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Error when running test script #3

Open szsctt opened 3 years ago

szsctt commented 3 years ago

I cloned the most recent commit (0e5e22f), and tried to run the gene-is test script on Ubuntu (18.04), but encountered several errors. Below is the output:

1) Targeted Sequencing Pair BWA  4) All
2) Targeted Sequencing Single    5) Clear
3) LAM-PCR           6) Quit
Please enter your choice: 1
......................................................
Mon Nov 23 03:19:03 Australia 2020
###################################################################
Pre-proceesing (Quality Filtering and Adapter Trimming) in progress...

perl /var/work/gene-is/scripts/filteringTrimming.pl  -f /var/work/gene-is/test/targetedSequencing/testData.TS.pair1.fastq.gz  -r /var/work/gene-is/test/targetedSequencing/testData.TS.pair2.fastq.gz -qual 20  -adaptF GATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -adaptR AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT    -sOut filtTrim -o /var/work/gene-is/test/targetedSequencing/results/pairedEnd -sk /var/work/gene-is/tools/bin/skewer

Quality value is 20.

Results will be stored in  /var/work/gene-is/test/targetedSequencing/results/pairedEnd
/var/work/gene-is/tools/bin/skewer -x GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -y AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 20 -l 50 -o /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtTrim /var/work/gene-is/test/targetedSequencing/testData.TS.pair1.fastq.gz /var/work/gene-is/test/targetedSequencing/testData.TS.pair2.fastq.gz
Parameters used:
-- 3' end adapter sequence (-x):    GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
-- maximum error ratio allowed (-r):    0.100
-- maximum indel error ratio allowed (-d):  0.030
-- end quality threshold (-q):      20
-- minimum read length allowed after trimming (-l): 20
-- file format (-f):        Sanger/Illumina 1.8+ FASTQ (auto detected)
Mon Nov 23 03:19:03 2020 >> started
|>                                                 | (0.66%)
Mon Nov 23 03:19:07 2020 >> done (4.053s)
50000 read pairs processed; of these:
   57 ( 0.11%) short read pairs filtered out after trimming by size control
10927 (21.85%) empty read pairs filtered out after trimming by size control
39016 (78.03%) read pairs available; of these:
35612 (91.28%) trimmed read pairs available after processing
 3404 ( 8.72%) untrimmed read pairs available after processing
log has been saved to "/var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtTrim.log".

###################################################################
Alignment in process...

=======>>>>>>>>>>>> 1
perl -I /var/work/gene-is/lib /var/work/gene-is/scripts/alignment.pl  -p 2 -f filtTrim-pair1.fastq -r filtTrim-pair2.fastq  -gv /var/work/gene-is/test/datasets/testGenomeVector.fa   -a /var/work/gene-is/tools/bin/bwa  -aOut completAlignment  -o /var/work/gene-is/test/targetedSequencing/results/pairedEnd -t AGILENT -s /var/work/gene-is/scripts -sam /var/work/gene-is/tools/bin/samtools 
Alignemnt type AGILENT
BWA is used as Aligner

/var/work/gene-is/tools/bin/bwa mem -M -t 2 /var/work/gene-is/test/datasets/testGenomeVector.fa  /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtTrim-pair1.fastq  /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtTrim-pair2.fastq  > /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sam 
[M::main_mem] read 78032 sequences (14192295 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 2490, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (76, 130, 202)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 454)
[M::mem_pestat] mean and std.dev: (147.89, 92.35)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 580)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::worker2@1] performed mate-SW for 14830 reads
[M::worker2@0] performed mate-SW for 14710 reads
[main] Version: 0.7.4-r385
[main] CMD: /var/work/gene-is/tools/bin/bwa mem -M -t 2 /var/work/gene-is/test/datasets/testGenomeVector.fa /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtTrim-pair1.fastq /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtTrim-pair2.fastq
[main] Real time: 7.795 sec; CPU: 15.021 sec
[samopen] SAM header is present: 6 sequences.
[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.
[bam_rmdup_core] processing reference VECTOR...
[bam_rmdup_core] processing reference chr1...
[bam_rmdup_core] 0 / 2 = 0.0000 in library '    '
[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.
###################################################################
IS extraction and post-processing in progress...

