Wed. Aug. 7, 2019 Geoduck genome paper BS analysis

Amb-low versus super low-low

This analysis focuses on 8 samples:

4 x animals reared in ambient conditions for 23 days
4 x animals reared in super low pH conditions for 23 days
following initial 23 day exposure, all animals were exposed to an ambient common garden indoors for 28 days, then an ambient common garden outdoors for 84 days, then underwent a secondary low pH exposure for 10 days after which they were preserved for methylome analysis.
- see Hollie’s experimental setup here

Compare coverage between v074 and v070

Ran alignment to v074 using same settings as past alignments to v070
- mox scripts here: 20190806_BmrkPgenr074.sh
- output here: https://gannet.fish.washington.edu/metacarcinus/Pgenerosa/analyses/20190806_v074/
Generate coverage reports for past analysis with v070
- mox script here: 20190807_BismarkCoverage2Cytosine.sh
- outupt here: https://gannet.fish.washington.edu/metacarcinus/Pgenerosa/analyses/20190807_Nov1_Pgenr_CytCov/
Generate coverage reports for v074 because that part of the mox script 20190806_BmrkPgenr074.sh failed
- cov report mox script here: 20190807_BmrkCytCov074.sh
- ouput here: https://gannet.fish.washington.edu/metacarcinus/Pgenerosa/analyses/20190806_v074/
Generate sorted bams for v074 analysis because that part of the mox script 20190806_BmrkPgenr074.sh failed
- sorted bams mox script here: 20190807_SortBams_Pgenr.sh
- output here: https://gannet.fish.washington.edu/metacarcinus/Pgenerosa/analyses/20190806_v074/
Ran jupyter notebook to plot coverage for v074
- notebook here: 20190806_Pgnr_cmpr_cov.ipynb
- didn’t get to run this on v070 yet so will do that later

Differential methylation analysis

Updated old methylkit analysis on these samples with v070 alignments to output the DMR files
- R script here: Pgenr_JuviOARRBS_low_vs_ambient.Rmd
- R project here: methylkit_JuviPgenr_allData.Rproj
- DMR files here:
  - v070_ALvSL-L_hyperDMR.tsv
  - v070_ALvSL-L_hypoDMR.tsv
***found this article about cov.bases that Yaamini and Mac have previously mentioned. Doesn’t seem like it makes a difference if this is set to 0 or 1.

Started running methylkit DMR analysis of v074 alignments on Emu

copied bams over to Emu:

 srlab@emu:~/GitHub/Shelly_Pgenerosa/analyses/JuviPgen_ALSL2lowd145/Get_DMRs_for_v074_alignments/dedup_bams$ scp strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Pgenerosa/analyses/20190806_v074/*_dedup.sorted.bam .

