ncbi / blast_plus_docs Goto Github PK

Hello and thank you for any assistance you can provide. After building Blast 2.15.0 using the typical commands ./configure, cd into the build dir, make all_r, I noticed that there are considerably less binaries in the 2.15.0 release than the 2.14.1 release.

2.15.0:
cleanup-blastdb-volumes.py lmdb_test1 lmdb_test5 update_blastdb.pl
datatool lmdb_test2 lmdbxx_sample windowmasker_2.2.22_adapter.py
get_species_taxids.sh lmdb_test3 project_tree_builder
legacy_blast.pl lmdb_test4 run_with_lock

2.14.1:
blastdb_aliastool dustmasker psiblast
blastdbcheck gene_info_reader rpsblast
blastdbcmd get_species_taxids.sh rpstblastn
blastdb_convert legacy_blast.pl run_with_lock
blastdbcp lmdb_test1 seedtop
blastdb_path lmdb_test2 segmasker
blast_formatter lmdb_test3 seqdb_demo
blastn lmdb_test4 seqdb_perf
blastp lmdb_test5 tblastn
blast_report lmdbxx_sample tblastx
blastx makeblastdb update_blastdb.pl
cleanup-blastdb-volumes.py makeclusterdb windowmasker
convert2blastmask makembindex windowmasker_2.2.22_adapter.py)
datatool makeprofiledb
deltablast project_tree_builder

Is this by design? Have tested with both .zip and tar.gz source code both look the same after building. Got them here: https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

Thank you for your assistance. Just wondering why the difference. Our faculty use the blastp and blastx binaries considerably

--
Sina Tashakkori (he/him/his)
Appalachian State University

Using the run BLAST via docker,
I have followed all the steps correctly, I install docker and download the database, as the samples.fa, however when calling:

docker run --rm --rm
-v /mnt/l/ENV_LINUX/BLAST/blastdb:/blast/blastdb:ro -v /mnt/l/ENV_LINUX/BLAST/blastdb_custom:/blast/blastdb_custom:ro \
-v /mnt/l/ENV_LINUX/BLAST/queries:/blast/queries:ro \ -v /mnt/l/ENV_LINUX/BLAST/blastdb_custom:ro
-v /mnt/l/ENV_LINUX/BLAST/results:/blast/results:rw \ -v /mnt/l/ENV_LINUX/BLAST/results:/blast/results:rw
ncbi/blast
blastn -query /blast/queries/query1.fa -db nt -num_threads 12
-out /blast/results/blastn.query1.denovo16s.out

gives me the following error:

Error: NCBI C++ Exception:
T0 "/root/ncbi-blast-2.13.0+-src/c++/src/corelib/ncbiobj.cpp", line 992: Critical: (CCoreException::eNullPtr) ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.
Stack trace:
/blast/lib/libxncbi.so ????:0 ncbi::CObject::ThrowNullPointerException() offset=0xAF addr=0x7fbdfe9941ef
/blast/lib/libxblast.so ???:0 ncbi::blast::CBlastTracebackSearch::Run() offset=0xB77 addr=0x7fbe01776c97
/blast/lib/libxblast.so ???:0 ncbi::blast::CLocalBlast::Run() offset=0x1E4F addr=0x7fbe0170d71f
blastn.REAL ????:0 CBlastnApp::x_RunMTBySplitDB() offset=0x180D addr=0x55c3e0c22fbd
blastn.REAL ????:0 CBlastnApp::Run() offset=0x44 addr=0x55c3e0c25d94
/blast/lib/libxncbi.so ???:0 ncbi::CNcbiApplicationAPI::x_TryMain(ncbi::EAppDiagStream, char const*, int*, bool*) offset=0x15B addr=0x7fbdfe8d5f6b
/blast/lib/libxncbi.so ??? :0 ncbi::CNcbiApplicationAPI::AppMain(int, char const* const*, char const* const*, ncbi::EAppDiagStream, char const*, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) offset=0x73D addr=0x7fbdfe8d983d
blastn.REAL ????:0 main offset=0x78 addr=0x55c3e0c17948
/lib/x86_64-linux-gnu/libc.so.6 ???:0 __libc_start_main offset=0xEB addr=0x7fbdfe49e09b
blastn.REAL ???:0 _start offset=0x2A addr=0x55c3e0c1828a

What could be the problem?

