Skip to content

Commit

Permalink
adding Dating dir
Browse files Browse the repository at this point in the history
  • Loading branch information
gabrielluishernandez committed Oct 27, 2021
1 parent 63bb6b5 commit 5b2aeb8
Show file tree
Hide file tree
Showing 52 changed files with 45,080 additions and 0 deletions.
Binary file added Dating divergence times/.DS_Store
View file
Binary file not shown.
9 changes: 9 additions & 0 deletions Dating divergence times/README.md
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
# Dated phylogenies

First, we created a dated phylogeny for the species tree. We included the node separating the species _S. fugax_ from the other _Solenopsis_ species. The directory `species_tree_dating` includes all scripts used for this, including:
* _De novo_ assembly of the genomes of different fire ants
* The use of BUSCO to identify single-copy orthologs between these species
* Multiple-sequence alignment between these single-copy orthologs
* Dated phylogeny with IQ-Tree

We then created dated tree with all samples in our analysis (for the supergene and the rest of the genome), calibrated with nodes retrieved from the tree above. The scripts used in this analysis are in the directory `supergene_dating`.
15 changes: 15 additions & 0 deletions Dating divergence times/species_tree_dating/01-assembly.txt
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@

#SAMPLE="SRR9008173"
#SAMPLE="SRR9008142"
#SAMPLE="SRR9008228"
#SAMPLE="SRR9008253"
#SAMPLE="SRR9008168"
#SAMPLE="SRR9008232"
#SAMPLE="SRR9008217"
#SAMPLE="SRR9008215"
#SAMPLE="SRR9008150"
#SAMPLE="SRR9008158"
#SAMPLE="SRR9008133"
#SAMPLE="SRR9008200"

qsub -pe smp 10 -q large.q,smalle.q,medium.q -v "SAMPLE=$SAMPLE" ~/scripts/2021.soli.masurca.assembly.sh
5 changes: 5 additions & 0 deletions Dating divergence times/species_tree_dating/02-busco.txt
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
conda activate busco_old_405
CPUs=50
INPUTFASTA="$PWD/NNNNNNNNNNNNNN.fa"
~/scripts/busco405.sh -t $CPUs -i $INPUTFASTA

54 changes: 54 additions & 0 deletions Dating divergence times/species_tree_dating/03-busco.gene.lists.common.to.all.samples.txt
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,54 @@

#chr1-15
cat Solenopsis.BUSCO.chr1-15.lst \
gng20170922.fa.busco405/gng20170922.fa.busco405.complete.lst \
GCF_016802725.1_UNIL_Sinv_3.0_genomic.fna.busco405/GCF_016802725.1_UNIL_Sinv_3.0_genomic.fna.busco405.complete.lst \
GCA_018691235.1_QMUL_Sinv_Sequel2_genomic.fna.busco405/GCA_018691235.1_QMUL_Sinv_Sequel2_genomic.fna.busco405.complete.lst \
GCA_010367695.1_ASM1036769v1_genomic.fna.busco405/GCA_010367695.1_ASM1036769v1_genomic.fna.busco405.complete.lst \
GCA_009299975.1_ASM929997v1_genomic.fna.busco405/GCA_009299975.1_ASM929997v1_genomic.fna.busco405.complete.lst \
GCA_009299965.1_ASM929996v1_genomic.fna.busco405/GCA_009299965.1_ASM929996v1_genomic.fna.busco405.complete.lst \
SRR9008133.masurca.3.3.7.fa.busco405/SRR9008133.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008142.masurca.3.3.7.fa.busco405/SRR9008142.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008150.masurca.3.3.7.fa.busco405/SRR9008150.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008158.masurca.3.3.7.fa.busco405/SRR9008158.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008168.masurca.3.3.7.fa.busco405/SRR9008168.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008173.masurca.3.3.7.fa.busco405/SRR9008173.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008200.masurca.3.3.7.fa.busco405/SRR9008200.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008215.masurca.3.3.7.fa.busco405/SRR9008215.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008217.masurca.3.3.7.fa.busco405/SRR9008217.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008228.masurca.3.3.7.fa.busco405/SRR9008228.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008232.masurca.3.3.7.fa.busco405/SRR9008232.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008253.masurca.3.3.7.fa.busco405/SRR9008253.masurca.3.3.7.fa.busco405.complete.lst \
Sgeminata.fa.busco405/Sgeminata.fa.busco405.complete.lst \
Spusillignis.fa.busco405/Spusillignis.fa.busco405.complete.lst \
Ssaevissima2.fa.busco405/Ssaevissima2.fa.busco405.complete.lst \
Sfugax.fa.busco405/Sfugax.fa.busco405.complete.lst | \
sort | uniq -c | sed -e 's/^[ \t]*//' | tr ' ' '\t' | awk '$1 == 23' | cut -f2 > common.buscos.chr1-15.lst
cat common.buscos.chr1-15.lst | wc -l

