Closed najouamghazli closed 6 years ago
Hello,
The error occur when the first command is submitted. It seems that it fail to get the version of flash.
Before using FROGS on you own data, did you test your installation with the script test.sh
cd <FROGS_PATH>/test
bash test.sh <FROGS_PATH> <NB_CPU> <JAVA_MEM> <OUT_FOLDER>
All dependancies listed in the Readme file are in your PATH or have a link in the
Hello @mariabernard ,
Thank you for your reply.
I did install all the dependencies listed in the Readme file, but when I run the test command I get somehow the same output as before:
gs-metagenomics/FROGS-2.0.0 2 3 /home/frogs-metagenomics/Out_Test Step preprocess Thu Feb 15 05:49:06 EST 2018 Process Process-2: Traceback (most recent call last): File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/home/frogs-metagenomics/FROGS-2.0.0/app/preprocess.py", line 604, in filter_process_multiples_files process_sample( R1_files[idx], R2_files[idx], samples_names[idx], out_files[idx], lengths_files[idx], log_files[idx], args ) File "/home/frogs-metagenomics/FROGS-2.0.0/app/preprocess.py", line 643, in process_sample flash_cmd.submit(log_file) File "/home/frogs-metagenomics/FROGS-2.0.0/lib/frogsUtils.py", line 135, in submit FH_log.write( '# ' + self.description + ' (' + os.path.basename(self.program) + ' version : ' + self.get_version() + ')\n' ) File "/home/frogs-metagenomics/FROGS-2.0.0/app/preprocess.py", line 81, in get_version return Cmd.get_version(self, 'stdout').split()[1].strip() IndexError: list index out of range Process Process-1: Traceback (most recent call last): File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/home/frogs-metagenomics/FROGS-2.0.0/app/preprocess.py", line 604, in filter_process_multiples_files process_sample( R1_files[idx], R2_files[idx], samples_names[idx], out_files[idx], lengths_files[idx], log_files[idx], args ) File "/home/frogs-metagenomics/FROGS-2.0.0/app/preprocess.py", line 643, in process_sample flash_cmd.submit(log_file) File "/home/frogs-metagenomics/FROGS-2.0.0/lib/frogsUtils.py", line 135, in submit FH_log.write( '# ' + self.description + ' (' + os.path.basename(self.program) + ' version : ' + self.get_version() + ')\n' ) File "/home/frogs-metagenomics/FROGS-2.0.0/app/preprocess.py", line 81, in get_version return Cmd.get_version(self, 'stdout').split()[1].strip() IndexError: list index out of range Traceback (most recent call last): File "/home/frogs-metagenomics/FROGS-2.0.0/app/preprocess.py", line 885, in <module> process( args ) File "/home/frogs-metagenomics/FROGS-2.0.0/app/preprocess.py", line 733, in process raise Exception( "Error in sub-process execution." ) Exception: Error in sub-process execution.
ok.
could you please give me the results of:
# if you linked binary dependancies in <FROGS_PATH>/libexec
export PATH=/home/frogs-metagenomics/FROGS-2.0.0/libexec:$PATH
# then
flash --version
The command
export PATH=/home/frogs-metagenomics/FROGS-2.0.0/libexec:$PATH
Doesn't have an output
flash --version
No command 'flash' found, did you mean: Command 'klash' from package 'klash' (universe) Command 'flasm' from package 'flasm' (universe) flash: command not found
I don't know why, even though I did install flash 1.2.11 !
Ok.
Let me know if you encountered other problem after installing Flash.
I just found out that flash wasn't in my $PATH
Here is the output of
flash --version `FLASH v1.2.11 Copyright (C) 2012 Tanja Magoc Copyright (C) 2012, 2013, 2014 Eric Biggers License GPLv3+; GNU GPL version 3 or later http://gnu.org/licenses/gpl.html. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.
