I was trying to use TEMP on a individual genome fragment (67 Mb), on which I was already able to detect TEs using RetroSeq. With TEMP however, it seems that nothing can be found. Attached is the programs output and the listing of generated files. Note that I masked some filenames.
I was always wondering how to deal with genomes that have different insert sizes (e.g. 200, 500, 800 in a single BAM file).
./TEMP_Insertion.sh -i bamfile -s . -r SINE.fasta -t bedfile -f 3 -f 200 -c 4
+ getopts hi:c:f:m:o:r:s:t: OPTION
+ case $OPTION in
+ BAM=
+ getopts hi:c:f:m:o:r:s:t: OPTION
+ case $OPTION in
+ BINDIR=.
+ getopts hi:c:f:m:o:r:s:t: OPTION
+ case $OPTION in
+ TESEQ=SINEC.fasta
+ getopts hi:c:f:m:o:r:s:t: OPTION
+ case $OPTION in
+ ANNO=bedfile
+ getopts hi:c:f:m:o:r:s:t: OPTION
+ case $OPTION in
+ INSERT=3
+ getopts hi:c:f:m:o:r:s:t: OPTION
+ case $OPTION in
+ INSERT=200
+ getopts hi:c:f:m:o:r:s:t: OPTION
+ case $OPTION in
+ CPU=4
+ getopts hi:c:f:m:o:r:s:t: OPTION
+ [[ -z bamfile ]]
+ [[ -z . ]]
+ [[ -z SINEC.fasta ]]
+ [[ -z bedfile ]]
+ '[' '!' -z 4 ']'
+ '[' '!' -z 200 ']'
+ '[' '!' -z '' ']'
+ MM=3
+ '[' '!' -z ']'
+ OUTDIR=/home/newuser/master_fritjof/programs/TEMP/scripts
+ mkdir -p /home/newuser/master_fritjof/programs/TEMP/scripts
+ cd /home/newuser/master_fritjof/programs/TEMP/scripts
+ touch /home/newuser/master_fritjof/programs/TEMP/scripts/.writting_permission
+ rm -rf /home/newuser/master_fritjof/programs/TEMP/scripts/.writting_permission
+ echo -e '\e[1;35mTesting required softwares/scripts:\e[0m'
Testing required softwares/scripts:
+ checkExist echo
+ echo -ne '\e[1;32m"echo" is using: \e[0m'
"echo" is using: + which echo
/bin/echo
+ [[ 0 != 0 ]]
+ checkExist rm
+ echo -ne '\e[1;32m"rm" is using: \e[0m'
"rm" is using: + which rm
/bin/rm
+ [[ 0 != 0 ]]
+ checkExist mkdir
+ echo -ne '\e[1;32m"mkdir" is using: \e[0m'
"mkdir" is using: + which mkdir
/bin/mkdir
+ [[ 0 != 0 ]]
+ checkExist date
+ echo -ne '\e[1;32m"date" is using: \e[0m'
"date" is using: + which date
/bin/date
+ [[ 0 != 0 ]]
+ checkExist mv
+ echo -ne '\e[1;32m"mv" is using: \e[0m'
"mv" is using: + which mv
/bin/mv
+ [[ 0 != 0 ]]
+ checkExist sort
+ echo -ne '\e[1;32m"sort" is using: \e[0m'
"sort" is using: + which sort
/usr/bin/sort
+ [[ 0 != 0 ]]
+ checkExist touch
+ echo -ne '\e[1;32m"touch" is using: \e[0m'
"touch" is using: + which touch
/usr/bin/touch
+ [[ 0 != 0 ]]
+ checkExist awk
+ echo -ne '\e[1;32m"awk" is using: \e[0m'
"awk" is using: + which awk
/usr/bin/awk
+ [[ 0 != 0 ]]
+ checkExist grep
+ echo -ne '\e[1;32m"grep" is using: \e[0m'
"grep" is using: + which grep
/bin/grep
+ [[ 0 != 0 ]]
+ checkExist bwa
+ echo -ne '\e[1;32m"bwa" is using: \e[0m'
"bwa" is using: + which bwa
/usr/bin/bwa
+ [[ 0 != 0 ]]
+ checkExist samtools
+ echo -ne '\e[1;32m"samtools" is using: \e[0m'
"samtools" is using: + which samtools
/usr/bin/samtools
+ [[ 0 != 0 ]]
+ checkExist bedtools
+ echo -ne '\e[1;32m"bedtools" is using: \e[0m'
"bedtools" is using: + which bedtools
/usr/bin/bedtools
+ [[ 0 != 0 ]]
+ echo -e '\e[1;35mDone with testing required softwares/scripts, starting pipeline...\e[0m'
Done with testing required softwares/scripts, starting pipeline...