#chr16nr
cat Solenopsis.BUSCO.chr16nr.lst \
gng20170922.fa.busco405/gng20170922.fa.busco405.complete.lst \
GCF_016802725.1_UNIL_Sinv_3.0_genomic.fna.busco405/GCF_016802725.1_UNIL_Sinv_3.0_genomic.fna.busco405.complete.lst \
GCA_018691235.1_QMUL_Sinv_Sequel2_genomic.fna.busco405/GCA_018691235.1_QMUL_Sinv_Sequel2_genomic.fna.busco405.complete.lst \
GCA_010367695.1_ASM1036769v1_genomic.fna.busco405/GCA_010367695.1_ASM1036769v1_genomic.fna.busco405.complete.lst \
GCA_009299975.1_ASM929997v1_genomic.fna.busco405/GCA_009299975.1_ASM929997v1_genomic.fna.busco405.complete.lst \
GCA_009299965.1_ASM929996v1_genomic.fna.busco405/GCA_009299965.1_ASM929996v1_genomic.fna.busco405.complete.lst \
SRR9008133.masurca.3.3.7.fa.busco405/SRR9008133.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008142.masurca.3.3.7.fa.busco405/SRR9008142.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008150.masurca.3.3.7.fa.busco405/SRR9008150.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008158.masurca.3.3.7.fa.busco405/SRR9008158.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008168.masurca.3.3.7.fa.busco405/SRR9008168.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008173.masurca.3.3.7.fa.busco405/SRR9008173.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008200.masurca.3.3.7.fa.busco405/SRR9008200.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008215.masurca.3.3.7.fa.busco405/SRR9008215.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008217.masurca.3.3.7.fa.busco405/SRR9008217.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008228.masurca.3.3.7.fa.busco405/SRR9008228.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008232.masurca.3.3.7.fa.busco405/SRR9008232.masurca.3.3.7.fa.busco405.complete.lst \
SRR9008253.masurca.3.3.7.fa.busco405/SRR9008253.masurca.3.3.7.fa.busco405.complete.lst \
Sgeminata.fa.busco405/Sgeminata.fa.busco405.complete.lst \
Spusillignis.fa.busco405/Spusillignis.fa.busco405.complete.lst \
Ssaevissima2.fa.busco405/Ssaevissima2.fa.busco405.complete.lst \
Sfugax.fa.busco405/Sfugax.fa.busco405.complete.lst | \
sort | uniq -c | sed -e 's/^[ \t]*//' | tr ' ' '\t' | awk '$1 == 23' | cut -f2 > common.buscos.chr16nr.lst
cat common.buscos.chr16nr.lst | wc -l
17 changes: 17 additions & 0 deletions Dating divergence times/species_tree_dating/04-extract.fasta.sequences.txt
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@

cd $INPUTFASTA.busco405
cat run_hymenoptera_odb10/full_table.tsv | grep -vP 'Missing|Duplicated|Fragmented|#|Sequence' > $INPUTFASTA.busco405.complete.tsv
cat run_hymenoptera_odb10/full_table.tsv | grep -vP 'Missing|Duplicated|Complete|#|Sequence' > $INPUTFASTA.busco405.fragmented.tsv
cat $INPUTFASTA.busco405.complete.tsv | tabtk cut -r -f 3,4,5,1 | tee $INPUTFASTA.busco405.complete.bed | cut -f4 > $INPUTFASTA.busco405.complete.lst
cat $INPUTFASTA.busco405.fragmented.tsv | tabtk cut -r -f 3,4,5,1 | tee $INPUTFASTA.busco405.fragmented.bed | cut -f4 > $INPUTFASTA.busco405.fragmented.lst

#test if files are there
cat $INPUTFASTA.busco405.complete.lst | head -n 50 | parallel -k "ls -1 run_hymenoptera_odb10/busco_sequences/single_copy_busco_sequences/{}.fna"

