cryptogenomicon
commented
5 years ago You ran out of space in /tmp (this is what theno space left on device error message is telling you).
You can set your ${TMPDIR} env variable to a different filesystem where you have plenty of available disk space, and try again.
For large indices, esl-sfetch --index needs to write some large temporary files and sort on disk.
I have been trying to use esl-sfetch to extract sequences from Metaclust database (https://metaclust.mmseqs.org/2018_06/). Since it requires creating SSI index file I was trying to create one but I get this output
Creating SSI index for metaclust_nr.fasta... sort: write failed: /tmp/sortVWzazq: No space left on device
Failed to write keys to ssi file metaclust_nr.fasta.ssi: external sort of primary keys failed
Moreover I see these SSI files being created.
-rw-r--r--. 1 rakesh sali 241G Jun 22 05:03 metaclust_nr.fasta -rw-r--r--. 1 rakesh sali 0 Dec 13 03:14 metaclust_nr.fasta.ssi.2 -rw-r--r--. 1 rakesh sali 71G Dec 13 04:04 metaclust_nr.fasta.ssi.1
Now when I use esl-seftch to extract sequences I get this output.
grep -v "^#" Cop9_msa.domtblout | awk '{print $1"/"$20"-"$21, $20, $21, $1}' | /home/rakesh/WORK/Softwares/Sequence_Alignment/hmmer3.2source/hmmer-3.2.1/easel/miniapps/esl-sfetch -Cf /salilab/park3/rakesh/Databases/metaclust/metaclust_nr.fasta - > yest Failed to open SSI index
How to resolve this ?