Rsync output from copying data from mox to gannet

[strigg@mox2 analyses]$ rsync --archive --progress --verbose /gscratch/scrubbed/strigg/analyses/20190806_v074 strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Pgenerosa/analyses
Password:
building file list ... 
145 files to consider
20190806_v074/
20190806_v074/CHG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,204,054,204 100%   47.20MB/s    0:00:24 (xfr#1, to-chk=143/145)
20190806_v074/CHG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,828,394,312 100%   47.43MB/s    0:00:36 (xfr#2, to-chk=142/145)
20190806_v074/CHG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  2,527,215,131 100%   43.31MB/s    0:00:55 (xfr#3, to-chk=141/145)
20190806_v074/CHG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,776,103,415 100%   44.71MB/s    0:00:37 (xfr#4, to-chk=140/145)
20190806_v074/CHG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,284,122,063 100%   40.32MB/s    0:00:30 (xfr#5, to-chk=139/145)
20190806_v074/CHG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,361,954,058 100%   45.55MB/s    0:00:28 (xfr#6, to-chk=138/145)
20190806_v074/CHG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,064,328,288 100%   44.16MB/s    0:00:22 (xfr#7, to-chk=137/145)
20190806_v074/CHG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,215,726,502 100%   38.94MB/s    0:00:29 (xfr#8, to-chk=136/145)
20190806_v074/CHG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,192,628,629 100%   40.42MB/s    0:00:28 (xfr#9, to-chk=135/145)
20190806_v074/CHG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,807,003,959 100%   43.49MB/s    0:00:39 (xfr#10, to-chk=134/145)
20190806_v074/CHG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  2,509,107,895 100%   44.63MB/s    0:00:53 (xfr#11, to-chk=133/145)
20190806_v074/CHG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,754,028,073 100%   44.31MB/s    0:00:37 (xfr#12, to-chk=132/145)
20190806_v074/CHG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,264,092,387 100%   43.35MB/s    0:00:27 (xfr#13, to-chk=131/145)
20190806_v074/CHG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,349,340,180 100%   44.17MB/s    0:00:29 (xfr#14, to-chk=130/145)
20190806_v074/CHG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,047,667,263 100%   45.74MB/s    0:00:21 (xfr#15, to-chk=129/145)
20190806_v074/CHG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,200,576,000 100%   43.86MB/s    0:00:26 (xfr#16, to-chk=128/145)
20190806_v074/CHH_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  3,658,775,548 100%   43.28MB/s    0:01:20 (xfr#17, to-chk=127/145)
20190806_v074/CHH_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  5,518,727,115 100%   44.28MB/s    0:01:58 (xfr#18, to-chk=126/145)
20190806_v074/CHH_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  7,848,248,612 100%   43.94MB/s    0:02:50 (xfr#19, to-chk=125/145)
20190806_v074/CHH_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  5,472,810,448 100%   41.03MB/s    0:02:07 (xfr#20, to-chk=124/145)
20190806_v074/CHH_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  4,100,955,167 100%   45.49MB/s    0:01:25 (xfr#21, to-chk=123/145)
20190806_v074/CHH_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  4,314,283,667 100%   43.87MB/s    0:01:33 (xfr#22, to-chk=122/145)
20190806_v074/CHH_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  3,392,446,875 100%   45.73MB/s    0:01:10 (xfr#23, to-chk=121/145)
20190806_v074/CHH_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  3,897,193,762 100%   43.08MB/s    0:01:26 (xfr#24, to-chk=120/145)
20190806_v074/CHH_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  3,628,543,634 100%   45.75MB/s    0:01:15 (xfr#25, to-chk=119/145)
20190806_v074/CHH_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  5,473,629,239 100%   42.08MB/s    0:02:04 (xfr#26, to-chk=118/145)
20190806_v074/CHH_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  7,798,653,297 100%   44.89MB/s    0:02:45 (xfr#27, to-chk=117/145)
20190806_v074/CHH_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  5,421,814,698 100%   42.69MB/s    0:02:01 (xfr#28, to-chk=116/145)
20190806_v074/CHH_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  4,061,692,626 100%   43.76MB/s    0:01:28 (xfr#29, to-chk=115/145)
20190806_v074/CHH_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  4,281,496,520 100%   42.04MB/s    0:01:37 (xfr#30, to-chk=114/145)
20190806_v074/CHH_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  3,358,482,102 100%   46.16MB/s    0:01:09 (xfr#31, to-chk=113/145)
20190806_v074/CHH_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  3,871,442,663 100%   44.25MB/s    0:01:23 (xfr#32, to-chk=112/145)
20190806_v074/CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
