%%bash
echo "TODAY'S DATE:"
date
echo "------------"
echo ""
lsb_release -a #Display operating system info
echo ""
echo "------------"
echo "HOSTNAME: "; hostname
echo ""
echo "------------"
echo "Computer Specs:"
echo ""
lscpu
echo ""
echo "------------"
echo ""
echo "Memory Specs"
echo ""
free -mh
TODAY'S DATE:
Wed May 23 09:58:07 PDT 2018
------------
Distributor ID: Ubuntu
Description: Ubuntu 16.04.4 LTS
Release: 16.04
Codename: xenial
------------
HOSTNAME:
roadrunner
------------
Computer Specs:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 16
On-line CPU(s) list: 0-15
Thread(s) per core: 2
Core(s) per socket: 4
Socket(s): 2
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family: 6
Model: 26
Model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz
Stepping: 5
CPU MHz: 2394.000
CPU max MHz: 2394.0000
CPU min MHz: 1596.0000
BogoMIPS: 4521.78
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 8192K
NUMA node0 CPU(s): 0-15
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts nopl xtopology nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca sse4_1 sse4_2 popcnt lahf_lm kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida
------------
Memory Specs
total used free shared buff/cache available
Mem: 47G 419M 40G 50M 6.5G 46G
Swap: 47G 0B 47G
No LSB modules are available.
%%bash
mkdir /home/sam/analyses/20180523_oly_repeatmasker
%%bash
mkdir /home/sam/data/oly_assemblies
cp /mnt/owl/Athaliana/20171130_oly_pbjelly/jelly.out.fasta /home/sam/data/oly_assemblies
cp: cannot stat '/mnt/owl/Athaliana/20171130_oly_pbjelly/jelly.out.fasta': No such file or directory
Forgot that I had restarted roadrunner - need to re-mount owl...
Needs sudo so will re-run outside of notebook.
%%bash
time \
cp /mnt/owl/Athaliana/20171130_oly_pbjelly/jelly.out.fasta /home/sam/data/oly_assemblies
real 0m18.276s user 0m0.000s sys 0m1.368s
%%bash
ls -l /home/sam/data/oly_assemblies/
total 1233740 -rw-rw-r-- 1 sam sam 1263344875 May 23 10:13 jelly.out.fasta
%%bash
mv /home/sam/analyses/20180523_oly_repeatmasker \
/home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01
-par 15 : Use 15 CPU threads
-gff : Create GFF output file (in addition to default files)
-excln : Adjusts output table calculations to exclude sequence runs of >=25Ns. Useful for draft genome assemblies.
1> : Send stdout to file instead of printing to notebook.
2> : Send stderr to file instead of printing to notebook.
%%bash
time \
/home/shared/RepeatMasker-4.0.7/RepeatMasker \
/home/sam/data/oly_assemblies/jelly.out.fasta \
-par 15 \
-gff \
-excln \
1> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stdout.out \
2> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stderr.err
sed '/^Subject:/ s/ / repeatmasker JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
real 398m44.441s user 4976m30.380s sys 1006m29.860s
%%bash
echo "------------"
echo "STANDARD OUT"
echo "------------"
tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stdout.out
echo ""
echo ""
echo "------------"
echo "STANDARD ERROR"
echo "------------"
tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stderr.err
echo ""
echo ""
echo "------------"
echo "REPEATMASKER TABLE"
echo "------------"
cat /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/jelly.out.fasta.tbl
------------ STANDARD OUT ------------ cycle 4 ....................................................................................................................................................................................................................................................................................................................................................................................................................... cycle 5 ....................................................................................................................................................................................................................................................................................................................................................................................................................... cycle 6 ....................................................................................................................................................................................................................................................................................................................................................................................................................... cycle 7 ....................................................................................................................................................................................................................................................................................................................................................................................................................... cycle 8 ............................................................................................................................................................................................................................................................................................................................................................................................................ cycle 9 ............................................................................................................................................................................................................................................................................................................................................................................................................ cycle 10 ............................................................................................................................................................................................................................................................................................................................................................................................................ Generating output... ......................................................................................................................................................................................................................................................................................................................................................................................................... masking done ------------ STANDARD ERROR ------------ ------------ REPEATMASKER TABLE ------------
cat: /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/jelly.out.fasta.tbl: No such file or directory
Oof. Ran this in the wrong directory AND started running repeatmasker after this. Can't tell if files are overwritten or what. Need to re-run. Grr.
