cblaster didn't create .dmnd out file???????

Question

[Neel]

Hi, i am running cblaster and it didn't create .dmnd diamond, however it only create sqlite3 and fasta file. if anyone know anything please let me know. It will be great help.

cblaster makedb -n localD -f $(ls ~/Neelam/43_strains_gbk/*.gbk)
[18:20:39] INFO - Starting makedb module
[18:20:39] INFO - Pre-existing files found, overwriting
[18:20:39] INFO - Overwriting pre-existing file at localD.sqlite3
[18:20:39] INFO - Parsing 44 genome files, in 1 batches of 44
[18:20:39] INFO - Processing batch 1
[18:20:39] INFO - P_aeruginosa_AR_0110.gbk
[18:20:39] INFO - P_aeruginosa_AR_0111.gbk
[18:20:39] INFO - P_aeruginosa_AR_455.gbk
[18:20:39] INFO - P_aeruginosa_ATCC_15692.gbk
[18:20:39] INFO - P_aeruginosa_ATCC_27853.gbk
[18:20:39] INFO - P_aeruginosa_CMCP_115.gbk
[18:20:39] INFO - P_aeruginosa_Cu1510.gbk
[18:20:39] INFO - P_aeruginosa_DHS01.gbk
[18:20:39] INFO - P_aeruginosa_DK2.gbk
[18:20:39] INFO - P_aeruginosa_DVT419.gbk
[18:20:39] INFO - P_aeruginosa_DVT421.gbk
[18:20:39] INFO - P_aeruginosa_DVT425.gbk
[18:20:39] INFO - P_aeruginosa_E90.gbk
[18:20:39] INFO - P_aeruginosa_F5677.gbk
[18:20:39] INFO - P_aeruginosa_FDAARGOS_1041.gbk
[18:20:39] INFO - P_aeruginosa_FDAARGOS_532.gbk
[18:20:39] INFO - P_aeruginosa_FDAARGOS_767.gbk
[18:20:39] INFO - P_aeruginosa_GIMC5015_PAKB6.gbk
[18:20:39] INFO - P_aeruginosa_HOU1.gbk
[18:20:39] INFO - P_aeruginosa_LIUYANGP_C.gbk
[18:20:39] INFO - P_aeruginosa_M1608.gbk
[18:20:39] INFO - P_aeruginosa_NCTC12903.gbk
[18:20:39] INFO - P_aeruginosa_NCTC13618.gbk
[18:20:39] INFO - P_aeruginosa_NCTC13620.gbk
[18:20:39] INFO - P_aeruginosa_NDTH10366.gbk
[18:20:39] INFO - P_aeruginosa_PA0750.gbk
[18:20:39] INFO - P_aeruginosa_PA1.gbk
[18:20:39] INFO - P_aeruginosa_PA1R.gbk
[18:20:39] INFO - P_aeruginosa_PA1RG.gbk
[18:20:39] INFO - P_aeruginosa_PAO1.gbk
[18:20:39] INFO - P_aeruginosa_PB353.gbk
[18:20:39] INFO - P_aeruginosa_PB369.gbk
[18:20:39] INFO - P_aeruginosa_QZPH21.gbk
[18:20:39] INFO - P_aeruginosa_SCAID_PLC1P_2021_16_222.gbk
[18:20:39] INFO - P_aeruginosa_SCAID_TSTP_2021_7_157.gbk
[18:20:39] INFO - P_aeruginosa_SE5357.gbk
[18:20:39] INFO - P_aeruginosa_SRRSH1101.gbk
[18:20:39] INFO - P_aeruginosa_TL3773.gbk
[18:20:39] INFO - P_aeruginosa_UNC_PaerCF05.gbk
[18:20:39] INFO - P_aeruginosa_UNC_PaerCF14.gbk
[18:20:39] INFO - P_aeruginosa_UNC_PaerCF17.gbk
[18:20:39] INFO - P_aeruginosa_VRFPA04.gbk
[18:20:39] INFO - P_aeruginosa_Y71.gbk
[18:20:39] INFO - P_aeruginosa_Y89.gbk
[18:20:41] INFO - Saving 269318 genes
[18:20:43] INFO - Writing FASTA to localD.fasta
[18:20:44] INFO - Building DIAMOND database at localD.dmnd
[18:20:44] INFO - Done!

This two file only created. localD.sqlite3 and localD.fasta

Thank you !

[GenoMax]

Since the log shows no errors, search for "local.dmnd" using find to see if it got written someplace else in the directories you are working in.

[Neel]

Hi, i have check it everywhere even tried to locate this diamond file but still unable to find it.

[GenoMax]

You seem to be using slightly different command line options than what is here: https://cblaster.readthedocs.io/en/latest/guide/makedb_module.html but I assume you have checked that they are correct. Do you have DIAMOND available in your $PATH?

[Neel]

Hi, i checked it again diamond is installed in usr/local/bin but still it give error, however i made separate file from diamond using fasta as a input to .dmnd file for further local search but it gives some other error.

cblaster search -m local -db db.dmnd  -qf query.fa 
[16:37:46] INFO - Starting cblaster in local mode
[16:37:48] INFO - Found 72 hits meeting score thresholds for local search
[16:37:48] INFO - Fetching genomic context of hits
[16:37:48] INFO - Querying local SQLite3 database: /home/bvs/Neelam/test/db.sqlite3
Traceback (most recent call last):
  File "/home/bvs/.local/bin/cblaster", line 8, in <module>
    sys.exit(main())
  File "/home/bvs/.local/lib/python3.8/site-packages/cblaster/main.py", line 432, in main
    cblaster(
  File "/home/bvs/.local/lib/python3.8/site-packages/cblaster/main.py", line 300, in cblaster
    organisms = context.search(
  File "/home/bvs/.local/lib/python3.8/site-packages/cblaster/context.py", line 591, in search
    organisms = query_local_DB(hits, sqlite_db)
  File "/home/bvs/.local/lib/python3.8/site-packages/cblaster/context.py", line 302, in query_local_DB
    ) in database.query_genes(list(hit_dict), db):
  File "/home/bvs/.local/lib/python3.8/site-packages/cblaster/database.py", line 104, in query_genes
    return _query(query, database)
  File "/home/bvs/.local/lib/python3.8/site-packages/cblaster/database.py", line 83, in _query
    query = cur.execute(query, values) if values else cur.execute(query)
sqlite3.OperationalError: no such column: NECIECAO_04165

Thank you!

[GenoMax]

Looks like the database did not get properly created.

[Neel]

Hi, i what i have found that whenever i am giving input gff files cblaster create .dmnd file but it gives warning like

WARNING - Found no CDS features in APOFNIMO_06355 [/home/bvs/Neelam/cblaster_input/P_aeruginosa_E90.gff] and when i ran this  .dmnd file then it give-

cblaster search -m local -db ps_db.dmnd  -qf ~/Neelam/output12type.fasta 
[11:30:45] INFO - Starting cblaster in local mode
[11:30:45] ERROR - Error: Incomplete database file. Database building did not complete successfully.

As much as i know CDS feature is annotated in GBK files however as above i said it didn't create .dmnd whenever i am giving gbk files. i think there must be something which i am missing but i don't know what it is........

Thank you