I am having trouble getting LMAT to run under OS X with Xcode 7.2 installed.
In the run_rl.sh file I had to change line 243 to use gnu-time (called with gtime) instead of the time in OS X. OS X does not allow for the -v option. I am running LMAT from the ./bin file included in the LMAT folder. There are some issues with compling LMAT directly under OS X.
Once I solved that I have a new error:
./bin/run_rl.sh --db_file=kML.v4-14.20.g10.db --query_file=../LMAT-1.2.4/CC1506261_S19.fasta
Using default null model list file for kML.v4-14.20.g10.db
Create output file from input parameters: ./CC1506261_S19.fasta.kML.v4-14.20.g10.db.lo.rl_output.0.30.fastsummary
Process ../LMAT-1.2.4/CC1506261_S19.fasta outputfile=./CC1506261_S19.fasta.kML.v4-14.20.g10.db.lo.rl_output.0.30.fastsummary
Error, did not create a fastsummary file [./CC1506261_S19.fasta.kML.v4-14.20.g10.db.lo.rl_output.0.30.fastsummary]
The log file is here:
/usr/local/bin/gtime: cannot run /../bin/read_label: No such file or directory
Command exited with non-zero status 127
Command being timed: "/../bin/read_label -f /m9.32To16.map -u /ncbi_taxonomy_rank.segment.pruned.txt -w /ncbi_taxid_to_rank.pruned.txt -x 0 -j 30 -l 0 -b 1.0 -n /kML.v4-14.20.g10.db.null_lst.txt -e /depth_for_ncbi_taxonomy.segment.pruned.dat -p -t 80 -i ../LMAT-1.2.4/CC1506261_S19.fasta -d kML.v4-14.20.g10.db -c /ncbi_taxonomy.segment.pruned.dat.nohl -o ./CC1506261_S19.fasta.kML.v4-14.20.g10.db.lo.rl_output"
User time (seconds): 0.00
System time (seconds): 0.00
Percent of CPU this job got: ?%
Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.00
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 1294336
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 103
Voluntary context switches: 0
Involuntary context switches: 1
Swaps: 0
File system inputs: 0
File system outputs: 0
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 127
It looks like it's looking for the read_label and not finding it.
I was wondering what might be a good next step to take.
Thanks,
ara
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thanks for the information. It maybe that the shell script syntax is slightly different in Mac OS X. I haven't not yet had an opportunity to confirm this.
It looks like the "bin_dir" environment variable was not set correctly.
It looks like it hit the line:
bin_dir="$LMAT_DIR/../bin/" in run_rl.sh
and LMAT_DIR is undefined. Make sure LMAT_DIR is set to point to the runtime_inputs directory.
In the run_rl.sh script you can try settting the LMAT_DIR and bin_dir directory, for example:
bin_dir=/YOUR_LMAT_DIR/bin/
make sure this is set after line 36 where bin_dir= is currently set.
--Jonathan
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello all,
I am having trouble getting LMAT to run under OS X with Xcode 7.2 installed.
In the run_rl.sh file I had to change line 243 to use gnu-time (called with gtime) instead of the time in OS X. OS X does not allow for the -v option. I am running LMAT from the ./bin file included in the LMAT folder. There are some issues with compling LMAT directly under OS X.
Once I solved that I have a new error:
./bin/run_rl.sh --db_file=kML.v4-14.20.g10.db --query_file=../LMAT-1.2.4/CC1506261_S19.fasta
Using default null model list file for kML.v4-14.20.g10.db
Create output file from input parameters: ./CC1506261_S19.fasta.kML.v4-14.20.g10.db.lo.rl_output.0.30.fastsummary
Process ../LMAT-1.2.4/CC1506261_S19.fasta outputfile=./CC1506261_S19.fasta.kML.v4-14.20.g10.db.lo.rl_output.0.30.fastsummary
Error, did not create a fastsummary file [./CC1506261_S19.fasta.kML.v4-14.20.g10.db.lo.rl_output.0.30.fastsummary]
The log file is here:
/usr/local/bin/gtime: cannot run /../bin/read_label: No such file or directory
Command exited with non-zero status 127
Command being timed: "/../bin/read_label -f /m9.32To16.map -u /ncbi_taxonomy_rank.segment.pruned.txt -w /ncbi_taxid_to_rank.pruned.txt -x 0 -j 30 -l 0 -b 1.0 -n /kML.v4-14.20.g10.db.null_lst.txt -e /depth_for_ncbi_taxonomy.segment.pruned.dat -p -t 80 -i ../LMAT-1.2.4/CC1506261_S19.fasta -d kML.v4-14.20.g10.db -c /ncbi_taxonomy.segment.pruned.dat.nohl -o ./CC1506261_S19.fasta.kML.v4-14.20.g10.db.lo.rl_output"
User time (seconds): 0.00
System time (seconds): 0.00
Percent of CPU this job got: ?%
Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.00
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 1294336
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 103
Voluntary context switches: 0
Involuntary context switches: 1
Swaps: 0
File system inputs: 0
File system outputs: 0
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 127
It looks like it's looking for the read_label and not finding it.
I was wondering what might be a good next step to take.
Thanks,
ara
Hi Ara,
thanks for the information. It maybe that the shell script syntax is slightly different in Mac OS X. I haven't not yet had an opportunity to confirm this.
It looks like the "bin_dir" environment variable was not set correctly.
It looks like it hit the line:
bin_dir="$LMAT_DIR/../bin/" in run_rl.sh
and LMAT_DIR is undefined. Make sure LMAT_DIR is set to point to the runtime_inputs directory.
In the run_rl.sh script you can try settting the LMAT_DIR and bin_dir directory, for example:
bin_dir=/YOUR_LMAT_DIR/bin/
make sure this is set after line 36 where bin_dir= is currently set.
--Jonathan
Hi,
Linux is required to run LMAT. We don't support OSX at this time. Sorry for the misunderstanding.
Best Regards,
Sasha
Last edit: Sasha 2016-02-19