%%bash
cd /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01
time \
/home/shared/RepeatMasker-4.0.7/RepeatMasker \
/home/sam/data/oly_assemblies/jelly.out.fasta \
-par 15 \
-gff \
-excln \
1> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stdout.out \
2> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stderr.err
sed '/^Subject:/ s/ / repeatmasker JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
real 408m50.418s user 4841m17.924s sys 1297m22.872s
%%bash
echo "------------"
echo "STANDARD OUT"
echo "------------"
tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stdout.out
echo ""
echo ""
echo "------------"
echo "STANDARD ERROR"
echo "------------"
tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stderr.err
echo ""
echo ""
echo "------------"
echo "REPEATMASKER TABLE"
echo "------------"
cat /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/jelly.out.fasta.tbl
------------ STANDARD OUT ------------ cycle 4 ....................................................................................................................................................................................................................................................................................................................................................................................................................... cycle 5 ....................................................................................................................................................................................................................................................................................................................................................................................................................... cycle 6 ....................................................................................................................................................................................................................................................................................................................................................................................................................... cycle 7 ....................................................................................................................................................................................................................................................................................................................................................................................................................... cycle 8 ............................................................................................................................................................................................................................................................................................................................................................................................................ cycle 9 ............................................................................................................................................................................................................................................................................................................................................................................................................ cycle 10 ............................................................................................................................................................................................................................................................................................................................................................................................................ Generating output... ......................................................................................................................................................................................................................................................................................................................................................................................................... masking done ------------ STANDARD ERROR ------------ ------------ REPEATMASKER TABLE ------------
cat: /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/jelly.out.fasta.tbl: No such file or directory
-species "crassostrea gigas" : Sets species to Crassostrea gigas
-par 15 : Use 15 CPU threads
-gff : Create GFF output file (in addition to default files)
-excln : Adjusts output table calculations to exclude sequence runs of >=25Ns. Useful for draft genome assemblies.
1> : Send stdout to file instead of printing to notebook.
2> : Send stderr to file instead of printing to notebook.
%%bash
mkdir /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02
cd /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02
time \
/home/shared/RepeatMasker-4.0.7/RepeatMasker \
/home/sam/data/oly_assemblies/jelly.out.fasta \
-species "crassostrea gigas" \
-par 15 \
-gff \
-excln \
1> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02/stdout.out \
2> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02/stderr.err
sed '/^Subject:/ s/ / repeatmasker JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
mkdir: cannot create directory ‘/home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02’: File exists real 391m39.372s user 4547m11.540s sys 1003m40.176s
%%bash
echo "------------"
echo "STANDARD OUT"
echo "------------"
tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02/stdout.out
echo ""
echo ""
echo "------------"
echo "STANDARD ERROR"
echo "------------"
tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02/stderr.err
echo ""
echo ""
echo "------------"
echo "REPEATMASKER C.GIGAS TABLE"
echo "------------"
cat /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02/jelly.out.fasta.tbl
------------ STANDARD OUT ------------ cycle 4 ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. cycle 5 cycle 6 ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. cycle 7 ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. cycle 8 ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. cycle 9 ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. cycle 10 ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ Generating output... .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... masking done ------------ STANDARD ERROR ------------ ------------ REPEATMASKER C.GIGAS TABLE ------------
cat: /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02/jelly.out.fasta.tbl: No such file or directory
-species "crassostrea virginica" : Sets species to Crassostrea virginica
-par 15 : Use 15 CPU threads
-gff : Create GFF output file (in addition to default files)
-excln : Adjusts output table calculations to exclude sequence runs of >=25Ns. Useful for draft genome assemblies.
