bowtie2-align exited with value 1 with example data

[niekwit]

I am trying to run the example data:

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?

[rhj1993119]

I am having the same issue. Did you solve it?

[niekwit]

Unfortunately not... They don't seem to update their code anymore since many years so I doubt we will get a response for this issue.