TYPEx:TIERED:STRATIFY:tier_one_ref crashes with error exit status 1

[MargotCh]

Hi,
I'm trying to run TYPEx on my user provided cell objects table with this command:

#!/bin/bash
#SBATCH --job-name=typex
#SBATCH --partition=cpu-single
#SBATCH --ntasks=1
#SBATCH --time=06:00:00
#SBATCH --mem=4gb
#LOAD MODULES
module load devel/java_jdk/1.18
module load system/singularity/3.9.2
# export cache directory for singularity
export NXF_SINGULARITY_CACHEDIR='.cache'

release="TYPEx_test"
nextflow run TYPEx/main.nf \
   -c $PWD/test.config \
   --input_dir $PWD/TYPEx/results/ \
   --input_table $PWD/TYPEx/data/cell_objects.txt \
   --sample_file $PWD/TYPEx/data/sample_file.txt \
   --release $release \
   --output_dir "$PWD/TYPEx/results/$release/" \
   --params_config "$PWD/TYPEx/data/typing_params.json" \
   --annotation_config "$PWD/TYPEx/data/cell_type_annotation.json" \
   --color_config $PWD/TYPEx/conf/celltype_colors.json \
   -profile singularity

I've tried running it both locally and on a cluster but it crashes every time at the TYPEx:TIERED:STRATIFY:tier_one_ref step with this error message:

ERROR ~ Error executing process > 'TYPEx:TIERED:STRATIFY:tier_one_ref'

Caused by:
  Process `TYPEx:TIERED:STRATIFY:tier_one_ref` terminated with an error exit status (1)

Command executed:

  export BASE_DIR=/gpfs/bwfor/work/ws/hd_qk451-typex/TYPEx
  export PARAMS_CONF=/gpfs/bwfor/work/ws/hd_qk451-typex/TYPEx/data/typing_params.json
  export ANN_CONF=/gpfs/bwfor/work/ws/hd_qk451-typex/TYPEx/data/cell_type_annotation.json
  export COL_CONF=/gpfs/bwfor/work/ws/hd_qk451-typex/TYPEx/conf/celltype_colors.json
  
  typing.R --wDir /gpfs/bwfor/work/ws/hd_qk451-typex/TYPEx/results/TYPEx_test/ 			--nfDir nfData 			--method cellassign  			--subset major 			--markers major_markers 			--run TYPEx_test 	--panel p1 			--regFile /gpfs/bwfor/work/ws/hd_qk451-typex/TYPEx/data/sample_file.txt 			--tissAreaDir "/gpfs/bwfor/work/ws/hd_qk451-typex/TYPEx/results/TYPEx_test//tissue_seg/" 			--celltypeModelFile /gpfs/bwfor/work/ws/hd_qk451-typex/TYPEx/results/TYPEx_test//review/p1_major_markers.RData 			--stratify true 		--mostFreqCellType "None" 			--major_markers "major_markers"

Command exit status:
  1

Command output:
  Reading cell-type annotation config /gpfs/bwfor/work/ws/hd_qk451-typex/TYPEx/data/cell_type_annotation.json 
  Reading typing config /gpfs/bwfor/work/ws/hd_qk451-typex/TYPEx/data/typing_params.json 
  Reading typing config /gpfs/bwfor/work/ws/hd_qk451-typex/TYPEx/conf/celltype_colors.json 

Command error:
  Error in read_fst(path, columns, from, to, as.data.table, old_format) : 
    Error opening fst file for reading, please check access rights and file availability
  Calls: <Anonymous> -> read_fst
  Execution halted

I've made sure that all three files the error message is mentioning ( cell_type_annotation.json, typing_params.json, celltype_colors.json) are available and have access rights -rwxr-xr-x

Have you encountered this error before and could point me to how to solve it? Please let me know if you need additional information from me.

Thank you very much!
Best,
Margot

[Precancer]

Hi Margot,

The tier_one_ref process has thrown this error because it depends on output that should have been generated with the preceding tier_one process, but this file doesn't seem to be there. Can you confirm that the tier_one process has completed successfully and you see the file results/major/major_markers/cellassign/*clusters.fst?

Best wishes

[MargotCh]

Hi, thanks for your answer!

So it seems that I have the folder results/TYPEx_test/major/major_markers/cellassign/ but it contains nothing save for an empty .log file. That means that the tier_one process did not run correctly? Do you know what might have caused it?