ValueError: could not convert string to float: '[0.5]' about open-cravat HOT 7 CLOSED

Hi Joshua,

Could you send the content of sample.vcf.log if available? When I ran the above steps, I got a different exception before reporter ran. Also, is your wget url in fact the raw text of sample.vcf at https://raw.githubusercontent.com/vcflib/vcflib/master/samples/sample.vcf ?

from open-cravat.

You're right, my URL for the vcf was incorrect. It should be https://raw.githubusercontent.com/vcflib/vcflib/master/samples/sample.vcf. Now I get a different error:

2020/02/13 07:05:10 cravat started: Thu Feb 13 07:05:10 2020
2020/02/13 07:05:10 cravat conf file: None
2020/02/13 07:05:10 cravat input files: /Users/jgould/Downloads/sample.vcf
2020/02/13 07:05:10 cravat input assembly: hg38
2020/02/13 07:05:10 cravat.converter started: Thu Feb 13 07:05:10 2020
2020/02/13 07:05:10 cravat.converter input files: /Users/jgould/Downloads/sample.vcf
2020/02/13 07:05:10 cravat.converter input format: vcf
2020/02/13 07:05:10 cravat.converter NoneType: None
2020/02/13 07:05:10 cravat.converter error lines: 0
2020/02/13 07:05:10 cravat.converter finished: Thu Feb 13 07:05:10 2020
2020/02/13 07:05:10 cravat.converter num input lines: 9
2020/02/13 07:05:10 cravat.converter runtime: 0.003
2020/02/13 07:05:10 cravat.mapper input file: /Users/jgould/Downloads/sample.vcf.crv
2020/02/13 07:05:10 cravat.mapper mapper database: /Users/Shared/open-cravat/modules/mappers/hg38/data/hg38.sqlite
2020/02/13 07:05:10 cravat.mapper started: Thu Feb 13 07:05:10 2020
2020/02/13 07:05:10 cravat.mapper finished: Thu Feb 13 07:05:10 2020
2020/02/13 07:05:10 cravat.mapper runtime: 0.044
2020/02/13 07:05:10 cravat num_workers: 15
2020/02/13 07:05:11 cravat.clinvar started: Thu Feb 13 07:05:11 2020
2020/02/13 07:05:11 cravat.clinvar finished: Thu Feb 13 07:05:11 2020
2020/02/13 07:05:11 cravat.clinvar runtime: 0.007s
2020/02/13 07:05:13 cravat.aggregator level: variant
2020/02/13 07:05:13 cravat.aggregator input directory: /Users/jgould/Downloads
2020/02/13 07:05:13 cravat.aggregator started: Thu Feb 13 07:05:13 2020
2020/02/13 07:05:13 cravat An unexpected exception occurred.
Traceback (most recent call last):
File "/opt/anaconda3/envs/cravat/lib/python3.8/site-packages/cravat/cravat_class.py", line 375, in main
self.result_path = self.run_aggregator()
File "/opt/anaconda3/envs/cravat/lib/python3.8/site-packages/cravat/cravat_class.py", line 761, in run_aggregator
v_aggregator.run()
File "/opt/anaconda3/envs/cravat/lib/python3.8/site-packages/cravat/aggregator.py", line 141, in run
for lnum, line, rd in reader.loop_data():
File "/opt/anaconda3/envs/cravat/lib/python3.8/site-packages/cravat/inout.py", line 120, in loop_data
out[col_name] = float(tok)
ValueError: could not convert string to float: '[0.5]'
2020/02/13 07:05:13 cravat finished with an exception: Thu Feb 13 07:05:13 2020
2020/02/13 07:05:13 cravat runtime: 2.901s

from open-cravat.

Hi Joshua,

vcf-converter 1.2.10 has been published with a fix for the issue you had. Can you try oc module install vcf-converter -v 1.2.10 and run the job again?

from open-cravat.

I now get a different error:

2020/02/13 14:37:20 cravat started: Thu Feb 13 14:37:20 2020
2020/02/13 14:37:20 cravat conf file: None
2020/02/13 14:37:20 cravat input files: /Users/jgould/sample.vcf
2020/02/13 14:37:20 cravat input assembly: hg38
2020/02/13 14:37:20 cravat.vcfreporter started: Thu Feb 13 14:37:20 2020
2020/02/13 14:37:20 cravat no such table: info
Traceback (most recent call last):
File "/opt/anaconda3/envs/cravat/lib/python3.8/site-packages/cravat/cravat_class.py", line 875, in run_reporter
await reporter.run()
File "/opt/anaconda3/envs/cravat/lib/python3.8/site-packages/cravat/cravat_report.py", line 346, in run
if self.setup() == False:
File "/Users/Shared/open-cravat/modules/reporters/vcfreporter/vcfreporter.py", line 33, in setup
self.cursor2.execute(q)
sqlite3.OperationalError: no such table: info
2020/02/13 14:37:20 cravat finished with an exception: Thu Feb 13 14:37:20 2020
2020/02/13 14:37:20 cravat runtime: 0.368s

from open-cravat.

Please try giving --repeat converter option to your run. The run did not do vcf-converter.

from open-cravat.

Running the following command works. Thanks.

oc run sample.vcf --repeat converter -t vcf -l hg38

from open-cravat.

Great! Let us know if you encounter any issue.

from open-cravat.