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Ecogenomics / CheckM

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
https://ecogenomics.github.io/CheckM/
GNU General Public License v3.0
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checkm ssu_finder #384

Closed mehmetdayi closed 4 months ago

mehmetdayi commented 10 months ago

Dear all,

I am trying to run ssu_finder as below, and errors occurred. Any idea?

checkm ssu_finder -x fa 36_Inf3_11dpi_metasapdes.metagenome.assembly.fasta

36_Inf3_11dpi_metasapdes.metagenome.assembly.fasta.metabat-bins ssu_finder [2024-01-10 15:30:59] INFO: CheckM v1.2.2 [2024-01-10 15:30:59] INFO: checkm ssu_finder -x fa 36_Inf3_11dpi_metasapdes.metagenome.assembly.fasta 36_Inf3_11dpi_metasapdes.metagenome.assembly.fasta.metabat-bins ssu_finder [2024-01-10 15:30:59] INFO: CheckM data: /home/mdayi/.checkm [2024-01-10 15:30:59] INFO: [CheckM - ssu_finder] Identifying SSU (16S/18S) rRNAs in sequences. [2024-01-10 15:31:14] INFO: Determining bin assignment of sequences. [2024-01-10 15:31:39] INFO: Identifying SSU rRNAs on sequences. [2024-01-10 15:31:39] INFO: Identifying bacterial 16S.

Error: File existence/permissions problem in trying to open query file /home/mdayi/.checkm/hmms_ssu/SSU_bacteria.hmm. HMM file /home/mdayi/.checkm/hmms_ssu/SSU_bacteria.hmm not found (nor an .h3m binary of it)

cat: write error: Broken pipe [2024-01-10 15:31:39] INFO: Identifying archaeal 16S.

Error: File existence/permissions problem in trying to open query file /home/mdayi/.checkm/hmms_ssu/SSU_archaea.hmm. HMM file /home/mdayi/.checkm/hmms_ssu/SSU_archaea.hmm not found (nor an .h3m binary of it)

cat: write error: Broken pipe [2024-01-10 15:31:39] INFO: Identifying eukaryotic 18S.

Error: File existence/permissions problem in trying to open query file /home/mdayi/.checkm/hmms_ssu/SSU_euk.hmm. HMM file /home/mdayi/.checkm/hmms_ssu/SSU_euk.hmm not found (nor an .h3m binary of it)

cat: write error: Broken pipe

Unexpected error: <class 'FileNotFoundError'> Traceback (most recent call last): File "/home/mdayi/Miniconda3/envs/checkm/bin/checkm", line 856, in checkmParser.parseOptions(args) File "/home/mdayi/Miniconda3/envs/checkm/lib/python3.9/site-packages/checkm/main.py", line 1027, in parseOptions self.ssuFinder(options) File "/home/mdayi/Miniconda3/envs/checkm/lib/python3.9/site-packages/checkm/main.py", line 928, in ssuFinder ssuFinder.run(options.seq_file, binFiles, options.output_dir, File "/home/mdayi/Miniconda3/envs/checkm/lib/python3.9/site-packages/checkm/ssuFinder.py", line 213, in run seqInfo = self._readHits(os.path.join(outputDir, 'ssu' + '.' + domain + '.txt'), domain, evalueThreshold) File "/home/mdayi/Miniconda3/envs/checkm/lib/python3.9/site-packages/checkm/ssuFinder.py", line 61, in _readHits for line in open(resultsFile): FileNotFoundError: [Errno 2] No such file or directory: 'ssu_finder/ssu.archaea.txt'

mehmetdayi commented 10 months ago

Sorry for mistyping command. The corrected one is below:

checkm ssu_finder -x fa 36_Inf3_11dpi_metasapdes.metagenome.assembly.fasta 36_Inf3_11dpi_metasapdes.metagenome.assembly.fasta.metabat-bins ssu_finder

mehmetdayi commented 10 months ago

I figured it out. All we need is to locate necessary directories (Error: File existence/permissions problem in trying to open query ) where checkm seeks.