drop: MAE fails with DESeq counts matrix should be numeric

For my Input files the MAE pipeline fails with Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode: logical

Maybe my Input files are off, but I’m unsure if this is a bug or I did configure the input wrong. (GATK has no output?!)

Full output:

Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/centos/miniconda3/envs/drop/share/gatk4-4.1.9.0-0/gatk-package-4.1.9.0-local.jar ASEReadCounter -R /mnt/breast_cancer/refs/GRCH37-Sarek/human_g1k_v37_decoy.fasta -I /mnt/breast_cancer/cinder_backups/qmrkh_data/bam/Probe/I18R008Rf04/QMRKH080A2_I18R008Rf04_accepted_hits.bam -V /mnt/breast_cancer/tests/test1/processed_data/mae/snvs/I18R008Df04–I18R008Rf04.vcf.gz -L Y --verbosity ERROR --QUIET true --disable-sequence-dictionary-validation True I18R008Df04–I18R008Rf04 contig position variantID refAllele altAllele refCount altCount totalCount lowMAPQDepth lowBaseQDepth rawDepth otherBases improperPairs ID [Thu Nov 5 10:14:09 2020] Finished job 46. 8 of 150 steps (5%) done

[Thu Nov 5 10:14:09 2020] rule MonoallelicExpression_pipeline_MAE_deseq_mae_R: input: /mnt/breast_cancer/tests/test1/processed_data/mae/allelic_counts/I18R008Df04–I18R008Rf04.csv.gz, Scripts/MonoallelicExpression/pipeline/MAE/deseq_mae.R output: /mnt/breast_cancer/tests/test1/processed_results/mae/samples/I18R008Df04–I18R008Rf04_res.Rds log: /mnt/breast_cancer/tests/test1/.drop/tmp/MAE/deseq/I18R008Df04–I18R008Rf04.Rds jobid: 10 wildcards: vcf=I18R008Df04, rna=I18R008Rf04

Started with deseq [1] “Running DESeq…” Error in DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode: logical Calls: DESeq4MAE … deseq_for_allele_specific_expression -> DESeqDataSetFromMatrix -> DESeqDataSet Execution halted [Thu Nov 5 10:14:21 2020] Error in rule MonoallelicExpression_pipeline_MAE_deseq_mae_R: jobid: 10 output: /mnt/breast_cancer/tests/test1/processed_results/mae/samples/I18R008Df04–I18R008Rf04_res.Rds log: /mnt/breast_cancer/tests/test1/.drop/tmp/MAE/deseq/I18R008Df04–I18R008Rf04.Rds (check log file(s) for error message)

RuleException: CalledProcessError in line 283 of /tmp/tmp9z1u6jop: Command ‘set -euo pipefail; Rscript --vanilla /mnt/breast_cancer/tests/test1/.snakemake/scripts/tmpcfvzautu.deseq_mae.R’ returned non-zero exit status 1. File “/home/centos/miniconda3/envs/drop/lib/python3.8/site-packages/snakemake/executors/init.py”, line 2208, in run_wrapper File “/tmp/tmp9z1u6jop”, line 283, in __rule_MonoallelicExpression_pipeline_MAE_deseq_mae_R File “/home/centos/miniconda3/envs/drop/lib/python3.8/site-packages/snakemake/executors/init.py”, line 551, in _callback File “/home/centos/miniconda3/envs/drop/lib/python3.8/concurrent/futures/thread.py”, line 57, in run File “/home/centos/miniconda3/envs/drop/lib/python3.8/site-packages/snakemake/executors/init.py”, line 537, in cached_or_run File “/home/centos/miniconda3/envs/drop/lib/python3.8/site-packages/snakemake/executors/init.py”, line 2239, in run_wrapper Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /mnt/breast_cancer/tests/test1/.snakemake/log/2020-11-05T095354.638278.snakemake.log