Error: tabix is required

[derekwong90]

Hello,

I am trying to get CragR working on our computing environment. However, I’m running into a bit of trouble at the IFS step (Stage 1). I was wondering if you would be able to help? Some information:

I’ve downloaded your CragR scripts (https://github.com/epifluidlab/cragr) onto our environment and call the cragr.R script from it’s location similar to in your wiki page.

#!/bin/bash

module load samtools/1.14
module load tabix/0.2.6
module load R/4.1.0

cd /cluster/projects/pughlab/projects/CHARM/NF1/cragr/output/frags

Rscript /cluster/projects/pughlab/bin/CragR/inst/extdata/scripts/cragr.R ifs -i /cluster/projects/pughlab/projects/CHARM/NF1/cragr/output/frags/TGL49_0166_Cf_n_PE_396_WG.downsample_frag.bed.gz -o /cluster/projects/pughlab/projects/CHARM/NF1/cragr/output/cragr/TGL49_0166_Cf_n_PE_396_WG.downsample_raw_ifs.chr1.bed.gz --gc-correct --genome GRCh38 --exclude-region /cluster/projects/pughlab/bin/CragR/inst/extdata/hg38-blacklist.v2.bed --chrom chr1

The script gets called fine and starts running but when it reads in the frag file I get an error and execution halted. I’ve copied the Error log below:

2023-01-13 12:29:11 INFO::Argument summary:
2023-01-13 12:29:11 INFO::cragr_version=0.1.8.17
2023-01-13 12:29:11 INFO::bedtorch_version=0.1.12.12
2023-01-13 12:29:11 INFO::timestamp=2023-01-13T12:29:11-0500
2023-01-13 12:29:11 INFO::input=/cluster/projects/pughlab/projects/CHARM/NF1/cragr/output/frags/TGL49_0166_Cf_n_PE_396_WG.downsample_frag.bed.gz
2023-01-13 12:29:11 INFO::output=/cluster/projects/pughlab/projects/CHARM/NF1/cragr/output/cragr/TGL49_0166_Cf_n_PE_396_WG.downsample_raw_ifs.chr1.bed.gz
2023-01-13 12:29:11 INFO::genome=GRCh38
2023-01-13 12:29:11 INFO::gc_correct=TRUE
2023-01-13 12:29:11 INFO::gc_correct_method=standard
2023-01-13 12:29:11 INFO::gc_correct_n=1000000
2023-01-13 12:29:11 INFO::chrom=chr1
2023-01-13 12:29:11 INFO::min_mapq=30
2023-01-13 12:29:11 INFO::min_fraglen=50
2023-01-13 12:29:11 INFO::max_fraglen=1000
2023-01-13 12:29:11 INFO::exclude_region=/cluster/projects/pughlab/bin/CragR/inst/extdata/hg38-blacklist.v2.bed
2023-01-13 12:29:11 INFO::window_size=200
2023-01-13 12:29:11 INFO::step_size=20
2023-01-13 12:29:11 INFO::verbose=FALSE
2023-01-13 12:29:11 INFO::help=FALSE
Loading required namespace: BSgenome.Hsapiens.NCBI.GRCh38
2023-01-13 12:29:27 INFO::Process chromosome chr1 ...
2023-01-13 12:29:27 INFO::Loading fragment file /cluster/projects/pughlab/projects/CHARM/NF1/cragr/output/frags/TGL49_0166_Cf_n_PE_396_WG.downsample_frag.bed.gz ...
Error: tabix is required.
Execution halted

I've double checked the input frag files (bed.gz) and they are the same format as in your example. The tabix index (bed.gz.tbi) file is also in the same directory as the frag file.

I'm not sure if this may be the issue but my computing cluster uses modularized tools. If I manually call tabix from the command line I'm able to do it but bedtorch doesn't seem to be able to call it from R even when I run the script from the command line instead of submitting it to a job handler.

Thanks

[dnaase]

Sorry about the late reply. Are you able to run the example fragment file at inst/extdata/ directory? Did you also have the similar problem?