Mon. Aug. 5, 2019 Salmon + Sea lice BS data analysis

Salmon + Sea lice data analysis

STEP 1. Copied data from mox to ostrich desktop via rsync in a screen

on mox:

screen -S rsync.TRIM1st5bp
	
rsync /gscratch/srlab/strigg/data/Salmo_Calig/TRIM_1st5bp/*.gz strigg@ostrich.fish.washington.edu:~/Desktop/Salmo_Calig

STEP 2. moved data to Gannet

ostrich:TRIM_1st5bp strigg$ pwd
/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_1st5bp

mv ~/Desktop/TRIM_1st5bp/ .

STEP 3. run check sums

on Gannet:

/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_1st5bp md5 * > checksums.md5 

on Mox:

cd /gscratch/srlab/strigg/data/Salmo_Calig/TRIM_1st5bp
md5sum *.gz > checksums.md5
  • this got delayed because of node maintenance

STEP 4. run fastqc on ostrich - see 20190722_SalmonSeaLice_FASTQC_TRIM.ipynb section “#run fastqc on trimmed 1st 5bp + adapter trimmed reads”

STEP 5. copy fastqc output to emu

srlab@emu:~/GitHub/Shelly_Pgenerosa/multiqc$ scp -r strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_1st5bp/FASTQC .
Password:
16C_32psu_2_S2_L002_R1_001_trimmed.5bp_3prime 100%  304KB 304.2KB/s   00:00    
16C_32psu_1_S1_L001_R1_001_trimmed.5bp_3prime 100%  321KB 321.4KB/s   00:00    
16C_32psu_4_S4_L001_R1_001_trimmed.5bp_3prime 100%  308KB 308.0KB/s   00:00    
8C_26psu_4_S12_L001_R1_001_trimmed.5bp_3prime 100%  421KB 420.6KB/s   00:00    
16C_32psu_4_S4_L001_R2_001_trimmed.5bp_3prime 100%  420KB 420.5KB/s   00:00    
16C_26psu_3_S15_L001_R2_001_trimmed.5bp_3prim 100%  424KB 423.9KB/s   00:00    
8C_26psu_3_S11_L001_R1_001_trimmed.5bp_3prime 100%  306KB 306.5KB/s   00:00    
8C_32psu_2_S6_L002_R2_001_trimmed.5bp_3prime_ 100%  308KB 307.6KB/s   00:00    
16C_26psu_4_S16_L002_R1_001_trimmed.5bp_3prim 100%  423KB 422.9KB/s   00:00    
8C_26psu_2_S10_L002_R1_001_trimmed.5bp_3prime 100%  422KB 421.8KB/s   00:00    
16C_32psu_1_S1_L002_R1_001_trimmed.5bp_3prime 100%  327KB 326.6KB/s   00:00    
8C_26psu_2_S10_L001_R2_001_trimmed.5bp_3prime 100%  420KB 420.4KB/s   00:00    
Sealice_F1_S20_L001_R1_001_trimmed.5bp_3prime 100%  414KB 414.1KB/s   00:00    
8C_32psu_1_S5_L002_R2_001_trimmed.5bp_3prime_ 100%  421KB 421.0KB/s   00:00    
16C_32psu_4_S4_L001_R2_001_trimmed.5bp_3prime 100%  313KB 313.1KB/s   00:00    
CTRL_8C_26psu_1_S17_L002_R2_001_trimmed.5bp_3 100%  312KB 312.3KB/s   00:00    
8C_26psu_4_S12_L002_R2_001_trimmed.5bp_3prime 100%  317KB 316.5KB/s   00:00    
16C_32psu_2_S2_L002_R1_001_trimmed.5bp_3prime 100%  419KB 418.6KB/s   00:00    
8C_32psu_2_S6_L001_R2_001_trimmed.5bp_3prime_ 100%  419KB 418.8KB/s   00:00    
16C_26psu_2_S14_L001_R1_001_trimmed.5bp_3prim 100%  420KB 419.7KB/s   00:00    
8C_26psu_3_S11_L001_R1_001_trimmed.5bp_3prime 100%  418KB 418.4KB/s   00:01    
8C_32psu_4_S8_L002_R1_001_trimmed.5bp_3prime_ 100%  421KB 420.6KB/s   00:00    
16C_32psu_3_S3_L002_R2_001_trimmed.5bp_3prime 100%  318KB 318.5KB/s   00:00    
CTRL_8C_26psu_1_S17_L002_R1_001_trimmed.5bp_3 100%  420KB 420.2KB/s   00:00    
CTRL_16C_26psu_1_S19_L001_R1_001_trimmed.5bp_ 100%  309KB 308.7KB/s   00:00    
