blast Segmentation fault

Question

[giulia.cosenza]

I am writing to seek your assistance regarding an issue I encountered while attempting to run blastn locally on my computer. I have downloaded and installed blast+ on my machine and all nt_euk* files from the blast_db. Onece the db files were all downloaded I decompressed them in a directory I have called blastdb and create the .ncbirc config file as:

[BLAST] 
BLASTDB=path_to_blastdb
DATA_LOADERS=blastdb

To launch the program I used the command line:

blastn -db nt_euk -query /mnt/adna/work/blast-test/empty-N0C0.fasta  -strand plus -outfmt "6 qacc qlen sacc evalue score length qcovus pident" -sorthits 0 -max_target_seqs 3

But I got the following error:

Error message: Segmentation Fault (core dumped)

Gdb stack trace:

(gdb) bt
#0  0x0000000000f56381 in ncbi::CSeqDBVol::x_GetSequence(int, char const**) const ()
#1  0x0000000000f48599 in ncbi::CSeqDBImpl::GetSequence(int, char const**) const ()
#2  0x0000000000ed339e in ?? ()
#3  0x0000000000dc2bc1 in BLAST_PreliminarySearchEngine ()
#4  0x0000000000dc3832 in Blast_RunPreliminarySearchWithInterrupt ()
#5  0x0000000000e7c55f in ncbi::blast::CBlastPrelimSearch::Run() ()
#6  0x0000000000e4a8e7 in ncbi::blast::CLocalBlast::Run() ()
#7  0x0000000000b15246 in CBlastnApp::x_RunMTBySplitDB() ()
#8  0x0000000000b17520 in CBlastnApp::Run() ()
#9  0x00000000016bfdc3 in ncbi::CNcbiApplicationAPI::x_TryMain(ncbi::EAppDiagStream, char const*, int*, bool*) ()
#10 0x00000000016c2478 in ncbi::CNcbiApplicationAPI::AppMain(int, char const* const*, char const* const*, ncbi::EAppDiagStream, char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) ()
#11 0x0000000000ae33b7 in main ()

Can someone help me resolve this issue?

Thank you very much for your attention to this matter.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or use one of (a) the option highlighted in the image below/ (b) fenced code blocks for multi-line code. Fenced code blocks are useful in syntax highlighting. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time. You'd used the double quote button this time and that is not the right way to format code.

[giulia.cosenza]

thank you!

Answer 1

[Mensur Dlakic]

Most segmentation errors indicate memory problems. How quickly did the error pop up? What is your available RAM and did you monitor its use? It appears you are running this on a Windows-based computer, which is generally more problematic in terms of memory management.

I suggest you run your command with a short nucleotide sequence, say an 18S rRNA from a eukaryote of your choice. Then type in the whole path to the database and use time to measure how long the command runs and its resource use:

time blastn -db /path/to/nt_euk -query /mnt/adna/work/blast-test/empty-N0C0.fasta ...

Make sure that you have properly formatted /path/to/nt_euk files and let us know about the output of the above command.

[giulia.cosenza]

It takes just a few seconds to return the error. I'm running it on a Linux-based computer.

I'm having doubts about whether I formatted the database correctly. How should I have done it? I simply downloaded all gzip files named nt_euk from the NCBI FTP and then unzipped each file.

[Ram]

I'm running it on a Linux-based computer.

That's quite vague. How much RAM does this machine have? Is it a local machine (laptop/desktop) or a server?