cblaster didn't create .dmnd out file???????
neelam19051 opened this issue · 8 comments
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 !
Hi @gamcil/ @brymerr921, @chasemc , please reply anyone if possible its urgent. i am facing this issue regarding cblaster local search-
cblaster search -m local -db mydb.dmnd -qf ~/Neelam/output12type.fasta
[19:03:06] INFO - Starting cblaster in local mode
[19:03:08] INFO - Found 6740 hits meeting score thresholds for local search
[19:03:08] INFO - Fetching genomic context of hits
[19:03:08] INFO - Querying local SQLite3 database: /home/bvs/Neelam/cblaster_input/mydb.sqlite3
Traceback (most recent call last):
File "/home/bvs/.local/bin/cblaster", line 8, in
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 !
Can you upload any of the files you used here? I downloaded some P. aeruginosa genomes from the NCBI and did not have any issues making/searching a local database with them. Are you on the newest version of cblaster?
Hi, @gamcil. Yes i am using latest version 1.3.18 and i have also check on NCBI file which accession number is GCF_000006765.1 but what i have found that .dmnd file isn't made by cblaster for this accession number of genome i.e PAO1 however when i used bua.gbk file as input cblaster work perfectly fine, i mean it made .dmnd file and sqlite3, fasta all three. Here i am attaching few files please have a look and let me know. On the other hand, can I use Clinker's input of whole genome gbk files to display just the genes of interest?
Thank you for your time!
P_aeruginosa_AR_0110.zip
P_aeruginosa_AR_0111.zip
P_aeruginosa_AR_455.zip
Hi, might be way off here, but your dmnd file could be getting saved in a different folder to the one you expect (it's the only one without a filepath). Try looking in your main user folder (C:) or searching for 'localD' in you base directory.
Hi,
I am having the exact same problem as the first message.
I am using both .gbff files created from Bakta or downloaded directly from NCBI (and have tried each individually with the same result) to create a database using the makedb tool. However, only the .sqlite3 and .fasta files are created and the .dmnd file is missing.
I have searched the entire hard drive for the .dmnd file and it is not placed elsewhere.
I have installed diamond (v4.0.515) before installing cblaster (v1.3.18)
Everything else seems to be working correctly.
Any help solving this issue would be great!
Replying to @neelam19051: I have recently encountered this issue. It seems that when diamond is not (properly) installed on your working environment, cblaster will not produce the .dmnd (diamond) file and also won't raise any errors. That's why it is hard to debug this issue.
You can simply fix it by installing diamond with pip install.
This did the trick for me. I hope it will help others too.
Thanks for the tip @hebalkaya, looks like cblaster needs a more robust check for the correct diamond. The 'diamond' available from PyPI is not related to the diamond aligner, but cblaster only looks for something named diamond/diamond-aligner on the system $PATH so it isn't catching this case correctly. In the meantime, installing diamond from the repo or via conda/homebrew/etc should solve this issue.
I found something realy strange about this
If you see my video, nearby 10s (at the left windows file directory), you can see that .dmnd file actually generated and suddenly disappeared
The command that I used was
cblaster makedb -cp 4 -n Sanghuangporus -f ./genomes/*.gbk
I think this can be clue to what is happening
Debug.mp4
* Edit after few more trials: I found .dmnd well generates if I put gbk files one by one instead of using wildcard
- Edit after few more trials: It was problem of specific invalid file included, in my case, Sanghuangporus_weigelae_GCA_036873625.gbk