I can use the image to create the relative directories and download the example database but I can not download the query db.
$ docker run --rm ncbi/blast efetch -db protein -format fasta
-id P01349 > queries/P01349.fsa
bash: queries/P01349.fsa: Permission denied
If the problem is related to not having a cloud account, then my question is why must I have a paid account in order to use the ncbi/blast docker image?
Thanks

However the following works the way I like!

docker ps

docker ps
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
6437c2fc9c4f 4afb1f585a96 "bash" 4 minutes ago Up 4 minutes friendly_swartz

docker exec -it friendly_swartz bash
root@6437c2fc9c4f:/blast# ls
bin blastdb blastdb_custom lib
root@6437c2fc9c4f:/blast# update_blastdb.pl --showall pretty --source gcp

Connected to GCP
BLASTDB DESCRIPTION SIZE (GB) LAST_UPDATED
swissprot Non-redundant UniProtKB/SwissProt sequences 0.3573 2023-04-29
nr All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects 364.0284 2023-04-27
refseq_protein NCBI Protein Reference Sequences 144.4754 2023-05-05
landmark Landmark database for SmartBLAST 0.3817 2023-04-25
pdbaa PDB protein database 0.1951 2023-04-29
nt Nucleotide collection (nt) 303.7546 2023-04-30
pdbnt PDB nucleotide database 0.0143 2023-04-23
patnt Nucleotide sequences derived from the Patent division of GenBank 15.7333 2023-04-28
refseq_rna NCBI Transcript Reference Sequences 46.6038 2023-05-01
ref_prok_rep_genomes Refseq prokaryote representative genomes (contains refseq assembly) 19.6809 2023-04-29
ref_viruses_rep_genomes Refseq viruses representative genomes 0.1320 2023-04-29
ref_viroids_rep_genomes Refseq viroids representative genomes 0.0001 2022-06-25
ref_euk_rep_genomes RefSeq Eukaryotic Representative Genome Database 350.4509 2023-04-13
split-cdd CDD split into 32 volumes 4.5709 2022-12-18
cdd CDD.v3.20 3.7088 2022-09-21
GCF_000001405.39_top_level Homo sapiens GRCh38.p13 [GCF_000001405.39] chromosomes plus unplaced and unlocalized scaffolds 1.1572 2021-06-02
GCF_000001635.27_top_level Mus musculus GRCm39 [GCF_000001635.27] chromosomes plus unplaced and unlocalized scaffolds 3.6543 2021-06-02
16S_ribosomal_RNA 16S ribosomal RNA (Bacteria and Archaea type strains) 0.0179 2023-04-15
18S_fungal_sequences 18S ribosomal RNA sequences (SSU) from Fungi type and reference material 0.0023 2023-05-04
28S_fungal_sequences 28S ribosomal RNA sequences (LSU) from Fungi type and reference material 0.0053 2023-05-04
ITS_RefSeq_Fungi Internal transcribed spacer region (ITS) from Fungi type and reference material 0.0067 2022-10-28
ITS_eukaryote_sequences ITS eukaryote BLAST 0.0331 2023-05-01
env_nt environmental samples 48.8039 2023-04-05
Betacoronavirus Betacoronavirus 54.0961 2023-05-06
pataa Protein sequences derived from the Patent division of GenBank 1.8011 2023-04-30
refseq_select_prot RefSeq Select proteins 34.3461 2023-04-30
refseq_select_rna RefSeq Select RNA sequences 0.0656 2023-04-30
env_nr Proteins from WGS metagenomic projects (env_nr). 3.9459 2023-04-30
LSU_eukaryote_rRNA Large subunit ribosomal nucleic acid for Eukaryotes 0.0053 2022-12-05
LSU_prokaryote_rRNA Large subunit ribosomal nucleic acid for Prokaryotes 0.0041 2022-12-05
SSU_eukaryote_rRNA Small subunit ribosomal nucleic acid for Eukaryotes 0.0063 2022-12-05
mito NCBI Genomic Mitochondrial Reference Sequences 0.1252 2023-04-20
tsa_nr Transcriptome Shotgun Assembly (TSA) sequences 5.1253 2023-04-30
tsa_nt Transcriptome Shotgun Assembly (TSA) sequences 6.3491 2023-04-27
nt_euk Eukaryota nt 197.6799 2023-04-26
nt_prok Prokaryota (bacteria and archaea) nt 51.1781 2023-05-01
nt_viruses Viruses nt 51.2685 2023-05-01
nt_others Artificial and other seqs nt 0.7473 2023-05-01
taxdb Taxonomy database 0.1670 2021-06-07

root@6437c2fc9c4f:/blast# efetch -db protein -format fasta
-id P01349 > queries/P01349.fsa

root@6437c2fc9c4f:/blast# ls
bin blastdb blastdb_custom fasta lib queries results

root@6437c2fc9c4f:/blast# cd queries

root@6437c2fc9c4f:/blast/queries# ls
P01349.fsa

root@6437c2fc9c4f:/blast/queries# cd ..

