When I try to execute mt-classifier.py -h I get this error.
Traceback (most recent call last):
File "/data/common_scripts/mtoolbox/MToolBox_v0.2/mt-classifier.py", line 5, in <module>
from bioinf.seqs import SeqList
File "/data/common_scripts/mtoolbox/MToolBox_v0.2/bioinf/seqs.py", line 25, in <module>
from files import write_funcs, load_funcs, check_funcs, file_types, plugins
File "/data/common_scripts/mtoolbox/MToolBox_v0.2/bioinf/files/init.py", line 43, in <module>
file_types[plugin] = getattr(mod, 'FILETYPE')
AttributeError: 'module' object has no attribute 'FILETYPE'
Has anyone else encountered this problem?
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
this is Domenico, one of the software developers. In order to better understand your issue, could you please post here the output of the following command?
ls -al /data/common_scripts/mtoolbox/MToolBox_v0.2/bioinf/files/
Thanks for using our tool
Domenico
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
OK. Those hidden files (the ones like .fasta.py) were accidentally
included in the package and they bother the module loading occurring during
the execution of the mt-classifier.py script. For your convenience, please
use the command rm .* to remove these hidden files from all package
subfolders. This should avoid the error.
OK. Those hidden files (the ones like .fasta.py) were accidentally included in the package and they bother the module loading occurring during the execution of the mt-classifier.py script. For your convenience, please use the command rm .* to remove these hidden files from all package subfolders. This should avoid the error.
Please let me know if you need further help.
Best regards
Last edit: Domenico Simone 2014-10-27
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I ran into the same issue and tried removing all the .* files from the package subfolders (basically removed all the hidden files from all the folders inside MToolBox/0.3). After doing this when I re-run MToolBox I am getting this error:
PREDICTING HAPLOGROUPS AND ANNOTATING/PRIORITIZING VARIANTS...
Haplogroup predictions based on RSRS Phylotree build 16
Your best results file is mt_classification_best_results.csv
Loading contig sequences from file LCM0001SE-contigs.fasta
Traceback (most recent call last):
File "/home/ssekar/MToolBox/0.3/mt-classifier.py", line 327, in <module>
main_mt_hpred()
File "/home/ssekar/MToolBox/0.3/mt-classifier.py", line 250, in main_mt_hpred
contig_array = load_sequences(contig_file)
File "/home/ssekar/MToolBox/0.3/mt-classifier.py", line 195, in load_sequences
a.load_file(fname)
File "/home/ssekar/MToolBox/0.3/bioinf/seqs.py", line 457, in load_file
super(SeqList, self).load_file(fname, self.add_seq)
File "/home/ssekar/MToolBox/0.3/bioinf/seqs.py", line 350, in load_file
raise TypeError("non e' stato possibile determinare il formato del file")
TypeError: non e' stato possibile determinare il formato del file
Not quite sure I understand what the error message means. Would really appreciate some help with this! This is the command I ran:
MToolBox.sh -i bam -p /scratch/ssekar/Mito/MToolbox_results/LCM0001SE.bam -a "-r /scratch/ssekar/Mito/Reference/ -s /packages/samtools/0.1.19/samtools"
Thanks in advance!
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
thanks for using our tool and for writing us to ask our help.
Could you please double check your file consistency with fasta format?
Apparently the pipeline does not recognize it as fasta.
Please note that I'm cc'ing this mail to our official support forum, ie the
MToolBox googlegroup. I kindly ask you to reply there.
I ran into the same issue and tried removing all the .* files from the
package subfolders (basically removed all the hidden files from all the
folders inside MToolBox/0.3). After doing this when I re-run MToolBox I am
getting this error:
PREDICTING HAPLOGROUPS AND ANNOTATING/PRIORITIZING VARIANTS...
Haplogroup predictions based on RSRS Phylotree build 16
Your best results file is mt_classification_best_results.csv
Loading contig sequences from file LCM0001SE-contigs.fasta
Traceback (most recent call last):
File "/home/ssekar/MToolBox/0.3/mt-classifier.py", line 327, in <module>
main_mt_hpred()
File "/home/ssekar/MToolBox/0.3/mt-classifier.py", line 250, in
main_mt_hpred
contig_array = load_sequences(contig_file)
File "/home/ssekar/MToolBox/0.3/mt-classifier.py", line 195, in
load_sequences
a.load_file(fname)
File "/home/ssekar/MToolBox/0.3/bioinf/seqs.py", line 457, in load_file
super(SeqList, self).load_file(fname, self.add_seq)
File "/home/ssekar/MToolBox/0.3/bioinf/seqs.py", line 350, in load_file
raise TypeError("non e' stato possibile determinare il formato del file")
TypeError: non e' stato possibile determinare il formato del file
Not quite sure I understand what the error message means. Would really
appreciate some help with this! This is the command I ran:
MToolBox.sh -i bam -p /scratch/ssekar/Mito/MToolbox_results/LCM0001SE.bam
-a "-r /scratch/ssekar/Mito/Reference/ -s
/packages/samtools/0.1.19/samtools"
--
Domenico Simone, PhD
Computational Biology Institute - The George Washington University
Innovation Hall, 45085 University Drive, Suite 305
Ashburn, VA 20147, US
When I try to execute mt-classifier.py -h I get this error.
