update_db crash
Opened this issue · 1 comments
pgcudahy commented
Hi Jody, hope you're well. I'm having trouble setting up a new install of NTM-profiler. I did
conda create -n ntmprofiler_v0.3.0 ntm-profiler=0.3.0 -y
conda activate ntmprofiler_v0.3.0
mkdir -p ntm_profiler/v0.3.0
cd ntm_profiler/v0.3.0
ntm-profiler update_db --logging DEBUG
And get
[03:54:39] DEBUG ntm-db ntm-profiler:186
DEBUG Directory ntm-db does not exist, cloning repo ntm-profiler:193
DEBUG Running command: git clone https://github.com/ntm-db/ntm-db.git utils.py:386
[03:54:45] DEBUG Running command: git checkout master utils.py:386
DEBUG Running command: zip -F species/sourmash-split.zip --out species/sourmash.sbt.zip utils.py:386
INFO ntm-profiler:205
Creating species DB
DEBUG Running command: ntm-profiler create_species_db -p ntmdb --sourmash_db sourmash.sbt.zip --accessions accessions.csv --load utils.py:386
[03:54:47] DEBUG Moving to Mycobacterium_abscessus ntm-profiler:211
INFO ntm-profiler:214
Creating DB for M
DEBUG Running command: ntm-profiler create_resistance_db --prefix M --csv resistance_variants.csv --barcode barcode.bed --load utils.py:386
[03:54:48] ERROR Traceback (most recent call last): utils.py:391
File "/home/pgc29/.conda/envs/ntmprofiler_v0.3.0/bin/ntm-profiler", line 390, in <module>
args.func(args)
File "/home/pgc29/.conda/envs/ntmprofiler_v0.3.0/bin/ntm-profiler", line 177, in create_resistance_db
pp.create_db(args,extra_files=extra_files)
File "/home/pgc29/.conda/envs/ntmprofiler_v0.3.0/lib/python3.10/site-packages/pathogenprofiler/db.py", line 417, in create_db
hgvs_variants = [r for r in csv.DictReader(open(args.csv))]
FileNotFoundError: [Errno 2] No such file or directory: 'resistance_variants.csv'
Cleaning up after failed run
Traceback (most recent call last):
File "/home/pgc29/.conda/envs/ntmprofiler_v0.3.0/bin/ntm-profiler", line 390, in <module>
args.func(args)
File "/home/pgc29/.conda/envs/ntmprofiler_v0.3.0/bin/ntm-profiler", line 216, in main_update_db
pp.run_cmd(f'ntm-profiler create_resistance_db --prefix {species.replace(" ","_")} --csv resistance_variants.csv {barcode_arg} --load')
File "/home/pgc29/.conda/envs/ntmprofiler_v0.3.0/lib/python3.10/site-packages/pathogenprofiler/utils.py", line 392, in run_cmd
raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,result.stderr.decode()))
ValueError: Command Failed:
/bin/bash -c set -o pipefail; ntm-profiler create_resistance_db --prefix M --csv resistance_variants.csv --barcode barcode.bed --load
stderr:
Traceback (most recent call last):
File "/home/pgc29/.conda/envs/ntmprofiler_v0.3.0/bin/ntm-profiler", line 390, in <module>
args.func(args)
File "/home/pgc29/.conda/envs/ntmprofiler_v0.3.0/bin/ntm-profiler", line 177, in create_resistance_db
pp.create_db(args,extra_files=extra_files)
File "/home/pgc29/.conda/envs/ntmprofiler_v0.3.0/lib/python3.10/site-packages/pathogenprofiler/db.py", line 417, in create_db
hgvs_variants = [r for r in csv.DictReader(open(args.csv))]
FileNotFoundError: [Errno 2] No such file or directory: 'resistance_variants.csv'
Cleaning up after failed run
Cleaning up after failed run
ERROR ntm-profiler:55
################################# ERROR #######################################
This run has failed. Please check all arguments and make sure all input files
exist. If no solution is found, please open up an issue at
https://github.com/jodyphelan/NTM-Profiler/issues/new and paste or attach the
contents of the error log (1d14c959-8c57-4537-9d0a-364d402ae24d.errlog.txt)
###############################################################################
The error log is
ntm-profiler error report
- OS: linux
- ntm-profiler version: 0.3.0
- pathogen-profiler version: 3.1.0
- Program call:
{'no_clean': False, 'logging': 'DEBUG', 'repo': 'https://github.com/ntm-db/ntm-db.git', 'branch': 'master', 'commit': None, 'dir': '.', 'temp': '.', 'func': <function main_update_db at 0x149324f12a70>, 'software_name': 'ntm-profiler', 'tmp_prefix': 'cb8c3dd4-29ec-49e7-9543-58eb6d414fce', 'files_prefix': './cb8c3dd4-29ec-49e7-9543-58eb6d414fce'}
Traceback:
File "/home/pgc29/.conda/envs/ntmprofiler_v0.3.0/bin/ntm-profiler", line 390, in <module>
args.func(args)
File "/home/pgc29/.conda/envs/ntmprofiler_v0.3.0/bin/ntm-profiler", line 216, in main_update_db
pp.run_cmd(f'ntm-profiler create_resistance_db --prefix {species.replace(" ","_")} --csv resistance_variants.csv {barcode_arg} --load')
File "/home/pgc29/.conda/envs/ntmprofiler_v0.3.0/lib/python3.10/site-packages/pathogenprofiler/utils.py", line 392, in run_cmd
raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,result.stderr.decode()))
Value:
Command Failed:
/bin/bash -c set -o pipefail; ntm-profiler create_resistance_db --prefix M --csv resistance_variants.csv --barcode barcode.bed --load
stderr:
Traceback (most recent call last):
File "/home/pgc29/.conda/envs/ntmprofiler_v0.3.0/bin/ntm-profiler", line 390, in <module>
args.func(args)
File "/home/pgc29/.conda/envs/ntmprofiler_v0.3.0/bin/ntm-profiler", line 177, in create_resistance_db
pp.create_db(args,extra_files=extra_files)
File "/home/pgc29/.conda/envs/ntmprofiler_v0.3.0/lib/python3.10/site-packages/pathogenprofiler/db.py", line 417, in create_db
hgvs_variants = [r for r in csv.DictReader(open(args.csv))]
FileNotFoundError: [Errno 2] No such file or directory: 'resistance_variants.csv'
Cleaning up after failed run
jodyphelan commented
Thanks @pgcudahy , I'm going to be releasing a new version shortly that will have this fixed!