perl -I /var/work/gene-is/lib /var/work/gene-is/scripts/extractIS.pl -l /var/work/gene-is/lib -p -aIn completAlignment.sorted.bam -o /var/work/gene-is/test/targetedSequencing/results/pairedEnd -s /var/work/gene-is/scripts -r /var/work/gene-is/test/datasets/VECTOR.fa -i /var/work/gene-is/test/datasets/testGenomeVector.fa.2bit -v VECTOR -t AGILENT   -bla /var/work/gene-is/tools/bin/blat -minIden 95 -range 3 -samtools /var/work/gene-is/tools/bin/samtools -specificity 0 

Results will be stored in  /var/work/gene-is/test/targetedSequencing/results/pairedEnd
bash /var/work/gene-is/scripts/extractIS.sh /var/work/gene-is/test/targetedSequencing/results/pairedEnd completAlignment.sorted.bam /var/work/gene-is/scripts /var/work/gene-is/test/datasets/VECTOR.fa VECTOR /var/work/gene-is/tools/bin/blat  /var/work/gene-is/lib /var/work/gene-is/test/datasets/testGenomeVector.fa.2bit 95 3 /var/work/gene-is/tools/bin/samtools 0 
mv: cannot stat '/var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.nodup.bam.bai': No such file or directory
/var/work/gene-is/tools/bin/samtools view /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sorted.bam | awk -v thr=20 -v specific=0 -f /var/work/gene-is/scripts/extractSClip.awk > /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sorted.bam.sclip.txt
awk: /var/work/gene-is/scripts/extractSClip.awk: line 29: illegal reference to array vect
awk: /var/work/gene-is/scripts/extractSClip.awk: line 37: illegal reference to array vect
awk: /var/work/gene-is/scripts/extractSClip.awk: line 43: illegal reference to array vect
awk: /var/work/gene-is/scripts/extractSClip.awk: line 52: illegal reference to array vect
awk: /var/work/gene-is/scripts/extractSClip.awk: line 57: illegal reference to array appoggio
Processing whole alignment
sort -k1,1 -k2,2n -k5,5 /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sorted.bam.sclip.txt > /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sorted.bam.sclip.txt.app; mv /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sorted.bam.sclip.txt.app /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sorted.bam.sclip.txt

BLAT alignment in process... 
/var/work/gene-is/tools/bin/blat /var/work/gene-is/test/datasets/testGenomeVector.fa.2bit /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.fa -out=blast8 -minIdentity=95 /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.bst
/var/work/gene-is/tools/bin/blat: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory
sort -k1,1 -k12,12nr /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.bst > /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.sort.bst
sort: cannot read: /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.bst: No such file or directory
awk -F"\t" -v vectorStr=VECTOR -f /var/work/gene-is/scripts/extractIS.awk /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.sort.bst |grep VECTOR > /var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDup.csv
sort -k1,1 -u /var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDup.csv > /var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDupSingle.csv

Clustering in process...
cut -d " " -f 1,2,3,4,5,6,7 /var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDupSingle.csv |awk -v vectorName=VECTOR -f /var/work/gene-is/scripts/formatIS.awk |sort -k4nr >/var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDup.csv.total
sort -k1,1 -k2,2n /var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDup.csv.total| awk -v range=3  -f /var/work/gene-is/scripts/solveIS.awk > /var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDup.csv.total.results
awk: /var/work/gene-is/scripts/solveIS.awk: line 5: illegal reference to local variable fields
awk: /var/work/gene-is/scripts/solveIS.awk: line 23: type error in arg(1) in call to getRunInfos

No extra filtering...
###################################################################
Multiple aligned reads processing TS ...

bash /var/work/gene-is/scripts/repeatsExtractTS.sh VECTOR /var/work/gene-is/test/targetedSequencing/results/pairedEnd /var/work/gene-is/scripts 0.95 /var/work/gene-is/tools/bin/blat /var/work/gene-is/test/datasets/testGenomeVector.fa.2bit 95 3
awk: cannot open /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.bst (No such file or directory)
cut: /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.bst: No such file or directory
/var/work/gene-is/tools/bin/blat: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory
awk: cannot open /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.temp.bst (No such file or directory)
awk: /var/work/gene-is/scripts/solveIS.awk: line 5: illegal reference to local variable fields
awk: /var/work/gene-is/scripts/solveIS.awk: line 23: type error in arg(1) in call to getRunInfos
awk: /var/work/gene-is/scripts/solveIS.awk: line 5: illegal reference to local variable fields
awk: /var/work/gene-is/scripts/solveIS.awk: line 23: type error in arg(1) in call to getRunInfos
###################################################################
IS annotation TS...