#get single gene fasta's and rename header to sample
mkdir $INPUTFASTA.busco405.complete.fasta
for GENE in $(ls -1 run_hymenoptera_odb10/busco_sequences/single_copy_busco_sequences/*.fna | rev | cut -d"/" -f1 | cut -d"." -f2- | rev)
do
cat run_hymenoptera_odb10/busco_sequences/single_copy_busco_sequences/$GENE.fna | seqtk seq -l 0 -C | sed -r "s,^>.+$,>$SAMPLENAME,g" > $INPUTFASTA.busco405.complete.fasta/$GENE.fa
done
cd ..
157 changes: 157 additions & 0 deletions Dating divergence times/species_tree_dating/05-multiple.sequence.alignment.txt
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,157 @@

## fuse fastas for alignment and relabel
rm -rf busco.fasta.fused.chr1-15
mkdir busco.fasta.fused.chr1-15

cat common.buscos.chr1-15.lst | parallel -j30 "echo {}; cat Sfugax.fa.busco405/Sfugax.fa.busco405.complete.fasta/{}.fa \
gng20170922.fa.busco405/gng20170922.fa.busco405.complete.fasta/{}.fa \
Sgeminata.fa.busco405/Sgeminata.fa.busco405.complete.fasta/{}.fa \
Spusillignis.fa.busco405/Spusillignis.fa.busco405.complete.fasta/{}.fa \
Ssaevissima2.fa.busco405/Ssaevissima2.fa.busco405.complete.fasta/{}.fa \
GCF_016802725.1_UNIL_Sinv_3.0_genomic.fna.busco405/GCF_016802725.1_UNIL_Sinv_3.0_genomic.fna.busco405.complete.fasta/{}.fa \
GCA_018691235.1_QMUL_Sinv_Sequel2_genomic.fna.busco405/GCA_018691235.1_QMUL_Sinv_Sequel2_genomic.fna.busco405.complete.fasta/{}.fa \
GCA_010367695.1_ASM1036769v1_genomic.fna.busco405/GCA_010367695.1_ASM1036769v1_genomic.fna.busco405.complete.fasta/{}.fa \
GCA_009299975.1_ASM929997v1_genomic.fna.busco405/GCA_009299975.1_ASM929997v1_genomic.fna.busco405.complete.fasta/{}.fa \
GCA_009299965.1_ASM929996v1_genomic.fna.busco405/GCA_009299965.1_ASM929996v1_genomic.fna.busco405.complete.fasta/{}.fa \
SRR9008133.masurca.3.3.7.fa.busco405/SRR9008133.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008142.masurca.3.3.7.fa.busco405/SRR9008142.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008150.masurca.3.3.7.fa.busco405/SRR9008150.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008158.masurca.3.3.7.fa.busco405/SRR9008158.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008168.masurca.3.3.7.fa.busco405/SRR9008168.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008173.masurca.3.3.7.fa.busco405/SRR9008173.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008200.masurca.3.3.7.fa.busco405/SRR9008200.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008215.masurca.3.3.7.fa.busco405/SRR9008215.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008217.masurca.3.3.7.fa.busco405/SRR9008217.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008228.masurca.3.3.7.fa.busco405/SRR9008228.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008232.masurca.3.3.7.fa.busco405/SRR9008232.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008253.masurca.3.3.7.fa.busco405/SRR9008253.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa |\
seqtk seq -l 0 > busco.fasta.fused.chr1-15/{}.fa"
cat busco.fasta.fused.chr1-15/9932at7399.fa | grep ">"
cat busco.fasta.fused.chr1-15/9932at7399.fa | grep ">" | wc -l
#22