    794,708,749 100%   43.74MB/s    0:00:17 (xfr#33, to-chk=111/145)
20190806_v074/CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,184,493,224 100%   44.26MB/s    0:00:25 (xfr#34, to-chk=110/145)
20190806_v074/CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,658,009,553 100%   44.12MB/s    0:00:35 (xfr#35, to-chk=109/145)
20190806_v074/CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,141,504,240 100%   39.77MB/s    0:00:27 (xfr#36, to-chk=108/145)
20190806_v074/CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
    823,494,640 100%   41.57MB/s    0:00:18 (xfr#37, to-chk=107/145)
20190806_v074/CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
    874,287,987 100%   35.48MB/s    0:00:23 (xfr#38, to-chk=106/145)
20190806_v074/CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
    681,089,281 100%   44.12MB/s    0:00:14 (xfr#39, to-chk=105/145)
20190806_v074/CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
    785,170,609 100%   42.86MB/s    0:00:17 (xfr#40, to-chk=104/145)
20190806_v074/CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
    782,298,004 100%   44.11MB/s    0:00:16 (xfr#41, to-chk=103/145)
20190806_v074/CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,164,180,284 100%   44.09MB/s    0:00:25 (xfr#42, to-chk=102/145)
20190806_v074/CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,635,665,583 100%   45.41MB/s    0:00:34 (xfr#43, to-chk=101/145)
20190806_v074/CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
  1,122,011,753 100%   40.03MB/s    0:00:26 (xfr#44, to-chk=100/145)
20190806_v074/CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
    806,463,320 100%   40.98MB/s    0:00:18 (xfr#45, to-chk=99/145)
20190806_v074/CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
    861,523,166 100%   44.34MB/s    0:00:18 (xfr#46, to-chk=98/145)
20190806_v074/CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
    667,210,945 100%   39.07MB/s    0:00:16 (xfr#47, to-chk=97/145)
20190806_v074/CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
    769,840,235 100%   44.94MB/s    0:00:16 (xfr#48, to-chk=96/145)
20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_PE_report.html
        365,790 100%  913.60kB/s    0:00:00 (xfr#49, to-chk=95/145)
20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_PE_report.txt
          2,010 100%    4.91kB/s    0:00:00 (xfr#50, to-chk=94/145)
20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam
  1,415,720,462 100%   45.33MB/s    0:00:29 (xfr#51, to-chk=93/145)
20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt
         16,688 100%   20.42kB/s    0:00:00 (xfr#52, to-chk=92/145)
20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam
  1,043,385,336 100%   44.58MB/s    0:00:22 (xfr#53, to-chk=91/145)
20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
     43,234,484 100%   32.80MB/s    0:00:01 (xfr#54, to-chk=90/145)
20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
     37,557,825 100%   33.44MB/s    0:00:01 (xfr#55, to-chk=89/145)
20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt
            879 100%   11.60kB/s    0:00:00 (xfr#56, to-chk=88/145)
20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt
            351 100%    3.33kB/s    0:00:00 (xfr#57, to-chk=87/145)
20190806_v074/EPI-205_S26_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    131,013,238 100%   42.58MB/s    0:00:02 (xfr#58, to-chk=86/145)
20190806_v074/EPI-205_S26_L004_dedup.sorted.bam
    875,133,911 100%   39.16MB/s    0:00:21 (xfr#59, to-chk=85/145)
20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_PE_report.html
        365,855 100%  773.33kB/s    0:00:00 (xfr#60, to-chk=84/145)
20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_PE_report.txt
          2,012 100%    4.14kB/s    0:00:00 (xfr#61, to-chk=83/145)
20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam
  2,032,293,966 100%   45.40MB/s    0:00:42 (xfr#62, to-chk=82/145)
20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt
         16,941 100%   22.30kB/s    0:00:00 (xfr#63, to-chk=81/145)
20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam
  1,537,982,344 100%   42.28MB/s    0:00:34 (xfr#64, to-chk=80/145)
20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
     55,459,884 100%   28.45MB/s    0:00:01 (xfr#65, to-chk=79/145)
20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
     49,266,400 100%   24.98MB/s    0:00:01 (xfr#66, to-chk=78/145)
20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt
            879 100%    0.98kB/s    0:00:00 (xfr#67, to-chk=77/145)
20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt
            351 100%    0.39kB/s    0:00:00 (xfr#68, to-chk=76/145)
20190806_v074/EPI-206_S27_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    133,539,018 100%   34.38MB/s    0:00:03 (xfr#69, to-chk=75/145)