8C_32psu_3_S7_L002_R2_001_trimmed.5bp_3prime_ 100%  322KB 322.1KB/s   00:00    
16C_32psu_1_S1_L002_R2_001_trimmed.5bp_3prime 100%  423KB 422.8KB/s   00:00    
16C_32psu_2_S2_L001_R2_001_trimmed.5bp_3prime 100%  313KB 313.2KB/s   00:00    
8C_26psu_3_S11_L002_R1_001_trimmed.5bp_3prime 100%  308KB 307.6KB/s   00:00    
8C_26psu_1_S9_L001_R1_001_trimmed.5bp_3prime_ 100%  307KB 306.7KB/s   00:00    
16C_32psu_4_S4_L002_R2_001_trimmed.5bp_3prime 100%  430KB 429.9KB/s   00:00    
16C_32psu_3_S3_L002_R2_001_trimmed.5bp_3prime 100%  421KB 421.1KB/s   00:00    
16C_26psu_4_S16_L002_R1_001_trimmed.5bp_3prim 100%  310KB 309.5KB/s   00:00    
16C_26psu_2_S14_L002_R2_001_trimmed.5bp_3prim 100%  319KB 318.9KB/s   00:00    
16C_32psu_2_S2_L002_R2_001_trimmed.5bp_3prime 100%  424KB 423.9KB/s   00:00    
16C_26psu_3_S15_L001_R1_001_trimmed.5bp_3prim 100%  425KB 425.0KB/s   00:00    
8C_26psu_2_S10_L001_R1_001_trimmed.5bp_3prime 100%  420KB 420.4KB/s   00:00    
16C_26psu_1_S13_L002_R2_001_trimmed.5bp_3prim 100%  314KB 314.2KB/s   00:00    
16C_26psu_4_S16_L001_R2_001_trimmed.5bp_3prim 100%  309KB 308.6KB/s   00:00    
16C_26psu_2_S14_L001_R2_001_trimmed.5bp_3prim 100%  418KB 418.4KB/s   00:00    
16C_32psu_1_S1_L002_R2_001_trimmed.5bp_3prime 100%  317KB 317.0KB/s   00:00    
8C_32psu_3_S7_L001_R1_001_trimmed.5bp_3prime_ 100%  306KB 305.5KB/s   00:00    
16C_32psu_2_S2_L001_R2_001_trimmed.5bp_3prime 100%  421KB 421.1KB/s   00:00    
CTRL_8C_26psu_2_S18_L001_R1_001_trimmed.5bp_3 100%  421KB 420.9KB/s   00:00    
CTRL_8C_26psu_1_S17_L001_R2_001_trimmed.5bp_3 100%  313KB 313.4KB/s   00:01    
Sealice_F1_S20_L002_R1_001_trimmed.5bp_3prime 100%  417KB 417.0KB/s   00:00    
8C_32psu_3_S7_L002_R2_001_trimmed.5bp_3prime_ 100%  424KB 423.7KB/s   00:00    
Sealice_F1_S20_L002_R2_001_trimmed.5bp_3prime 100%  312KB 311.6KB/s   00:00    
Sealice_F2_S22_L002_R1_001_trimmed.5bp_3prime 100%  421KB 421.5KB/s   00:00    
CTRL_8C_26psu_1_S17_L001_R1_001_trimmed.5bp_3 100%  309KB 309.2KB/s   00:00    
8C_32psu_1_S5_L001_R2_001_trimmed.5bp_3prime_ 100%  306KB 306.0KB/s   00:00    
CTRL_16C_26psu_2_S21_L002_R1_001_trimmed.5bp_ 100%  311KB 310.6KB/s   00:00    
Sealice_F1_S20_L001_R2_001_trimmed.5bp_3prime 100%  306KB 306.2KB/s   00:00    
16C_32psu_4_S4_L002_R1_001_trimmed.5bp_3prime 100%  419KB 419.0KB/s   00:00    
8C_32psu_4_S8_L001_R2_001_trimmed.5bp_3prime_ 100%  308KB 307.5KB/s   00:00    
16C_26psu_3_S15_L001_R2_001_trimmed.5bp_3prim 100%  315KB 315.0KB/s   00:00    
CTRL_8C_26psu_2_S18_L001_R2_001_trimmed.5bp_3 100%  413KB 412.8KB/s   00:00    
16C_26psu_2_S14_L001_R1_001_trimmed.5bp_3prim 100%  311KB 310.6KB/s   00:00    
CTRL_8C_26psu_2_S18_L002_R1_001_trimmed.5bp_3 100%  317KB 317.5KB/s   00:00    
8C_26psu_2_S10_L002_R2_001_trimmed.5bp_3prime 100%  317KB 317.1KB/s   00:00    
Sealice_F1_S20_L002_R2_001_trimmed.5bp_3prime 100%  425KB 425.1KB/s   00:00    
8C_26psu_1_S9_L002_R2_001_trimmed.5bp_3prime_ 100%  425KB 424.9KB/s   00:00    
8C_26psu_4_S12_L002_R1_001_trimmed.5bp_3prime 100%  424KB 423.6KB/s   00:00    
