Open fletchec99 opened 5 years ago
wwood
commented
5 years ago Hi,
It looks like you are specifying the path to the refpkg, not the gpkg (the refpkg lives inside the gpkg folder). How did you run graftM create? Ben Woodcroft DECRA Recipient & Post-doctoral Research Fellow Australian Centre for Ecogenomics, UQ (https://maps.google.com/?q=Australian%20Centre%20for%20Ecogenomics%2C%20UQ) http://www.ecogenomic.org
fletchec99
commented
5 years ago Hi Dr. Woodcroft,
Thank you very much for your quick response! Unfortunately, the graftM create command did not return a gpkg, just a refpkg, which itself is a folder. To run graftM create, I extracted the sequences and taxonomies for my gene of interest from some metagenomic and metatranscriptomic assemblies available in my lab, making sure they were in the correct format, and also specified an extant HMM. Do you think it possible that graftM create did not work? Thank you for any clarification here, and please let me know if I can provide you with more information.
Best, Colette
-- Colette Fletcher Hoppe Vassar College Class of 2015 c.fletcher.hoppe@gmail.com
wwood
commented
5 years ago Hi, GraftM create is supposed to generate gpkgs including refpkgs. It is hard to know what is happening though without the command line you used or the output from create. Would you mind sending that, or otherwise try it again? Thanks, ben
fletchec99
commented
5 years ago Hello again Dr. Woodcroft,
I subsampled my input fasta and taxonomy files, taking sequences from the top 100 taxonomies. Please find the input files attached. I ran GraftM create again on the sub-sampled files, as below: [image: image.png]
The output I got did not include a gpkg, just a refpkg, as shown below: [image: image.png] Thanks for any insights as to what is going on here.
Best, Colette
On Sat, Mar 16, 2019 at 2:20 PM Ben J Woodcroft notifications@github.com wrote:
Hi, GraftM create is supposed to generate gpkgs including refpkgs. It is hard to know what is happening though without the command line you used or the output from create. Would you mind sending that, or otherwise try it again? Thanks, ben
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/geronimp/graftM/issues/259#issuecomment-473593710, or mute the thread https://github.com/notifications/unsubscribe-auth/AoIUBZcmIwRphxPUMQcQLfGz1Du60N2Nks5vXWAKgaJpZM4b1fqU .
-- Colette Fletcher Hoppe Vassar College Class of 2015 c.fletcher.hoppe@gmail.com
NODE_320420_length_511_cov_0.591146 dBacteria; punknown; cunknown; ounknown; funknown; gunknown; suncultured bacterium
NODE_4821_length_2897_cov_1.650181 dBacteria; pCyanobacteria; cunknown; oSynechococcales; fSynechococcaceae; gSynechococcus; s__uncultured marine type-A Synechococcus 4O4
NODE_42246_length_1070_cov_1.477200 dBacteria; pProteobacteria; cAlphaproteobacteria; oRhizobiales; fMethylobacteriaceae; gMethylobacterium; sMethylobacterium oryzae
NODE_65319_length_896_cov_0.384915 dBacteria; pProteobacteria; cAlphaproteobacteria; oRhizobiales; fMethylobacteriaceae; gMethylobacterium; sMethylobacterium aquaticum
NODE_147685_length_663_cov_1.444030 dBacteria; pProteobacteria; cAlphaproteobacteria; oRhodobacterales; fRhodobacteraceae; gRhodovulum; s__Rhodovulum sulfidophilum
NODE_323094_length_510_cov_0.271540 dBacteria; pProteobacteria; cAlphaproteobacteria; oRhodobacterales; fRhodobacteraceae; gRhodobacter; sRhodobacter sphaeroides
NODE_310388_length_517_cov_0.158974 dBacteria; pCyanobacteria; cunknown; oSynechococcales; fSynechococcaceae; gSynechococcus; suncultured marine type-A Synechococcus 4O4
NODE_1095489_length_338_cov_0.909953 dBacteria; pProteobacteria; cAlphaproteobacteria; oRhodobacterales; fRhodobacteraceae; gRhodobacter; s__Rhodobacter sphaeroides
NODE_917699_length_360_cov_0.515021 dBacteria; pProteobacteria; cAlphaproteobacteria; oRhizobiales; fMethylobacteriaceae; gMethylobacterium; sMethylobacterium aquaticum
NODE_1313581_length_317_cov_0.042105 dBacteria; pProteobacteria; cAlphaproteobacteria; oRhizobiales; fMethylobacteriaceae; gMethylobacterium; sMethylobacterium aquaticum
NODE_17679_length_1577_cov_1.000000 dBacteria; pActinobacteria
wwood
commented
5 years ago Hi, I don't think your images are coming through, perhaps because they are being filtered through GitHub issues. Would you mind copying the text or finding a way to send images? Feel free to email me directly if that helps. ben
fletchec99
commented
5 years ago Hi again,
The first image shows the GraftM command I ran, copied below: graftM create --sequences 100seqs_sequences.fasta --taxonomy 100seqs_taxonomy.txt --hmm TIGR01287.HMM --output custom_graftM_package_100seqs
The second image shows the output of the command (“ls custom_graftM_package_100seqs”); I included it to demonstrate that the output included a .refpkg folder, and no gpkg folder. Please let me know if I can provide more information.
