I am noticing there are differences in the number of counts reported by the search_otu_table.txt and the combined_count_table.txt. Could you explain why there is a discrepancy between the two tables. I am primarily interested in the number of reads per sample that is detected by the HMM, so which numbers should I go with? I've included the two tables.
I've read earlier there is a way to pass multiple search HMMs into graftm. When I tried using a command like below I get the following logs. To note, the _search.hmms come from different gpkgs. When I try to pass the _align.hmm with the --aln_hmm_file from the gpkgs, the error logs are still the same. How can I successfully get multiple hmms to run?
graftM graft --foward R1.fastq --reverse R2.fastq --search_hmm_files hmm1_search.hmm hmm2_search.hmm --search_only
GraftM 0.15.1
Traceback (most recent call last):
File "/home/robcli/.conda/envs/graftm/bin/graftM", line 420, in
Run(args).main()
File "/home/robcli/.conda/envs/graftm/lib/python3.10/site-packages/graftm/run.py", line 56, in init
self.setattributes(self.args)
File "/home/robcli/.conda/envs/graftm/lib/python3.10/site-packages/graftm/run.py", line 66, in setattributes
self.hk.set_attributes(self.args)
File "/home/robcli/.conda/envs/graftm/lib/python3.10/site-packages/graftm/housekeeping.py", line 204, in set_attributes
raise Exception("Multiple search HMMs specified, but aln_hmm_file not specified")
Exception: Multiple search HMMs specified, but aln_hmm_file not specified
Hello,
I am noticing there are differences in the number of counts reported by the search_otu_table.txt and the combined_count_table.txt. Could you explain why there is a discrepancy between the two tables. I am primarily interested in the number of reads per sample that is detected by the HMM, so which numbers should I go with? I've included the two tables.
search_otu_table.txt combined_count_table.txt
I've read earlier there is a way to pass multiple search HMMs into graftm. When I tried using a command like below I get the following logs. To note, the _search.hmms come from different gpkgs. When I try to pass the _align.hmm with the --aln_hmm_file from the gpkgs, the error logs are still the same. How can I successfully get multiple hmms to run?
graftM graft --foward R1.fastq --reverse R2.fastq --search_hmm_files hmm1_search.hmm hmm2_search.hmm --search_only GraftM 0.15.1 Traceback (most recent call last): File "/home/robcli/.conda/envs/graftm/bin/graftM", line 420, in
Run(args).main()
File "/home/robcli/.conda/envs/graftm/lib/python3.10/site-packages/graftm/run.py", line 56, in init
self.setattributes(self.args)
File "/home/robcli/.conda/envs/graftm/lib/python3.10/site-packages/graftm/run.py", line 66, in setattributes
self.hk.set_attributes(self.args)
File "/home/robcli/.conda/envs/graftm/lib/python3.10/site-packages/graftm/housekeeping.py", line 204, in set_attributes
raise Exception("Multiple search HMMs specified, but aln_hmm_file not specified")
Exception: Multiple search HMMs specified, but aln_hmm_file not specified
Thanks, Robert