+ cp SINEC.fasta ./
cp: `SINEC.fasta' and `./SINEC.fasta' are the same file
++ basename bamfile
+ name=13_new_reAligned.scaffold1.sorted.bam
++ basename SINEC.fasta
+ te=SINEC.fasta
+ i=13_new_reAligned.scaffold1
+ echo 13_new_reAligned.scaffold1.sorted.bam
13_new_reAligned.scaffold1.sorted.bam
+ echo 13_new_reAligned.scaffold1
13_new_reAligned.scaffold1
+ [[ ! -s 13_new_reAligned.scaffold1.sorted.bam ]]
+ [[ ! -s 13_new_reAligned.scaffold1.sorted.bam.bai ]]
+ samtools view -XF 0x2 13_new_reAligned.scaffold1.sorted.bam
+ perl ./pickUniqPairFastq.pl 13_new_reAligned.scaffold1.unpair.sam 13_new_reAligned.scaffold1.unpair.uniq
+ perl ./pickUniqPos.pl 13_new_reAligned.scaffold1.unpair.sam
+ bwa index -a is SINEC.fasta
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[main] Version: 0.6.1-r104
[main] CMD: bwa index -a is SINEC.fasta
[main] Real time: 0.004 sec; CPU: 0.004 sec
+ bwa aln -t 4 -n 3 -l 100 -R 1000 SINEC.fasta 13_new_reAligned.scaffold1.unpair.uniq.1.fastq
[main] Version: 0.6.1-r104
[main] CMD: bwa aln -t 4 -n 3 -l 100 -R 1000 SINEC.fasta 13_new_reAligned.scaffold1.unpair.uniq.1.fastq
[main] Real time: 0.000 sec; CPU: 0.000 sec
+ bwa aln -t 4 -n 3 -l 100 -R 1000 SINEC.fasta 13_new_reAligned.scaffold1.unpair.uniq.2.fastq
[main] Version: 0.6.1-r104
[main] CMD: bwa aln -t 4 -n 3 -l 100 -R 1000 SINEC.fasta 13_new_reAligned.scaffold1.unpair.uniq.2.fastq
[main] Real time: 0.000 sec; CPU: 0.000 sec
+ bwa sampe -P SINEC.fasta 13_new_reAligned.scaffold1.unpair.uniq.1.sai 13_new_reAligned.scaffold1.unpair.uniq.2.sai 13_new_reAligned.scaffold1.unpair.uniq.1.fastq 13_new_reAligned.scaffold1.unpair.uniq.2.fastq
[main] Version: 0.6.1-r104
[main] CMD: bwa sampe -P SINEC.fasta 13_new_reAligned.scaffold1.unpair.uniq.1.sai 13_new_reAligned.scaffold1.unpair.uniq.2.sai 13_new_reAligned.scaffold1.unpair.uniq.1.fastq 13_new_reAligned.scaffold1.unpair.uniq.2.fastq
[main] Real time: 0.001 sec; CPU: 0.000 sec
+ samtools view -hSXF 0x2 13_new_reAligned.scaffold1.unpair.uniq.transposons.sam
[samopen] SAM header is present: 16 sequences.
[sam_read1] reference 'ID:bwa PN:bwa VN:0.6.1-r104
' is recognized as '*'.
[main_samview] truncated file.
