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samtools sort: failed to create "lgs.part001.sort.bam": Stale file handle #144
I do not have permission to write temporary files in the cloud platform
No permission to write temporary files in the cloud platform
How to enable software such as samtools to write to local directories
this is problem.
hostname
hostname
cd /data/work/pipeline_assemble_env/test/test_megahit_opera_ms/polished_output1/00.lgs_polish/02.map.ref.sh.work/map_genome2
Try your own alignment pipeline, see here
Thank you very much for your answer, but I just looked at the document and I want to use mixed reading to perform polishing, but he doesn't have any examples. I would like to know how to assemble the final polishing fasta file after both polishing
where PREFIX: Write temporary files to PREFIX.nnnn.bam.
After saving the change, execute the shell script manually, and then run the main NextPolish command again.
Thank you very much for your answer, but this operation can only solve this one. If I need to use it in batches in the future, this problem will still occur
于心
***@***.***
Are you saying that I now need to modify the 02.map.ref.sh file to make the data run smoothly before modifying the source code to solve my current problem? However, I ran the test data without any problem, and when I replaced it with my own data, the above error occurred. If I were to modify the source code, would it be enough to only modify the path in map_genome? Thank you for your answer
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moold commentedon Aug 8, 2025
Try your own alignment pipeline, see here
Peterhhb commentedon Aug 8, 2025
moold commentedon Aug 8, 2025
You can edit the bash file
/data/work/pipeline_assemble_env/test/test_megahit_opera_ms/polished_output1/00.lgs_polish/02.map.ref.shso that it runs:
where
PREFIX: Write temporary files to PREFIX.nnnn.bam.After saving the change, execute the shell script manually, and then run the main NextPolish command again.
Peterhhb commentedon Aug 8, 2025
moold commentedon Aug 8, 2025
Yes, edit the source code here
Peterhhb commentedon Aug 8, 2025
Are you saying that I now need to modify the 02.map.ref.sh file to make the data run smoothly before modifying the source code to solve my current problem? However, I ran the test data without any problem, and when I replaced it with my own data, the above error occurred. If I were to modify the source code, would it be enough to only modify the path in map_genome? Thank you for your answer
Peterhhb commentedon Aug 8, 2025
If we only modify the file path without modifying the source code, can we solve this problem? Is there a corresponding one in the configuration file