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License: Apache License 2.0
Generate an enhanced VCF files from ClinVar XML Full releases
License: Apache License 2.0
Dear developers,
I'ive installed all packages required for clinvcf compiling but when I launch the command "nimble install" the process fails with the following message:
"Executing /home/rpracella/.nimble/bin/nim c --colors:on --noNimblePath -d:release -d:NimblePkgVersion=0.0.1 --path:/home/rpracella/.nimble/pkgs2/unicodedb-0.12.0-4452416471e2fe8726eb6070ed6ea7368171cc09 --path:/home/rpracella/.nimble/pkgs2/regex-0.23.0-89466caa353b571cdcd8271f2c797ba2c15a89f2 --path:/home/rpracella/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9 --path:/home/rpracella/.nimble/pkgs2/tiny_sqlite-0.2.0-0efd42349aa1792d82a82b833014311b51be8051 --path:/home/rpracella/.nimble/pkgs2/q-0.0.8-398d2298391a06be1151dcaa6aadd50d84a327ec --path:/home/rpracella/.nimble/pkgs2/hts-0.2.23-d282c5a3bd0e70cdba01bb5809e8435ba7771ca7 -o:/home/rpracella/clinvcf/clinvcf /home/rpracella/clinvcf/src/clinvcf.nim
Hint: used config file '/home/rpracella/.choosenim/toolchains/nim-2.0.2/config/nim.cfg' [Conf]
Hint: used config file '/home/rpracella/.choosenim/toolchains/nim-2.0.2/config/config.nims' [Conf]
......................................................................................................................................................................
/home/rpracella/.nimble/pkgs2/hts-0.2.23-d282c5a3bd0e70cdba01bb5809e8435ba7771ca7/hts/private/hts_concat.nim(1, 2) Error: invalid indentation
nimble.nim(229) buildFromDir
Error: Build failed for the package: clinvcf
Info: Nimble data file "/home/rpracella/.nimble/nimbledata2.json" has been saved."
What's the problem?
Best Wishes,
Riccardo Pracella
Hi,
I am trying to install and use clinVCF however, at the time of compilation I am getting an error. Can you please help?
$ nimble install --verbose
Warning: Package 'clinvcf' has an incorrect structure. The top level of the package source directory should contain at most one module, named 'clinvcf.nim', but a file named 'extractClinvarSet.nim' was found. This will be an error in the future.
Hint: If this is the primary source file in the package, rename it to 'clinvcf.nim'. If it's a source file required by the main module, or if it is one of several modules exposed by 'clinvcf', then move it into a 'clinvcfpkg/' subdirectory. If it's a test file or otherwise not required to build the the package 'clinvcf.nim', prevent its installation by adding `skipFiles = @["extractClinvarSet.nim"]` to the .nimble file. See https://github.com/nim-lang/nimble#libraries for more info.
Verifying dependencies for [email protected]
Reading official package list
Checking for hts@>= 0.2.20 & <= 0.2.23
Installing hts@>= 0.2.20 & <= 0.2.23
Reading official package list
Downloading https://github.com/brentp/hts-nim using git
Cloning latest tagged version: v0.2.23
Error: Could not read package info file in /tmp/nimble_496/githubcom_brentphtsnim_0.2.20_0.2.23/hts.nimble;
... Reading as ini file failed with:
... Invalid section: .
... Evaluating as NimScript file failed with:
... usr/lib/nim/pure/times.nim(79, 9) Error: cannot 'importc' variable at compile time.
When launching clinvcf script I get SIGSEGV error:
./clinvcf --coding-first --genome GRCh37 ClinVarFullRelease_00-latest.xml.gz | bgzip -c > clinvar_GRCh37.vcf.gz
[2022-05-18T14:35:59] - clinvcf - INFO : [main] Genome assembly GRCh37
[2022-05-18T14:35:59] - clinvcf - INFO : [main] Parsing variants from ClinVarFullRelease_00-latest.xml.gz
[2022-05-18T14:39:44] - clinvcf - INFO : [main] clinvarSet=100000
[2022-05-18T14:42:47] - clinvcf - INFO : [main] clinvarSet=200000
[2022-05-18T14:45:20] - clinvcf - INFO : [main] clinvarSet=300000
[2022-05-18T14:48:15] - clinvcf - INFO : [main] clinvarSet=400000
[2022-05-18T14:51:18] - clinvcf - INFO : [main] clinvarSet=500000
[2022-05-18T14:54:01] - clinvcf - INFO : [main] clinvarSet=600000
[2022-05-18T14:56:50] - clinvcf - INFO : [main] clinvarSet=700000
[2022-05-18T14:59:34] - clinvcf - INFO : [main] clinvarSet=800000
[2022-05-18T15:02:20] - clinvcf - INFO : [main] clinvarSet=900000
[2022-05-18T15:04:48] - clinvcf - INFO : [main] clinvarSet=1000000
[2022-05-18T15:07:38] - clinvcf - INFO : [main] clinvarSet=1100000
[2022-05-18T15:10:19] - clinvcf - INFO : [main] clinvarSet=1200000
[2022-05-18T15:12:51] - clinvcf - INFO : [main] clinvarSet=1300000
[2022-05-18T15:15:16] - clinvcf - INFO : [main] clinvarSet=1400000
[2022-05-18T15:17:43] - clinvcf - INFO : [main] clinvarSet=1500000
[2022-05-18T15:20:10] - clinvcf - INFO : [main] clinvarSet=1600000
[2022-05-18T15:23:02] - clinvcf - INFO : [main] clinvarSet=1700000
[2022-05-18T15:25:36] - clinvcf - INFO : [main] clinvarSet=1800000
[2022-05-18T15:28:19] - clinvcf - INFO : [main] clinvarSet=1900000
[2022-05-18T15:31:30] - clinvcf - INFO : [main] clinvarSet=2000000
[2022-05-18T15:32:38] - clinvcf - INFO : [main] Sorting variants
[2022-05-18T15:32:44] - clinvcf - INFO : [main] Printing variants
SIGSEGV: Illegal storage access. (Attempt to read from nil?)
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