16C_32psu_2_S2_L001_R1_001_trimmed.5bp_3prime 100%  416KB 415.8KB/s   00:00    
8C_32psu_4_S8_L001_R2_001_trimmed.5bp_3prime_ 100%  420KB 419.7KB/s   00:00    
16C_26psu_1_S13_L002_R1_001_trimmed.5bp_3prim 100%  425KB 425.2KB/s   00:00    
CTRL_8C_26psu_2_S18_L002_R1_001_trimmed.5bp_3 100%  428KB 427.9KB/s   00:00    
16C_32psu_3_S3_L001_R1_001_trimmed.5bp_3prime 100%  416KB 416.1KB/s   00:00    
Sealice_F2_S22_L001_R2_001_trimmed.5bp_3prime 100%  422KB 421.9KB/s   00:00    
Sealice_F1_S20_L001_R1_001_trimmed.5bp_3prime 100%  299KB 299.0KB/s   00:00    
CTRL_16C_26psu_2_S21_L002_R2_001_trimmed.5bp_ 100%  413KB 413.3KB/s   00:00    
8C_26psu_1_S9_L002_R2_001_trimmed.5bp_3prime_ 100%  314KB 314.2KB/s   00:00    
16C_26psu_2_S14_L002_R1_001_trimmed.5bp_3prim 100%  424KB 424.4KB/s   00:01    
8C_32psu_2_S6_L001_R1_001_trimmed.5bp_3prime_ 100%  308KB 307.6KB/s   00:00    
8C_32psu_2_S6_L001_R1_001_trimmed.5bp_3prime_ 100%  417KB 417.1KB/s   00:00    
16C_26psu_2_S14_L001_R2_001_trimmed.5bp_3prim 100%  305KB 305.2KB/s   00:00    
8C_32psu_2_S6_L001_R2_001_trimmed.5bp_3prime_ 100%  304KB 303.8KB/s   00:00    
16C_26psu_2_S14_L002_R1_001_trimmed.5bp_3prim 100%  311KB 310.8KB/s   00:00    
8C_32psu_4_S8_L001_R1_001_trimmed.5bp_3prime_ 100%  306KB 306.3KB/s   00:00    
8C_26psu_1_S9_L001_R2_001_trimmed.5bp_3prime_ 100%  424KB 424.5KB/s   00:00    
CTRL_16C_26psu_1_S19_L002_R2_001_trimmed.5bp_ 100%  314KB 314.2KB/s   00:00    
16C_32psu_3_S3_L002_R1_001_trimmed.5bp_3prime 100%  306KB 305.9KB/s   00:00    
8C_26psu_2_S10_L002_R1_001_trimmed.5bp_3prime 100%  309KB 309.0KB/s   00:00    
Sealice_F2_S22_L001_R1_001_trimmed.5bp_3prime 100%  417KB 417.2KB/s   00:00    
8C_26psu_4_S12_L002_R2_001_trimmed.5bp_3prime 100%  422KB 421.9KB/s   00:00    
16C_32psu_4_S4_L002_R2_001_trimmed.5bp_3prime 100%  322KB 322.4KB/s   00:00    
CTRL_16C_26psu_2_S21_L001_R2_001_trimmed.5bp_ 100%  306KB 305.8KB/s   00:00    
CTRL_8C_26psu_2_S18_L002_R2_001_trimmed.5bp_3 100%  307KB 307.5KB/s   00:00    
8C_32psu_3_S7_L002_R1_001_trimmed.5bp_3prime_ 100%  422KB 422.0KB/s   00:00    
16C_26psu_1_S13_L002_R2_001_trimmed.5bp_3prim 100%  424KB 423.9KB/s   00:00    
8C_26psu_4_S12_L001_R2_001_trimmed.5bp_3prime 100%  417KB 417.1KB/s   00:00    
8C_32psu_3_S7_L001_R2_001_trimmed.5bp_3prime_ 100%  314KB 314.1KB/s   00:00    
16C_26psu_4_S16_L001_R1_001_trimmed.5bp_3prim 100%  419KB 418.7KB/s   00:00    
16C_32psu_3_S3_L002_R1_001_trimmed.5bp_3prime 100%  418KB 418.4KB/s   00:00    
Sealice_F1_S20_L002_R1_001_trimmed.5bp_3prime 100%  299KB 298.8KB/s   00:00    
16C_32psu_3_S3_L001_R2_001_trimmed.5bp_3prime 100%  422KB 421.6KB/s   00:00    
CTRL_8C_26psu_1_S17_L002_R1_001_trimmed.5bp_3 100%  304KB 304.0KB/s   00:00    
CTRL_8C_26psu_1_S17_L001_R2_001_trimmed.5bp_3 100%  426KB 425.6KB/s   00:00    
16C_32psu_2_S2_L002_R2_001_trimmed.5bp_3prime 100%  317KB 317.3KB/s   00:00    
8C_26psu_3_S11_L002_R2_001_trimmed.5bp_3prime 100%  316KB 315.6KB/s   00:00    