20190806_v074/EPI-206_S27_L004_dedup.sorted.bam
  1,252,773,646 100%   44.58MB/s    0:00:26 (xfr#70, to-chk=74/145)
20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_PE_report.html
        365,982 100%  416.56kB/s    0:00:00 (xfr#71, to-chk=73/145)
20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_PE_report.txt
          2,013 100%    2.23kB/s    0:00:00 (xfr#72, to-chk=72/145)
20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam
  2,921,053,627 100%   45.53MB/s    0:01:01 (xfr#73, to-chk=71/145)
20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt
         17,235 100%  180.98kB/s    0:00:00 (xfr#74, to-chk=70/145)
20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam
  2,135,882,869 100%   45.79MB/s    0:00:44 (xfr#75, to-chk=69/145)
20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
     70,347,871 100%   30.13MB/s    0:00:02 (xfr#76, to-chk=68/145)
20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
     63,718,431 100%   37.28MB/s    0:00:01 (xfr#77, to-chk=67/145)
20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt
            882 100%    1.36kB/s    0:00:00 (xfr#78, to-chk=66/145)
20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt
            353 100%    0.54kB/s    0:00:00 (xfr#79, to-chk=65/145)
20190806_v074/EPI-214_S30_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    136,509,692 100%   35.45MB/s    0:00:03 (xfr#80, to-chk=64/145)
20190806_v074/EPI-214_S30_L004_dedup.sorted.bam
  1,701,814,404 100%   41.84MB/s    0:00:38 (xfr#81, to-chk=63/145)
20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_PE_report.html
        365,857 100%  973.52kB/s    0:00:00 (xfr#82, to-chk=62/145)
20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_PE_report.txt
          2,013 100%    5.17kB/s    0:00:00 (xfr#83, to-chk=61/145)
20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam
  2,126,356,975 100%   42.82MB/s    0:00:47 (xfr#84, to-chk=60/145)
20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt
         16,939 100%  120.74kB/s    0:00:00 (xfr#85, to-chk=59/145)
20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam
  1,503,368,044 100%   45.64MB/s    0:00:31 (xfr#86, to-chk=58/145)
20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
     53,761,313 100%   34.14MB/s    0:00:01 (xfr#87, to-chk=57/145)
20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
     47,824,286 100%   30.12MB/s    0:00:01 (xfr#88, to-chk=56/145)
20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt
            879 100%    1.67kB/s    0:00:00 (xfr#89, to-chk=55/145)
20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt
            352 100%    0.65kB/s    0:00:00 (xfr#90, to-chk=54/145)
20190806_v074/EPI-215_S31_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    133,434,500 100%   38.08MB/s    0:00:03 (xfr#91, to-chk=53/145)
20190806_v074/EPI-215_S31_L004_dedup.sorted.bam
  1,217,722,626 100%   43.99MB/s    0:00:26 (xfr#92, to-chk=52/145)
20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_PE_report.html
        365,799 100%  840.53kB/s    0:00:00 (xfr#93, to-chk=51/145)
20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_PE_report.txt
          2,011 100%    4.46kB/s    0:00:00 (xfr#94, to-chk=50/145)
20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam
  1,646,052,864 100%   44.74MB/s    0:00:35 (xfr#95, to-chk=49/145)
20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt
         16,786 100%  145.07kB/s    0:00:00 (xfr#96, to-chk=48/145)
20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam
  1,099,806,886 100%   45.55MB/s    0:00:23 (xfr#97, to-chk=47/145)
20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
     44,928,221 100%   42.85MB/s    0:00:01 (xfr#98, to-chk=46/145)
20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
     39,035,250 100%   37.95MB/s    0:00:00 (xfr#99, to-chk=45/145)
20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt
            879 100%    0.87kB/s    0:00:00 (xfr#100, to-chk=44/145)
20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt
            351 100%    0.35kB/s    0:00:00 (xfr#101, to-chk=43/145)
20190806_v074/EPI-220_S32_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    131,227,349 100%   33.24MB/s    0:00:03 (xfr#102, to-chk=42/145)
20190806_v074/EPI-220_S32_L004_dedup.sorted.bam
    916,828,880 100%   36.49MB/s    0:00:23 (xfr#103, to-chk=41/145)
20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_PE_report.html
        365,808 100%  675.30kB/s    0:00:00 (xfr#104, to-chk=40/145)
20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_PE_report.txt
          2,011 100%    3.64kB/s    0:00:00 (xfr#105, to-chk=39/145)
20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam
  1,637,659,455 100%   45.28MB/s    0:00:34 (xfr#106, to-chk=38/145)
20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt
         16,797 100%   32.48kB/s    0:00:00 (xfr#107, to-chk=37/145)
20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam
  1,164,916,000 100%   40.76MB/s    0:00:27 (xfr#108, to-chk=36/145)
20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
     47,256,049 100%   21.85MB/s    0:00:02 (xfr#109, to-chk=35/145)
20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
     41,216,575 100%   33.86MB/s    0:00:01 (xfr#110, to-chk=34/145)
20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt
            879 100%    5.33kB/s    0:00:00 (xfr#111, to-chk=33/145)
20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt
            351 100%    1.85kB/s    0:00:00 (xfr#112, to-chk=32/145)
20190806_v074/EPI-221_S33_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    131,667,804 100%   35.43MB/s    0:00:03 (xfr#113, to-chk=31/145)
20190806_v074/EPI-221_S33_L004_dedup.sorted.bam
    971,611,127 100%   39.40MB/s    0:00:23 (xfr#114, to-chk=30/145)
20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_PE_report.html
        365,720 100%  670.07kB/s    0:00:00 (xfr#115, to-chk=29/145)
20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_PE_report.txt
          2,010 100%    3.61kB/s    0:00:00 (xfr#116, to-chk=28/145)
20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam
  1,252,453,489 100%   40.06MB/s    0:00:29 (xfr#117, to-chk=27/145)
20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt
         16,666 100%   20.02kB/s    0:00:00 (xfr#118, to-chk=26/145)
20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam
    903,432,465 100%   40.24MB/s    0:00:21 (xfr#119, to-chk=25/145)
20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
     38,858,828 100%   26.25MB/s    0:00:01 (xfr#120, to-chk=24/145)
20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
     33,470,064 100%   28.27MB/s    0:00:01 (xfr#121, to-chk=23/145)
20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt
            876 100%    6.74kB/s    0:00:00 (xfr#122, to-chk=22/145)
20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt
            350 100%    2.67kB/s    0:00:00 (xfr#123, to-chk=21/145)
20190806_v074/EPI-226_S34_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    130,079,212 100%   31.25MB/s    0:00:03 (xfr#124, to-chk=20/145)
20190806_v074/EPI-226_S34_L004_dedup.sorted.bam
    753,681,291 100%   36.42MB/s    0:00:19 (xfr#125, to-chk=19/145)
20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_PE_report.html
        365,777 100%  404.53kB/s    0:00:00 (xfr#126, to-chk=18/145)
20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_PE_report.txt
          2,009 100%    2.15kB/s    0:00:00 (xfr#127, to-chk=17/145)
20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam
  1,441,673,440 100%   43.08MB/s    0:00:31 (xfr#128, to-chk=16/145)
20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.M-bias.txt
         16,749 100%   18.50kB/s    0:00:00 (xfr#129, to-chk=15/145)
20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam
  1,039,075,931 100%   44.06MB/s    0:00:22 (xfr#130, to-chk=14/145)
20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
     44,195,627 100%   30.02MB/s    0:00:01 (xfr#131, to-chk=13/145)
20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
     38,291,186 100%   30.06MB/s    0:00:01 (xfr#132, to-chk=12/145)
20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt
            878 100%    3.95kB/s    0:00:00 (xfr#133, to-chk=11/145)
20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplication_report.txt
            351 100%    1.54kB/s    0:00:00 (xfr#134, to-chk=10/145)
20190806_v074/EPI-227_S35_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    131,022,369 100%   32.29MB/s    0:00:03 (xfr#135, to-chk=9/145)
20190806_v074/EPI-227_S35_L004_dedup.sorted.bam
    871,297,403 100%   39.97MB/s    0:00:20 (xfr#136, to-chk=8/145)
20190806_v074/bismark_summary_report.html
        272,185 100%  373.85kB/s    0:00:00 (xfr#137, to-chk=7/145)
20190806_v074/bismark_summary_report.txt
          1,545 100%    2.12kB/s    0:00:00 (xfr#138, to-chk=6/145)
20190806_v074/bme.err
        208,573 100%  279.02kB/s    0:00:00 (xfr#139, to-chk=5/145)
20190806_v074/dedup.err
          5,869 100%    7.67kB/s    0:00:00 (xfr#140, to-chk=4/145)
20190806_v074/mapping_dedup_summary.txt
            704 100%    0.91kB/s    0:00:00 (xfr#141, to-chk=3/145)
20190806_v074/slurm-1154897.out
        189,204 100%  233.00kB/s    0:00:00 (xfr#142, to-chk=2/145)
20190806_v074/slurm-1156605.out
            505 100%    0.62kB/s    0:00:00 (xfr#143, to-chk=1/145)
20190806_v074/slurm-1156661.out
         39,001 100%   46.91kB/s    0:00:00 (xfr#144, to-chk=0/145)

