problem with medakka polishing

[jhgffhgjf]

every time my instance of NGSspeciesID runs, it will never finish the medakka polishing 2 consensus formed. Saving spoa references to files: 945021|NC_016052.1/consensus_reference_X.fasta running medaka on spoa reference 3 using 18 reads for polishing. creating 945021|NC_016052.1/medaka_cl_id_3 Traceback (most recent call last): File "/home/marc/anaconda3/envs/ngspeciesid/bin/NGSpeciesID", line 294, in main(args) File "/home/marc/anaconda3/envs/ngspeciesid/bin/NGSpeciesID", line 145, in main centers_polished = consensus.polish_sequences(centers_filtered, args) File "/home/marc/anaconda3/envs/ngspeciesid/lib/python3.6/site-packages/modules/consensus.py", line 224, in polish_sequences run_medaka(all_reads_file, spoa_center_file, polishing_outfolder, "1", args.medaka_model) File "/home/marc/anaconda3/envs/ngspeciesid/lib/python3.6/site-packages/modules/consensus.py", line 109, in run_medaka subprocess.check_call(['medaka_consensus', '-i', reads_to_center, "-d", center_file, "-o", outfolder, "-t", cores], stdout=output_file, stderr=medaka_stderr) File "/home/marc/anaconda3/envs/ngspeciesid/lib/python3.6/subprocess.py", line 311, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['medaka_consensus', '-i', '945021|NC_016052.1/reads_to_consensus_3.fastq', '-d', '945021|NC_016052.1/consensus_reference_3.fasta', '-o', '945021|NC_016052.1/medaka_cl_id_3', '-t', '1']' returned non-zero exit status 1.

I did notice in your other thread about the medakka problems that in the last line there is a difference in this part: raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['medaka_consensus', '-i', '945021|NC_016052.1/reads_to_consensus_3.fastq', '-d', '945021|NC_016052.1/consensus_reference_3.fasta', '-o', '945021|NC_016052.1/medaka_cl_id_3', '-t', '1']' returned non-zero exit status 1.

whilst in a past thread of yours: subprocess.CalledProcessError: Command '['medaka_consensus', '-i', './ngspouts_liverbiduck/reads_to_consensus_1.fasta', '-d', './ngspouts_liverbiduck/consensus_reference_1.fasta', '-o', './ngspouts_liverbiduck/medaka_cl_id_1', '-t', '1', '-m', 'r941_min_high_g330']' returned non-zero exit status 1.

the "-m', 'r941_min_high_g330']'" part is missing, but i have no idea if this is normal or not.

Thanks in advance! -Marc

[ksahlin]

Hi @jhgffhgjf ,

Could you please run

medaka_consensus -i 945021|NC_016052.1/reads_to_consensus_3.fastq -d 945021|NC_016052.1/consensus_reference_3.fasta -o 945021|NC_016052.1/medaka_cl_id_3 -t 1

directly from the terminal to identify whether the error is something with installation or input?

As you may know, you may also rpecify --racon instead of --medaka to use a different polishing algorithm.

[mtva0001]

Hi,

I have the same issue specifying medaka (1.5.0): NGSpeciesID --ont --fastq sample_h1.fastq --outfolder ./sample_h1 --consensus --medaka Error: Saving spoa references to files: ./sample_h1/consensus_reference_X.fasta running medaka on spoa reference 17 using 256 reads for polishing. creating ./sample_h1/medaka_cl_id_17 Traceback (most recent call last): File "/opt/anaconda3/envs/NGSpeciesID/bin/NGSpeciesID", line 291, in <module> main(args) File "/opt/anaconda3/envs/NGSpeciesID/bin/NGSpeciesID", line 142, in main centers_polished = consensus.polish_sequences(centers_filtered, args) File "/opt/anaconda3/envs/NGSpeciesID/lib/python3.6/site-packages/modules/consensus.py", line 224, in polish_sequences run_medaka(all_reads_file, spoa_center_file, polishing_outfolder, "1", args.medaka_model) File "/opt/anaconda3/envs/NGSpeciesID/lib/python3.6/site-packages/modules/consensus.py", line 109, in run_medaka subprocess.check_call(['medaka_consensus', '-i', reads_to_center, "-d", center_file, "-o", outfolder, "-t", cores], stdout=output_file, stderr=medaka_stderr) File "/opt/anaconda3/envs/NGSpeciesID/lib/python3.6/subprocess.py", line 311, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['medaka_consensus', '-i', './sample_h1/reads_to_consensus_17.fastq', '-d', './sample_h1/consensus_reference_17.fasta', '-o', './sample_h1/medaka_cl_id_17', '-t', '1']' returned non-zero exit status 1.

I tried to run the above-mentioned command: medaka_consensus -i ./sample_h1/reads_to_consensus_17.fastq -d ./sample_h1/consensus_reference_17.fasta -o ./sample_h1/medaka_cl_id_17 -t 1

and I got this: readlink: illegal option -- f usage: readlink [-n] [file ...]

I'd prefer to use medaka for my new experiment, but don't know how I could make it work. Do you have any new idea? I attach the list of packages installed.