Report bugs to flash.comment@gmail.com or https://sourceforge.net/p/flashpage/bugs `
But I'm now having problem with removing chimera when running the command
bash test/test.sh
Step preprocess Thu Feb 15 17:19:45 EST 2018
Step clustering Thu Feb 15 17:21:24 EST 2018
Step remove_chimera Thu Feb 15 17:22:21 EST 2018
Process Process-2:
Traceback (most recent call last):
File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "/home/frogs-metagenomics/FROGS-2.0.0/libexec/parallelChimera.py", line 369, in chimera
chimera_by_sample( sample_names[idx], input_fasta, input_abund, outputs_fasta[idx], outputs_chimera[idx], log_chimera[idx], user_size_separator )
File "/home/frogs-metagenomics/FROGS-2.0.0/libexec/parallelChimera.py", line 411, in chimera_by_sample
submit_cmd( ["vsearch", "--uchime_denovo", tmp_fasta, "--nonchimeras", output_fasta, "--uchimeout", tmp_log], tmp_stdout, tmp_stderr )
File "/home/frogs-metagenomics/FROGS-2.0.0/libexec/parallelChimera.py", line 152, in submit_cmd
p = Popen(cmd, stdout=PIPE, stderr=PIPE)
File "/usr/lib/python2.7/subprocess.py", line 711, in __init__
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Process Process-1:
Traceback (most recent call last):
File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "/home/frogs-metagenomics/FROGS-2.0.0/libexec/parallelChimera.py", line 369, in chimera
chimera_by_sample( sample_names[idx], input_fasta, input_abund, outputs_fasta[idx], outputs_chimera[idx], log_chimera[idx], user_size_separator )
File "/home/frogs-metagenomics/FROGS-2.0.0/libexec/parallelChimera.py", line 411, in chimera_by_sample
submit_cmd( ["vsearch", "--uchime_denovo", tmp_fasta, "--nonchimeras", output_fasta, "--uchimeout", tmp_log], tmp_stdout, tmp_stderr )
File "/home/frogs-metagenomics/FROGS-2.0.0/libexec/parallelChimera.py", line 152, in submit_cmd
p = Popen(cmd, stdout=PIPE, stderr=PIPE)
File "/usr/lib/python2.7/subprocess.py", line 711, in __init__
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Traceback (most recent call last):
File "/home/frogs-metagenomics/FROGS-2.0.0/app/remove_chimera.py", line 212, in <module>
ParallelChimera( args.input_fasta, args.input_biom, args.non_chimera, args.out_abundance, tmp_chimera_summary, "biom", args.nb_cpus, tmp_log, size_separator ).submit( args.log_file )
File "/home/frogs-metagenomics/FROGS-2.0.0/lib/frogsUtils.py", line 140, in submit
subprocess.check_output( self.get_cmd(), shell=True )
File "/usr/lib/python2.7/subprocess.py", line 574, in check_output
raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command 'parallelChimera.py --lenient-filter --nb-cpus 2 --sequences /home/frogs-metagenomics/Out_Test/02-clustering.fasta --biom /home/frogs-metagenomics/Out_Test/02-clustering.biom --non-chimera /home/frogs-metagenomics/Out_Test/03-chimera.fasta --out-abundance /home/frogs-metagenomics/Out_Test/03-chimera.biom --summary /home/frogs-metagenomics/Out_Test/1518733342.04_30118_03-chimera.fasta_summary.tsv --log-file /home/frogs-metagenomics/Out_Test/1518733342.04_30118_03-chimera.fasta_tmp.log' returned non-zero exit status 1
Error in remove_chimera
Good morning,
Could you :
See you later.
feel free to reopen it if you have some troubles
Hello community,
I'm still new to FROGS, and I'm using the command lines version but when I try to run the preprocess command I got an error:
Here is the command:
And here is the output error:
I'm using:
I searched around and it seems that python can't multiprocessing, but I don't really know how to solve this !
PS: I'm not using the Galaxy version because my data is heavier than the allocated memory.
Your feedback is appreciated, thank you.