Loading required namespace: GenomicFiles
Using local VCF.
File already tabix-indexed.
Finding empty VCF columns based on first 10,000 rows.
Dropping 1 duplicate column(s).
1 sample detected: EBI-a-GCST005898
Constructing ScanVcfParam object.
VCF contains: 417,240 variant(s) x 1 sample(s)
Reading VCF file: multi-threaded (4 threads)
Timing stopped at: 0.528 0.39 0.386
BiocParallel errors
  4 remote errors, element index: 1, 2, 3, 4
  0 unevaluated and other errors
  first remote error:
Error: scanVcf: scanVcf: scanTabix: '1' not present in tabix index
 path: /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/VCFs/ebi-a-GCST005898.vcf.gz
 index: /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/VCFs/ebi-a-GCST005898.vcf.gz.tbi
  path: /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/VCFs/ebi-a-GCST005898.vcf.gz

Done with all processing in 0.11 minutes.
===================== 🦠🌋🦠 Welcome to MAGMA.Celltyping 🦠🌋🦠 =====================
This package uses MAGMA:
https://ctg.cncr.nl/software/magma

To cite MAGMA.Celltyping, please use:
* Skene, N.G., Bryois, J., Bakken, T.E. et al. Genetic identification of
     brain cell types underlying schizophrenia. Nat Genet 50, 825-833 (2018).
     https://doi.org/10.1038/s41588-018-0129-5
* de Leeuw CA, Mooij JM, Heskes T, Posthuma D (2015) MAGMA: Generalized
     Gene-Set Analysis of GWAS Data. PLOS Computational Biology 11(4): e1004219.
     https://doi.org/10.1371/journal.pcbi.1004219

Please report any bugs or feature requests by filling out an Issues template:
     https://github.com/neurogenomics/MAGMA_Celltyping/issues
===================== 🦠🌋🦠 =========================== 🦠🌋🦠 =====================

Installed MAGMA version: v1.10
Skipping MAGMA installation.
The desired_version of MAGMA is currently installed: v1.10
Using: magma_v1.10
Using existing genome_ref found in storage_dir.
Error in path.expand(x) : invalid 'path' argument
Calls: lapply -> FUN -> <Anonymous> -> fix_path -> path.expand
Execution halted
Loading required namespace: GenomicFiles
Using local VCF.
File already tabix-indexed.
Finding empty VCF columns based on first 10,000 rows.
Dropping 1 duplicate column(s).
1 sample detected: EBI-a-GCST005898
Constructing ScanVcfParam object.
VCF contains: 417,240 variant(s) x 1 sample(s)
Reading VCF file: multi-threaded (4 threads)
Timing stopped at: 0.584 0.395 0.403
BiocParallel errors
  4 remote errors, element index: 1, 2, 3, 4
  0 unevaluated and other errors
  first remote error:
Error: scanVcf: scanVcf: scanTabix: '1' not present in tabix index
 path: /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/VCFs/ebi-a-GCST005898.vcf.gz
 index: /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/VCFs/ebi-a-GCST005898.vcf.gz.tbi
  path: /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/VCFs/ebi-a-GCST005898.vcf.gz

Done with all processing in 0.1 minutes.
Registered S3 methods overwritten by 'treeio':
  method              from    
  MRCA.phylo          tidytree
  MRCA.treedata       tidytree
  Nnode.treedata      tidytree
  Ntip.treedata       tidytree
  ancestor.phylo      tidytree
  ancestor.treedata   tidytree
  child.phylo         tidytree
  child.treedata      tidytree
  full_join.phylo     tidytree
  full_join.treedata  tidytree
  groupClade.phylo    tidytree
  groupClade.treedata tidytree
  groupOTU.phylo      tidytree
  groupOTU.treedata   tidytree
  is.rooted.treedata  tidytree
  nodeid.phylo        tidytree
  nodeid.treedata     tidytree
  nodelab.phylo       tidytree
  nodelab.treedata    tidytree
  offspring.phylo     tidytree
  offspring.treedata  tidytree
  parent.phylo        tidytree
  parent.treedata     tidytree
  root.treedata       tidytree
  rootnode.phylo      tidytree
  sibling.phylo       tidytree
===================== 🦠🌋🦠 Welcome to MAGMA.Celltyping 🦠🌋🦠 =====================
This package uses MAGMA:
https://ctg.cncr.nl/software/magma

To cite MAGMA.Celltyping, please use:
* Skene, N.G., Bryois, J., Bakken, T.E. et al. Genetic identification of
     brain cell types underlying schizophrenia. Nat Genet 50, 825-833 (2018).
     https://doi.org/10.1038/s41588-018-0129-5
* de Leeuw CA, Mooij JM, Heskes T, Posthuma D (2015) MAGMA: Generalized
     Gene-Set Analysis of GWAS Data. PLOS Computational Biology 11(4): e1004219.
     https://doi.org/10.1371/journal.pcbi.1004219

Please report any bugs or feature requests by filling out an Issues template:
     https://github.com/neurogenomics/MAGMA_Celltyping/issues
===================== 🦠🌋🦠 =========================== 🦠🌋🦠 =====================

Installed MAGMA version: v1.10
Skipping MAGMA installation.
The desired_version of MAGMA is currently installed: v1.10
Using: magma_v1.10
genome_ref not found in storage_dir. Downloading from remote server instead ==> /rds/general/project/neurogenomics-lab/ephemeral/magma_storage.20f09b25c2ce8c/g1000_eur
Unzipping file.
Error in path.expand(x) : invalid 'path' argument
Calls: lapply -> FUN -> <Anonymous> -> fix_path -> path.expand
In addition: Warning messages:
1: In utils::download.file(url = input_url, destfile = zipfile) :
  URL https://ctg.cncr.nl/software/MAGMA/ref_data/g1000_eur.zip: cannot open destfile '/rds/general/project/neurogenomics-lab/ephemeral/magma_storage.20f09b25c2ce8c/g1000_eur.zip', reason 'No such file or directory'
2: In utils::download.file(url = input_url, destfile = zipfile) :
  download had nonzero exit status
3: In utils::unzip(zipfile = zipfile, exdir = genome_ref_dir, overwrite = TRUE) :
  error 1 in extracting from zip file
Execution halted