Traceback (most recent call last):
File "/data/common_scripts/mtoolbox/MToolBox_v0.2/mt-classifier.py", line 5, in <module>
from bioinf.seqs import SeqList
File "/data/common_scripts/mtoolbox/MToolBox_v0.2/bioinf/seqs.py", line 25, in <module>
from files import write_funcs, load_funcs, check_funcs, file_types, plugins
File "/data/common_scripts/mtoolbox/MToolBox_v0.2/bioinf/files/init.py", line 43, in <module>
file_types[plugin] = getattr(mod, 'FILETYPE')
AttributeError: 'module' object has no attribute 'FILETYPE'
Has anyone else encountered this problem?
Dear Tom,
this is Domenico, one of the software developers. In order to better understand your issue, could you please post here the output of the following command?
ls -al /data/common_scripts/mtoolbox/MToolBox_v0.2/bioinf/files/
Thanks for using our tool
Domenico
Output=
total 60
drwxr-xr-x 2 sander users 4096 okt 20 13:44 .
drwxr-xr-x 3 sander users 4096 okt 20 13:44 ..
-rwxr-xr-x 1 sander users 197 mei 30 17:03 ._fasta.py
-rwxr-xr-x 1 sander users 4213 mei 30 17:03 fasta.py
-rwxr-xr-x 1 sander users 197 mei 30 17:03 ._genedoc.py
-rwxr-xr-x 1 sander users 2311 mei 30 17:03 genedoc.py
-rwxr-xr-x 1 sander users 1252 mei 30 17:03 init.py
-rwxr-xr-x 1 sander users 197 mei 30 17:03 ._init.py
-rwxr-xr-x 1 sander users 197 mei 30 17:03 ._ncbi_flat.py
-rwxr-xr-x 1 sander users 9288 mei 30 17:03 ncbi_flat.py
-rwxr-xr-x 1 sander users 197 mei 30 17:03 ._phylip.py
-rwxr-xr-x 1 sander users 2549 mei 30 17:03 phylip.py
OK. Those hidden files (the ones like .fasta.py) were accidentally
included in the package and they bother the module loading occurring during
the execution of the mt-classifier.py script. For your convenience, please
use the command rm .* to remove these hidden files from all package
subfolders. This should avoid the error.
Please let me know if you need further help.
Best regards
2014-10-27 11:31 GMT+01:00 Tom Brumby yorkietom@users.sf.net:
--
Domenico Simone, PhD
Istituto di Biomembrane e Bioenergetica (IBBE), CNR - Bari
Dipartimento di Bioscienze, Università degli Studi di Milano - Milano
Skype: berliner_08
OK. Those hidden files (the ones like .fasta.py) were accidentally included in the package and they bother the module loading occurring during the execution of the mt-classifier.py script. For your convenience, please use the command rm .* to remove these hidden files from all package subfolders. This should avoid the error.
Please let me know if you need further help.
Best regards
Last edit: Domenico Simone 2014-10-27
That has cleared up the issue, cheers.
I am glad to hear this. We'll fix the problem in the next release.
Thank you again for using our tool, please don't hesitate to contact us if you need further help.
Cheers
Hi,
I ran into the same issue and tried removing all the .* files from the package subfolders (basically removed all the hidden files from all the folders inside MToolBox/0.3). After doing this when I re-run MToolBox I am getting this error:
PREDICTING HAPLOGROUPS AND ANNOTATING/PRIORITIZING VARIANTS...
Haplogroup predictions based on RSRS Phylotree build 16
Your best results file is mt_classification_best_results.csv
Loading contig sequences from file LCM0001SE-contigs.fasta
Traceback (most recent call last):
File "/home/ssekar/MToolBox/0.3/mt-classifier.py", line 327, in <module>
main_mt_hpred()
File "/home/ssekar/MToolBox/0.3/mt-classifier.py", line 250, in main_mt_hpred
contig_array = load_sequences(contig_file)
File "/home/ssekar/MToolBox/0.3/mt-classifier.py", line 195, in load_sequences
a.load_file(fname)
File "/home/ssekar/MToolBox/0.3/bioinf/seqs.py", line 457, in load_file
super(SeqList, self).load_file(fname, self.add_seq)
File "/home/ssekar/MToolBox/0.3/bioinf/seqs.py", line 350, in load_file
raise TypeError("non e' stato possibile determinare il formato del file")
TypeError: non e' stato possibile determinare il formato del file
Not quite sure I understand what the error message means. Would really appreciate some help with this! This is the command I ran:
MToolBox.sh -i bam -p /scratch/ssekar/Mito/MToolbox_results/LCM0001SE.bam -a "-r /scratch/ssekar/Mito/Reference/ -s /packages/samtools/0.1.19/samtools"
Thanks in advance!
Dear Shobana,
thanks for using our tool and for writing us to ask our help.
Could you please double check your file consistency with fasta format?
Apparently the pipeline does not recognize it as fasta.
Please note that I'm cc'ing this mail to our official support forum, ie the
MToolBox googlegroup. I kindly ask you to reply there.
Best,
Domenico
2015-04-06 23:22 GMT-04:00 Shobana shobus88@users.sf.net:
--
Domenico Simone, PhD
Computational Biology Institute - The George Washington University
Innovation Hall, 45085 University Drive, Suite 305
Ashburn, VA 20147, US
Skype: berliner_08