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allAmb_DMRfind1222.log
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allAmb_DMRfind1222.log
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methylpy DMRfind --allc-files EPI-41_S38_L005_5xmerg_allc.tsv EPI-42_S39_L005_5xmerg_allc.tsv EPI-43_S40_L005_5xmerg_allc.tsv EPI-44_S41_L005_5xmerg_allc.tsv EPI-119_S31_L005_5xmerg_allc.tsv EPI-120_S32_L005_5xmerg_allc.tsv EPI-135_S35_L005_5xmerg_allc.tsv EPI-136_S36_L005_5xmerg_allc.tsv EPI-151_S2_L002_5xmerg_allc.tsv EPI-152_S3_L002_5xmerg_allc.tsv EPI-153_S4_L002_5xmerg_allc.tsv EPI-154_S5_L002_5xmerg_allc.tsv EPI-181_S16_L003_5xmerg_allc.tsv EPI-182_S17_L003_5xmerg_allc.tsv EPI-184_S18_L003_5xmerg_allc.tsv EPI-185_S19_L003_5xmerg_allc.tsv --samples EPI-41 EPI-42 EPI-43 EPI-44 EPI-119 EPI-120 EPI-135 EPI-136 EPI-151 EPI-152 EPI-153 EPI-154 EPI-181 EPI-182 EPI-184 EPI-185 --mc-type "CGN" --num-procs 8 --output-prefix amb_AllTimes_DMR250bp_MCmax25_cov5x --mc-max-dist 25 --dmr-max-dist 250 --min-num-dms 3 --sample-category 0 0 0 0 1 1 1 1 2 2 2 2 3 3 3 3
Adding Methylation Levels
Sun Dec 22 18:18:49 2019
Done
Sun Dec 22 18:19:37 2019
bash-3.2$ ls
EPI-103_S27_L005_5xmerg_allc.tsv
EPI-104_S28_L005_5xmerg_allc.tsv
EPI-111_S29_L005_5xmerg_allc.tsv
EPI-113_S30_L005_5xmerg_allc.tsv
EPI-119_S31_L005_5xmerg_allc.tsv
EPI-120_S32_L005_5xmerg_allc.tsv
EPI-127_S33_L005_5xmerg_allc.tsv
EPI-128_S34_L005_5xmerg_allc.tsv
EPI-135_S35_L005_5xmerg_allc.tsv
EPI-136_S36_L005_5xmerg_allc.tsv
EPI-143_S37_L005_5xmerg_allc.tsv
EPI-145_S38_L005_5xmerg_allc.tsv
EPI-151_S2_L002_5xmerg_allc.tsv
EPI-152_S3_L002_5xmerg_allc.tsv
EPI-153_S4_L002_5xmerg_allc.tsv
EPI-154_S5_L002_5xmerg_allc.tsv
EPI-159_S6_L002_5xmerg_allc.tsv
EPI-160_S7_L002_5xmerg_allc.tsv
EPI-161_S8_L002_5xmerg_allc.tsv
EPI-162_S9_L002_5xmerg_allc.tsv
EPI-167_S10_L002_5xmerg_allc.tsv
EPI-168_S11_L002_5xmerg_allc.tsv
EPI-169_S12_L002_5xmerg_allc.tsv
EPI-170_S13_L002_5xmerg_allc.tsv
EPI-175_S14_L003_5xmerg_allc.tsv
EPI-176_S15_L003_5xmerg_allc.tsv
EPI-181_S16_L003_5xmerg_allc.tsv
EPI-182_S17_L003_5xmerg_allc.tsv
EPI-184_S18_L003_5xmerg_allc.tsv
EPI-185_S19_L003_5xmerg_allc.tsv
EPI-187_S20_L003_5xmerg_allc.tsv
EPI-188_S21_L003_5xmerg_allc.tsv
EPI-193_S22_L003_5xmerg_allc.tsv
EPI-194_S23_L003_5xmerg_allc.tsv
EPI-199_S24_L003_5xmerg_allc.tsv
EPI-200_S25_L003_5xmerg_allc.tsv
EPI-205_S26_L004_5xmerg_allc.tsv
EPI-206_S27_L004_5xmerg_allc.tsv
EPI-208_S28_L004_5xmerg_allc.tsv
EPI-209_S29_L004_5xmerg_allc.tsv
EPI-214_S30_L004_5xmerg_allc.tsv
EPI-215_S31_L004_5xmerg_allc.tsv
EPI-220_S32_L004_5xmerg_allc.tsv
