samtools sort: failed to create "lgs.part001.sort.bam": Stale file handle

[Peterhhb]

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
• cd /data/work/pipeline_assemble_env/test/test_megahit_opera_ms/polished_output1/00.lgs_polish/02.map.ref.sh.work/map_genome2
  minimap2 --split-prefix tmp -a -x map-ont -t 4 /data/work/pipeline_assemble_env/test/test_megahit_opera_ms/polished_output1/00.lgs_polish/input.genome.fasta /data/work/pipeline_assemble_env/test/test_megahit_opera_ms/polished_output1/input.lgspart.001.fasta.gz|samtools view --threads 5 -F 0x4 -b - |samtools sort - -m 2g --threads 4 -o lgs.part001.sort.bam
• minimap2 --split-prefix tmp -a -x map-ont -t 4 /data/work/pipeline_assemble_env/test/test_megahit_opera_ms/polished_output1/00.lgs_polish/input.genome.fasta /data/work/pipeline_assemble_env/test/test_megahit_opera_ms/polished_output1/input.lgspart.001.fasta.gz
• samtools view --threads 5 -F 0x4 -b -
• samtools sort - -m 2g --threads 4 -o lgs.part001.sort.bam
  [M::mm_idx_gen::0.3810.98] collected minimizers
  [M::mm_idx_gen::0.4641.39] sorted minimizers
  [M::main::0.4641.39] loaded/built the index for 2571 target sequence(s)
  [M::mm_mapopt_update::0.4951.36] mid_occ = 10
  [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2571
  [M::mm_idx_stat::0.516*1.34] distinct minimizers: 1395384 (96.62% are singletons); average occurrences: 1.041; average spacing: 5.386; total length: 7824854
  [ERROR]�[1;31m failed to write to temporary file 'tmp.0000.tmp'�[0m: Stale file handle
  [E::hts_open_format] Failed to open file "lgs.part001.sort.bam" : Stale file handle
  samtools sort: failed to create "lgs.part001.sort.bam": Stale file handle

[moold]

Try your own alignment pipeline, see here

[Peterhhb]

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

[moold]

You can edit the bash file
/data/work/pipeline_assemble_env/test/test_megahit_opera_ms/polished_output1/00.lgs_polish/02.map.ref.sh
so that it runs:

samtools sort -T PREFIX - -m 2g --threads 4 -o lgs.part001.sort.bam

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]

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 ***@***.***

[moold]

Yes, edit the source code here

[Peterhhb]

是的，在这里编辑源代码

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]

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