cannot create my custom database

[jxlabWzZ]

hi, i installed the latest version of adVNTR （v1.32） using miniconda: conda install -c bioconda advntr, and erverything is well but i cannot add (create) a new .db ohh! i created a new folder : vntr_data

my code is : advntr addmodel -r sus.fa -p GGGGTCATG -s 14859 -e 14889 -c chr1

error info: Traceback (most recent call last): File "/home/miniconda2/envs/py36/bin/advntr", line 11, in sys.exit(main()) File "/home/miniconda2/envs/py36/lib/python3.6/site-packages/advntr/main.py", line 138, in main add_model(args, addmodel_parser) File "/home/miniconda2/envs/py36/lib/python3.6/site-packages/advntr/advntr_commands.py", line 184, in add_model create_vntrs_database(settings.TRAINED_MODELS_DB) File "/home/miniconda2/envs/py36/lib/python3.6/site-packages/advntr/models.py", line 115, in create_vntrs_database ''') sqlite3.OperationalError: disk I/O error

it will generate a new file (hg19_selected_VNTRs_Illumina.db) under vntr_data, if change the permission to 777 (chmod 777 *) ,another error encounterd:

Traceback (most recent call last): File "/home/miniconda2/envs/py36/bin/advntr", line 11, in sys.exit(main()) File "/home/miniconda2/envs/py36/lib/python3.6/site-packages/advntr/main.py", line 138, in main add_model(args, addmodel_parser) File "/home/miniconda2/envs/py36/lib/python3.6/site-packages/advntr/advntr_commands.py", line 186, in add_model vntr_id = get_largest_id_in_database() + 1 File "/home/miniconda2/envs/py36/lib/python3.6/site-packages/advntr/models.py", line 207, in get_largest_id_in_database cursor.execute('''SELECT MAX(id) FROM vntrs''') sqlite3.OperationalError: disk I/O error

although，I saw the same question, I didn't get any exact solution。 Thank you in advance

[mehrdadbakhtiari]

Hello,

Could you try to run advntr addmodel -r sus.fa -p GGGGTCATG -s 14859 -e 14889 -c chr1 -m my_db.db? without -m parameter it tries to create the database in a default directory to which you may not have access. (This will solve your first problem) Also, can you check the access permission of "hg19_selected_VNTRs_Illumina.db" or my_db.db (in case you specified the name) after getting the second error?

[jxlabWzZ]

Thank you for your reply.

If i run: advntr addmodel -r sus.fa -p GGGGTCATG -s 14859 -e 14889 -c chr1 it will generate a file under vntr_data/ ,the access is: -rw-r--r-- 1 useid useid 0 Nov 8 11:12 hg19_selected_VNTRs_Illumina.db and the error info is: Traceback (most recent call last): File "/home/miniconda3/envs/str/bin/advntr", line 11, in sys.exit(main()) File "/home/miniconda3/envs/str/lib/python2.7/site-packages/advntr/main.py", line 138, in main add_model(args, addmodel_parser) File "/home/miniconda3/envs/str/lib/python2.7/site-packages/advntr/advntr_commands.py", line 184, in add_mode create_vntrs_database(settings.TRAINED_MODELS_DB) File "/home/miniconda3/envs/str/lib/python2.7/site-packages/advntr/models.py", line 118, in create_vntrs_data ''') sqlite3.OperationalError: disk I/O error

If i run:advntr addmodel -r sus.fa -p GGGGTCATG -s 14859 -e 14889 -c chr1 -m my_db.db no file or folder were generated the error info is:

Traceback (most recent call last): File "/home/miniconda3/envs/str/bin/advntr", line 11, in sys.exit(main()) File "/home/miniconda3/envs/str/lib/python2.7/site-packages/advntr/main.py", line 138, in main add_model(args, addmodel_parser) File "/home/miniconda3/envs/str/lib/python2.7/site-packages/advntr/advntr_commands.py", line 184, in add_mode create_vntrs_database(settings.TRAINED_MODELS_DB) File "/home/miniconda3/envs/str/lib/python2.7/site-packages/advntr/models.py", line 112, in create_vntrs_data os.makedirs(os.path.dirname(db_file)) File "/home/miniconda3/envs/str/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 2] No such file or directory: '' nohup.out (END)

[Jong-hun-Park]

Hi,

I know that you've tried it many times, but could you please double-check in which folder you are running adVNTR? As Mehrdad mentioned, if you run 'advntr addmodel' without -m parameter, it will generate a folder and file under wherever you launch adVNTR. I just want to make sure that we are looking at the same folder and file. In addition to that, can you please let us know which OS are you trying to run on?