1> : Send stdout to file instead of printing to notebook.
2> : Send stderr to file instead of printing to notebook.
%%bash
mkdir /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03
cd /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03
time \
/home/shared/RepeatMasker-4.0.7/RepeatMasker \
/home/sam/data/oly_assemblies/jelly.out.fasta \
-species "crassostrea virginica" \
-par 15 \
-gff \
-excln \
1> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03/stdout.out \
2> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03/stderr.err
sed '/^Subject:/ s/ / repeatmasker JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
real 301m41.551s user 3123m55.312s sys 1092m28.468s
%%bash
echo "------------"
echo "STANDARD OUT"
echo "------------"
tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03/stdout.out
echo ""
echo ""
echo "------------"
echo "STANDARD ERROR"
echo "------------"
tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03/stderr.err
echo ""
echo ""
echo "------------"
echo "REPEATMASKER C.VIRGINICA TABLE"
echo "------------"
cat /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03/jelly.out.fasta.tbl
------------ STANDARD OUT ------------ cycle 4 .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... cycle 5 cycle 6 .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... cycle 7 .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... cycle 8 .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. cycle 9 .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. cycle 10 ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Generating output... ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... masking done ------------ STANDARD ERROR ------------ ------------ REPEATMASKER C.VIRGINICA TABLE ------------
cat: /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03/jelly.out.fasta.tbl: No such file or directory
-species "ostrea lurida" : Sets species to Ostrea lurida
-par 15 : Use 15 CPU threads
-gff : Create GFF output file (in addition to default files)
-excln : Adjusts output table calculations to exclude sequence runs of >=25Ns. Useful for draft genome assemblies.
1> : Send stdout to file instead of printing to notebook.
2> : Send stderr to file instead of printing to notebook.
%%bash
mkdir /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04
cd /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04
time \
/home/shared/RepeatMasker-4.0.7/RepeatMasker \
/home/sam/data/oly_assemblies/jelly.out.fasta \
-species "ostrea lurida" \
-par 15 \
-gff \
-excln \
1> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04/stdout.out \
2> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04/stderr.err
sed '/^Subject:/ s/ / repeatmasker JOB COMPLETE/' ~/.default-subject.mail | msmtp "$EMAIL"
real 297m9.951s user 3102m3.256s sys 1096m47.180s
%%bash
echo "------------"
echo "STANDARD OUT"
echo "------------"
tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04/stdout.out
echo ""
echo ""
echo "------------"
echo "STANDARD ERROR"
echo "------------"
tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04/stderr.err
echo ""
echo ""
echo "------------"
echo "REPEATMASKER O.LURIDA TABLE"
echo "------------"
cat /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04/jelly.out.fasta.tbl
------------ STANDARD OUT ------------ cycle 4 .................................................................................................................................................................................................................................................................................................................................................................................................. cycle 5 cycle 6 .................................................................................................................................................................................................................................................................................................................................................................................................. cycle 7 .................................................................................................................................................................................................................................................................................................................................................................................................. cycle 