Thur. Jul. 25, 2019 Salmon sea lice methylome data

trimming 5bp from 5’ end of each read

  1. copied data to mox
rsync --archive --progress --verbose strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_adapt/*.fq.gz /gscratch/srlab/strigg/data/Salmo-Calig/
Password:
receiving file list ... 
88 files to consider
16C_26psu_1_S13_L001_R1_001_trimmed.fq.gz
  1,181,815,682 100%   34.40MB/s    0:00:32 (xfr#1, to-chk=87/88)
16C_26psu_1_S13_L001_R2_001_trimmed.fq.gz
  1,244,658,686 100%   33.42MB/s    0:00:35 (xfr#2, to-chk=86/88)
16C_26psu_1_S13_L002_R1_001_trimmed.fq.gz
  1,197,062,541 100%   33.61MB/s    0:00:33 (xfr#3, to-chk=85/88)
16C_26psu_1_S13_L002_R2_001_trimmed.fq.gz
  1,262,286,154 100%   33.07MB/s    0:00:36 (xfr#4, to-chk=84/88)
16C_26psu_2_S14_L001_R1_001_trimmed.fq.gz
    931,644,174 100%   33.56MB/s    0:00:26 (xfr#5, to-chk=83/88)
16C_26psu_2_S14_L001_R2_001_trimmed.fq.gz
    971,546,034 100%   33.68MB/s    0:00:27 (xfr#6, to-chk=82/88)
16C_26psu_2_S14_L002_R1_001_trimmed.fq.gz
    944,608,696 100%   33.11MB/s    0:00:27 (xfr#7, to-chk=81/88)
16C_26psu_2_S14_L002_R2_001_trimmed.fq.gz
    986,091,662 100%   33.97MB/s    0:00:27 (xfr#8, to-chk=80/88)
16C_26psu_3_S15_L001_R1_001_trimmed.fq.gz
    785,839,823 100%   33.19MB/s    0:00:22 (xfr#9, to-chk=79/88)
16C_26psu_3_S15_L001_R2_001_trimmed.fq.gz
    832,267,326 100%   33.12MB/s    0:00:23 (xfr#10, to-chk=78/88)
16C_26psu_3_S15_L002_R1_001_trimmed.fq.gz
    795,555,186 100%   32.82MB/s    0:00:23 (xfr#11, to-chk=77/88)
16C_26psu_3_S15_L002_R2_001_trimmed.fq.gz
    843,634,759 100%   33.87MB/s    0:00:23 (xfr#12, to-chk=76/88)
16C_26psu_4_S16_L001_R1_001_trimmed.fq.gz
    904,443,257 100%   33.07MB/s    0:00:26 (xfr#13, to-chk=75/88)
16C_26psu_4_S16_L001_R2_001_trimmed.fq.gz
    945,294,549 100%   33.66MB/s    0:00:26 (xfr#14, to-chk=74/88)
16C_26psu_4_S16_L002_R1_001_trimmed.fq.gz
    916,864,454 100%   33.28MB/s    0:00:26 (xfr#15, to-chk=73/88)
16C_26psu_4_S16_L002_R2_001_trimmed.fq.gz
    959,381,024 100%   33.95MB/s    0:00:26 (xfr#16, to-chk=72/88)
16C_32psu_1_S1_L001_R1_001_trimmed.fq.gz
    988,175,387 100%   33.00MB/s    0:00:28 (xfr#17, to-chk=71/88)
16C_32psu_1_S1_L001_R2_001_trimmed.fq.gz
  1,032,928,925 100%   33.02MB/s    0:00:29 (xfr#18, to-chk=70/88)
16C_32psu_1_S1_L002_R1_001_trimmed.fq.gz
  1,002,406,038 100%   33.41MB/s    0:00:28 (xfr#19, to-chk=69/88)
16C_32psu_1_S1_L002_R2_001_trimmed.fq.gz
  1,049,057,808 100%   33.56MB/s    0:00:29 (xfr#20, to-chk=68/88)
16C_32psu_2_S2_L001_R1_001_trimmed.fq.gz
    892,974,026 100%   33.13MB/s    0:00:25 (xfr#21, to-chk=67/88)
16C_32psu_2_S2_L001_R2_001_trimmed.fq.gz
    931,742,732 100%   33.57MB/s    0:00:26 (xfr#22, to-chk=66/88)
16C_32psu_2_S2_L002_R1_001_trimmed.fq.gz
    906,032,069 100%   33.58MB/s    0:00:25 (xfr#23, to-chk=65/88)
16C_32psu_2_S2_L002_R2_001_trimmed.fq.gz
    946,108,643 100%   33.23MB/s    0:00:27 (xfr#24, to-chk=64/88)
16C_32psu_3_S3_L001_R1_001_trimmed.fq.gz
    672,513,019 100%   33.92MB/s    0:00:18 (xfr#25, to-chk=63/88)
16C_32psu_3_S3_L001_R2_001_trimmed.fq.gz
    718,296,782 100%   32.60MB/s    0:00:21 (xfr#26, to-chk=62/88)
16C_32psu_3_S3_L002_R1_001_trimmed.fq.gz
    683,707,914 100%   34.10MB/s    0:00:19 (xfr#27, to-chk=61/88)
16C_32psu_3_S3_L002_R2_001_trimmed.fq.gz