16C_32psu_2_S2_L001_R1_001_trimmed.5bp_3prime 100%  303KB 302.8KB/s   00:00    
8C_32psu_2_S6_L002_R1_001_trimmed.5bp_3prime_ 100%  308KB 307.7KB/s   00:00    
16C_32psu_3_S3_L001_R1_001_trimmed.5bp_3prime 100%  305KB 305.1KB/s   00:01    
16C_26psu_3_S15_L002_R2_001_trimmed.5bp_3prim 100%  323KB 323.4KB/s   00:00    
CTRL_16C_26psu_1_S19_L001_R1_001_trimmed.5bp_ 100%  419KB 419.5KB/s   00:00    
CTRL_16C_26psu_1_S19_L001_R2_001_trimmed.5bp_ 100%  306KB 306.0KB/s   00:00    
16C_26psu_4_S16_L002_R2_001_trimmed.5bp_3prim 100%  424KB 423.9KB/s   00:00    
8C_32psu_3_S7_L001_R1_001_trimmed.5bp_3prime_ 100%  417KB 416.9KB/s   00:00    
16C_26psu_1_S13_L001_R2_001_trimmed.5bp_3prim 100%  315KB 314.8KB/s   00:00    
CTRL_8C_26psu_2_S18_L001_R2_001_trimmed.5bp_3 100%  309KB 309.0KB/s   00:00    
16C_32psu_4_S4_L002_R1_001_trimmed.5bp_3prime 100%  305KB 305.0KB/s   00:00    
8C_32psu_4_S8_L002_R1_001_trimmed.5bp_3prime_ 100%  308KB 307.9KB/s   00:00    
8C_26psu_1_S9_L002_R1_001_trimmed.5bp_3prime_ 100%  311KB 310.7KB/s   00:00    
16C_32psu_1_S1_L002_R1_001_trimmed.5bp_3prime 100%  433KB 432.6KB/s   00:00    
CTRL_16C_26psu_2_S21_L002_R1_001_trimmed.5bp_ 100%  421KB 420.7KB/s   00:00    
16C_26psu_3_S15_L002_R1_001_trimmed.5bp_3prim 100%  318KB 317.5KB/s   00:00    
8C_26psu_4_S12_L001_R2_001_trimmed.5bp_3prime 100%  303KB 303.1KB/s   00:00    
Sealice_F2_S22_L002_R1_001_trimmed.5bp_3prime 100%  306KB 306.3KB/s   00:00    
8C_32psu_1_S5_L001_R1_001_trimmed.5bp_3prime_ 100%  416KB 416.5KB/s   00:00    
16C_26psu_4_S16_L002_R2_001_trimmed.5bp_3prim 100%  314KB 313.5KB/s   00:00    
CTRL_8C_26psu_2_S18_L001_R1_001_trimmed.5bp_3 100%  310KB 309.9KB/s   00:00    
Sealice_F2_S22_L002_R2_001_trimmed.5bp_3prime 100%  310KB 309.7KB/s   00:00    
CTRL_16C_26psu_1_S19_L002_R1_001_trimmed.5bp_ 100%  426KB 425.8KB/s   00:00    
8C_26psu_1_S9_L002_R1_001_trimmed.5bp_3prime_ 100%  424KB 423.6KB/s   00:00    
Sealice_F2_S22_L002_R2_001_trimmed.5bp_3prime 100%  423KB 423.3KB/s   00:00    
16C_32psu_4_S4_L001_R1_001_trimmed.5bp_3prime 100%  419KB 418.8KB/s   00:00    
CTRL_8C_26psu_1_S17_L002_R2_001_trimmed.5bp_3 100%  424KB 424.3KB/s   00:00    
CTRL_16C_26psu_1_S19_L002_R2_001_trimmed.5bp_ 100%  424KB 424.3KB/s   00:00    
CTRL_16C_26psu_2_S21_L002_R2_001_trimmed.5bp_ 100%  311KB 310.7KB/s   00:00    
16C_26psu_2_S14_L002_R2_001_trimmed.5bp_3prim 100%  425KB 425.1KB/s   00:00    
8C_32psu_1_S5_L002_R1_001_trimmed.5bp_3prime_ 100%  310KB 309.8KB/s   00:00    
8C_26psu_1_S9_L001_R1_001_trimmed.5bp_3prime_ 100%  419KB 419.2KB/s   00:01    
8C_26psu_3_S11_L002_R2_001_trimmed.5bp_3prime 100%  426KB 425.9KB/s   00:00    
8C_32psu_4_S8_L002_R2_001_trimmed.5bp_3prime_ 100%  423KB 423.5KB/s   00:00    
8C_32psu_4_S8_L001_R1_001_trimmed.5bp_3prime_ 100%  415KB 414.9KB/s   00:00    
8C_32psu_2_S6_L002_R2_001_trimmed.5bp_3prime_ 100%  420KB 420.3KB/s   00:00    
Sealice_F2_S22_L001_R1_001_trimmed.5bp_3prime 100%  303KB 303.1KB/s   00:00    
8C_26psu_4_S12_L002_R1_001_trimmed.5bp_3prime 100%  311KB 310.7KB/s   00:00    
