RScript crash

[dashgenomics]

I tried to run the parser with the newest ClinVar may release

I was stuck at the 1.32. RScript crashed after a few second of run.

Any idea how it happened?

Thanks for developing the tool.

[May 17 12:05:49]: --> Exec 1.32: Rscript join_data.R variant_summary.txt.gz output_tmp/clinvar_alleles_grouped.single.b37.tsv.gz output_tmp/tmp.2017-05-17_11.05.29.clinvar_alleles_combine[May 17 12:05:49]: --> Exec 1.32: Rscript join_data.R variant_summary.txt.gz output_tmp/clinvar_alleles_grouped.single.b37.tsv.gz output_tmp/tmp.2017-05-17_11.05.29.clinvar_alleles_combined.single.b37.tsv.gz
[May 17 12:05:49]: Output (last mod N/A): output_tmp/clinvar_alleles_combined.single.b37.tsv.gz [doesn't exist yet]
[May 17 12:06:13]: [1] 282106 25
[May 17 12:06:37]: [1] 634027 30
[May 17 12:06:44]: Error in write.table(combined, output_table, sep = "\t", row.names = F, :
[May 17 12:06:44]: unimplemented type 'list' in 'EncodeElement'
[May 17 12:06:54]: $write.table(combined, output_table, sep = "\\t", row.names = F, col.names =
[May 17 12:06:54]: <environment: 0x7fc00382c120>
[May 17 12:06:54]: attr(,"error.message")
[May 17 12:06:54]: [1] "Error in write.table(combined, output_table, sep = "\t", row.names = F, : \n unimplemented type 'list' in 'EncodeElement'\n"
[May 17 12:06:54]: attr(,"class")
[May 17 12:06:54]: [1] "dump.frames"
[May 17 12:06:54]: Finished 1.32. Running time: 0:01:04.242256 sec.d.single.b37.tsv.gz
[May 17 12:05:49]: Output (last mod N/A): output_tmp/clinvar_alleles_combined.single.b37.tsv.gz [doesn't exist yet]
[May 17 12:06:13]: [1] 282106 25
[May 17 12:06:37]: [1] 634027 30
[May 17 12:06:44]: Error in write.table(combined, output_table, sep = "\t", row.names = F, :
[May 17 12:06:44]: unimplemented type 'list' in 'EncodeElement'
[May 17 12:06:54]: $write.table(combined, output_table, sep = "\\t", row.names = F, col.names =
[May 17 12:06:54]: <environment: 0x7fc00382c120>
[May 17 12:06:54]: attr(,"error.message")
[May 17 12:06:54]: [1] "Error in write.table(combined, output_table, sep = "\t", row.names = F, : \n unimplemented type 'list' in 'EncodeElement'\n"
[May 17 12:06:54]: attr(,"class")
[May 17 12:06:54]: [1] "dump.frames"
[May 17 12:06:54]: Finished 1.32. Running time: 0:01:04.242256 sec.

[kristjaneerik]

See #33 (comment) -- it's an issue with the newest variant_summary table, you might want to use an older version.