Errors from find_batch_effects.shard_helper.R called in Module07XfBatchEffect

[LNGDingj]

Bug Report

Affected module(s) or script(s)

Module07XfBatchEffect/find_batch_effects.shard_helper.R

How to solve: upgrade R on docker images to R 4.1.x, the errors will disappear

Description

Background: Re-run Module07 with a modified minGQ lookup table on a call set completed last year, Module07MinGQ and follow-up Module07FilterOutlierSamples were completed successfully, however, ran into R script errors in Module07XfBatchEffect

When running XfBatchEffect --> call-check_batch_effects --> check_batch_effects --> call-CompareBatches --> sv-pipeline/scripts/downstream_analysis_and_filtering/find_batch_effects.shard_helper.R script, all shards stopped with the following error message. Command repeated error

/opt/sv-pipeline/scripts/downstream_analysis_and_filtering/find_batch_effects.shard_helper.R \
  freq_table_shard_00001.txt.gz \
  "Batch_1" \
  "Batch_2" \
  "Batch_1_vs_Batch_2.results.txt"

And when running XfBatchEffect --> call-one_vs_all_comparison --> check_batch_effects --> call-CompareBatches --> sv-pipeline/scripts/downstream_analysis_and_filtering/find_batch_effects.shard_helper.R script, all shards stopped with following error message. Command repeated error

/opt/sv-pipeline/scripts/downstream_analysis_and_filtering/find_batch_effects.shard_helper.R \
  freq_table_shard_00001.txt.gz \
  "Batch_1" \
  "ALL_OTHERS" \
  "Batch_1_vs_ALL_OTHERS.results.txt"

freq_table_shard_00001.txt.gz

Docker images used: "XfBatchEffect.sv_pipeline_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:20220302-9bf5ca3b" "XfBatchEffect.sv_pipeline_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:rlc_posthoc_filtering_cnv_mcnv_compatability_9a8561"

Run "find_batch_effects.shard_helper.R" locally in R 4.1.x, all errors disappear, please help to upgrade R on docker images