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CSB5 / OPERA-MS

OPERA-MS - Hybrid Metagenomic Assembler
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Reference clustering - Nucmer error #63

Open niexiaoqing opened 3 years ago

niexiaoqing commented 3 years ago

image

jsgounot commented 3 years ago

Hi,

thanks for using Opera-MS. Are you able to access the file with a terminal ?

Regards, jsgounot

niexiaoqing commented 3 years ago

Hi,

thanks for using Opera-MS. Are you able to access the file with a terminal ?

Regards, jsgounot

no，nothing find in the dir

Unaimend commented 3 years ago

I have the same problem. But its seems that I am able to open the file with for example vim, but its not in temp folder but instead in the NUCMER_OUT folder.

/scratch/SlurmTMP/sukem127.2123121/OPERA-MS/scratch/SlurmTMP/sukem127.2123121/RESULTS/intermediate_files/reference_clustering/NUCMER_OUT/temp_genome/119591-vs-121716_0.fa Check your paths and file permissions and try again

But at least for me the temp_genome folder is empty

jsgounot commented 3 years ago

Hi, can you past the last part of the logs ? Which Opera-MS options did you used ?

niexiaoqing commented 3 years ago

I have the same problem. But its seems that I am able to open the file with for example vim, but its not in temp folder but instead in the NUCMER_OUT folder.

/scratch/SlurmTMP/sukem127.2123121/OPERA-MS/scratch/SlurmTMP/sukem127.2123121/RESULTS/intermediate_files/reference_clustering/NUCMER_OUT/temp_genome/119591-vs-121716_0.fa Check your paths and file permissions and try again

But at least for me the temp_genome folder is empty

me too, the same problem

niexiaoqing commented 3 years ago

Hi, can you past the last part of the logs ? Which Opera-MS options did you used ?

in intermediate_files/reference_clustering/NUCMER_OUT/log.txt image in workdir there is a nucmer.error contains some error messages image Opera-MS options image

niexiaoqing commented 3 years ago

Hi, can you past the last part of the logs ? Which Opera-MS options did you used ?

in intermediate_files/reference_clustering/NUCMER_OUT/log.txt image in workdir there is a nucmer.error contains some error messages image Opera-MS options image

and --contig-len-thr seems doesn't work

jsgounot commented 3 years ago

Hi, sorry, my schedule is a bit busy but I'm working on this issue, please don't close it.

niexiaoqing commented 3 years ago

Hi, sorry, my schedule is a bit busy but I'm working on this issue, please don't close it.

i think i find why i got error message,maybe i should add --no-ref-clusting option.

niexiaoqing commented 3 years ago

I have the same problem. But its seems that I am able to open the file with for example vim, but its not in temp folder but instead in the NUCMER_OUT folder.

/scratch/SlurmTMP/sukem127.2123121/OPERA-MS/scratch/SlurmTMP/sukem127.2123121/RESULTS/intermediate_files/reference_clustering/NUCMER_OUT/temp_genome/119591-vs-121716_0.fa Check your paths and file permissions and try again

But at least for me the temp_genome folder is empty

i think i find why i got error message,maybe i should add --no-ref-clusting option.

Unaimend commented 3 years ago

Yes, but I would like to have this ref/strain clustering OPERA-MS offers, that's one of the reasons I picked this assembler in my latest projects

rhysnewell commented 2 years ago

Look at the filepath that nucmer is trying to look at: /scratch/SlurmTMP/sukem127.2123121/OPERA-MS/scratch/SlurmTMP/sukem127.2123121/RESULTS/intermediate_files/reference_clustering/NUCMER_OUT/temp_genome/119591-vs-121716_0.fa That file path does not exist, it's appending the directory where OPERA-MS is installed onto your working directory. It's wild. OPERA-MS install: /scratch/SlurmTMP/sukem127.2123121/OPERA-MS/ Working dir: /scratch/SlurmTMP/sukem127.2123121/RESULTS/intermediate_files/reference_clustering/NUCMER_OUT/temp_genome/119591-vs-121716_0.fa

I've posted this in another thread, but thought I should post it here too so they can see it. Just change whatever code is messing with the file paths like that

jsgounot commented 2 years ago

Hi everyone. First, thanks to @rhysnewell for his comment on this thread. I just pushed a fix for this on github, please let me know if this does fix your problem. You don't need to recompile everything.

Unaimend commented 2 years ago

Sorry, I stopped working on this project, but I will try to redo it in the next few days and give you some feedback.