root@6437c2fc9c4f:/blast# efetch -db protein -format fasta
-id Q90523,P80049,P83981,P83982,P83983,P83977,P83984,P83985,P27950
> fasta/nurse-shark-proteins.fsa

root@6437c2fc9c4f:/blast# ls
bin blastdb blastdb_custom fasta lib queries results

root@6437c2fc9c4f:/blast# makeblastdb -in /blast/fasta/nurse-shark-proteins.fsa -dbtype prot
-parse_seqids -out nurse-shark-proteins -title "Nurse shark proteins"
-taxid 7801 -blastdb_version 5

Building a new DB, current time: 05/07/2023 05:51:28
New DB name: /blast/nurse-shark-proteins
New DB title: Nurse shark proteins
Sequence type: Protein
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 7 sequences in 0.000834227 seconds.

root@6437c2fc9c4f:/blast# blastdbcmd -entry all -db nurse-shark-proteins -outfmt "%a %l %T"
Q90523.1 106 7801
P80049.1 132 7801
P83981.1 53 7801
P83977.1 95 7801
P83984.1 190 7801
P83985.1 195 7801
P27950.1 151 7801

root@6437c2fc9c4f:/blast# blastdbcmd -list /blast/blastdb -remove_redundant_dbs ##### this does not work

root@6437c2fc9c4f:/blast# blastp -query /blast/queries/P01349.fsa -db nurse-shark-proteins
-out /blast/results/blastp.out

root@6437c2fc9c4f:/blast# cd results

root@6437c2fc9c4f:/blast/results# ls
blastp.out

root@6437c2fc9c4f:/blast/results# cat blastp.out
BLASTP 2.14.0+

Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.

Reference for composition-based statistics: Alejandro A. Schaffer,
L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri
I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001),
"Improving the accuracy of PSI-BLAST protein database searches with
composition-based statistics and other refinements", Nucleic Acids
Res. 29:2994-3005.

Database: Nurse shark proteins
7 sequences; 922 total letters

Query= sp|P01349.2|RELX_CARTA RecName: Full=Relaxin; Contains: RecName:
Full=Relaxin B chain; Contains: RecName: Full=Relaxin A chain

Length=44
Score E
Sequences producing significant alignments: (Bits) Value

P80049.1 RecName: Full=Fatty acid-binding protein, liver; AltName... 14.2 0.96

P80049.1 RecName: Full=Fatty acid-binding protein, liver; AltName: Full=Liver-type
fatty acid-binding protein; Short=L-FABP
Length=132

Score = 14.2 bits (25), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 3/9 (33%), Positives = 6/9 (67%), Gaps = 0/9 (0%)

Query 2 LCGRGFIRA 10
+C R ++R
Sbjct 123 VCTREYVRE 131

Lambda K H a alpha
0.334 0.143 0.520 0.792 4.96

Gapped
Lambda K H a alpha sigma
0.267 0.0410 0.140 1.90 42.6 43.6

Effective search space used: 22680

Database: Nurse shark proteins
Posted date: May 7, 2023 5:51 AM
Number of letters in database: 922
Number of sequences in database: 7

Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Neighboring words threshold: 11
Window for multiple hits: 40

root@6437c2fc9c4f:/blast/results#

The ncbi Docker Hub org lists no (public) repositories:

https://hub.docker.com/u/ncbi

$ docker pull docker.io/ncbi/blast:latest
Error response from daemon: pull access denied for ncbi/blast, repository does not exist or may require 'docker login': denied: requested access to the resource is denied

Hello,

I am following the documentation to download a ncbi database nt. The files are dowloaded but when I try to check the available databases in local nothing appears. I try also with the pdbaa database as shown in the example but it does not work. Is there any step missing?