8 ............................................................................................................................................................................................................................................................................................................................................................................... cycle 9 ............................................................................................................................................................................................................................................................................................................................................................................... cycle 10 ............................................................................................................................................................................................................................................................................................................................................................................... Generating output... ........................................................................................................................................................................................................................................................................................................................................................................... masking done ------------ STANDARD ERROR ------------ ------------ REPEATMASKER O.LURIDA TABLE ------------
cat: /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04/jelly.out.fasta.tbl: No such file or directory
%%bash
ls /home/sam/data/oly_assemblies/
jelly.out.fasta jelly.out.fasta.preThuMay240214172018.RMoutput jelly.out.fasta.preThuMay240845562018.RMoutput jelly.out.fasta.preThuMay241347382018.RMoutput jelly.out.fasta.preThuMay241644392018.RMoutput
%%bash
cat /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay240214172018.RMoutput/jelly.out.fasta.tbl
==================================================
file name: jelly.out.fasta
sequences: 696946
total length: 1253001795 bp (1172226648 bp excl N/X-runs)
GC level: 36.51 %
bases masked: 20002806 bp ( 1.71 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
SINEs: 17794 1061170 bp 0.09 %
ALUs 363 31340 bp 0.00 %
MIRs 1166 92129 bp 0.01 %
LINEs: 4456 888114 bp 0.08 %
LINE1 976 103929 bp 0.01 %
LINE2 813 82891 bp 0.01 %
L3/CR1 699 63627 bp 0.01 %
LTR elements: 1187 199118 bp 0.02 %
ERVL 155 15828 bp 0.00 %
ERVL-MaLRs 200 20737 bp 0.00 %
ERV_classI 379 42833 bp 0.00 %
ERV_classII 66 6896 bp 0.00 %
DNA elements: 2290 196866 bp 0.02 %
hAT-Charlie 190 15468 bp 0.00 %
TcMar-Tigger 732 37473 bp 0.00 %
Unclassified: 101 12946 bp 0.00 %
Total interspersed repeats: 2358214 bp 0.20 %
Small RNA: 5954 433422 bp 0.04 %
Satellites: 366 55705 bp 0.00 %
Simple repeats: 310641 14322152 bp 1.22 %
Low complexity: 47381 2844279 bp 0.24 %
==================================================
* most repeats fragmented by insertions or deletions
have been counted as one element
Runs of >=20 X/Ns in query were excluded in % calcs
The query species was assumed to be homo sapiens
RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127
run with rmblastn version 2.6.0+
%%bash
cat /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay240845562018.RMoutput/jelly.out.fasta.tbl
==================================================
file name: jelly.out.fasta
sequences: 696946
total length: 1253001795 bp (1172226648 bp excl N/X-runs)
GC level: 36.51 %
bases masked: 160759267 bp ( 13.71 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
Retroelements 213132 69887654 bp 5.96 %
SINEs: 2374 311974 bp 0.03 %
Penelope 171792 57862186 bp 4.94 %
LINEs: 195605 63430615 bp 5.41 %
CRE/SLACS 0 0 bp 0.00 %
L2/CR1/Rex 731 357995 bp 0.03 %
R1/LOA/Jockey 0 0 bp 0.00 %
R2/R4/NeSL 13 11377 bp 0.00 %
RTE/Bov-B 8085 1948581 bp 0.17 %
L1/CIN4 0 0 bp 0.00 %
LTR elements: 15153 6145065 bp 0.52 %
BEL/Pao 2119 955773 bp 0.08 %
Ty1/Copia 101 75372 bp 0.01 %
Gypsy/DIRS1 11776 4815361 bp 0.41 %
Retroviral 0 0 bp 0.00 %
DNA transposons 256292 35689117 bp 3.04 %
hobo-Activator 19847 2059651 bp 0.18 %
Tc1-IS630-Pogo 43269 6806311 bp 0.58 %
En-Spm 0 0 bp 0.00 %
MuDR-IS905 0 0 bp 0.00 %
PiggyBac 7935 1060296 bp 0.09 %
Tourist/Harbinger 9503 887332 bp 0.08 %
Other (Mirage, 0 0 bp 0.00 %
P-element, Transib)
Rolling-circles 0 0 bp 0.00 %
Unclassified: 174943 38299211 bp 3.27 %
Total interspersed repeats: 143875982 bp 12.27 %
Small RNA: 280 78768 bp 0.01 %
Satellites: 7383 1362194 bp 0.12 %
Simple repeats: 278809 12982714 bp 1.11 %
Low complexity: 44078 2622506 bp 0.22 %
==================================================
* most repeats fragmented by insertions or deletions
have been counted as one element
Runs of >=20 X/Ns in query were excluded in % calcs
The query species was assumed to be crassostrea gigas
RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127
run with rmblastn version 2.6.0+
%%bash
cat /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay241347382018.RMoutput/jelly.out.fasta.tbl
==================================================
file name: jelly.out.fasta
sequences: 696946
total length: 1253001795 bp (1172226648 bp excl N/X-runs)
GC level: 36.51 %
bases masked: 39598953 bp ( 3.38 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
Retroelements 63882 10327611 bp 0.88 %
SINEs: 63882 10327611 bp 0.88 %
Penelope 0 0 bp 0.00 %
LINEs: 0 0 bp 0.00 %
CRE/SLACS 0 0 bp 0.00 %
L2/CR1/Rex 0 0 bp 0.00 %
R1/LOA/Jockey 0 0 bp 0.00 %
R2/R4/NeSL 0 0 bp 0.00 %
RTE/Bov-B 0 0 bp 0.00 %
L1/CIN4 0 0 bp 0.00 %
LTR elements: 0 0 bp 0.00 %
BEL/Pao 0 0 bp 0.00 %
Ty1/Copia 0 0 bp 0.00 %
Gypsy/DIRS1 0 0 bp 0.00 %
Retroviral 0 0 bp 0.00 %
DNA transposons 9433 2307292 bp 0.20 %
hobo-Activator 0 0 bp 0.00 %
Tc1-IS630-Pogo 0 0 bp 0.00 %
En-Spm 0 0 bp 0.00 %
MuDR-IS905 0 0 bp 0.00 %
PiggyBac 0 0 bp 0.00 %
Tourist/Harbinger 0 0 bp 0.00 %
Other (Mirage, 0 0 bp 0.00 %
P-element, Transib)
Rolling-circles 0 0 bp 0.00 %
Unclassified: 51558 9836468 bp 0.84 %
Total interspersed repeats: 22471371 bp 1.92 %
Small RNA: 64164 10406776 bp 0.89 %
Satellites: 10 5985 bp 0.00 %
Simple repeats: 298612 14185090 bp 1.21 %
Low complexity: 47510 2866522 bp 0.24 %
==================================================
* most repeats fragmented by insertions or deletions
have been counted as one element
Runs of >=20 X/Ns in query were excluded in % calcs
The query species was assumed to be crassostrea virginica
RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127
run with rmblastn version 2.6.0+
%%bash
cat /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay241644392018.RMoutput/jelly.out.fasta.tbl
==================================================
file name: jelly.out.fasta
sequences: 696946
total length: 1253001795 bp (1172226648 bp excl N/X-runs)
GC level: 36.51 %
bases masked: 17617763 bp ( 1.50 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
Retroelements 0 0 bp 0.00 %
SINEs: 0 0 bp 0.00 %
Penelope 0 0 bp 0.00 %
LINEs: 0 0 bp 0.00 %
CRE/SLACS 0 0 bp 0.00 %
L2/CR1/Rex 0 0 bp 0.00 %
R1/LOA/Jockey 0 0 bp 0.00 %
R2/R4/NeSL 0 0 bp 0.00 %
RTE/Bov-B 0 0 bp 0.00 %
L1/CIN4 0 0 bp 0.00 %
LTR elements: 0 0 bp 0.00 %
BEL/Pao 0 0 bp 0.00 %
Ty1/Copia 0 0 bp 0.00 %
Gypsy/DIRS1 0 0 bp 0.00 %
Retroviral 0 0 bp 0.00 %
DNA transposons 0 0 bp 0.00 %
hobo-Activator 0 0 bp 0.00 %
Tc1-IS630-Pogo 0 0 bp 0.00 %
En-Spm 0 0 bp 0.00 %
MuDR-IS905 0 0 bp 0.00 %
PiggyBac 0 0 bp 0.00 %
Tourist/Harbinger 0 0 bp 0.00 %
Other (Mirage, 0 0 bp 0.00 %
P-element, Transib)
Rolling-circles 0 0 bp 0.00 %
Unclassified: 3 189 bp 0.00 %
Total interspersed repeats: 189 bp 0.00 %
Small RNA: 282 79165 bp 0.01 %
Satellites: 10 5985 bp 0.00 %
Simple repeats: 313082 14662647 bp 1.25 %
Low complexity: 47785 2878201 bp 0.25 %
==================================================
* most repeats fragmented by insertions or deletions
have been counted as one element
Runs of >=20 X/Ns in query were excluded in % calcs
The query species was assumed to be ostrea lurida
RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127
run with rmblastn version 2.6.0+
%%bash
cp -pR /home/sam/data/oly_assemblies/jelly.out.fasta.* /mnt/owl/Athaliana/
ls /mnt/owl/Athaliana/jelly.out.fasta.*
cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput/jelly.out.fasta.masked': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput/jelly.out.fasta.tbl': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput/jelly.out.fasta.out': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput/readme.txt': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput/jelly.out.fasta.cat.gz': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput/jelly.out.fasta.out.gff': Permission denied cp: preserving times for '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput': Operation not permitted cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput/jelly.out.fasta.masked': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput/jelly.out.fasta.out.gff': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput/jelly.out.fasta.cat.gz': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput/jelly.out.fasta.tbl': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput/jelly.out.fasta.out': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput/readme.txt': Permission denied cp: preserving times for '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput': Operation not permitted cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput/jelly.out.fasta.masked': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput/jelly.out.fasta.out.gff': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput/jelly.out.fasta.cat.gz': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput/jelly.out.fasta.tbl': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput/jelly.out.fasta.out': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput/readme.txt': Permission denied cp: preserving times for '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput': Operation not permitted cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput/jelly.out.fasta.masked': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput/jelly.out.fasta.out.gff': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput/jelly.out.fasta.cat.gz': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput/jelly.out.fasta.tbl': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput/jelly.out.fasta.out': Permission denied cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput/readme.txt': Permission denied cp: preserving times for '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput': Operation not permitted ls: cannot open directory '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput': Permission denied ls: cannot open directory '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput': Permission denied ls: cannot open directory '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput': Permission denied ls: cannot open directory '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput': Permission denied
Ugh. Ran copy command with sudo outside of notebok.
%%bash
ls /mnt/owl/Athaliana/jelly.out.fasta.*
/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput: jelly.out.fasta.cat.gz jelly.out.fasta.masked jelly.out.fasta.out jelly.out.fasta.out.gff jelly.out.fasta.tbl readme.txt /mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput: jelly.out.fasta.cat.gz jelly.out.fasta.masked jelly.out.fasta.out jelly.out.fasta.out.gff jelly.out.fasta.tbl readme.txt /mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput: jelly.out.fasta.cat.gz jelly.out.fasta.masked jelly.out.fasta.out jelly.out.fasta.out.gff jelly.out.fasta.tbl readme.txt /mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput: jelly.out.fasta.cat.gz jelly.out.fasta.masked jelly.out.fasta.out jelly.out.fasta.out.gff jelly.out.fasta.tbl readme.txt
Copied folders to wrong locations. Re-doing. Will need to use sudo outside of notebook.
%%bash
cp -pR /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay240214172018.RMoutput \
/home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/
cp -pR /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay240845562018.RMoutput \
/home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02/
cp -pR /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay241347382018.RMoutput \
/home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03/
cp -pR /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay241644392018.RMoutput \
/home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04/
%%bash
ls /mnt/owl/Athaliana/20180523_oly_repeatmasker_pbjelly_sjw_01-0*
/mnt/owl/Athaliana/20180523_oly_repeatmasker_pbjelly_sjw_01-01: jelly.out.fasta.preThuMay240214172018.RMoutput readme.txt stderr.err stdout.out /mnt/owl/Athaliana/20180523_oly_repeatmasker_pbjelly_sjw_01-02: jelly.out.fasta.preThuMay240845562018.RMoutput stderr.err stdout.out /mnt/owl/Athaliana/20180523_oly_repeatmasker_pbjelly_sjw_01-03: jelly.out.fasta.preThuMay241347382018.RMoutput stderr.err stdout.out /mnt/owl/Athaliana/20180523_oly_repeatmasker_pbjelly_sjw_01-04: jelly.out.fasta.preThuMay241644392018.RMoutput stderr.err stdout.out