Bug running diffTF with RNAseq count data

Dear Christian,

I was trying to run diffTF with RNAseq count data these days. It was facing a problem when trying to incorporate the count data during the summary-final step:

WARN [2019-08-14 12:06:42] Could not find the parameter designContrastRNA in the configuration file. The default of "~conditionSummary" will be taken as formula. If you know about confounding variables,
rerun this step and add the parameter (see the Documentation for details)
Parsed with column specification:
cols(
ENSEMBL = col_character(),
wt_16_LPS = col_integer(),
wt_17_LPS = col_integer(),
tg_17_LPS = col_integer(),
wt_18_LPS = col_integer(),
tg_18_LPS = col_integer(),
tg_19_LPS = col_integer()
)
WARN [2019-08-14 12:06:48] Filtered 6 sample IDs after comparising sample names with RNA-Seq table
WARN [2019-08-14 12:06:48] Could not find the parameter designContrastRNA in the configuration file. The default of "~conditionSummary" will be taken as formula. If you know about confounding variables, rerun this step and add the parameter (see the Documentation for details)
Error in DESeqDataSet(se, design = design, ignoreRank) :
counts matrix should be numeric, currently it has mode: logical
Calls: DESeqDataSetFromMatrix -> DESeqDataSet
Execution halted
[Wed Aug 14 14:06:48 2019]
Error in rule summaryFinal:
jobid: 1
output: output/FINAL_OUTPUT/extension100/wt_LPSvstg_LPS.all.summary.tsv.gz, output/FINAL_OUTPUT/extension100/wt_LPSvstg_LPS.all.summary.volcano.pdf, output/FINAL_OUTPUT/extension100/wt_LPSvstg_LPS.all.diagnosticPlots.pdf, output/FINAL_OUTPUT/extension100/wt_LPSvstg_LPS.all.diagnosticPlotsClassification1.pdf, output/FINAL_OUTPUT/extension100/wt_LPSvstg_LPS.all.diagnosticPlotsClassification2.pdf, output/FINAL_OUTPUT/extension100/wt_LPSvstg_LPS.all.summary.plots.rds
log: output/LOGS_AND_BENCHMARKS/summaryFinal.R.log (check log file(s) for error message)

RuleException:
CalledProcessError in line 664 of /home/heyj/tools/diffTF/src/Snakefile:
Command ' singularity exec --home /home/heyj/c010-datasets/Internal/COPD/ATAC/190612_3rep_MedLPS/diffTF/LPS_comp_RNA --bind /home/heyj/tools/diffTF/,./,/home/heyj/c010-datasets/Internal/COPD/ATAC/190612_3rep_MedLPS/diffTF/190711/ --bind /home/heyj/miniconda3/lib/python3.7/site-packages:/mnt/snakemake /home/heyj/tools/singularity_containers/bc12f9f5dd66bf5a09489dfa07c45231.simg bash -c 'set -euo pipefail; Rscript --vanilla /home/heyj/c010-datasets/Internal/COPD/ATAC/190612_3rep_MedLPS/diffTF/LPS_comp_RNA/.snakemake/scripts/tmptvl8qi71.summaryFinal.R'' returned non-zero exit status 1.
File "/home/heyj/tools/diffTF/src/Snakefile", line 664, in __rule_summaryFinal
File "/home/heyj/miniconda3/lib/python3.7/concurrent/futures/thread.py", line 57, in run
Removing output files of failed job summaryFinal since they might be corrupted:
output/FINAL_OUTPUT/extension100/wt_LPSvstg_LPS.all.diagnosticPlots.pdf
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

‌

I crosschecked the count input and it seems fine to me:

ENSEMBL wt_16_LPS wt_17_LPS tg_17_LPS wt_18_LPS tg_18_LPS tg_19_LPS
ENSMUSG00000028180 2339 2591 2431 2564 2381 2284
ENSMUSG00000028182 5 5 0 7 10 5
ENSMUSG00000028184 1975 2938 2525 2122 1653 1838
ENSMUSG00000028187 1821 1793 1842 1966 2051 1882
ENSMUSG00000028189 961 1022 1336 981 1338 1183
ENSMUSG00000028188 42 62 24 68 41 77
ENSMUSG00000070074 0 0 0 0 0 1
ENSMUSG00000020755 2291 2615 2556 2228 1930 2172
ENSMUSG00000070077 0 2 0 0 0 2

Thank you for your support.

Best,

Joschka

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