rm -rf ./config/
rm -rf ./data/
rm -rf .Rproj.user
rm -rf _config.yml
rm -rf .gitignore
rm -rf .Rhistory
rm -rf index.md
rm -rf guinea_pore_c.Rproj
rm -rf ./docs/
rm -rf ./logs/
rm -rf ./scripts/
rm -rf ./results/02_basecalling/
rm -rf ./results/03_initial_qc/
rm -rf ./results/04_pore_c_snakemake_pipeline_run/reference_genome/
rm -rf ./results/04_pore_c_snakemake_pipeline_run/Pore-C-Snakemake/
rm -rf ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/basecall/
rm -rf ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/benchmarks/
rm -rf ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/juicebox/juicer_tools.jar
rm -rf ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/logs/
rm -rf ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/mapping/*.txt
rm -rf ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/merged_contacts/NlaIII_run01_Cavpor3.0_unphased.concatemer_summary.csv
rm -rf ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/merged_contacts/NlaIII_run01_Cavpor3.0_unphased.fofn.txt
rm -rf ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/virtual_digest/NlaIII_Cavpor3.0.vd.catalog.yaml
rm -rf ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/pipeline_dag.png
rm -rf ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/pipeline_rulegraph.png
rm -rf ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/contacts/
rm -rf ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/align_table/
rm -rf ./results/README.md
rm -rf ./results/05_look_at_outputs/
rm -rf ./results/06_data_visualisation/
rm -rf ./scripts/
rm -rf ./seq_reports/
rm -rf ./index.md
rm -rf ./_config.yml
rm -rf ./.gitignore
rm -rf ./.git/
cd /NGS/scratch/KSCBIOM/HumanGenomics/
mv /NGS/scratch/KSCBIOM/HumanGenomics/guinea_pore_c/ /NGS/clinicalgenomics/archive/2022/results/Additional files remaining after cleaning up (everything kept and not included in the github repo)
cd /NGS/clinicalgenomics/archive/2022/results/guinea_pore_c/
ls -lhv ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/mapping/My output (click to expand)
total 64G
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.5G Aug 23 2022 NlaIII_run01_batch1_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch1_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.5G Aug 23 2022 NlaIII_run01_batch2_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch2_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.6G Aug 23 2022 NlaIII_run01_batch3_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch3_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.5G Aug 23 2022 NlaIII_run01_batch4_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch4_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.5G Aug 23 2022 NlaIII_run01_batch5_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch5_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.5G Aug 23 2022 NlaIII_run01_batch6_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch6_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.4G Aug 23 2022 NlaIII_run01_batch7_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch7_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.4G Aug 23 2022 NlaIII_run01_batch8_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch8_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.5G Aug 23 2022 NlaIII_run01_batch9_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch9_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.5G Aug 23 2022 NlaIII_run01_batch10_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch10_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.5G Aug 23 2022 NlaIII_run01_batch11_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch11_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.5G Aug 23 2022 NlaIII_run01_batch12_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch12_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.5G Aug 23 2022 NlaIII_run01_batch13_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch13_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.9G Aug 23 2022 NlaIII_run01_batch14_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch14_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.8G Aug 23 2022 NlaIII_run01_batch15_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch15_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.8G Aug 23 2022 NlaIII_run01_batch16_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch16_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.8G Aug 23 2022 NlaIII_run01_batch17_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch17_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.7G Aug 23 2022 NlaIII_run01_batch18_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch18_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.9G Aug 23 2022 NlaIII_run01_batch19_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch19_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.9G Aug 23 2022 NlaIII_run01_batch20_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch20_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.9G Aug 23 2022 NlaIII_run01_batch21_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch21_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.8G Aug 23 2022 NlaIII_run01_batch22_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch22_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.8G Aug 23 2022 NlaIII_run01_batch23_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch23_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.8G Aug 23 2022 NlaIII_run01_batch24_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch24_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.7G Aug 23 2022 NlaIII_run01_batch25_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch25_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.8G Aug 23 2022 NlaIII_run01_batch26_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch26_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.8G Aug 23 2022 NlaIII_run01_batch27_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch27_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.7G Aug 23 2022 NlaIII_run01_batch28_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch28_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.7G Aug 23 2022 NlaIII_run01_batch29_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.4M Aug 23 2022 NlaIII_run01_batch29_Cavpor3.0.coord_sort.bam.bai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 739M Aug 23 2022 NlaIII_run01_batch30_Cavpor3.0.coord_sort.bam
