'data/lca/tmp/alignment/alignment.stat' -> Will output lca weight in file: 'data/lca/tmp/alignment/alignment.wlca' -> Will output log info (problems) in file: 'data/lca/tmp/alignment/alignment.log' -> -bam raw_data/alignment.bam -> -names raw_data/names-mdmg.dmp -> -nodes raw_data/nodes-mdmg.dmp -> -acc2tax raw_data/acc2taxid.map.gz -> -simscoreLow 0.000000 -> -simscoreHigh 1.000000 -> -editdistMin 0 -> -editdistMax 10 -> -outnames data/lca/tmp/alignment/alignment -> -minmapq 0 -> -lca_rank species -> -norank2species 0 -> -howmany 5 -> -fix_ncbi 0 -> -weighttype 0 -> -tempfolder 28299616 -> Starting to extract (acc->taxid) from binary file: 'raw_data/acc2taxid.map.gz' -> Checking if exits: 'data/lca/tmp/alignment/acc2taxid.map.gzalignment.bam.bin' -> Checking if bimnary file exists. dodump=1 -> opening file: 'data/lca/tmp/alignment/acc2taxid.map.gzalignment.bam.bin' mode: 'wb' -> Setting threads to: 4 -> opening file: 'raw_data/acc2taxid.map.gz' mode: 'rb' -> Setting threads to: 2 -> At linenr: 200001 in 'raw_data/acc2taxid.map.gz' -> Number of entries to use from accesion to taxid: 2, time taken: 0.00 sec -> [raw_data/names-mdmg.dmp] Number of unique names (column1): 65949 with third column 'scientific name' -> Number of unique names (column1): 65949 from file: raw_data/nodes-mdmg.dmp parent.size():65949 child.size():0 -> Number of entries with level information: 46 [hts] -> editMin:0 editmMax:10 scoreLow:0.000000 scoreHigh:1.000000 minlength:-1 discard: 516 prefix: data/lca/tmp/alignment/alignment howmany: 5 skipnorank: 1 weighttype: 0 -> Will dump: 'data/lca/tmp/alignment/alignment.bdamage.gz' this contains damage patterns for: 2 items -> Setting threads to: 4 -> Number of species with reads that map uniquely: 2 -> [ALL done] walltime used = 1.00 sec
Not a major issue since the .bin is not really used by my end of the pipeline, however, I was just curious about it.
.bin
This should not be an issue in new versions.
When I run the same command, the name of the generated files differ between Mac and Linux (i.e. on my local laptop vs the server).
In particular, I run:
./metaDMG-cpp lca -bam raw_data/alignment.bam -outnames data/lca/tmp/alignment/alignment -names raw_data/names-mdmg.dmp -nodes raw_data/nodes-mdmg.dmp -acc2tax raw_data/acc2taxid.map.gz -fix_ncbi 0 -tempfolder data/lca/tmp/alignment/
which either generates
alignment.bamalignment.bam.bin
on my Mac oracc2taxid.map.gzalignment.bam.bin
on the server.The output of my Mac is:
and the output on Linux is: