# Failure download reference databases and setup IGDATA directory

when I try to execute AssignGenes.py ,BLAST Database error: No alias or index file found for nucleotide database [/root/share/igblast/database/imgt_human_ig_v] in search path [/root/share/igblast::]

AssignGenes.py igblast -s ~/changeo/pbmcHC/all_contig.fasta -b ~/share/igblast --organism human --loci ig --format blast
START> AssignGenes
COMMAND> igblast
VERSION> 1.18.0
FILE> all_contig.fasta
ORGANISM> human
LOCI> ig
NPROC> 2

PROGRESS> 14:48:16 |Running IgBLAST | 0.0 minERROR> Running command: igblastn -query /root/changeo/pbmcHC/all_contig.fasta -out /root/changeo/pbmcHC/all_contig_igblast.fmt7 -num_threads 2 -ig_seqtype Ig -organism human -auxiliary_data /root/share/igblast/optional_file/human_gl.aux -germline_db_V /root/share/igblast/database/imgt_human_ig_v -germline_db_D /root/share/igblast/database/imgt_human_ig_d -germline_db_J /root/share/igblast/database/imgt_human_ig_j -outfmt 7 std qseq sseq btop -domain_system imgt
BLAST Database error: No alias or index file found for nucleotide database [/root/share/igblast/database/imgt_human_ig_v] in search path [/root/share/igblast::]

It’s wrong in search path [/root/share/igblast::]

~/share/igblast# ls -lh
total 20K
drwxr-xr-x 2 root root 4.0K May 23 14:34 database
drwxr-xr-x 2 root root 4.0K May 23 14:43 fasta
drwxr-xr-x 7 root root 4.0K May 23 00:53 internal_data
drwxr-xr-x 2 root root 4.0K May 23 00:53 optional_file

database/ folder is listed as below

fasta/ folder is empty

~/share/igblast/database# ls
mouse_gl_D.nhr mouse_gl_D.nsi mouse_gl_J.nog mouse_gl_VDJ.tar mouse_gl_V.nsd mouse_gl_V.pin mouse_gl_V.psq rhesus_monkey_J.nog rhesus_monkey_VJ.tar rhesus_monkey_V.nsd rhesus_monkey_V.pin rhesus_monkey_V.psq
mouse_gl_D.nin mouse_gl_D.nsq mouse_gl_J.nsd mouse_gl_V.nhr mouse_gl_V.nsi mouse_gl_V.pog ncbi_human_c_genes.tar rhesus_monkey_J.nsd rhesus_monkey_V.nhr rhesus_monkey_V.nsi rhesus_monkey_V.pog
mouse_gl_D.nog mouse_gl_J.nhr mouse_gl_J.nsi mouse_gl_V.nin mouse_gl_V.nsq mouse_gl_V.psd rhesus_monkey_J.nhr rhesus_monkey_J.nsi rhesus_monkey_V.nin rhesus_monkey_V.nsq rhesus_monkey_V.psd
mouse_gl_D.nsd mouse_gl_J.nin mouse_gl_J.nsq mouse_gl_V.nog mouse_gl_V.phr mouse_gl_V.psi rhesus_monkey_J.nin rhesus_monkey_J.nsq rhesus_monkey_V.nog rhesus_monkey_V.phr rhesus_monkey_V.psi

~/share/igblast/fasta# ls -lh
total 0

trace back to #download reference databases and setup IGDATA directory

have executed successfully

fetch_igblastdb.sh -o ~/share/igblast

fetch_imgtdb.sh -o ~/share/germlines/imgt

but error: BLAST options error: File /root/share/igblast/fasta/imgt_human_ig_c.fasta does not exist

imgt2igblast.sh -i ~/share/germlines/imgt -o ~/share/igblast

Traceback (most recent call last):
File "/root/changeo/scripts/clean_imgtdb.py", line 5, in <module>
import Bio
ModuleNotFoundError: No module named 'Bio'

Building a new DB, current time: 05/23/2022 14:43:54
New DB name: /root/share/igblast/database/imgt_human_ig_c
New DB title: /root/share/igblast/fasta/imgt_human_ig_c.fasta
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 3000000000B
BLAST options error: File /root/share/igblast/fasta/imgt_human_ig_c.fasta does not exist
Traceback (most recent call last):
File "/root/changeo/scripts/clean_imgtdb.py", line 5, in <module>
import Bio
ModuleNotFoundError: No module named 'Bio'

............

So I failed to download /root/share/igblast/fasta/ folder. It can be done by fetch_igblastdb.sh? I repeated fetch_igblastdb.sh, but the result and error didn’t change.

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