    731,201,146 100%   34.27MB/s    0:00:20 (xfr#28, to-chk=60/88)
16C_32psu_4_S4_L001_R1_001_trimmed.fq.gz
    885,169,706 100%   33.67MB/s    0:00:25 (xfr#29, to-chk=59/88)
16C_32psu_4_S4_L001_R2_001_trimmed.fq.gz
    936,641,517 100%   33.89MB/s    0:00:26 (xfr#30, to-chk=58/88)
16C_32psu_4_S4_L002_R1_001_trimmed.fq.gz
    894,824,608 100%   33.89MB/s    0:00:25 (xfr#31, to-chk=57/88)
16C_32psu_4_S4_L002_R2_001_trimmed.fq.gz
    947,373,865 100%   33.83MB/s    0:00:26 (xfr#32, to-chk=56/88)
8C_26psu_1_S9_L001_R1_001_trimmed.fq.gz
    974,034,711 100%   33.51MB/s    0:00:27 (xfr#33, to-chk=55/88)
8C_26psu_1_S9_L001_R2_001_trimmed.fq.gz
  1,018,657,916 100%   33.47MB/s    0:00:29 (xfr#34, to-chk=54/88)
8C_26psu_1_S9_L002_R1_001_trimmed.fq.gz
    985,253,509 100%   34.05MB/s    0:00:27 (xfr#35, to-chk=53/88)
8C_26psu_1_S9_L002_R2_001_trimmed.fq.gz
  1,030,941,630 100%   33.67MB/s    0:00:29 (xfr#36, to-chk=52/88)
8C_26psu_2_S10_L001_R1_001_trimmed.fq.gz
    956,467,174 100%   33.91MB/s    0:00:26 (xfr#37, to-chk=51/88)
8C_26psu_2_S10_L001_R2_001_trimmed.fq.gz
  1,008,088,446 100%   33.04MB/s    0:00:29 (xfr#38, to-chk=50/88)
8C_26psu_2_S10_L002_R1_001_trimmed.fq.gz
    968,170,140 100%   34.43MB/s    0:00:26 (xfr#39, to-chk=49/88)
8C_26psu_2_S10_L002_R2_001_trimmed.fq.gz
  1,021,486,222 100%   33.20MB/s    0:00:29 (xfr#40, to-chk=48/88)
8C_26psu_3_S11_L001_R1_001_trimmed.fq.gz
    837,731,084 100%   33.78MB/s    0:00:23 (xfr#41, to-chk=47/88)
8C_26psu_3_S11_L001_R2_001_trimmed.fq.gz
    889,418,330 100%   33.48MB/s    0:00:25 (xfr#42, to-chk=46/88)
8C_26psu_3_S11_L002_R1_001_trimmed.fq.gz
    850,364,774 100%   33.60MB/s    0:00:24 (xfr#43, to-chk=45/88)
8C_26psu_3_S11_L002_R2_001_trimmed.fq.gz
    903,827,163 100%   34.18MB/s    0:00:25 (xfr#44, to-chk=44/88)
8C_26psu_4_S12_L001_R1_001_trimmed.fq.gz
    685,099,286 100%   33.23MB/s    0:00:19 (xfr#45, to-chk=43/88)
8C_26psu_4_S12_L001_R2_001_trimmed.fq.gz
    733,810,895 100%   33.32MB/s    0:00:21 (xfr#46, to-chk=42/88)
8C_26psu_4_S12_L002_R1_001_trimmed.fq.gz
    692,157,022 100%   32.45MB/s    0:00:20 (xfr#47, to-chk=41/88)
8C_26psu_4_S12_L002_R2_001_trimmed.fq.gz
    741,931,963 100%   33.90MB/s    0:00:20 (xfr#48, to-chk=40/88)
8C_32psu_1_S5_L001_R1_001_trimmed.fq.gz
    644,038,625 100%   32.17MB/s    0:00:19 (xfr#49, to-chk=39/88)
8C_32psu_1_S5_L001_R2_001_trimmed.fq.gz
    672,902,856 100%   33.86MB/s    0:00:18 (xfr#50, to-chk=38/88)
8C_32psu_1_S5_L002_R1_001_trimmed.fq.gz
    654,261,760 100%   32.61MB/s    0:00:19 (xfr#51, to-chk=37/88)
8C_32psu_1_S5_L002_R2_001_trimmed.fq.gz
    684,609,880 100%   34.25MB/s    0:00:19 (xfr#52, to-chk=36/88)
8C_32psu_2_S6_L001_R1_001_trimmed.fq.gz
    677,336,284 100%   33.56MB/s    0:00:19 (xfr#53, to-chk=35/88)
8C_32psu_2_S6_L001_R2_001_trimmed.fq.gz
    713,511,534 100%   33.63MB/s    0:00:20 (xfr#54, to-chk=34/88)
8C_32psu_2_S6_L002_R1_001_trimmed.fq.gz
    685,482,650 100%   33.52MB/s    0:00:19 (xfr#55, to-chk=33/88)
8C_32psu_2_S6_L002_R2_001_trimmed.fq.gz
    722,777,166 100%   32.77MB/s    0:00:21 (xfr#56, to-chk=32/88)
8C_32psu_3_S7_L001_R1_001_trimmed.fq.gz
    714,966,190 100%   33.70MB/s    0:00:20 (xfr#57, to-chk=31/88)
8C_32psu_3_S7_L001_R2_001_trimmed.fq.gz
    744,503,502 100%   33.57MB/s    0:00:21 (xfr#58, to-chk=30/88)