sent 151,528,699,160 bytes  received 3,198 bytes  46,036,367.11 bytes/sec
total size is 151,510,187,727  speedup is 1.00

[strigg@mox2 analyses]$ rsync --archive --progress --verbose /gscratch/srlab/strigg/jobs/ strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/mox_jobs/
Password:
building file list ... 
32 files to consider
./
20190806_BmrkPgenr074.sh
          3,445 100%    2.62MB/s    0:00:00 (xfr#1, to-chk=4/32)
20190807_BismarkCoverage2Cytosine.sh
          1,096 100%    1.05MB/s    0:00:00 (xfr#2, to-chk=2/32)
20190807_BmrkCytCov074.sh
          1,042 100% 1017.58kB/s    0:00:00 (xfr#3, to-chk=1/32)
20190807_SortBams_Pgenr.sh
            906 100%  884.77kB/s    0:00:00 (xfr#4, to-chk=0/32)

sent 6,053 bytes  received 310 bytes  1,818.00 bytes/sec
total size is 116,252  speedup is 18.27

[strigg@mox2 20190807_Nov1_Pgenr_CytCov]$ rsync --archive --progress --verbose --exclude "data" /gscratch/scrubbed/strigg/analyses/20190807_Nov1_Pgenr_CytCov strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Pgenerosa/analyses
Password:
building file list ... 
10 files to consider
20190807_Nov1_Pgenr_CytCov/
20190807_Nov1_Pgenr_CytCov/EPI-205_S26_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    327,334,629 100%   46.42MB/s    0:00:06 (xfr#1, to-chk=8/10)
20190807_Nov1_Pgenr_CytCov/EPI-206_S27_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    330,554,417 100%   41.89MB/s    0:00:07 (xfr#2, to-chk=7/10)
20190807_Nov1_Pgenr_CytCov/EPI-214_S30_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    334,319,152 100%   41.36MB/s    0:00:07 (xfr#3, to-chk=6/10)
20190807_Nov1_Pgenr_CytCov/EPI-215_S31_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    330,368,526 100%   41.65MB/s    0:00:07 (xfr#4, to-chk=5/10)
20190807_Nov1_Pgenr_CytCov/EPI-220_S32_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    327,572,369 100%   42.38MB/s    0:00:07 (xfr#5, to-chk=4/10)
20190807_Nov1_Pgenr_CytCov/EPI-221_S33_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    328,162,365 100%   43.61MB/s    0:00:07 (xfr#6, to-chk=3/10)
20190807_Nov1_Pgenr_CytCov/EPI-226_S34_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    326,096,618 100%   34.42MB/s    0:00:09 (xfr#7, to-chk=2/10)
20190807_Nov1_Pgenr_CytCov/EPI-227_S35_L004_cytosine_CpG_cov_report.CpG_report.txt.gz
    327,322,006 100%   40.39MB/s    0:00:07 (xfr#8, to-chk=1/10)
20190807_Nov1_Pgenr_CytCov/slurm-1156627.out
    400,017,493 100%   40.20MB/s    0:00:09 (xfr#9, to-chk=0/10)

sent 3,032,118,715 bytes  received 228 bytes  44,920,280.64 bytes/sec
total size is 3,031,747,575  speedup is 1.00

ouput from copying data from gannet to mox

[strigg@mox2 data]$ scp strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Pgenerosa/analyses/20181101/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz .
Password:
EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz           100%   45MB  40.9MB/s   00:01    
[strigg@mox2 data]$ scp strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Pgenerosa/analyses/20181101/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz .
Password:
EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz           100%   59MB  42.8MB/s   00:01    
[strigg@mox2 data]$ scp strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Pgenerosa/analyses/20181101/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz .
Password:
EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz           100%   77MB  39.2MB/s   00:01    
[strigg@mox2 data]$ scp strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Pgenerosa/analyses/20181101/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz .
Password:
EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz           100%   57MB  41.0MB/s   00:01    
[strigg@mox2 data]$ scp strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Pgenerosa/analyses/20181101/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz .
Password:
EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz           100%   47MB  40.6MB/s   00:01    
[strigg@mox2 data]$ scp strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Pgenerosa/analyses/20181101/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz .
Password:
EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz           100%   49MB  37.0MB/s   00:01    
[strigg@mox2 data]$ scp strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Pgenerosa/analyses/20181101/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz .
Password:
EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz           100%   40MB  39.3MB/s   00:01    
[strigg@mox2 data]$ scp strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Pgenerosa/analyses/20181101/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz .
Password:
EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz           100%   46MB  41.3MB/s   00:01  