CTRL_8C_26psu_1_S17_L001_R1_001_trimmed.5bp_3 100%  420KB 419.6KB/s   00:00    
8C_32psu_1_S5_L001_R1_001_trimmed.5bp_3prime_ 100%  307KB 307.1KB/s   00:00    
8C_32psu_1_S5_L002_R2_001_trimmed.5bp_3prime_ 100%  308KB 308.0KB/s   00:00    
16C_26psu_1_S13_L001_R1_001_trimmed.5bp_3prim 100%  421KB 420.9KB/s   00:00    
CTRL_16C_26psu_1_S19_L001_R2_001_trimmed.5bp_ 100%  418KB 418.3KB/s   00:00    
8C_32psu_3_S7_L002_R1_001_trimmed.5bp_3prime_ 100%  310KB 310.3KB/s   00:00    
8C_26psu_2_S10_L001_R2_001_trimmed.5bp_3prime 100%  307KB 306.6KB/s   00:00    
16C_26psu_3_S15_L002_R2_001_trimmed.5bp_3prim 100%  427KB 426.8KB/s   00:00    
16C_26psu_4_S16_L001_R1_001_trimmed.5bp_3prim 100%  309KB 308.5KB/s   00:00    
16C_26psu_1_S13_L001_R1_001_trimmed.5bp_3prim 100%  312KB 312.0KB/s   00:00    
CTRL_8C_26psu_2_S18_L002_R2_001_trimmed.5bp_3 100%  418KB 418.1KB/s   00:00    
8C_26psu_3_S11_L001_R2_001_trimmed.5bp_3prime 100%  420KB 420.5KB/s   00:00    
8C_26psu_3_S11_L002_R1_001_trimmed.5bp_3prime 100%  420KB 420.5KB/s   00:00    
8C_26psu_4_S12_L001_R1_001_trimmed.5bp_3prime 100%  308KB 308.4KB/s   00:00    
16C_26psu_1_S13_L002_R1_001_trimmed.5bp_3prim 100%  314KB 313.7KB/s   00:00    
16C_32psu_1_S1_L001_R2_001_trimmed.5bp_3prime 100%  423KB 423.3KB/s   00:00    
16C_26psu_3_S15_L001_R1_001_trimmed.5bp_3prim 100%  318KB 318.0KB/s   00:00    
8C_32psu_1_S5_L001_R2_001_trimmed.5bp_3prime_ 100%  419KB 418.6KB/s   00:00    
8C_32psu_4_S8_L002_R2_001_trimmed.5bp_3prime_ 100%  319KB 318.9KB/s   00:00    
CTRL_16C_26psu_2_S21_L001_R1_001_trimmed.5bp_ 100%  315KB 315.2KB/s   00:00    
8C_26psu_3_S11_L001_R2_001_trimmed.5bp_3prime 100%  310KB 310.0KB/s   00:01    
8C_32psu_2_S6_L002_R1_001_trimmed.5bp_3prime_ 100%  421KB 420.8KB/s   00:00    
16C_26psu_1_S13_L001_R2_001_trimmed.5bp_3prim 100%  425KB 425.5KB/s   00:00    
8C_32psu_1_S5_L002_R1_001_trimmed.5bp_3prime_ 100%  422KB 421.7KB/s   00:00    
16C_32psu_3_S3_L001_R2_001_trimmed.5bp_3prime 100%  316KB 316.4KB/s   00:00    
8C_26psu_1_S9_L001_R2_001_trimmed.5bp_3prime_ 100%  314KB 313.7KB/s   00:00    
16C_26psu_3_S15_L002_R1_001_trimmed.5bp_3prim 100%  428KB 428.2KB/s   00:00    
8C_26psu_2_S10_L001_R1_001_trimmed.5bp_3prime 100%  313KB 312.6KB/s   00:00    
CTRL_16C_26psu_2_S21_L001_R1_001_trimmed.5bp_ 100%  420KB 420.3KB/s   00:00    
CTRL_16C_26psu_1_S19_L002_R1_001_trimmed.5bp_ 100%  316KB 316.0KB/s   00:00    
Sealice_F1_S20_L001_R2_001_trimmed.5bp_3prime 100%  422KB 421.7KB/s   00:00    
16C_32psu_1_S1_L001_R1_001_trimmed.5bp_3prime 100%  424KB 424.4KB/s   00:00    
16C_26psu_4_S16_L001_R2_001_trimmed.5bp_3prim 100%  421KB 421.2KB/s   00:00    
CTRL_16C_26psu_2_S21_L001_R2_001_trimmed.5bp_ 100%  415KB 415.2KB/s   00:00    
16C_32psu_1_S1_L001_R2_001_trimmed.5bp_3prime 100%  312KB 312.1KB/s   00:00    
8C_26psu_2_S10_L002_R2_001_trimmed.5bp_3prime 100%  425KB 424.6KB/s   00:00    
Sealice_F2_S22_L001_R2_001_trimmed.5bp_3prime 100%  307KB 307.3KB/s   00:00    
8C_32psu_3_S7_L001_R2_001_trimmed.5bp_3prime_ 100%  424KB 424.4KB/s   00:00 