Best, Colette
On Mar 18, 2019, at 2:54 PM, Ben J Woodcroft notifications@github.com wrote:
Hi, I don't think your images are coming through, perhaps because they are being filtered through GitHub issues. Would you mind copying the text or finding a way to send images? Feel free to email me directly if that helps. ben
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/geronimp/graftM/issues/259#issuecomment-474116576, or mute the thread https://github.com/notifications/unsubscribe-auth/AoIUBQdDXWK0Na9-y7hcounGpNOkq_5yks5vYAsfgaJpZM4b1fqU.
wwood
commented
5 years ago Oh I see.
When you specify --output that's specifying the gpkg. So conventionally, you'd specify e.g. --output custom_graftM_package_100seqs.gpkg but there's there's nothing in GraftM that requires the output to end in .gpkg. So, maybe you'd run mv custom_graftM_package_100seqs custom_graftM_package_100seqs.gpkg and then specify that gpkg to graftM graft. Let me know if that doesn't work out. ben
fletchec99
commented
5 years ago Hi Dr. Woodcroft,
Thank you for the clarification! I did rename the custom package, and tried running GraftM graft, just as you suggested. However, I got the following error message:
graftM: error: unrecognized arguments: --graftM_package custom_graftM_package_100seqs.gpkg/
It seems GraftM graft does not recognize the custom package. Do you have any further suggestions? Can I provide you with more information about this issue? Thanks for any clarification you can offer!
Best, Colette
On Mar 18, 2019, at 3:10 PM, Ben J Woodcroft notifications@github.com wrote:
Oh I see.
When you specify --output that's specifying the gpkg. So conventionally, you'd specify e.g. --output custom_graftM_package_100seqs.gpkg but there's there's nothing in GraftM that requires the output to end in .gpkg. So, maybe you'd run mv custom_graftM_package_100seqs custom_graftM_package_100seqs.gpkg and then specify that gpkg to graftM graft. Let me know if that doesn't work out. ben — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/geronimp/graftM/issues/259#issuecomment-474121089, or mute the thread https://github.com/notifications/unsubscribe-auth/AoIUBXnOBqZsSVo4fwzfTx84uEZtpkDqks5vYA7dgaJpZM4b1fqU.
wwood
commented
5 years ago GraftM is not recognizing the option, rather than the package --graftM_package should be --graftm_package
fletchec99
commented
5 years ago Hi Dr. Woodcroft,
GraftM graft is now working with my custom package. Thank you for your patience and help with my question!
Best, Colette
On Mar 18, 2019, at 5:32 PM, Ben J Woodcroft notifications@github.com wrote:
GraftM is not recognizing the option, rather than the package --graftM_package should be --graftm_package — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/geronimp/graftM/issues/259#issuecomment-474152803, or mute the thread https://github.com/notifications/unsubscribe-auth/AoIUBY7TE_uEzTdYyZigwaTL0LVqdxOwks5vYDAvgaJpZM4b1fqU.
Hello! I have created a new GraftM package using "graftM create;" I followed the sample protocol on the Wiki to do so. I am now trying to run "graftM graft" using my output package. I keep getting the following error message: KeyError: "graftm_package_version"
Here is the error message in full:
graftM graft --forward 01_input_fastq/JUL-2009_repaired_1.fastq.gz --reverse 01_input_fastq/JUL-2009_repaired_2.fastq.gz --graftm_package /db/graftm/7/7.60.marine_nifH_graftM.refpkg --threads 30 --evalue 1e-5 --search_method hmmsearch --assignment_method pplacer --log 02_graftM_results/JUL-2009_repaired_graftM.log --force --output_directory 02_graftM_results/JUL-2009_repaired
Traceback (most recent call last): File "/opt/conda/bin/graftM", line 411, in
Run(args).main()
File "/opt/conda/lib/python2.7/site-packages/graftm/run.py", line 56, in init
self.setattributes(self.args)
File "/opt/conda/lib/python2.7/site-packages/graftm/run.py", line 66, in setattributes
self.hk.set_attributes(self.args)
File "/opt/conda/lib/python2.7/site-packages/graftm/housekeeping.py", line 163, in set_attributes
gpkg = GraftMPackage.acquire(args.graftm_package)
File "/opt/conda/lib/python2.7/site-packages/graftm/graftm_package.py", line 78, in acquire
v=contents_hash[GraftMPackage.VERSION_KEY]
KeyError: 'graftm_package_version'
Any suggestions would be greatly appreciated!