+ perl ./pickUniqMate.pl 13_new_reAligned.scaffold1.unpair.uniq.transposons.unpair.sam 13_new_reAligned.scaffold1.unpair.uniq.bed
+ cp 13_new_reAligned.scaffold1.unpair.uniq.transposons.bed 13_new_reAligned.scaffold1.unpair.uniq.transposons.filtered.bed
+ awk -F '\t' -v sample=13_new_reAligned.scaffold1 '{OFS="\t"; print $1,$2,$3,sample,$5,$6}' 13_new_reAligned.scaffold1.unpair.uniq.transposons.filtered.bed
+ perl ./mergeTagsWithoutGap.pl tmp
+ perl ./mergeTagsWithGap.pl 13_new_reAligned.scaffold1.uniq.transposons.filtered.woGap.bed 200
+ rm tmp
+ perl ./get_class.pl 13_new_reAligned.scaffold1.uniq.transposons.filtered.wGap.bed 13_new_reAligned.scaffold1
+ perl ./make.bp.bed.pl 13_new_reAligned.scaffold1.uniq.transposons.filtered.wGap.class.bed
+ rm 13_new_reAligned.scaffold1.unpair.sam 13_new_reAligned.scaffold1.unpair.uniq.bed 13_new_reAligned.scaffold1.unpair.uniq.1.fastq 13_new_reAligned.scaffold1.unpair.uniq.2.fastq 13_new_reAligned.scaffold1.unpair.uniq.1.sai 13_new_reAligned.scaffold1.unpair.uniq.2.sai
+ rm 13_new_reAligned.scaffold1.unpair.uniq.transposons.sam 13_new_reAligned.scaffold1.unpair.uniq.transposons.unpair.sam 13_new_reAligned.scaffold1.uniq.transposons.filtered.woGap.bed 13_new_reAligned.scaffold1.uniq.transposons.filtered.wGap.bed
+ samtools view -bf 0x2 13_new_reAligned.scaffold1.sorted.bam
+ samtools index 13_new_reAligned.scaffold1.pair.bam
+ perl ./pickClippedFastq.pl 13_new_reAligned.scaffold1 SINEC.fasta
+ perl ./refine_breakpoint.in.pl
+ rm 13_new_reAligned.scaffold1.pair.bam 13_new_reAligned.scaffold1.pair.bam.bai
+ perl ./pickOverlapPair.in.pl 13_new_reAligned.scaffold1.insertion.refined.bp 200
+ awk -F '\t' '{OFS="\t"; if ($5=="antisense") $5="-"; if ($5=="sense") $5="+"; if ($1 ~ /^chr/) print $1,$2,$3,$4,".",$5}' 13_new_reAligned.scaffold1.insertion.refined.bp.summary
+ bedtools intersect -a tmp -b bedfile -f 0.1 -wo -s
Error: tmp is an empty file.
+ awk -F '\t' '{OFS="\t"; if (($4==$10)&&($6==$12)) print $1,$2,$3,$4,$5,$6}' tmp1
+ [[ -s tmp2 ]]
+ rm tmp tmp1 tmp2
4.0K -rw-rw-r-- 1 newuser newuser 156 Jun 13 16:07 13_new_reAligned.scaffold1.insertion.refined.bp.summary
0 -rw-rw-r-- 1 newuser newuser 0 Jun 13 16:07 13_new_reAligned.scaffold1.insertion.refined.bp
4.0K -rw-rw-r-- 1 newuser newuser 163 Jun 13 16:06 13_new_reAligned.scaffold1.uniq.transposons.filtered.wGap.class.bed
0 -rw-rw-r-- 1 newuser newuser 0 Jun 13 16:06 13_new_reAligned.scaffold1.unpair.uniq.transposons.filtered.bed
0 -rw-rw-r-- 1 newuser newuser 0 Jun 13 16:06 13_new_reAligned.scaffold1.unpair.uniq.transposons.bed
0 -rw-rw-r-- 1 newuser newuser 0 Jun 13 15:48 13_new_reAligned.scaffold1.clipped.reads.aln
0 -rw-rw-r-- 1 newuser newuser 0 Jun 13 15:47 13_new_reAligned.scaffold1.insertion.bp.bed
764K -rw-r--r-- 1 newuser newuser 762K Jun 13 15:46 13_new_reAligned.scaffold1.sorted.bam.bai
503M -rw-r--r-- 1 newuser newuser 503M Jun 13 15:46 13_new_reAligned.scaffold1.sorted.ba
Hi,
I was trying to use TEMP on a individual genome fragment (67 Mb), on which I was already able to detect TEs using RetroSeq. With TEMP however, it seems that nothing can be found. Attached is the programs output and the listing of generated files. Note that I masked some filenames.
I was always wondering how to deal with genomes that have different insert sizes (e.g. 200, 500, 800 in a single BAM file).