EPI-221_S33_L004_5xmerg_allc.tsv
EPI-226_S34_L004_5xmerg_allc.tsv
EPI-227_S35_L004_5xmerg_allc.tsv
EPI-229_S36_L004_5xmerg_allc.tsv
EPI-230_S37_L004_5xmerg_allc.tsv
EPI-41_S38_L005_5xmerg_allc.tsv
EPI-42_S39_L005_5xmerg_allc.tsv
EPI-43_S40_L005_5xmerg_allc.tsv
EPI-44_S41_L005_5xmerg_allc.tsv
amb_AllTimes_DMR250bp_MCmax25_cov5x_rms_results.tsv.gz
amb_AllTimes_DMR250bp_MCmax25_cov5x_rms_results_collapsed.tsv
amb_AllTimes_DMR250bp_MCmax25_cov5x_rms_results_collapsed.tsv.DMR.bed
amb_AllTimes_DMR250bp_MCmax25_cov5x_rms_results_collapsed.tsv.DMS.bed
day10_AllpH_DMR250bp_MCmax25_cov5x_rms_results.tsv.gz
day10_AllpH_DMR250bp_MCmax25_cov5x_rms_results_collapsed.tsv
day10_AllpH_DMR250bp_MCmax25_cov5x_rms_results_collapsed.tsv.DMR.bed
day10_AllpH_DMR250bp_MCmax25_cov5x_rms_results_collapsed.tsv.DMS.bed
bash-3.2$ ls
EPI-103_S27_L005_5xmerg_allc.tsv EPI-175_S14_L003_5xmerg_allc.tsv
EPI-41_S38_L005_5xmerg_allc.tsv EPI-104_S28_L005_5xmerg_allc.tsv EPI-176_S15_L003
_5xmerg_allc.tsv EPI-42_S39_L005_5xmerg_allc.tsv EPI-111_S29_L005_5xmerg_allc.tsv
EPI-181_S16_L003_5xmerg_allc.tsv EPI-43_S40_L005_5xmerg_allc.tsv
EPI-113_S30_L005_5xmerg_allc.tsv EPI-182_S17_L003_5xmerg_allc.tsv EPI-44_S41_L005_5xmerg_allc.tsv
EPI-119_S31_L005_5xmerg_allc.tsv EPI-184_S18_L003_5xmerg_allc.tsv amb_AllTimes_DMR250bp_MCmax25_co
v5x_rms_results.tsv.gz
EPI-120_S32_L005_5xmerg_allc.tsv EPI-185_S19_L003_5xmerg_allc.tsv amb_AllTimes_DMR250bp_MCmax25_co
v5x_rms_results_collapsed.tsv
EPI-127_S33_L005_5xmerg_allc.tsv EPI-187_S20_L003_5xmerg_allc.tsv amb_AllTimes_DMR250bp_MCmax25_co
v5x_rms_results_collapsed.tsv.DMR.bed
EPI-128_S34_L005_5xmerg_allc.tsv EPI-188_S21_L003_5xmerg_allc.tsv amb_AllTimes_DMR250bp_MCmax25_co
v5x_rms_results_collapsed.tsv.DMS.bed
EPI-135_S35_L005_5xmerg_allc.tsv EPI-193_S22_L003_5xmerg_allc.tsv day10_AllpH_DMR250bp_MCmax25_cov
5x_rms_results.bed
EPI-136_S36_L005_5xmerg_allc.tsv EPI-194_S23_L003_5xmerg_allc.tsv day10_AllpH_DMR250bp_MCmax25_cov
5x_rms_results.short.bed
EPI-143_S37_L005_5xmerg_allc.tsv EPI-199_S24_L003_5xmerg_allc.tsv day10_AllpH_DMR250bp_MCmax25_cov
5x_rms_results.tsv.gz
EPI-145_S38_L005_5xmerg_allc.tsv EPI-200_S25_L003_5xmerg_allc.tsv day10_AllpH_DMR250bp_MCmax25_cov
5x_rms_results_collapsed.bed
EPI-151_S2_L002_5xmerg_allc.tsv EPI-205_S26_L004_5xmerg_allc.tsv day10_AllpH_DMR250bp_MCmax25_cov
5x_rms_results_collapsed.tsv
EPI-152_S3_L002_5xmerg_allc.tsv EPI-206_S27_L004_5xmerg_allc.tsv day10_AllpH_DMR250bp_MCmax25_cov
5x_rms_results_collapsed.tsv.DMR.bed
EPI-153_S4_L002_5xmerg_allc.tsv EPI-208_S28_L004_5xmerg_allc.tsv day10_AllpH_DMR250bp_MCmax25_cov