Download Protein Data Bank amino acid database (pdbaa)

docker run --rm
-v $HOME/blastdb:/blast/blastdb:rw
-w /blast/blastdb
ncbi/blast
update_blastdb.pl pdbaa

Display database(s) in $HOME/blastdb

docker run --rm
-v $HOME/blastdb:/blast/blastdb:ro
ncbi/blast
blastdbcmd -list /blast/blastdb -remove_redundant_dbs

Hi, could you create instructions on how to import BLAST+ as a layer in my multistage build? I am copying from this layer in my Dockerfile but something isn't quite right. Thank you!

Here are the relevant lines from my Dockerfile

FROM ncbi/blast:2.10.1 AS blast
COPY --from=blast     /blast                /blast
ENV PATH="${PATH}:/blast" BLASTDB=/blast/blastdb

I get an error when I try to run blastn:

blastn.REAL: error while loading shared libraries: liblmdb.so.0: cannot open shared object file: No such file or directory

Dear everyone.

+I try to run Blast with Singularity.
+Firstly, I downloaded the datatbase :
wget https://ftp.ncbi.nlm.nih.gov/blast/db/nr.00.tar.gz
tar zxvf nr.00.tar.gz
+In this directory:
daomhai 394620928 Jan 29 22:01 blast_latest.sif
daomhai 785474112 Jan 29 21:01 Catfish22a.scaffolds.fa
daomhai 21758439844 Jan 23 22:41 nr.00.tar.gz
daomhai 16398992 Jan 23 13:45 taxdb.bti
daomhai 154795652 Jan 23 13:45 taxdb.btd
daomhai 545 Jan 21 14:07 nr.pal
daomhai 39369916416 Jan 21 14:07 nr.pdb
daomhai 13595021718 Jan 21 12:58 nr.pos
daomhai 130220032 Jan 21 12:54 nr.ptf
daomhai 2678679080 Jan 21 12:53 nr.pto
daomhai 6306876900 Jan 21 12:50 nr.pot
daomhai 66710822 Jan 21 11:07 nr.00.pin
daomhai 155170935 Jan 21 08:36 nr.00.phd
daomhai 3466580 Jan 21 08:36 nr.00.phi
daomhai 33355348 Jan 21 08:36 nr.00.pog
daomhai 66710632 Jan 21 08:36 nr.00.ppd
daomhai 260636 Jan 21 08:36 nr.00.ppi
daomhai 2009755978 Jan 21 08:36 nr.00.phr
daomhai 3175349590 Jan 21 08:36 nr.00.psq
+Then, I run blastp:
/scratch/ulg/bbasv/daomhai/BlastAnalyse/DownloadNR $ singularity run -B
/scratch/users/d/a/daomhai/BlastAnalyse/DownloadNR/ /scratch/users/d/a/daomhai/BlastAnalyse/DownloadNR/blast_latest.sif
blastp -db /scratch/ulg/bbasv/daomhai/BlastAnalyse/DownloadNR/nr -query
/scratch/users/d/a/daomhai/BlastAnalyse/DownloadNR/Catfish22a.scaffolds.fa -out catfish.out
+But I get error:
BLAST Database error: No alias or index file found for protein database
[/scratch/ulg/bbasv/daomhai/BlastAnalyse/DownloadNR/nr] in search path
[/home/ulg/bbasv/daomhai:/blast/blastdb:/blast/blastdb_custom:]
+I also make :
export blastdb='/scratch/users/d/a/daomhai/BlastAnalyse/DownloadNR'
+But it was still a problem.

Please help me to figure out what I am doing wrong ??

Sincerely
Hai

Will N have an impact on blast n if RepeatMask uses hard masking and generates N from repeated sequences? For example, is ATCGGGCTNNTTT the same sequence as ATCGGGCTTTT? Or is it true that ATCGGGCTNNNNTTT and ATCGGGCTTTTT have the same effect in inputting blast n

How do you use/set up a configuration file for blast+ to indicate the database directory? I want to change the search path from [blast:/blast/blastdb:/blast/blastdb_custom:] to a different directory. I tried creating a config file that named config.ncbirc and says says:

[BLAST]
BLASTDB=db/pdbaa

but didnt know if I was meant to export the config file or is there a flag to add to the command line?