Thanks for your response in advance! Best, Máté

condalist.txt

[ksahlin]

Hi @mtva0001 ,

This error is discussed in this comment https://github.com/ksahlin/NGSpeciesID/issues/1#issuecomment-605871762 (older medaka version), and the solution is presented in the same post (or in the post after by another user).

Best, Kristoffer

[mtva0001]

I re-installed NGSpeciesID following: https://github.com/ksahlin/NGSpeciesID/issues/1#issuecomment-644698902 So the medaka version is 1.0.3 right now, and I got this error message: Saving spoa references to files: ./sample_h1/consensus_reference_X.fasta running medaka on spoa reference 17 using 256 reads for polishing. creating ./sample_h1/medaka_cl_id_17 Traceback (most recent call last): File "/opt/anaconda3/envs/ngspeciesid/bin/NGSpeciesID", line 294, in <module> main(args) File "/opt/anaconda3/envs/ngspeciesid/bin/NGSpeciesID", line 145, in main centers_polished = consensus.polish_sequences(centers_filtered, args) File "/opt/anaconda3/envs/ngspeciesid/lib/python3.6/site-packages/modules/consensus.py", line 224, in polish_sequences run_medaka(all_reads_file, spoa_center_file, polishing_outfolder, "1", args.medaka_model) File "/opt/anaconda3/envs/ngspeciesid/lib/python3.6/site-packages/modules/consensus.py", line 109, in run_medaka subprocess.check_call(['medaka_consensus', '-i', reads_to_center, "-d", center_file, "-o", outfolder, "-t", cores], stdout=output_file, stderr=medaka_stderr) File "/opt/anaconda3/envs/ngspeciesid/lib/python3.6/subprocess.py", line 311, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['medaka_consensus', '-i', './sample_h1/reads_to_consensus_17.fastq', '-d', './sample_h1/consensus_reference_17.fasta', '-o', './sample_h1/medaka_cl_id_17', '-t', '1']' returned non-zero exit status 2.

And after running medaka (medaka_consensus -i ./sample_h1/reads_to_consensus_17.fastq -d ./sample_h1/consensus_reference_17.fasta -o ./sample_h1/medaka_cl_id_17 -t 1):

/opt/anaconda3/envs/ngspeciesid/bin/medaka_consensus: line 16: 91633 Illegal instruction: 4 medaka tools list_models Checking program versions This is medaka 1.0.3 Program Version Required Pass bcftools 1.10.2 1.9 True bgzip 1.10.2 1.9 True minimap2 2.24 2.11 True samtools 1.10 1.9 True tabix 1.10.2 1.9 True Warning: Output ./sample_h1/medaka_cl_id_17 already exists, may use old results. usage: medaka tools is_rle_model [-h] [--model MODEL] [--disable_cudnn] medaka tools is_rle_model: error: argument --model: expected 1 argument

[mtva0001]

Ah okay, now I specified the model: -m r941_min_high_g330. It seems working. But could it be specified somehow already in the NGSpeciesID run?

[ksahlin]

Great, thanks for reporting back. Yes, that sounds reasonable - will do.

[mtva0001]

Oh no, I was wrong, it didn't work: /opt/anaconda3/envs/ngspeciesid/bin/medaka_consensus: line 16: 93427 Illegal instruction: 4 medaka tools list_models There's some issues with the model but I couldn't figure out how to get a list of models because the command suggested on the medaka site does not work either (medaka tools list_models). Also, they have medaka 1.6.x now, so would be great to use the newest version in NGSpeciesID, if it is possible.

[jhgffhgjf]

I resolved the issue by making sure the path to the working directory did not contain any spaces or symbols. Rookie ubuntu user mistake ;)

On Wed, Aug 10, 2022 at 11:10 AM mtva0001 @.***> wrote:

Oh no, I was wrong, it didn't work: /opt/anaconda3/envs/ngspeciesid/bin/medaka_consensus: line 16: 93427 Illegal instruction: 4 medaka tools list_models There's some issues with the model but I couldn't figure out how to get a list of models because the command suggested on the medaka site does not work either (medaka tools list_models). Also, they have medaka 1.6.x now, so would be great to use the newest version in NGSpeciesID, if it is possible.

— Reply to this email directly, view it on GitHub https://github.com/ksahlin/NGSpeciesID/issues/21#issuecomment-1210387302, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFQ7357T4X4TDFRYVWEIQY3VYNWYTANCNFSM5UC4BGFQ . You are receiving this because you were mentioned.Message ID: @.***>

[ksahlin]

I googled "line 16: 93427 Illegal instruction: 4 medaka tools list_models" and I found this issue https://github.com/nanoporetech/medaka/issues/261 and this https://github.com/nanoporetech/medaka/issues/119

The first issue is even for medaka through NGSpeciesID. Perhaps they are relevant?

[mtva0001]

Thanks! Yes, I saw all these comments and tried to install medaka in many different ways but did not fix the problem. I tried running the test fastq file on our server (HPC2N) since the NGSpeciesID (v.0.1.2.2) is installed there, but medaka produces the same error there, too. :(