5x_rms_results_collapsed.tsv.DMS.bed
EPI-154_S5_L002_5xmerg_allc.tsv EPI-209_S29_L004_5xmerg_allc.tsv day10_DMS_scaffold_position
EPI-159_S6_L002_5xmerg_allc.tsv EPI-214_S30_L004_5xmerg_allc.tsv day135_AllpH_DMR250bp_MCmax25_co
v5x_rms_results.tsv.gz
EPI-160_S7_L002_5xmerg_allc.tsv EPI-215_S31_L004_5xmerg_allc.tsv day135_AllpH_DMR250bp_MCmax25_co
v5x_rms_results_collapsed.tsv
EPI-161_S8_L002_5xmerg_allc.tsv EPI-220_S32_L004_5xmerg_allc.tsv day135_AllpH_DMR250bp_MCmax25_co
v5x_rms_results_collapsed.tsv.DMR.bed
EPI-162_S9_L002_5xmerg_allc.tsv EPI-221_S33_L004_5xmerg_allc.tsv day135_AllpH_DMR250bp_MCmax25_co
v5x_rms_results_collapsed.tsv.DMS.bed
EPI-167_S10_L002_5xmerg_allc.tsv EPI-226_S34_L004_5xmerg_allc.tsv day145_AllpH_DMR250bp_MCmax25_co
v5x_rms_results.tsv.gz
EPI-168_S11_L002_5xmerg_allc.tsv EPI-227_S35_L004_5xmerg_allc.tsv day145_AllpH_DMR250bp_MCmax25_co
v5x_rms_results_collapsed.tsv
EPI-169_S12_L002_5xmerg_allc.tsv EPI-229_S36_L004_5xmerg_allc.tsv day145_AllpH_DMR250bp_MCmax25_co
v5x_rms_results_collapsed.tsv.DMR.bed
EPI-170_S13_L002_5xmerg_allc.tsv EPI-230_S37_L004_5xmerg_allc.tsv day145_AllpH_DMR250bp_MCmax25_co
v5x_rms_results_collapsed.tsv.DMS.bed
bash-3.2$ history | head
7 methylpy call-methylation-state -h
8 exit
9 cd /Volumes/web/metacarcinus/Salmo_Calig/
10 ls
11 cd analyses/
12 ls
13 cd 20190828_Salmo/
14 ls
15 history | grep rsync
16 rsync --verbose *.sorted.bam strigg@mox.hyak.uw.edu:/gscratch/scrubbed/strigg/analyses/20190828_Salmo
bash-3.2$ history | tail
498 ls
499 top
500 ls
501 cd ~/Documents/GitHub/Shelly_Pgenerosa/analyses/20191222/
502 ls
503 methylpy DMRfind --allc-files EPI-41_S38_L005_5xmerg_allc.tsv EPI-42_S39_L005_5xmerg_allc.tsv EPI-43_S40_L005_5xmerg_allc.tsv EPI-44_S41_L005_5xmerg_allc.tsv EPI-119_S31
_L005_5xmerg_allc.tsv EPI-120_S32_L005_5xmerg_allc.tsv EPI-135_S35_L005_5xmerg_allc.tsv EPI-136_S36_L005_5xmerg_allc.tsv EPI-151_S2_L002_5xmerg_allc.tsv EPI-152_S3_L002_5xmerg_
allc.tsv EPI-153_S4_L002_5xmerg_allc.tsv EPI-154_S5_L002_5xmerg_allc.tsv EPI-181_S16_L003_5xmerg_allc.tsv EPI-182_S17_L003_5xmerg_allc.tsv EPI-184_S18_L003_5xmerg_allc.tsv EPI-
185_S19_L003_5xmerg_allc.tsv --samples EPI-41 EPI-42 EPI-43 EPI-44 EPI-119 EPI-120 EPI-135 EPI-136 EPI-151 EPI-152 EPI-153 EPI-154 EPI-181 EPI-182 EPI-184 EPI-185 --mc-type "CG
N" --num-procs 8 --output-prefix amb_AllTimes_DMR250bp_MCmax25_cov5x --mc-max-dist 25 --dmr-max-dist 250 --min-num-dms 3 --sample-category 0 0 0 0 1 1 1 1 2 2 2 2 3 3 3 3
504 ls
505 ls
506 history | head
507 history | tail
bash-3.2$