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 2.8M Aug 23 2022 NlaIII_run01_batch30_Cavpor3.0.coord_sort.bam.bails -lhv ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/assembly/My output (click to expand)
total 4.0G
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 3.0G Aug 23 2022 NlaIII_run01_Cavpor3.0_unphased.salsa.bedls -lhv ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/matrix/My output (click to expand)
total 371M
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 43M Aug 23 2022 NlaIII_run01_Cavpor3.0_unphased.matrix.cool
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 234M Aug 23 2022 NlaIII_run01_Cavpor3.0_unphased.matrix.mcoolls -lhv ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/merged_contacts/My output (click to expand)
total 82M
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 62M Aug 23 2022 NlaIII_run01_Cavpor3.0_unphased.concatemers.parquet
drwxrws--- 2 lkemp SEC_lab_KSCBIOM 1.1K Aug 23 2022 NlaIII_run01_Cavpor3.0_unphased.contacts.parquetls -lhv ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/merged_contacts/NlaIII_run01_Cavpor3.0_unphased.contacts.parquet/My output (click to expand)
total 1.6G
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 38M Aug 23 2022 part.0.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 38M Aug 23 2022 part.1.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 39M Aug 23 2022 part.2.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 38M Aug 23 2022 part.3.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 39M Aug 23 2022 part.4.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 38M Aug 23 2022 part.5.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 36M Aug 23 2022 part.6.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 36M Aug 23 2022 part.7.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 39M Aug 23 2022 part.8.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 38M Aug 23 2022 part.9.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 38M Aug 23 2022 part.10.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 38M Aug 23 2022 part.11.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 38M Aug 23 2022 part.12.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 46M Aug 23 2022 part.13.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 44M Aug 23 2022 part.14.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 43M Aug 23 2022 part.15.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 43M Aug 23 2022 part.16.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 42M Aug 23 2022 part.17.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 47M Aug 23 2022 part.18.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 46M Aug 23 2022 part.19.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 45M Aug 23 2022 part.20.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 45M Aug 23 2022 part.21.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 43M Aug 23 2022 part.22.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 44M Aug 23 2022 part.23.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 42M Aug 23 2022 part.24.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 43M Aug 23 2022 part.25.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 44M Aug 23 2022 part.26.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 41M Aug 23 2022 part.27.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 43M Aug 23 2022 part.28.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 15M Aug 23 2022 part.29.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 19K Aug 23 2022 _common_metadata
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 140K Aug 23 2022 _metadatals -lhv ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/pairs/My output (click to expand)
total 3.5G
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 537M Aug 23 2022 NlaIII_run01_Cavpor3.0_unphased.sorted.pairs.gz
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 23M Aug 23 2022 NlaIII_run01_Cavpor3.0_unphased.sorted.pairs.gz.px2
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 2.1G Aug 23 2022 NlaIII_run01_Cavpor3.0_unphased.unsorted.pairsls -lhv ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/refgenome/My output (click to expand)
total 9.4G
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 71K Aug 23 2022 Cavpor3.0.rg.catalog.yaml
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 55K Aug 23 2022 Cavpor3.0.rg.chromsizes
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 2.6G Aug 23 2022 Cavpor3.0.rg.fa
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 962K Aug 23 2022 Cavpor3.0.rg.fa.amb
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 468K Aug 23 2022 Cavpor3.0.rg.fa.ann
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 2.6G Aug 23 2022 Cavpor3.0.rg.fa.bwt
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 100K Aug 23 2022 Cavpor3.0.rg.fa.fai
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 650M Aug 23 2022 Cavpor3.0.rg.fa.pac
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 1.3G Aug 23 2022 Cavpor3.0.rg.fa.sa
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 55K Aug 23 2022 Cavpor3.0.rg.metadata.csvls -lhv ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/virtual_digest/My output (click to expand)
total 214M
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 160M Aug 23 2022 NlaIII_Cavpor3.0.vd.fragments.parquet
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 140K Aug 23 2022 NlaIII_Cavpor3.0.vd.digest_stats.csvls -lhv ./results/04_pore_c_snakemake_pipeline_run/pipeline_run/juicebox/My output (click to expand)
total 6.2G
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 97M Aug 23 2022 NlaIII_Cavpor3.0.hicRef
-rw-rw---- 1 lkemp SEC_lab_KSCBIOM 4.5G Aug 23 2022 NlaIII_run01_Cavpor3.0_unphased.mnd.txtLocally we have:
- Partial Pore-C-Snakemake pipeline outputs
In the github repo we have: