jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Error in Step4 #662

Closed liuyinan19922 closed 1 year ago

liuyinan19922 commented 1 year ago

Hello! I am a beginner in metagenomics, and I tried to analyze my samples with a commond that

(base) [yinan@ln-0001 seqshares]$ SqueezeMeta.pl -m coassembly -p wormPlastic1 -s 230403.samples -f 230403data

Unfortunately, when it came to Step 4, an error message was showed and the program was stopped, as follows

  Setting block size for Diamond
  AVAILABLE (free) RAM memory: 231.64 Gb
  We will set Diamond block size to 16 (Gb RAM/8, Max 16).
  You can override this setting using the -b option when starting the project, or changing
  the $blocksize variable in SqueezeMeta_conf.pl
 taxaDisk quota exceeded
terminate called after throwing an instance of 'File_write_exception'
  what():  Error writing file /gpfs1/scratch/yinan/230403metagenomeData/grid.scelse.ntu.edu.sg/seqshares/wormPlastic1/intermediate/diamond-tmp-eYQRGR
Error running command:    /home/yinan/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/diamond blastp -q /gpfs1/scratch/yinan/230403metagenomeData/grid.scelse.ntu.edu.sg/seqshares/wormPlastic1/results/03.wormPlastic1.faa -p 12 -d /gpfs1/scratch/yinan/squeezemetadownload/db/nr.dmnd -e 0.001 --id 40 -f tab -b 16 --quiet -o /gpfs1/scratch/yinan/230403metagenomeData/grid.scelse.ntu.edu.sg/seqshares/wormPlastic1/intermediate/04.wormPlastic1.nr.diamond at /home/yinan/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/04.rundiamond.pl line 72.
Stopping in STEP4 -> 04.rundiamond.pl. Program finished abnormally

  If you don't know what went wrong or want further advice, please look for similar issues in https://github.com/jtamames/SqueezeMeta/issues
  Feel free to open a new issue if you don't find the answer there. Please add a brief description of the problem and upload the /gpfs1/scratch/yinan/230403metagenomeData/grid.scelse.ntu.edu.sg/seqshares/wormPlastic1/syslog file (zip it first)
Died at /home/yinan/miniconda3/envs/SqueezeMeta/bin/SqueezeMeta.pl line 921.

As a beginner, I have a little knowledge of SqueezeMeta, and have no idea how to fix such an error. Does it cause by my limited quota space on the cluster I used? Could I trouble you to give me some advice?

Thanks very much! Regards, Yinan

fpusan commented 1 year ago

Indeed it is because you exceeded your quota.

liuyinan19922 commented 1 year ago

Indeed it is because you exceeded your quota.

Thanks for your prompt reply! I will check it.