| ... | ... | @@ -933,6 +933,31 @@ done | paste - - - | awk '$4=100*$2/$3' | \ |
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sed $'1 i\\\nsample\tmapped_reads\ttotal\tpercent_mapped' > mappability_over_5000bp.txt
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```
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###############
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# Troubleshooting - SNAKEMAKE wanting to run everything #
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# DIAMOND - RE-RUN #
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###############
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- When trying to run a single step., i.e. "TEST_DIAMOND" from the "ASSEMBLY_ANNOTATION_RULES"
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- SNAKEMAKE wanted to re-run everything including assemblies
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- using the `-r` flag in a dry-run we saw that some files had a newer timestamp
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## TODO: figure out why certain folders have a newer timestamp
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- The "WORKAROUND" for this is presented below
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```
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# Looking at timestamp with "stat" and editing "timestamp" with touch
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1. stat results/annotation/proteins/flye/lr/merged/no_barcode/assembly.faa
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2. # saved the original fasta file
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cp results/assembly/flye/lr/merged/no_barcode/assembly.fasta results/assembly/flye/lr/merged/no_barcode/assembly.fasta.orig
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3. # replacing the timestamp
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touch -d '14 May 2020 05:17' results/assembly/flye/lr/merged/no_barcode/assembly.fasta
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4. # dry-run
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snakemake -npr -s workflows/assembly_annotation.smk results/annotation/diamond/flye/lr/merged/no_barcode/assembly.tsv
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# created a new bash script to RE-RUN "DIAMOND with the "nr_uniprot_trembl" database
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./src/run_diamond_only.sh "results/annotation/diamond/metaspades_hybrid/lr_no_barcode-sr_ONT3_MG_xx_Rashi_S11/contigs.tsv \
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results/annotation/diamond/megahit/ONT3_MG_xx_Rashi_S11/final.contigs.tsv \
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results/annotation/diamond/flye/lr/merged/no_barcode/assembly.tsv"
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```
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##### Notes - for 2019_GDB data #####
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1. Since **diamond** was inadvertently run on the "new_nr.dmnd (BLAST nucleotide database), the folder was renamed ```mv diamond diamond_new_nr```
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| ... | ... | |
