Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

#Classify_bin_BLASTN Segmentation fault #569

Open
AVIK9875 opened this issue Feb 24, 2025 · 0 comments
Open

#Classify_bin_BLASTN Segmentation fault #569

AVIK9875 opened this issue Feb 24, 2025 · 0 comments

Comments

@AVIK9875
Copy link

metawrap classify_bins -b /home/rmvcc/INITIAL_BINNING/BIN_REASSEMBLY/reassembled_bins/ -o bin_classify
metawrap classify_bins -b /home/rmvcc/INITIAL_BINNING/BIN_REASSEMBLY/reassembled_bins/ -o bin_classify

########################################################################################################################

ALIGN CONTIGS TO DATABASE WITH MEGABLAST

########################################################################################################################


----- setting up ouput folder bin_classify and merging contigs from all bins... -----

Warning: bin_classify already exists.


----- aligning bin_classify/all_contigs.fa to /media/rmvcc/Vivekananda/NCBI_nt/ncbi_nt_db -----
----- database with MEGABLAST. This is the longest step - please be patient. You may look at the -----
----- classification progress in bin_classify/megablast_out.raw.tab -----

/home/rmvcc/miniconda3/envs/metawrap-py27/bin/metawrap-modules/classify_bins.sh: line 126: 3444798 Segmentation fault (core dumped) blastn -task megablast -num_threads $threads -db ${BLASTDB}/nt -outfmt '6 qseqid qstart qend qlen sseqid staxids sstart send bitscore evalue nident length' -query ${out}/all_contigs.fa > ${out}/megablast_out.raw.tab


***** Failed to run megablast. Exiting... *****


real 844m59.282s
user 599m56.630s
sys 17m36.518s

Even i try to run separately:
blastn -task megablast -num_threads 5 -db /media/rmvcc/Vivekananda/NCBI_nt/ncbi_nt_db/nt -outfmt 6 -query /media/rmvcc/Vivekananda/NCBI_nt/all_contigs.fa > output.tab
Segmentation fault (core dumped)

my system have 40 core 80 threads and 256 gb memory. Please help me.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant