search

bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
MIT License
396 stars 190 forks source link

metaWRAP classify_bins Segmentation fault (core dumped) #499

Open xubiy opened 1 year ago

xubiy commented 1 year ago

Hi, An error was encountered while running the module classify_bins.sh. The metawrap version is MetaWRAP v=1.3.2. Unfortunately, I have no idea how to debug this. I will really appreciate any help you can provide. The error is as follows:

/home/xuby/anaconda3/envs/metawrap2/bin/metawrap-modules/classify_bins.sh: line 126: 219799 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...                                     *****
************************************************************************************************************************
Joedhy commented 3 months ago

hello， I got the same error.Did you have any solution yet ？

xubiy commented 3 months ago

hello， I got the same error.Did you have any solution yet ？

Sorry for the late reply.

In the latest version of the NCBI nt database, the .nhr file has replaced the .nhd file and serves as the new index file for the BLAST database. After decompressing, you will obtain six files in total: .nsq, .nog, .nni, .nnd, .nin, and .nhr.

If you are using the classify_bins.sh module in the metaWRAP software for species annotation and encounter one or all of the following issues: 【1】nt.00.nhd doesn't exist 【2】Segmentation fault (core dumped)

It is recommended to update the NCBI nt database and change the corresponding files in line 79 and line 80 of classify_bins.sh. After these steps, there should be no more errors.