Open niexiaoqing opened 3 years ago
Hi,
thanks for using Opera-MS. Are you able to access the file with a terminal ?
Regards, jsgounot
Hi,
thanks for using Opera-MS. Are you able to access the file with a terminal ?
Regards, jsgounot
no,nothing find in the dir
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
Hi, can you past the last part of the logs ? Which Opera-MS options did you used ?
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
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 in workdir there is a nucmer.error contains some error messages Opera-MS options
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 in workdir there is a nucmer.error contains some error messages Opera-MS options
and --contig-len-thr seems doesn't work
Hi, sorry, my schedule is a bit busy but I'm working on this issue, please don't close it.
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.
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.
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
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
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.
Sorry, I stopped working on this project, but I will try to redo it in the next few days and give you some feedback.