rm -rf busco.fasta.fused.chr16nr
mkdir busco.fasta.fused.chr16nr
cat common.buscos.chr16nr.lst | parallel -j30 "echo {}; cat Sfugax.fa.busco405/Sfugax.fa.busco405.complete.fasta/{}.fa \
gng20170922.fa.busco405/gng20170922.fa.busco405.complete.fasta/{}.fa \
Sgeminata.fa.busco405/Sgeminata.fa.busco405.complete.fasta/{}.fa \
Spusillignis.fa.busco405/Spusillignis.fa.busco405.complete.fasta/{}.fa \
Ssaevissima2.fa.busco405/Ssaevissima2.fa.busco405.complete.fasta/{}.fa \
GCF_016802725.1_UNIL_Sinv_3.0_genomic.fna.busco405/GCF_016802725.1_UNIL_Sinv_3.0_genomic.fna.busco405.complete.fasta/{}.fa \
GCA_018691235.1_QMUL_Sinv_Sequel2_genomic.fna.busco405/GCA_018691235.1_QMUL_Sinv_Sequel2_genomic.fna.busco405.complete.fasta/{}.fa \
GCA_010367695.1_ASM1036769v1_genomic.fna.busco405/GCA_010367695.1_ASM1036769v1_genomic.fna.busco405.complete.fasta/{}.fa \
GCA_009299975.1_ASM929997v1_genomic.fna.busco405/GCA_009299975.1_ASM929997v1_genomic.fna.busco405.complete.fasta/{}.fa \
GCA_009299965.1_ASM929996v1_genomic.fna.busco405/GCA_009299965.1_ASM929996v1_genomic.fna.busco405.complete.fasta/{}.fa \
SRR9008133.masurca.3.3.7.fa.busco405/SRR9008133.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008142.masurca.3.3.7.fa.busco405/SRR9008142.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008150.masurca.3.3.7.fa.busco405/SRR9008150.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008158.masurca.3.3.7.fa.busco405/SRR9008158.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008168.masurca.3.3.7.fa.busco405/SRR9008168.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008173.masurca.3.3.7.fa.busco405/SRR9008173.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008200.masurca.3.3.7.fa.busco405/SRR9008200.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008215.masurca.3.3.7.fa.busco405/SRR9008215.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008217.masurca.3.3.7.fa.busco405/SRR9008217.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008228.masurca.3.3.7.fa.busco405/SRR9008228.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008232.masurca.3.3.7.fa.busco405/SRR9008232.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa \
SRR9008253.masurca.3.3.7.fa.busco405/SRR9008253.masurca.3.3.7.fa.busco405.complete.fasta/{}.fa |\
seqtk seq -l 0 > busco.fasta.fused.chr16nr/{}.fa"
cat busco.fasta.fused.chr16nr/531at7399.fa | grep ">"
cat busco.fasta.fused.chr16nr/531at7399.fa | grep ">" | wc -l
#22



## run parallel alignments and sort by ID (phyx pxsort)
mkdir run1/dating.msa.chr16nr
mkdir run1/dating.msa.chr16nr.sorted
cat common.buscos.chr16nr.lst | parallel -j 91 "echo {}; prank -d=busco.fasta.fused.chr16nr/{}.fa -f=fasta -DNA -iterate=10 -o=run1/dating.msa.chr16nr/{} && cat run1/dating.msa.chr16nr/{}.best.fas | pxssort --sortby 1 > run1/dating.msa.chr16nr.sorted/{}.fa"


mkdir run1/dating.msa.chr1-15
mkdir run1/dating.msa.chr1-15.sorted
cat common.buscos.chr1-15.lst | parallel -j 100 "echo {}; prank -d=busco.fasta.fused.chr1-15/{}.fa -f=fasta -DNA -iterate=10 -o=run1/dating.msa.chr1-15/{}; cat run1/dating.msa.chr1-15/{}.best.fas | pxssort --sortby 1 > run1/dating.msa.chr1-15.sorted/{}.fa"



## remove alignment sites with gaps
INPUTLIST="common.buscos.chr16nr.lst"
mkdir run1/dating.msa.chr16nr.sorted.pxclsq
rm -f run1/dating.msa.chr16nr.sorted.pxclsq/stats.txt

N=$(cat $INPUTLIST | wc -l) && echo $N
for (( i = 1 ; i < $N+1 ; i++))
do
BUSCOGENE=$(cat $INPUTLIST | sed -n $i'p')
echo $i". "$BUSCOGENE
cat run1/dating.msa.chr16nr.sorted/$BUSCOGENE.fa | pxclsq -p 1.0 > run1/dating.msa.chr16nr.sorted.pxclsq/$BUSCOGENE.fa
cat run1/dating.msa.chr16nr.sorted.pxclsq/$BUSCOGENE.fa | pxlssq > run1/dating.msa.chr16nr.sorted.pxclsq/$BUSCOGENE.fa.stats
echo $BUSCOGENE >> run1/dating.msa.chr16nr.sorted.pxclsq/stats.txt
cat run1/dating.msa.chr16nr.sorted.pxclsq/$BUSCOGENE.fa.stats >> run1/dating.msa.chr16nr.sorted.pxclsq/stats.txt
done

cat run1/dating.msa.chr16nr.sorted.pxclsq/stats.txt | grep -B 2 "Number of sequences: " | grep -vP 'Number of|File type|--' > run1/dating.msa.chr16nr.sorted.pxclsq/stats.short.txt

cat run1/dating.msa.chr16nr.sorted.pxclsq/stats.txt | grep " -"
cat run1/dating.msa.chr16nr.sorted.pxclsq/stats.txt | grep " ?"
cat run1/dating.msa.chr16nr.sorted.pxclsq/stats.txt | grep "Number of sequences: " | wc -l
cat run1/dating.msa.chr16nr.sorted.pxclsq/stats.txt | grep -B 2 "Number of sequences: " | grep -vP 'Number of|File type|--' | wc -l

### concat alignment
FOLDERCONCAT="run1/dating.msa.chr16nr.sorted.pxclsq.concat"
mkdir $FOLDERCONCAT
pxcat -s run1/dating.msa.chr16nr.sorted.pxclsq/*.fa -p $FOLDERCONCAT/busco.dating.chr16nr.partitions -o $FOLDERCONCAT/busco.dating.chr16nr.supermatrix.fa
pxlssq -s $FOLDERCONCAT/busco.dating.chr16nr.supermatrix.fa > $FOLDERCONCAT/busco.dating.chr16nr.supermatrix.fa.stats
cat $FOLDERCONCAT/busco.dating.chr16nr.supermatrix.fa.stats




## remove alignment sites with gaps
#INPUTLIST="common.buscos.chr1-15.lst"
cat common.buscos.chr1-15.lst | grep -vwP '3303at7399|850at7399' > common.buscos.chr1-15.removed.3303.850.lst
INPUTLIST="common.buscos.chr1-15.removed.3303.850.lst"
#2161 samples
mkdir run1/dating.msa.chr1-15.sorted.pxclsq
rm -f run1/dating.msa.chr1-15.sorted.pxclsq/stats.txt

N=$(cat $INPUTLIST | wc -l) && echo $N
for (( i = 1 ; i < $N+1 ; i++))
do
BUSCOGENE=$(cat $INPUTLIST | sed -n $i'p')
echo $i". "$BUSCOGENE
cat run1/dating.msa.chr1-15.sorted/$BUSCOGENE.fa | pxclsq -p 1.0 > run1/dating.msa.chr1-15.sorted.pxclsq/$BUSCOGENE.fa
cat run1/dating.msa.chr1-15.sorted.pxclsq/$BUSCOGENE.fa | pxlssq > run1/dating.msa.chr1-15.sorted.pxclsq/$BUSCOGENE.fa.stats
echo $BUSCOGENE >> run1/dating.msa.chr1-15.sorted.pxclsq/stats.txt
cat run1/dating.msa.chr1-15.sorted.pxclsq/$BUSCOGENE.fa.stats >> run1/dating.msa.chr1-15.sorted.pxclsq/stats.txt
done

cat run1/dating.msa.chr1-15.sorted.pxclsq/stats.txt | grep -B 2 "Number of sequences: " | grep -vP 'Number of|File type|--' > run1/dating.msa.chr1-15.sorted.pxclsq/stats.short.txt

cat run1/dating.msa.chr1-15.sorted.pxclsq/stats.txt | grep " -"
cat run1/dating.msa.chr1-15.sorted.pxclsq/stats.txt | grep " ?"
cat run1/dating.msa.chr1-15.sorted.pxclsq/stats.txt | grep "Number of sequences: " | wc -l
cat run1/dating.msa.chr1-15.sorted.pxclsq/stats.txt | grep -B 2 "Number of sequences: " | grep -vP 'Number of|File type|--' | wc -l
#2161

### concat alignment
FOLDERCONCAT="run1/dating.msa.chr1-15.sorted.pxclsq.concat"
mkdir $FOLDERCONCAT
pxcat -s run1/dating.msa.chr1-15.sorted.pxclsq/*.fa -p $FOLDERCONCAT/busco.dating.chr1-15.partitions -o $FOLDERCONCAT/busco.dating.chr1-15.supermatrix.fa
pxlssq -s $FOLDERCONCAT/busco.dating.chr1-15.supermatrix.fa > $FOLDERCONCAT/busco.dating.chr1-15.supermatrix.fa.stats
cat $FOLDERCONCAT/busco.dating.chr1-15.supermatrix.fa.stats




### 2 genes cause segfault because during filtering for 0% gaps no sequence is left. lets remove these from the analysis
1635. 3303at7399
Segmentation fault (core dumped)
2042. 850at7399
Segmentation fault (core dumped)
run1/dating.msa.chr1-15.sorted.pxclsq/850at7399.fa
run1/dating.msa.chr1-15.sorted.pxclsq/3303at7399.fa

## these genes were removed from further analysis (above)



Loading

0 comments on commit 5b2aeb8

Please sign in to comment.