run-gen-ref

[StefanoLise]

Hello,

just flagging that 'bwa.kit/run-gen-ref hs38DH' can not find the remote directory (see below error message). I have modified the url38 variable in the script
url38="ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz" and now it seems OK.

Stefano

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bwa.kit/run-gen-ref hs38DH --2023-01-24 11:09:24-- ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz => ‘-’ Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.13, 130.14.250.12, 2607:f220:41f:250::229, ... Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.13|:21... connected. Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /genomes/all/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids ... No such directory ‘genomes/all/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids’.

gzip: stdin: unexpected end of file

Please run 'bwa index hs38DH.fa'...