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konradjk / loftee

MIT License
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Failed to compile plugin LoF: Can't locate List/MoreUtils.pm in @INC #62

Open jielab opened 4 years ago

jielab commented 4 years ago

Hi, I am trying to run loftee on Linux. Below is my command and error message.

Can someone please kindly let me know what is wrong here?

Thank you & best regards, jie

=== my command === vep -i all.tmp6.vcf --vcf --cache --dir /mnt/d/data/vep_cache --offline --assembly GRCh38 -o all.tmp7.vcf --force_overwrite --sift b --canonical --symbol --plugin LoF,loftee_path:/mnt/d/software_lin/loftee,human_ancestor_fa:/d/mnt/data/gatk_bundle/hg38/Homo_sapiens_assembly38.fasta.gz --dir_plugins /mnt/d/software_lin/loftee

=== the error === Smartmatch is experimental at /mnt/d/software_lin/loftee/de_novo_donor.pl line 175. Smartmatch is experimental at /mnt/d/software_lin/loftee/de_novo_donor.pl line 214. Smartmatch is experimental at /mnt/d/software_lin/loftee/splice_site_scan.pl line 191. Smartmatch is experimental at /mnt/d/software_lin/loftee/splice_site_scan.pl line 194. Smartmatch is experimental at /mnt/d/software_lin/loftee/splice_site_scan.pl line 238. Smartmatch is experimental at /mnt/d/software_lin/loftee/splice_site_scan.pl line 241. WARNING: Failed to compile plugin LoF: Can't locate List/MoreUtils.pm in @INC (you may need to install the List::MoreUtils module) (@INC contains: /mnt/d/software_lin/loftee /mnt/d/software_lin/ensembl_vep/modules /mnt/d/software_lin/ensembl_vep /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /mnt/d/software_lin/loftee/svm.pl line 5. BEGIN failed--compilation aborted at /mnt/d/software_lin/loftee/svm.pl line 5. Compilation failed in require at /mnt/d/software_lin/loftee/LoF.pm line 34. Compilation failed in require at (eval 32) line 2. BEGIN failed--compilation aborted at (eval 32) line 2.

Ninjahelicopter commented 4 years ago

Hi, I have the similar problem. Did you fix your issue?

jielab commented 4 years ago

yes, after i followed "Additional components" instruction at https://useast.ensembl.org/info/docs/tools/vep/script/vep_download.html