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Use of uninitialized value $returnString in concatenation (.) or string at build_genome_index.pl line 141 #46

Closed Cdk29 closed 5 years ago

Cdk29 commented 5 years ago

Good evening,

I get the following error when running :

perl build_genome_index.pl -f hg38.fa -s human -l H. Sapiens -v hg38

build_genome_index.pl: problem encountered running command "build_genome_index.pl/validate_reference.pl -f hg38.fa 2>&1" Failed to execute command: Not a directory

Use of uninitialized value $returnString in concatenation (.) or string at build_genome_index.pl line 141.

build_genome_index.pl: Invalid fasta file supplied, fix and retry.

Died at build_genome_index.pl line 143.

Does someone have a clue about this ? Everything seems to be okay

Cdk29 commented 5 years ago

Good evening,

I would like to add on my previous post that I have construct the reference genome in the usual way getting the fasta files from http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/hg38.analysisSet.chroms.tar.gz and using the usual cat *.fa > hg38.fa to concatenate all chromosomes into one file.

I have also tried today with the fasta file from the human genome from Ensembl but it does not work either.

uma-ramasubramanian commented 5 years ago

Thank you for reporting the issue. Please follow the below support channels based on your region for further support: ngs-amsupport@thermofisher.com (Americas) ngs-eusupport@thermofisher.com (EMEA) ngs-gcsupport@thermofisher.com (Greater China) ngs-sasiasupport@thermofisher.com (South Asia) jptech@thermofisher.com (Japan) APAC customers, please contact your local sales representative, Field Service Engineer or Field Bioinformatics Specialist .