Closed HenrikBengtsson closed 4 years ago
$ module load CBI sratoolkit 2020-04-01 18:57:05 ⌚ qb3-dev3 in ~/repositories/UCSF-CBC/CBI-software/CBI/sratoolkit ± → fastq-dump --help Can't locate JSON/PP.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /wynton/home/cbi/shared/software/CBI/sratoolkit-2.10.0/bin/fastq-dump line 12. BEGIN failed--compilation aborted at /wynton/home/cbi/shared/software/CBI/sratoolkit-2.10.0/bin/fastq-dump line 12.
The installation is in https://github.com/HenrikBengtsson/CBI-software/blob/develop/CBI/sratoolkit/
Installing 2.10.5 fixed the problem. It looks the above bug was specific to 2.10.0, cf. https://github.com/ncbi/sra-tools/issues/219
Issue
Troubleshooting
The installation is in https://github.com/HenrikBengtsson/CBI-software/blob/develop/CBI/sratoolkit/