Open yesitsjess opened 5 years ago
Hi Jessica,
It looks like the bowtie and samtools issues you're seeing are just that your shell isn't finding them. The function prepare_inputs accepts arguments for bowtie_exe and samtools_exe. You can just pass the absolute paths to these tools in those arguments.
Best,
Josh
Is there no way to run it directly with inputs as described in my question? I still get errors:
prepare_ceres_inputs(inputs_dir="ceres_inputs",
dep_file="ceres_inputs/ceres_LFC_input.gct",
cn_seg_file="ceres_inputs/ceres_CN_input.tsv",
gene_annot_file="example_data/CCDS.current.txt",
rep_map_file="ceres_inputs/ceres_rep_input.tsv",
genome_id="hg19",
chromosomes=paste0("chr", 1:22),
dep_normalize="zmad",
bowtie_exe="/software/bioinf/bowtie2_v2.2.3/bowtie2",
samtools_exe="/software/bioinf/samtools_v1.4.1/bin/samtools")
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2_v2.2.3/bowtie2-align-s --wrapper basic-0 -t -p 4 -a -v 0 -f -S hg19 /tmp/RtmpDk2HXp/guides.fa /tmp/RtmpDk2HXp/guides.sam
(ERR): bowtie2-align exited with value 1
[E::hts_open_format] fail to open file '/tmp/RtmpDk2HXp/guides.sam'
samtools view: failed to open "/tmp/RtmpDk2HXp/guides.sam" for reading: No such file or directory
Error in value[[3L]](cond) :
failed to open BamFile: file(s) do not exist:
'/tmp/RtmpDk2HXp/guides.bam'
I'm running into similar issues as well. With the same error message. Any solutions to this?
Just an update that I was able to run the example prepare_ceres_inputs()
!
In case anyone else stumbles on this issue in the future, I used the following bowtie and samtools versions:
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="/gsc/software/linux-x86_64-centos7/bowtie-1.2.3/bowtie",
samtools_exe="/gsc/software/linux-x86_64-centos7/samtools-1.9/bin/samtools")
Just an update that I was able to run the example
prepare_ceres_inputs()
!In case anyone else stumbles on this issue I used the following bowtie and samtools versions:
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="/gsc/software/linux-x86_64-centos7/bowtie-1.2.3/bowtie", samtools_exe="/gsc/software/linux-x86_64-centos7/samtools-1.9/bin/samtools")
Thanks for sharing this! :)
I can't get
prepare_ceres_inputs
to work consistently with my proxy settings and, on the rare occasion I do, I can't get it to work with my bowtie and samtools:As a result, I've tried to put together the correct data and supply it directly to
run_ceres
. It fails with error:and the warnings are:
Obviously I'm using real data, but I thought dummy data would help you to spot what I'm doing wrong: