%%bash
echo "TODAY'S DATE:"
date
echo "------------"
echo ""
#Display operating system info
lsb_release -a
echo ""
echo "------------"
echo "HOSTNAME: "; hostname
echo ""
echo "------------"
echo "Computer Specs:"
echo ""
lscpu
echo ""
echo "------------"
echo ""
echo "Memory Specs"
echo ""
free -mh
TODAY'S DATE:
Tue Dec 17 07:00:28 PST 2019
------------
LSB Version: core-9.20170808ubuntu1-noarch:security-9.20170808ubuntu1-noarch
Distributor ID: Ubuntu
Description: Ubuntu 18.04.3 LTS
Release: 18.04
Codename: bionic
------------
HOSTNAME:
computer
------------
Computer Specs:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 4
On-line CPU(s) list: 0-3
Thread(s) per core: 2
Core(s) per socket: 2
Socket(s): 1
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family: 6
Model: 58
Model name: Intel(R) Core(TM) i7-3517U CPU @ 1.90GHz
Stepping: 9
CPU MHz: 1795.794
CPU max MHz: 3000.0000
CPU min MHz: 800.0000
BogoMIPS: 4788.78
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 4096K
NUMA node0 CPU(s): 0-3
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 rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm cpuid_fault epb pti ssbd ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms xsaveopt dtherm ida arat pln pts md_clear flush_l1d
------------
Memory Specs
total used free shared buff/cache available
Mem: 7.5G 1.8G 320M 628M 5.4G 4.8G
Swap: 7.7G 12K 7.7G
%env are best for bash
%env wd=/home/samb/analyses/20191214_olur_genome_feature_and_intron_splitting
wd="/home/samb/analyses/20191214_olur_genome_feature_and_intron_splitting"
# File download
%env downloads_list=Olurida_v081.fa.fai Olurida_v081_genome_snap02.all.renamed.putative_function.domain_added.gff Olurida_v081-20190709.exon.gff Olurida_v081-20190709.gene.gff
%env rsync_owl=owl:/volume1/web/halfshell/genomic-databank/
# Input/output files
%env chrome_sizes=Olurida_v081.sizes.txt
%env fa_index=Olurida_v081.fa.fai
%env maker_gff=Olurida_v081_genome_snap02.all.renamed.putative_function.domain_added.gff
%env base_name=Olurida_v081-20190709
%env exon_gff=Olurida_v081-20190709.exon.gff
%env exon_gff_sorted=Olurida_v081-20190709.exon.sorted.gff3
%env gene_gff=Olurida_v081-20190709.gene.gff
%env gene_gff_sorted=Olurida_v081-20190709.gene.sorted.gff3
%env exon_comp_bed=Olurida_v081-20190709.exon.sorted.comp.bed
%env intron_bed=Olurida_v081-20190709.introns.bed
%env intergenic_bed=Olurida_v081-20190709.intergenic.bed
# Programs
%env bedtools_dir=/home/samb/programs/bedtools-2.29.0/bin
%env samtools=/home/samb/programs/samtools-1.10
env: wd=/home/samb/analyses/20191214_olur_genome_feature_and_intron_splitting env: downloads_list=Olurida_v081.fa.fai Olurida_v081_genome_snap02.all.renamed.putative_function.domain_added.gff Olurida_v081-20190709.exon.gff Olurida_v081-20190709.gene.gff env: rsync_owl=owl:/volume1/web/halfshell/genomic-databank/ env: chrome_sizes=Olurida_v081.sizes.txt env: fa_index=Olurida_v081.fa.fai env: maker_gff=Olurida_v081_genome_snap02.all.renamed.putative_function.domain_added.gff env: base_name=Olurida_v081-20190709 env: exon_gff=Olurida_v081-20190709.exon.gff env: exon_gff_sorted=Olurida_v081-20190709.exon.sorted.gff3 env: gene_gff=Olurida_v081-20190709.gene.gff env: gene_gff_sorted=Olurida_v081-20190709.gene.sorted.gff3 env: exon_comp_bed=Olurida_v081-20190709.exon.sorted.comp.bed env: intron_bed=Olurida_v081-20190709.introns.bed env: intergenic_bed=Olurida_v081-20190709.intergenic.bed env: bedtools_dir=/home/samb/programs/bedtools-2.29.0/bin env: samtools=/home/samb/programs/samtools-1.10
%%bash
mkdir --parents ${wd}
cd {wd}
/home/samb/analyses/20191214_olur_genome_feature_and_intron_splitting
%%bash
# Create array of files to download from list
mapfile -t downloads_array < <(echo ${downloads_list} | tr " " "\n")
for file in "${downloads_array[@]}"
do
rsync \
--archive \
--verbose \
"${rsync_owl}${file}" \
.
## Uncomment lines below if need to use wget for downloads
# wget --quiet \
# --no-check-certificate \
# https://owl.fish.washington.edu/halfshell/genomic-databank/${file}
done
echo ""
echo ""
echo "----------------------------------------------------------"
echo ""
ls -lh
receiving incremental file list sent 11 bytes received 63 bytes 11.38 bytes/sec total size is 6,103,215 speedup is 82,475.88 receiving incremental file list Olurida_v081_genome_snap02.all.renamed.putative_function.domain_added.gff sent 30 bytes received 3,105,037,889 bytes 3,625,263.19 bytes/sec total size is 3,104,658,743 speedup is 1.00 receiving incremental file list sent 11 bytes received 75 bytes 13.23 bytes/sec total size is 9,248,086 speedup is 107,535.88 ---------------------------------------------------------- total 3.0G -rw-r--r-- 1 samb samb 16M Jul 16 07:10 Olurida_v081-20190709.exon.gff -rw-r--r-- 1 samb samb 8.9M Jul 16 07:10 Olurida_v081-20190709.gene.gff -rw-rw-rw- 1 samb samb 5.9M Aug 24 2018 Olurida_v081.fa.fai -rw-rw-r-- 1 samb samb 2.9G Dec 13 21:30 Olurida_v081_genome_snap02.all.renamed.putative_function.domain_added.gff
X11 forwarding request failed on channel 0 X11 forwarding request failed on channel 0 Connection closed by 128.95.149.83 port 22 rsync: connection unexpectedly closed (0 bytes received so far) [Receiver] rsync error: unexplained error (code 255) at io.c(235) [Receiver=3.1.2] X11 forwarding request failed on channel 0
%%bash
# Create UTR array
utr_array=(five_prime_UTR three_prime_UTR)
echo "Here are the features and their counts in ${maker_gff}:"
awk 'NR>1 {print $3}' "${maker_gff}" | sort | uniq -c
echo ""
echo ""
echo "----------------------------------------------"
# Create GFFs
for feature in "${utr_array[@]}"
do
output="${base_name}.${feature}.gff3"
head -n 1 "${maker_gff}" >> "${output}"
awk -v feature="$feature" '$3 == feature {print}' "${maker_gff}" \
>> "${output}"
echo ""
echo ""
echo "${output}"
echo "----------------------------------------------"
head -n 5 "${output}"
done
Here are the features and their counts in Olurida_v081_genome_snap02.all.renamed.putative_function.domain_added.gff: 19565118 163637 CDS 159429 contig 170394 exon 1214512 expressed_sequence_match 14903 five_prime_UTR 32210 gene 2099176 match 7027538 match_part 32210 mRNA 332676 protein_match 13838 three_prime_UTR ---------------------------------------------- Olurida_v081-20190709.five_prime_UTR.gff3 ---------------------------------------------- ##gff-version 3 Contig58217 maker five_prime_UTR 11504 11541 . - . ID=OLUR_00019127-RA:five_prime_utr;Parent=OLUR_00019127-RA; Contig9540 maker five_prime_UTR 10078 10179 . - . ID=OLUR_00018391-RA:five_prime_utr;Parent=OLUR_00018391-RA; Contig36645 maker five_prime_UTR 2185 2225 . + . ID=OLUR_00022996-RA:five_prime_utr;Parent=OLUR_00022996-RA; Contig3008 maker five_prime_UTR 5726 6482 . - . ID=OLUR_00018754-RA:five_prime_utr;Parent=OLUR_00018754-RA; Olurida_v081-20190709.three_prime_UTR.gff3 ---------------------------------------------- ##gff-version 3 Contig1111 maker three_prime_UTR 24968 25427 . - . ID=OLUR_00006628-RA:three_prime_utr;Parent=OLUR_00006628-RA; Contig2046 maker three_prime_UTR 17809 17955 . + . ID=OLUR_00011450-RA:three_prime_utr;Parent=OLUR_00011450-RA; Contig2046 maker three_prime_UTR 18030 18113 . + . ID=OLUR_00011450-RA:three_prime_utr;Parent=OLUR_00011450-RA; Contig2046 maker three_prime_UTR 18333 18394 . + . ID=OLUR_00011450-RA:three_prime_utr;Parent=OLUR_00011450-RA;
%%bash
echo ${exon_gff}
head ${exon_gff}
echo ""
echo "----------------------"
echo ""
echo ${gene_gff}
head ${gene_gff}
Olurida_v081-20190709.exon.gff ##gff-version 3 Contig61093 maker exon 7493 7773 . + . ID=OLUR_00020575-RA:exon:1553;Parent=OLUR_00020575-RA; Contig61093 maker exon 7814 7946 . + . ID=OLUR_00020575-RA:exon:1554;Parent=OLUR_00020575-RA; Contig1111 maker exon 24968 25494 . - . ID=OLUR_00006628-RA:exon:209;Parent=OLUR_00006628-RA; Contig1111 maker exon 26015 26277 . - . ID=OLUR_00006628-RA:exon:208;Parent=OLUR_00006628-RA; Contig1111 maker exon 26889 27080 . - . ID=OLUR_00006628-RA:exon:207;Parent=OLUR_00006628-RA; Contig1111 maker exon 27651 27803 . - . ID=OLUR_00006628-RA:exon:206;Parent=OLUR_00006628-RA; Contig1111 maker exon 28523 28696 . - . ID=OLUR_00006628-RA:exon:205;Parent=OLUR_00006628-RA; Contig214118 maker exon 201 290 . + . ID=OLUR_00032161-RA:exon:2219;Parent=OLUR_00032161-RA; Contig214118 maker exon 807 926 . + . ID=OLUR_00032161-RA:exon:2220;Parent=OLUR_00032161-RA; ---------------------- Olurida_v081-20190709.gene.gff ##gff-version 3 Contig61093 maker gene 7493 7946 . + . ID=OLUR_00020575;Name=OLUR_00020575;Alias=maker-Contig61093-snap-gene-0.2;Note=Protein of unknown function; Contig1111 maker gene 24968 28696 . - . ID=OLUR_00006628;Name=OLUR_00006628;Alias=maker-Contig1111-snap-gene-0.1;Note=Similar to Spag6: Sperm-associated antigen 6 (Mus musculus OX%3D10090);Dbxref=Gene3D:G3DSA:1.25.10.10,InterPro:IPR000225,InterPro:IPR000357,InterPro:IPR011989,InterPro:IPR016024,Pfam:PF02985,SMART:SM00185,SUPERFAMILY:SSF48371;Ontology_term=GO:0005515; Contig214118 maker gene 201 926 . + . ID=OLUR_00032161;Name=OLUR_00032161;Alias=maker-Contig214118-snap-gene-0.0;Note=Protein of unknown function;Dbxref=Gene3D:G3DSA:3.10.450.10; Contig58217 maker gene 9736 11541 . - . ID=OLUR_00019127;Name=OLUR_00019127;Alias=snap_masked-Contig58217-processed-gene-0.2;Note=Protein of unknown function;Dbxref=MobiDBLite:mobidb-lite; Contig2046 maker gene 2295 18394 . + . ID=OLUR_00011450;Name=OLUR_00011450;Alias=maker-Contig2046-snap-gene-0.5;Note=Protein of unknown function; Contig9540 maker gene 4303 10179 . - . ID=OLUR_00018391;Name=OLUR_00018391;Alias=maker-Contig9540-snap-gene-0.1;Note=Protein of unknown function;Dbxref=Gene3D:G3DSA:2.170.300.10; Contig52254 maker gene 8908 11733 . + . ID=OLUR_00011614;Name=OLUR_00011614;Alias=maker-Contig52254-snap-gene-0.1;Note=Similar to MM_0045: Putative ankyrin repeat protein MM_0045 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88) OX%3D192952);Dbxref=CDD:cd00204,Gene3D:G3DSA:1.25.40.20,InterPro:IPR002110,InterPro:IPR020683,InterPro:IPR036770,PRINTS:PR01415,Pfam:PF12796,Pfam:PF13606,Pfam:PF13857,ProSiteProfiles:PS50088,ProSiteProfiles:PS50297,SMART:SM00248,SUPERFAMILY:SSF48403;Ontology_term=GO:0005515; Contig36645 maker gene 2185 3340 . + . ID=OLUR_00022996;Name=OLUR_00022996;Alias=maker-Contig36645-snap-gene-0.1;Note=Protein of unknown function;Dbxref=MobiDBLite:mobidb-lite; Contig3008 maker gene 532 6482 . - . ID=OLUR_00018754;Name=OLUR_00018754;Alias=maker-Contig3008-snap-gene-0.1;Note=Protein of unknown function;Dbxref=InterPro:IPR015919,SUPERFAMILY:SSF49313;Ontology_term=GO:0005509,GO:0016020;
%%bash
# Change LC_COLLATE to use C for proper sorting of file
export LC_COLLATE=C
cut -f1,2 ${fa_index} | sort > ${chrome_sizes}
head ${chrome_sizes}
Contig0 116746 Contig1 87411 Contig10 79314 Contig100 58076 Contig1000 25824 Contig10000 6887 Contig100000 1518 Contig100001 5004 Contig100002 1810 Contig100003 1990
%%bash
gff_array=("${exon_gff}" "${gene_gff}")
sorted_gff_array=("${exon_gff_sorted}" "${gene_gff_sorted}")
for index in "${!gff_array[@]}"
do
{ awk 'NR<2 {print}' "${gff_array[index]}"
awk 'NR>1 {print}' "${gff_array[index]}" | "${bedtools_dir}"/bedtools sort -i -
} >> "${sorted_gff_array[index]}"
# Check out sorted GFFs
echo "Previewing ${sorted_gff_array[index]}:"
echo ""
head "${sorted_gff_array[index]}"
echo ""
echo "Confirming sort order of ${sorted_gff_array[index]}:"
echo ""
cut -f1 "${sorted_gff_array[index]}" | uniq | head
echo ""
done
Previewing Olurida_v081-20190709.exon.sorted.gff3: ##gff-version 3 Contig0 maker exon 12497 12571 . + . ID=OLUR_00000039-RA:exon:17;Parent=OLUR_00000039-RA; Contig0 maker exon 13175 13233 . + . ID=OLUR_00000039-RA:exon:18;Parent=OLUR_00000039-RA; Contig0 maker exon 16209 16373 . + . ID=OLUR_00000039-RA:exon:19;Parent=OLUR_00000039-RA; Contig0 maker exon 18857 18959 . + . ID=OLUR_00000039-RA:exon:20;Parent=OLUR_00000039-RA; Contig0 maker exon 26493 26574 . + . ID=OLUR_00000039-RA:exon:21;Parent=OLUR_00000039-RA; Contig0 maker exon 27806 27862 . + . ID=OLUR_00000039-RA:exon:22;Parent=OLUR_00000039-RA; Contig0 maker exon 28510 28590 . + . ID=OLUR_00000039-RA:exon:23;Parent=OLUR_00000039-RA; Contig0 maker exon 28735 28775 . + . ID=OLUR_00000039-RA:exon:24;Parent=OLUR_00000039-RA; Contig0 maker exon 34306 34366 . + . ID=OLUR_00000039-RA:exon:25;Parent=OLUR_00000039-RA; Confirming sort order of Olurida_v081-20190709.exon.sorted.gff3: ##gff-version 3 Contig0 Contig1 Contig100 Contig1000 Contig10000 Contig100011 Contig100018 Contig100052 Contig100054 Previewing Olurida_v081-20190709.gene.sorted.gff3: ##gff-version 3 Contig0 maker gene 12497 93068 . + . ID=OLUR_00000039;Name=OLUR_00000039;Alias=maker-Contig0-snap-gene-0.8;Note=Similar to WDR87: WD repeat-containing protein 87 (Homo sapiens OX%3D9606);Dbxref=Coils:Coil,Gene3D:G3DSA:1.25.10.10,Gene3D:G3DSA:2.130.10.10,InterPro:IPR001680,InterPro:IPR011989,InterPro:IPR015943,InterPro:IPR016024,InterPro:IPR017986,InterPro:IPR036322,MobiDBLite:mobidb-lite,Pfam:PF00400,ProSiteProfiles:PS50082,ProSiteProfiles:PS50294,SMART:SM00320,SUPERFAMILY:SSF48371,SUPERFAMILY:SSF50978;Ontology_term=GO:0005515; Contig0 maker gene 95722 104318 . + . ID=OLUR_00000040;Name=OLUR_00000040;Alias=maker-Contig0-snap-gene-0.9;Note=Similar to SSB: Lupus La protein homolog (Bos taurus OX%3D9913);Dbxref=CDD:cd12291,Gene3D:G3DSA:1.10.10.10,Gene3D:G3DSA:3.30.70.330,InterPro:IPR000504,InterPro:IPR002344,InterPro:IPR006630,InterPro:IPR012677,InterPro:IPR014886,InterPro:IPR035979,InterPro:IPR036388,InterPro:IPR036390,MobiDBLite:mobidb-lite,PRINTS:PR00302,Pfam:PF00076,Pfam:PF05383,Pfam:PF08777,ProSiteProfiles:PS50102,ProSiteProfiles:PS50961,SMART:SM00360,SMART:SM00715,SUPERFAMILY:SSF46785,SUPERFAMILY:SSF54928;Ontology_term=GO:0003676,GO:0003723,GO:0005634,GO:0006396,GO:1990904; Contig0 maker gene 115731 116730 . + . ID=OLUR_00000041;Name=OLUR_00000041;Alias=maker-Contig0-snap-gene-0.10;Note=Protein of unknown function;Dbxref=CDD:cd00096,Gene3D:G3DSA:2.60.40.10,InterPro:IPR013783,InterPro:IPR036179,SUPERFAMILY:SSF48726; Contig1 maker gene 7358 13988 . + . ID=OLUR_00000198;Name=OLUR_00000198;Alias=maker-Contig1-snap-gene-0.10;Note=Similar to GPATCH3: G patch domain-containing protein 3 (Homo sapiens OX%3D9606);Dbxref=InterPro:IPR000467,Pfam:PF01585,ProSiteProfiles:PS50174,SMART:SM00443;Ontology_term=GO:0003676; Contig1 maker gene 33348 47451 . - . ID=OLUR_00000199;Name=OLUR_00000199;Alias=maker-Contig1-snap-gene-0.13;Note=Similar to CAMKK1: Calcium/calmodulin-dependent protein kinase kinase 1 (Homo sapiens OX%3D9606);Dbxref=Gene3D:G3DSA:1.10.510.10,InterPro:IPR000719,InterPro:IPR011009,MobiDBLite:mobidb-lite,Pfam:PF00069,ProSiteProfiles:PS50011,SMART:SM00220,SUPERFAMILY:SSF56112;Ontology_term=GO:0004672,GO:0005524,GO:0006468; Contig1 maker gene 37655 62707 . + . ID=OLUR_00000200;Name=OLUR_00000200;Alias=maker-Contig1-snap-gene-0.11;Note=Similar to PTH1R: Parathyroid hormone/parathyroid hormone-related peptide receptor (Didelphis virginiana OX%3D9267);Dbxref=Gene3D:G3DSA:1.20.1070.10,Gene3D:G3DSA:4.10.1240.10,InterPro:IPR000832,InterPro:IPR017981,InterPro:IPR017983,InterPro:IPR036445,MobiDBLite:mobidb-lite,PRINTS:PR00249,Pfam:PF00002,ProSitePatterns:PS00650,ProSiteProfiles:PS50261;Ontology_term=GO:0004888,GO:0004930,GO:0007166,GO:0007186,GO:0016020,GO:0016021; Contig1 maker gene 74421 78081 . + . ID=OLUR_00000201;Name=OLUR_00000201;Alias=maker-Contig1-snap-gene-0.12;Note=Protein of unknown function;Dbxref=CDD:cd00033,Gene3D:G3DSA:2.10.70.10,InterPro:IPR000436,InterPro:IPR035976,MobiDBLite:mobidb-lite,Pfam:PF00084,ProSiteProfiles:PS50923,SMART:SM00032,SUPERFAMILY:SSF57535; Contig100 maker gene 39284 49191 . - . ID=OLUR_00001175;Name=OLUR_00001175;Alias=maker-Contig100-snap-gene-0.7;Note=Protein of unknown function;Dbxref=Coils:Coil,Gene3D:G3DSA:3.40.50.10140,InterPro:IPR000157,InterPro:IPR035897,MobiDBLite:mobidb-lite,Pfam:PF13676,SUPERFAMILY:SSF52200;Ontology_term=GO:0005515,GO:0007165; Contig100 maker gene 50322 57773 . - . ID=OLUR_00001176;Name=OLUR_00001176;Alias=maker-Contig100-snap-gene-0.6;Note=Protein of unknown function; Confirming sort order of Olurida_v081-20190709.gene.sorted.gff3: ##gff-version 3 Contig0 Contig1 Contig100 Contig1000 Contig10000 Contig100011 Contig100018 Contig100052 Contig100054
%%bash
"${bedtools_dir}"/complementBed \
-i "${gene_gff_sorted}" \
-g "${chrome_sizes}" \
> "${intergenic_bed}"
echo "Previewing ${intergenic_bed}:"
echo ""
head "${intergenic_bed}"
Previewing Olurida_v081-20190709.intergenic.bed: Contig0 0 12496 Contig0 93068 95721 Contig0 104318 115730 Contig0 116730 116746 Contig1 0 7357 Contig1 13988 33347 Contig1 62707 74420 Contig1 78081 87411 Contig10 0 79314 Contig100 0 39283
Error: Sorted input specified, but the file Olurida_v081-20190709.gene.sorted.gff3 has the following out of order record Contig0 maker gene 12497 93068 . + . ID=OLUR_00000039;Name=OLUR_00000039;Alias=maker-Contig0-snap-gene-0.8;Note=Similar to WDR87: WD repeat-containing protein 87 (Homo sapiens OX%3D9606);Dbxref=Coils:Coil,Gene3D:G3DSA:1.25.10.10,Gene3D:G3DSA:2.130.10.10,InterPro:IPR001680,InterPro:IPR011989,InterPro:IPR015943,InterPro:IPR016024,InterPro:IPR017986,InterPro:IPR036322,MobiDBLite:mobidb-lite,Pfam:PF00400,ProSiteProfiles:PS50082,ProSiteProfiles:PS50294,SMART:SM00320,SUPERFAMILY:SSF48371,SUPERFAMILY:SSF50978;Ontology_term=GO:0005515;
%%bash
"${bedtools_dir}"/complementBed \
-i "${exon_gff_sorted}" \
-g "${chrome_sizes}" \
> "${exon_comp_bed}"
echo "Previewing ${exon_comp_bed}:"
echo ""
head "${exon_comp_bed}"
echo ""
echo "---------------------"
"${bedtools_dir}"/intersectBed \
-a "${gene_gff_sorted}" \
-b "${exon_comp_bed}" \
| awk -v OFS='\t' '{print $1,$4,$5}' \
> "${intron_bed}"
echo ""
echo "Previewing ${intron_bed}:"
echo ""
head "${intron_bed}"
Previewing Olurida_v081-20190709.exon.sorted.comp.bed: Contig0 0 12496 Contig0 12571 13174 Contig0 13233 16208 Contig0 16373 18856 Contig0 18959 26492 Contig0 26574 27805 Contig0 27862 28509 Contig0 28590 28734 Contig0 28775 34305 Contig0 34366 35487 --------------------- Previewing Olurida_v081-20190709.introns.bed: Contig0 12572 13174 Contig0 13234 16208 Contig0 18960 26492 Contig0 26575 27805 Contig0 27863 28509 Contig0 28591 28734 Contig0 34367 35487 Contig0 35641 36030 Contig0 36139 36864 Contig0 36941 42921
Error: Sorted input specified, but the file Olurida_v081-20190709.exon.sorted.gff3 has the following out of order record Contig0 maker exon 12497 12571 . + . ID=OLUR_00000039-RA:exon:17;Parent=OLUR_00000039-RA;
%%bash
rm "${maker_gff}" \
"${exon_comp_bed}" \
"${exon_gff}" \
"${exon_gff_sorted}" \
"${gene_gff}" \
"${gene_gff_sorted}" \
"${fa_index}"
ls -ltrh
total 16M -rw-r--r-- 1 samb samb 1.6M Dec 17 07:44 Olurida_v081-20190709.five_prime_UTR.gff3 -rw-r--r-- 1 samb samb 1.5M Dec 17 07:44 Olurida_v081-20190709.three_prime_UTR.gff3 -rw-r--r-- 1 samb samb 3.7M Dec 17 07:51 Olurida_v081-20190709.intergenic.bed -rw-r--r-- 1 samb samb 6.3M Dec 17 08:09 Olurida_v081-20190709.introns.bed -rw-r--r-- 1 samb samb 2.7M Dec 17 08:15 Olurida_v081.sizes.txt