8C_32psu_3_S7_L002_R1_001_trimmed.fq.gz
    725,444,860 100%   34.04MB/s    0:00:20 (xfr#59, to-chk=29/88)
8C_32psu_3_S7_L002_R2_001_trimmed.fq.gz
    756,001,219 100%   33.21MB/s    0:00:21 (xfr#60, to-chk=28/88)
8C_32psu_4_S8_L001_R1_001_trimmed.fq.gz
    809,062,238 100%   32.79MB/s    0:00:23 (xfr#61, to-chk=27/88)
8C_32psu_4_S8_L001_R2_001_trimmed.fq.gz
    852,912,896 100%   32.72MB/s    0:00:24 (xfr#62, to-chk=26/88)
8C_32psu_4_S8_L002_R1_001_trimmed.fq.gz
    819,373,965 100%   32.32MB/s    0:00:24 (xfr#63, to-chk=25/88)
8C_32psu_4_S8_L002_R2_001_trimmed.fq.gz
    864,649,829 100%   33.60MB/s    0:00:24 (xfr#64, to-chk=24/88)
CTRL_16C_26psu_1_S19_L001_R1_001_trimmed.fq.gz
    995,914,609 100%   33.05MB/s    0:00:28 (xfr#65, to-chk=23/88)
CTRL_16C_26psu_1_S19_L001_R2_001_trimmed.fq.gz
  1,046,653,483 100%   32.18MB/s    0:00:31 (xfr#66, to-chk=22/88)
CTRL_16C_26psu_1_S19_L002_R1_001_trimmed.fq.gz
  1,008,505,467 100%   33.89MB/s    0:00:28 (xfr#67, to-chk=21/88)
CTRL_16C_26psu_1_S19_L002_R2_001_trimmed.fq.gz
  1,061,172,085 100%   33.24MB/s    0:00:30 (xfr#68, to-chk=20/88)
CTRL_16C_26psu_2_S21_L001_R1_001_trimmed.fq.gz
    665,572,349 100%   32.74MB/s    0:00:19 (xfr#69, to-chk=19/88)
CTRL_16C_26psu_2_S21_L001_R2_001_trimmed.fq.gz
    690,395,926 100%   32.57MB/s    0:00:20 (xfr#70, to-chk=18/88)
CTRL_16C_26psu_2_S21_L002_R1_001_trimmed.fq.gz
    676,120,755 100%   33.61MB/s    0:00:19 (xfr#71, to-chk=17/88)
CTRL_16C_26psu_2_S21_L002_R2_001_trimmed.fq.gz
    702,212,516 100%   33.12MB/s    0:00:20 (xfr#72, to-chk=16/88)
CTRL_8C_26psu_1_S17_L001_R1_001_trimmed.fq.gz
    745,922,132 100%   33.33MB/s    0:00:21 (xfr#73, to-chk=15/88)
CTRL_8C_26psu_1_S17_L001_R2_001_trimmed.fq.gz
    786,658,607 100%   33.21MB/s    0:00:22 (xfr#74, to-chk=14/88)
CTRL_8C_26psu_1_S17_L002_R1_001_trimmed.fq.gz
    750,447,738 100%   32.95MB/s    0:00:21 (xfr#75, to-chk=13/88)
CTRL_8C_26psu_1_S17_L002_R2_001_trimmed.fq.gz
    792,166,507 100%   30.98MB/s    0:00:24 (xfr#76, to-chk=12/88)
CTRL_8C_26psu_2_S18_L001_R1_001_trimmed.fq.gz
    774,541,704 100%   33.00MB/s    0:00:22 (xfr#77, to-chk=11/88)
CTRL_8C_26psu_2_S18_L001_R2_001_trimmed.fq.gz
    809,441,360 100%   32.88MB/s    0:00:23 (xfr#78, to-chk=10/88)
CTRL_8C_26psu_2_S18_L002_R1_001_trimmed.fq.gz
    787,527,047 100%   33.07MB/s    0:00:22 (xfr#79, to-chk=9/88)
CTRL_8C_26psu_2_S18_L002_R2_001_trimmed.fq.gz
    824,186,923 100%   32.31MB/s    0:00:24 (xfr#80, to-chk=8/88)
Sealice_F1_S20_L001_R1_001_trimmed.fq.gz
  6,433,683,881 100%   33.48MB/s    0:03:03 (xfr#81, to-chk=7/88)
Sealice_F1_S20_L001_R2_001_trimmed.fq.gz
  6,759,833,320 100%   34.14MB/s    0:03:08 (xfr#82, to-chk=6/88)
Sealice_F1_S20_L002_R1_001_trimmed.fq.gz
  6,506,965,617 100%   33.94MB/s    0:03:02 (xfr#83, to-chk=5/88)
Sealice_F1_S20_L002_R2_001_trimmed.fq.gz
  6,838,839,438 100%   33.82MB/s    0:03:12 (xfr#84, to-chk=4/88)
Sealice_F2_S22_L001_R1_001_trimmed.fq.gz
  4,604,859,459 100%   33.92MB/s    0:02:09 (xfr#85, to-chk=3/88)
Sealice_F2_S22_L001_R2_001_trimmed.fq.gz
  4,868,920,579 100%   33.94MB/s    0:02:16 (xfr#86, to-chk=2/88)
Sealice_F2_S22_L002_R1_001_trimmed.fq.gz
  4,662,251,378 100%   33.92MB/s    0:02:11 (xfr#87, to-chk=1/88)
Sealice_F2_S22_L002_R2_001_trimmed.fq.gz
  4,932,290,570 100%   33.79MB/s    0:02:19 (xfr#88, to-chk=0/88)
	
