Did not create fast summary file

[singhbhavya]

Hi there. I've been trying to solve this problem the entire week, but nothing is working.

This is what I ran:
export LMAT_DIR=/home/bsingh/bin/LMAT/runtime_inputs
/home/bsingh/bin/LMAT/bin/run_rl.sh --db_file=/home/bsingh/bin/LMAT/data/kML.v4-14.20.g10.db --query_file=/home/bsingh/bin/LMAT/example/simple_list.1000.fna --odir=/home/bsingh/bin/LMAT/tmp --threads=8

This is the error I receive:
Using default null model list file for kML.v4-14.20.g10.db
Create output file from input parameters: /home/bsingh/bin/LMAT/tmp/simple_list.1000.fna.kML.v4-14.20.g10.db.lo.rl_output.0.30.fastsummary
Process /home/bsingh/bin/LMAT/example/simple_list.1000.fna outputfile=/home/bsingh/bin/LMAT/tmp/simple_list.1000.fna.kML.v4-14.20.g10.db.lo.rl_output.0.30.fastsummary
Error, did not create a fastsummary file [/home/bsingh/bin/LMAT/tmp/simple_list.1000.fna.kML.v4-14.20.g10.db.lo.rl_output.0.30.fastsummary]

This is what the log file says:
/home/bsingh/bin/LMAT/bin/run_rl.sh: line 243: /usr/bin/time: No such file or directory

I went into the run_rl.sh code and changed the directory from /usr/bin/time to the actual directory on my server where time is. Ran the same stuff again, and got this error:

Using default null model list file for kML.v4-14.20.g10.db
Create output file from input parameters: /home/bsingh/bin/LMAT/tmp/simple_list.1000.fna.kML.v4-14.20.g10.db.lo.rl_output.0.30.fastsummary
Process /home/bsingh/bin/LMAT/example/simple_list.1000.fna outputfile=/home/bsingh/bin/LMAT/tmp/simple_list.1000.fna.kML.v4-14.20.g10.db.lo.rl_output.0.30.fastsummary 
ERROR! Missing depth_file
ERROR! Missing ofbase
ERROR! Missing n_threads
ERROR! Missing kmer_db_fn
ERROR! Missing query_fn
Params:  0   
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==============================================
  Livermore  Metagenomics  Analysis  Toolkit  
==============================================

Taxonomic classification module usage:
/home/bsingh/bin/LMAT/runtime_inputs/../bin/read_label -d <input db file (list)> -i <query fasta file> -t <number of threads>
-o <output path> [-l <human bias>] [-v <pct cutoff>]  -c <tax tree file> -k <kmer size>
[-y:verbose] [-r:rank table] [-m <rank/tid-map-file>] [-g <tid-cutoff>]
[-w <with-strain-species-map> (affects -m option)] [-h:turn phiX screening off]
[-V:print version and exit] [-H:print this usage help and exit]
Command exited with non-zero status 255
	Command being timed: "/home/bsingh/bin/LMAT/runtime_inputs/../bin/read_label -f /home/bsingh/bin/LMAT/runtime_inputs/m9.32To16.map -u /home/bsingh/bin/LMAT/runtime_inputs/ncbi_taxonomy_rank.segment.pruned.txt -w /home/bsingh/bin/LMAT/runtime_inputs/ncbi_taxid_to_rank.pruned.txt -x 0 -j 30 -l 0 -b 1.0 -n /home/bsingh/bin/LMAT/runtime_inputs/kML.v4-14.20.g10.db.null_lst.txt"
	User time (seconds): 0.00
	System time (seconds): 0.00
	Percent of CPU this job got: 26%
	Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.01
	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): 1872
	Average resident set size (kbytes): 0
	Major (requiring I/O) page faults: 33
	Minor (reclaiming a frame) page faults: 459
	Voluntary context switches: 126
	Involuntary context switches: 51
	Swaps: 0
	File system inputs: 8224
	File system outputs: 0
	Socket messages sent: 0
	Socket messages received: 0
	Signals delivered: 0
	Page size (bytes): 4096
	Exit status: 255
Error, did not create a fastsummary file [/home/bsingh/bin/LMAT/tmp/simple_list.1000.fna.kML.v4-14.20.g10.db.lo.rl_output.0.30.fastsummary]

This is what the log says:
/home/bsingh/bin/LMAT/bin/run_rl.sh: line 244: -e: command not found