data_dir <- "/home/niek/Downloads/example_data"
cn_seg_file <- file.path(data_dir, "/CCLE_copynumber_2013-12-03.seg.txt")
gene_annot_file <- file.path(data_dir, "/CCDS.current.txt")
# Set bowtie index directory. Not needed if $BOWTIE_INDEXES environmental variable is set and includes hg19 index.
Sys.setenv(BOWTIE_INDEXES = file.path(data_dir, "bowtie_indexes")) #bowtie indexes were downloaded to this folder
gecko_dep_file <- file.path(data_dir, "Gecko.gct")
gecko_rep_map <- file.path(data_dir, "Gecko_replicate_map.tsv")
wang_dep_file <- file.path(data_dir, "Wang2017.gct")
wang_rep_map <- file.path(data_dir, "Wang2017_replicate_map.tsv")
### Run CERES on Gecko data
gecko_inputs_dir <- file.path("./data/gecko_ceres_inputs", Sys.Date())
prepare_ceres_inputs(inputs_dir=gecko_inputs_dir,
dep_file=gecko_dep_file,
cn_seg_file=cn_seg_file,
gene_annot_file=gene_annot_file,
rep_map_file=gecko_rep_map,
chromosomes=paste0("chr", 1:22),
dep_normalize="zmad",
bowtie_exe = "/home/niek/Downloads/example_data/bowtie2-2.4.2-linux-x86_64/bowtie2",
samtools_exe = "/home/niek/Downloads/example_data/samtools-1.12/bin/samtools")
gecko_ceres <-
wrap_ceres(sg_path=file.path(gecko_inputs_dir, "guide_sample_dep.Rds"),
cn_path=file.path(gecko_inputs_dir, "locus_sample_cn.Rds"),
guide_locus_path=file.path(gecko_inputs_dir, "guide_locus.Rds"),
locus_gene_path=file.path(gecko_inputs_dir, "locus_gene.Rds"),
replicate_map_path=file.path(gecko_inputs_dir, "replicate_map.Rds"),
run_id="Gecko",
params=list(lambda_g=0.68129207))
gecko_ceres_scaled <-
scale_to_essentials(gecko_ceres$gene_essentiality_results$ge_fit)
But I get the following error when trying to run prepare_ceres_inputs():
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home/niek/Downloads/example_data/bowtie2-2.4.2-linux-x86_64/bowtie2-align-s --wrapper basic-0 -t -p 4 -a -v 0 -f -S hg19 /tmp/RtmpU3W3In/guides.fa /tmp/RtmpU3W3In/guides.sam
(ERR): bowtie2-align exited with value 1
[E::hts_open_format] Failed to open file "/tmp/RtmpU3W3In/guides.sam" : No such file or directory
samtools view: failed to open "/tmp/RtmpU3W3In/guides.sam" for reading: No such file or directory
Error in value[[3L]](cond) :
failed to open BamFile: file(s) do not exist:
‘/tmp/RtmpU3W3In/guides.bam’
I have seen this problem in another issue but there was no response. How can I solve this issue?
I am trying to run the example data:
But I get the following error when trying to run
prepare_ceres_inputs()
:I have seen this problem in another issue but there was no response. How can I solve this issue?