sent 1,956 bytes  received 114,700,514,200 bytes  35,582,601.57 bytes/sec
total size is 114,686,507,361  speedup is 1.00
  1. Ran mox script https://gannet.fish.washington.edu/metacarcinus/mox_jobs/20190725_Trim1st5bp.sh

    • I had tried for a while to make this code as a loop with xargs (see code below), but because i needed to pass a few piped commands including awk and a redirect into xargs, I couldn’t get it to work correctly
!find /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_adapt/*R1_001_trimmed.fq.gz \
| xargs basename -s _L001_R1_001_trimmed.fq.gz | xargs -I{} sh -c \
'gzcat /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_adapt/{}_L001_R1_001_trimmed.fq.gz;awk '\''{if(($1 !~ /^@A00177\:/) && ($1 !~ /^\+$/))print substr($1,6,length($1));else print $1}'\'';gzip > /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_1st5bp/{}_L001_R1_001_trimmed.5bp_3prime.fq.gz

Remaining steps:

  1. copy data from mox to gannet
  2. start fastqc on ostrich
  3. copy fastqc data to emu and run multiqc
  4. see what the quality of data is like

Test Apex

  • got everything plugged in, but never got light to turn on on the Apex controller. Apparently this is the unresolved problem that happened to Sam Gurr too. Will need to call Neptune systems to troubleshoot this. convo with Sam here
Written on July 25, 2019