ssu_finder

[joao1980]

Hi, I am trying to get the 16S sequences from my bins.

Here is the log file. (i replaced my folder names with x).

[2022-11-17 10:00:27] INFO: CheckM v1.1.2
[2022-11-17 10:00:27] INFO: checkm ssu_finder /xxs/A-1-O-60_assembly.fa /x/final_bins/A.1.O.60 /xx/A.1.O.60/ssu_finder -x fa
[2022-11-17 10:00:27] INFO: [CheckM - ssu_finder] Identifying SSU (16S/18S) rRNAs in sequences.
[2022-11-17 10:00:27] INFO: Determining bin assignment of sequences.
[2022-11-17 10:00:32] INFO: Identifying SSU rRNAs on sequences.
[2022-11-17 10:00:32] INFO: Identifying bacterial 16S.
sh: nhmmer: command not found
cat: write error: Broken pipe
[2022-11-17 10:00:32] INFO: Identifying archaeal 16S.
sh: nhmmer: command not found
cat: write error: Broken pipe
[2022-11-17 10:00:32] INFO: Identifying eukaryotic 18S.
sh: nhmmer: command not found
cat: write error: Broken pipe

Unexpected error: <class 'FileNotFoundError'>
Traceback (most recent call last):
File "/gpfs1/data/msb/tools/checkm/new_install/checkm/bin/checkm", line 611, in
checkmParser.parseOptions(args)
File "/gpfs1/data/msb/tools/checkm/new_install/checkm/lib/python3.7/site-packages/checkm/main.py", line 905, in parseOptions
self.ssuFinder(options)
File "/gpfs1/data/msb/tools/checkm/new_install/checkm/lib/python3.7/site-packages/checkm/main.py", line 810, in ssuFinder
ssuFinder.run(options.seq_file, binFiles, options.output_dir, options.evalue, options.concatenate)
File "/gpfs1/data/msb/tools/checkm/new_install/checkm/lib/python3.7/site-packages/checkm/ssuFinder.py", line 213, in run
seqInfo = self.__readHits(os.path.join(outputDir, 'ssu' + '.' + domain + '.txt'), domain, evalueThreshold)
File "/gpfs1/data/msb/tools/checkm/new_install/checkm/lib/python3.7/site-packages/checkm/ssuFinder.py", line 61, in __readHits
for line in open(resultsFile):
FileNotFoundError: [Errno 2] No such file or directory: '/x/final_bins/A.1.O.60/ssu_finder/ssu.archaea.txt'

Any idea why I am getting this error?

Thanks.

[donovan-h-parks]

Hi. Looks like you need to get nhmmer on your system path. This is part of the HMMER package.