I have the error below:

Bio.Application.ApplicationError: Non-zero return code 2 from ‘psiblast -out 7NDB_B_WT.out -query 7NDB_B_WT.fasta -db /mnt/research/common-data/Bio/blastdb/nr -evalue 5000 -num_iterations 3 -out_ascii_pssm 7NDB_B_WT.pssm’, message ‘BLAST Database error: No alias or index file found for protein database [/mnt/research/common-data/Bio/blastdb/nr] in search path [/media/leon//Machine_learning_model_binding_free_energy_BFE_change_predictions/TopNetmAb/7NDB/features/7NDB_B_A_344_S::]’

I downloaded the “nr” file from the blast database and created a database link in the directory [/mnt/research/common-data/Bio/blastdb/nr]. But the error persists.

Please, can anyone help me?

Hello,

I am having trouble running BLASTn (via command line) with my Flye (de novo genome assembler). I am not getting any results in my output file. Has anyone had the same issue? Please advise why this is not work.

My apologies if this is not the correct place to report this, but I would expect the issue to show up in this project too.

I am running blastn in a docker container, copying it in from the binary tarball from https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+.

Since upgrading to 2.11.0, blastn calls take excessively long to finish, or do not complete at all.

Setting BLAST_USAGE_REPORT=false resolves the issue. This raises the strong suspicion that the new usage reporting feature is the culprit.

The issue can be reproduced by creating a docker image with a simple Dockerfile:

FROM ubuntu  # or your preferred starting image
COPY blastn /usr/local/bin
USER nobody:nogroup

After building the container with docker build -t test-bug ".", observe the difference between:

docker run -ti --rm --read-only -e BLAST_USAGE_REPORT=false test-bug blastn -help

and

docker run -ti --rm --read-only test-bug blastn -help

The hiccup is sub-second but already noticeable. Start a longer running local blastn call, and runtimes of normally e.g. 15s go up to many minutes, while top shows the processes as mostly sleeping.

Update for the record: the excessively long run times were not for single runs of blastn. They happened in our pipeline where we do a few dozen calls in series. These should take ~20s altogether, but their added up "hang time" made the job timeout after 20mn.

Hi there, I've followed all the instructions for running a local blast search within a GCP vm instance on the suggested hardware. Trying to follow the instructions for using bind mounts did not work for me, as needed files remained unavailable to the container. I also preferred to keep the containers, so I used docker cp to transfer the files instead, dropped the --rm flag, and otherwise modified the commands for execution from within the container. This all works fine. The problem is that after a day or two, the image and stopped container inexplicably disappear from the vm (at least according to the results of docker ps -a and docker images ls), and I lose a bunch of work. They do, however, persist across reboots. I'm very confused by this problem and any help would be much appreciated.

Apaprently outputfilenames for blast are limited to maximum 256 characters. This should be explicitely mentioned (or better: fixed)

I blasted two protein sequences of simillar lengths (1902 aa and 1901aa) which looked pretty similar. We tried to used -softmask options too but blast didn't give any significant results and matched only 29 amino acids.
blastp -soft_masking false -query orf0324_prot.fasta -subject h37rv_pgrs54_prot.fasta > blastp_orf0324_pgrs54.out

Score = 24.6 bits (52),  Expect = 0.14, Method: Compositional matrix adjust.
 Identities = 29/29 (100%), Positives = 29/29 (100%), Gaps = 0/29 (0%)

The nucleotide sequences of these proteins had an identity of 85.20% using blastn.

I tried to align those sequences again using the global aligner needle and got an alignment with an identity of 79.9%.
needle -asequence orf0324_prot.fasta -bsequence h37rv_pgrs54_prot.fasta -outfile needle_orf0324_54.out
Length: 2097 Identity: 1676/2097 (79.9%) Similarity: 1680/2097 (80.1%) Gaps: 391/2097 (18.6%) Score: 8713.0

Are there some other options in blastp that could be used to get around this issue?

