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songweizhi / MetaCHIP

Horizontal gene transfer (HGT) identification pipeline
GNU Affero General Public License v3.0
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Issue when parsing the Ranger-DTL2 output, no circos created #36

Open polinanvkv opened 2 years ago

polinanvkv commented 2 years ago

Hi,

I am using MetaCHIP 1.10.9 and there's an issue at the BP step:

[2022-07-04 10:53:41] Filtered blastn results detected, filtration step skipped.
[2022-07-04 10:53:41] Detect HGT among species: input genomes were clustered into 2 species.
[2022-07-04 10:53:42] Detect HGT among species: Best-match approach.
[2022-07-04 10:53:42] Detect HGT among species: get group-to-group identities with 128 cores.
[2022-07-04 10:53:45] Detect HGT among species: analyzing Blast hits with 128 cores.
[2022-07-04 10:53:46] Detect HGT among species: plotting flanking regions with 128 cores.

[2022-07-04 10:55:38] Detect HGT among species: get sequences of BM predicted HGT candidates.
[2022-07-04 10:55:41] Detect HGT among species: done for BM approach!
[2022-07-04 10:55:41] Detect HGT among species: get gene/genome members in gene/species tree for BM predicted HGT candidates.
[2022-07-04 10:55:41] Detect HGT among species: prepare genomes_s_combined_faa.fasta subset.
[2022-07-04 10:55:42] Detect HGT among species: get species and gene tree for 21 BM approach identified HGTs.
[2022-07-04 10:55:43] Detect HGT among species: running Ranger-DTL2.
[2022-07-04 10:55:44] Detect HGT among species: parsing Ranger-DTL2 outputs.
[2022-07-04 10:55:44] Detect HGT among species: add Ranger-DTL predicted direction to genomes_s2_HGTs_PG.txt
Error in contrib.url(repos, type) : 
  trying to use CRAN without setting a mirror
Calls: suppressMessages ... check.packages -> install.packages -> startsWith -> contrib.url
Execution halted

May you please have any suggestions? Thank you :)

vichy123 commented 3 months ago

hello,have you already solved this problem? I have the same issue.