RefineM
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donovan-h-parks
ssu_erroneous issue
Hi Donovan,
Am having an issue with the ssu_erroneous command. The output is given below. What seems o be the issue here? $ refinem ssu_erroneous -x fasta metagenome_test/ taxon_profile_output/ gtdb_r80_ssu_db.2018-01-18.fna/ gtdb_r95_taxonomy.2020-07-30.tsv/ ssu_output [2021-09-28 15:15:07] INFO: RefineM v0.1.2 [2021-09-28 15:15:07] INFO: refinem ssu_erroneous -x fasta /mnt/disk2/xbb/metagenome_test /mnt/disk2/xbb/jibowen/TD/yuanshitaxon_profile_output /mnt/disk2/xbb/RefineM_db/gtdb_r80_ssu_db.2018-01-18.fna /mnt/disk2/xbb/RefineM_db/gtdb_r95_taxonomy.2020-07-30.tsv /mnt/disk2/xbb/jibowen/TD/yuanshissu_output [2021-09-28 15:15:07] INFO: Identifying SSU rRNA genes. [2021-09-28 15:26:18] INFO: Extracting SSU rRNA genes. [2021-09-28 15:26:21] INFO: Classifying SSU rRNA genes. Warning: [blastn] Examining 5 or more matches is recommended Warning: [blastn] Examining 5 or more matches is recommended Warning: [blastn] Examining 5 or more matches is recommended Warning: [blastn] Examining 5 or more matches is recommended
Unexpected error: <class 'KeyError'>
Traceback (most recent call last):
File "/usr/local/bin/refinem", line 398, in
Thanks!
Unfortunately, I no longer have time to continue support for RefineM. GUNC https://github.com/grp-bork/gunc or MAGpurify https://github.com/snayfach/MAGpurify may meet your needs.
On Tue, Sep 28, 2021 at 2:24 AM Bowenji147 @.***> wrote:
Hi Donovan,
Am having an issue with the ssu_erroneous command. The output is given below. What seems o be the issue here? $ refinem ssu_erroneous -x fasta metagenome_test/ taxon_profile_output/ gtdb_r80_ssu_db.2018-01-18.fna/ gtdb_r95_taxonomy.2020-07-30.tsv/ ssu_output [2021-09-28 15:15:07] INFO: RefineM v0.1.2 [2021-09-28 15:15:07] INFO: refinem ssu_erroneous -x fasta /mnt/disk2/xbb/metagenome_test /mnt/disk2/xbb/jibowen/TD/yuanshitaxon_profile_output /mnt/disk2/xbb/RefineM_db/gtdb_r80_ssu_db.2018-01-18.fna /mnt/disk2/xbb/RefineM_db/gtdb_r95_taxonomy.2020-07-30.tsv /mnt/disk2/xbb/jibowen/TD/yuanshissu_output [2021-09-28 15:15:07] INFO: Identifying SSU rRNA genes. [2021-09-28 15:26:18] INFO: Extracting SSU rRNA genes. [2021-09-28 15:26:21] INFO: Classifying SSU rRNA genes. Warning: [blastn] Examining 5 or more matches is recommended Warning: [blastn] Examining 5 or more matches is recommended Warning: [blastn] Examining 5 or more matches is recommended Warning: [blastn] Examining 5 or more matches is recommended
Unexpected error: <class 'KeyError'> Traceback (most recent call last): File "/usr/local/bin/refinem", line 398, in parser.parse_options(args) File "/usr/local/lib/python3.6/dist-packages/refinem/main.py", line 687, in parse_options self.ssu_erroneous(options) File "/usr/local/lib/python3.6/dist-packages/refinem/main.py", line 318, in ssu_erroneous ssu_classifications = ssu.classify(ssu_seq_files, options.ssu_db, options.ssu_taxonomy_file, options.evalue, options.output_dir) File "/usr/local/lib/python3.6/dist-packages/refinem/ssu.py", line 419, in classify taxonomy_str = ';'.join(taxonomy[subject_id]) KeyError: 'RS_GCF_000808615.1'
Thanks!
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