wglab / icages Goto Github PK

Thanks for your works about ICAGES.
but when I utility it to analysis tumor-normal paired sequencing data in VCF files from GATK4 Metect2. I configure the -t tumor -g normal,then got the following message ,somewhere is likely wrong.
.....
Querying done. Found 1143 matches in 3444 queries.
Average database lookup: 6.93960511033682
Querying done. Found 436 matches in 3444 queries.
Average database lookup: 3.84262485481998
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 356, line 69.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 357, line 69.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 358, line 69.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 359, line 69.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 363, line 69.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 356, line 2093.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 357, line 2093.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 358, line 2093.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 359, line 2093.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 363, line 2093.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 356, line 2293.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 357, line 2293.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 358, line 2293.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 359, line 2293.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 363, line 2293.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 356, line 2508.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 357, line 2508.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 358, line 2508.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 359, line 2508.
Use of uninitialized value within @printGene in hash element at icages/bin/icagesMutationNew.pl line 363, line 2508.

1、Installation: before using iCAGES, please first install it by 'perl icagesInitiate.pl' command.

I run the command line perl icages.pl --help , then got the message. But I can not find the icagesInitiate.pl,

2、WARNING to old ANNOVAR users: this program no longer does line-to-line conversion for multi-sample VCF files. If you want to include all variants in output, use '-format vcf4old' or use '-format vcf4 -allsample -withfreq' instead.NOTICE: Finished reading 252 lines from VCF file。

To add '-format vcf4old' or use '-format vcf4 -allsample -withfreq' to icages.pl , It does not work!

hi~ I had got a problem. It feels like there are something wrong with the database. I had downloaded the database twice.
tar -xzvf /Workspace/Software/icages-1.0.2/db.tar.gz
./db/
./db/cgc.gene
./db/drug.score
./db/hg19_example_db_generic.txt
./db/hg19_example_db_gff3.txt
./db/hg19_funseq2.txt

gzip: stdin: invalid compressed data--format violated
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now
How can I fit it? Thanks~