When I execute: ncbi-blast-2.12.0+/bin/update_blastdb.pl --showall --verbose --verbose
I get the following

Net::FTP>>> Net::FTP(3.08_01)
Net::FTP>>> Exporter(5.72)
Net::FTP>>> Net::Cmd(3.08_01)
Net::FTP>>> IO::Socket::SSL(2.044)
Net::FTP>>> IO::Socket::IP(0.37)
Net::FTP>>> IO::Socket(1.38)
Net::FTP>>> IO::Handle(1.36)
Net::FTP=GLOB(0x55ec7173d4f8)<<< 220-
Net::FTP=GLOB(0x55ec7173d4f8)<<< This warning banner provides privacy and security notices consistent with
Net::FTP=GLOB(0x55ec7173d4f8)<<< applicable federal laws, directives, and other federal guidance for accessing
Net::FTP=GLOB(0x55ec7173d4f8)<<< this Government system, which includes all devices/storage media attached to
Net::FTP=GLOB(0x55ec7173d4f8)<<< this system. This system is provided for Government-authorized use only.
Net::FTP=GLOB(0x55ec7173d4f8)<<< Unauthorized or improper use of this system is prohibited and may result in
Net::FTP=GLOB(0x55ec7173d4f8)<<< disciplinary action and/or civil and criminal penalties. At any time, and for
Net::FTP=GLOB(0x55ec7173d4f8)<<< any lawful Government purpose, the government may monitor, record, and audit
Net::FTP=GLOB(0x55ec7173d4f8)<<< your system usage and/or intercept, search and seize any communication or data
Net::FTP=GLOB(0x55ec7173d4f8)<<< transiting or stored on this system. Therefore, you have no reasonable
Net::FTP=GLOB(0x55ec7173d4f8)<<< expectation of privacy. Any communication or data transiting or stored on this
Net::FTP=GLOB(0x55ec7173d4f8)<<< system may be disclosed or used for any lawful Government purpose.
Net::FTP=GLOB(0x55ec7173d4f8)<<< 220 FTP Server ready.
Net::FTP=GLOB(0x55ec7173d4f8)>>> USER anonymous
Net::FTP=GLOB(0x55ec7173d4f8)<<< 331 Anonymous login ok, send your complete email address as your password
Net::FTP=GLOB(0x55ec7173d4f8)>>> PASS ....
Net::FTP=GLOB(0x55ec7173d4f8)<<< 230 Anonymous access granted, restrictions apply
Net::FTP=GLOB(0x55ec7173d4f8)>>> CWD /blast/db
Net::FTP=GLOB(0x55ec7173d4f8)<<< 250 CWD command successful
Net::FTP=GLOB(0x55ec7173d4f8)>>> TYPE I
Net::FTP=GLOB(0x55ec7173d4f8)<<< 200 Type set to I
Connected to NCBI
Net::FTP=GLOB(0x55ec7173d4f8)>>> PASV
Net::FTP=GLOB(0x55ec7173d4f8)<<< 227 Entering Passive Mode (130,14,250,10,195,109).
Net::FTP=GLOB(0x55ec7173d4f8)>>> NLST
Net::FTP=GLOB(0x55ec7173d4f8)<<< 421 No transfer timeout (60 seconds): closing control connection
Net::FTP=GLOB(0x55ec7173d4f8)>>> PASV
Net::FTP: Net::Cmd::getline(): unexpected EOF on command channel: at /home/ncbi-blast-2.12.0+/bin/update_blastdb.pl line 370.
Net::FTP: Net::Cmd::_is_closed(): unexpected EOF on command channel: at /home/ncbi-blast-2.12.0+/bin/update_blastdb.pl line 337.
Net::FTP: Net::Cmd::_is_closed(): unexpected EOF on command channel: at /home/ncbi-blast-2.12.0+/bin/update_blastdb.pl line 337.

Any help?

Thanks

Hi! First of all, thank you so much for this tutorial.

Everything works great until I get to step 3 of section 3 (running blastn with nt and the 59 KB or 422 KB input file). I keep getting segfaults:

/blast/bin/blastn: line 25: 9 Segmentation fault (core dumped) blastn.REAL "$@"

I've tried changing the output format and I've tried changing the number of threads to 32, 16, or 1. I've tried Ubuntu 18.04 LTS with 500 GB and Ubuntu 20.04 LTS with 500 GB. I'm using a n1-highmem-32 us-east4c. Do you have any suggestions for what could be going wrong?

Thank you so much!

This is a really excellent guide, and was extremely helpful. I noticed while experimenting with the blast commands that running blastn as shown here takes as much time as after adding -task megablast. My understanding (though I could be wrong) is that running blastn by default as described in this guide, ncbi/blast blastn, actually runs megablast, and that to run blastn it is necessary to specify -task blastn. I think it would be helpful to add a note clarifying that the commands in this document run megablast, not blastn. Thank you so much.