MG detuplication step not appearing in snakemake stdout.
Files generated, but there seems to be not stdout for that step...
Looks like it does appear in the log, but it appears after the annotation rule... I wonder if the analysis went fine, if this was the case...
This behaviour seems consistent across all analyses samples. Wonder if the analysis itself is fine...
rule ANALYSIS_ANNOTATE:
input: /output/Assembly/MGMT.assembly.merged.fa, /databases/cm/Bacteria.i1i, /databases/genus/Staphylococcus.phr, /databases/hmm/CLUSTERS.hmm.h3f, /databases/kingdom/Archaea/sprot.phr
output: /output/Analysis/annotation/annotation.filt.gff
log: /output/Analysis/Analysis.log
benchmark: /output/Analysis/benchmarks/ANALYSIS_ANNOTATE.json
Softlinking /usr/bin/../db to /databases
18 of 40 steps (45%) done
rule PREPROCESSING_MG_DEDUPLICATE:
input: /output/Preprocessing/MG.R1.fq, /output/Preprocessing/MG.R2.fq
output: /output/Preprocessing/MG.R1.uniq.fq, /output/Preprocessing/MG.R2.uniq.fq
log: /output/Preprocessing/Preprocessing.log
benchmark: /output/Preprocessing/benchmarks/PREPROCESSING_MG_DEDUPLICATE.json
19 of 40 steps (48%) done
rule ANALYSIS_MG_READ_COUNT:
input: /output/Preprocessing/MG.R1.fq, /output/Preprocessing/MG.R2.fq, /output/Preprocessing/MG.R1.uniq.fq, /output/Preprocessing/MG.R2.uniq.fq, /output/Preprocessing/MG.R1.uniq.trimmed.fq, /output/Preprocessing/MG.R2.uniq.trimmed.fq, /output/Preprocessing/MG.SE.uniq.trimmed.fq, /output/Preprocessing/MG.R1.uniq.trimmed.hg38.fq, /output/Preprocessing/MG.R2.uniq.trimmed.hg38.fq, /output/Preprocessing/MG.SE.uniq.trimmed.hg38.fq
output: /output/Analysis/MG.read_counts.txt
log: /output/Analysis/Analysis.log
benchmark: /output/Analysis/benchmarks/ANALYSIS_MG_READ_COUNT.json