STEP 6. run multiqc

srlab@emu:~/GitHub/Shelly_Pgenerosa/multiqc$ multiqc .
[INFO   ]         multiqc : This is MultiQC v0.9
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching '.'
[INFO   ]          fastqc : Found 88 reports
[INFO   ]         multiqc : Report      : multiqc_report.html
[INFO   ]         multiqc : Data        : multiqc_data
[INFO   ]         multiqc : MultiQC complete

STEP 7. copy back to Gannet via ostrich

srlab@emu:~/GitHub/Shelly_Pgenerosa/multiqc$ ls
FASTQC  multiqc_data  multiqc_report.html
srlab@emu:~/GitHub/Shelly_Pgenerosa/multiqc$ mv multiqc_report.html multiqc_data/
srlab@emu:~/GitHub/Shelly_Pgenerosa/multiqc$ ls
FASTQC  multiqc_data
srlab@emu:~/GitHub/Shelly_Pgenerosa/multiqc$ scp -r multiqc_data/ strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_1st5bp/FASTQC
Password:
multiqc_report.html                           100% 1842KB   1.8MB/s   00:00    
.multiqc.log                                  100% 7012     6.9KB/s   00:00    
multiqc_sources.txt                           100%   15KB  15.2KB/s   00:00    
multiqc_general_stats.txt                     100% 8352     8.2KB/s   00:00    
multiqc_fastqc.txt                            100%   22KB  22.0KB/s   00:00    

STEP 8. check multiqc report - multiqc report here: https://gannet.fish.washington.edu/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_1st5bp/FASTQC/multiqc_data/multiqc_report.html

CONCLUSIONS:

Next steps:

Written on August 5, 2019