perl -I /var/work/gene-is/lib /var/work/gene-is/scripts/annotation.pl -o /var/work/gene-is/test/targetedSequencing/results/pairedEnd -s /var/work/gene-is/scripts -t /var/work/gene-is/tools/bin/bedtools -a1 /var/work/gene-is/test/datasets/UCSC.anno.table_hg38.txt  -r1 /var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDup.csv.total.results
perl -I /var/work/gene-is/lib /var/work/gene-is/scripts/annotation.pl -o /var/work/gene-is/test/targetedSequencing/results/pairedEnd -s /var/work/gene-is/scripts -t /var/work/gene-is/tools/bin/bedtools -a1 /var/work/gene-is/test/datasets/UCSC.anno.table_hg38.txt  -r1 /var/work/gene-is/test/targetedSequencing/results/pairedEnd/repeats.resultsNoDup.csv.total.results
Error: The requested bed file (/var/work/gene-is/test/targetedSequencing/results/pairedEnd/ISFileMod1.bed) could not be opened. Exiting!
awk: line 1: regular expression compile failed (missing operand)
+
awk: line 1: regular expression compile failed (missing operand)
+
awk: line 1: regular expression compile failed (missing operand)
+
awk: line 1: regular expression compile failed (missing operand)
+
awk: line 1: regular expression compile failed (missing operand)
+
awk: line 1: regular expression compile failed (missing operand)
+
awk: line 1: regular expression compile failed (missing operand)
+
/var/work/gene-is/test/targetedSequencing/results/pairedEnd
Error: The requested bed file (/var/work/gene-is/test/targetedSequencing/results/pairedEnd/anno9.bed) could not be opened. Exiting!
Error: The requested bed file (/var/work/gene-is/test/targetedSequencing/results/pairedEnd/anno9.bed) could not be opened. Exiting!
Error: The requested bed file (/var/work/gene-is/test/targetedSequencing/results/pairedEnd/ISFileMod1.bed) could not be opened. Exiting!
awk: line 1: regular expression compile failed (missing operand)
+
awk: line 1: regular expression compile failed (missing operand)
+
awk: line 1: regular expression compile failed (missing operand)
+
awk: line 1: regular expression compile failed (missing operand)
+
awk: line 1: regular expression compile failed (missing operand)
+
awk: line 1: regular expression compile failed (missing operand)
+
awk: line 1: regular expression compile failed (missing operand)
+
/var/work/gene-is/test/targetedSequencing/results/pairedEnd
Error: The requested bed file (/var/work/gene-is/test/targetedSequencing/results/pairedEnd/anno9.bed) could not be opened. Exiting!
Error: The requested bed file (/var/work/gene-is/test/targetedSequencing/results/pairedEnd/anno9.bed) could not be opened. Exiting!
###################################################################
###################################################################
Generating General Statistics ...

Finished.
###################################################################
##################### Testing Pair-ends Output #########################
Generated Output File /var/work/gene-is/test/targetedSequencing/results/testDataTS.pair.csv
Template Output File /var/work/gene-is/test/targetedSequencing/results/pairedEnd/testDataTS.ResultsClusteredAnnotated.csv
!!! Assertion failed !!!
Output File /var/work/gene-is/test/targetedSequencing/results/testDataTS.pair.csv is not the same as expected
###################################################################

Any insights would be appreciated!

eritema commented 3 years ago

Il giorno lun 23 nov 2020 alle ore 06:55 szsctt notifications@github.com ha scritto:

/var/work/gene-is/tools/bin/samtools view /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sorted.bam | awk -v thr=20 -v specific=0 -f /var/work/gene-is/scripts/extractSClip.awk > /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sorted.bam.sclip.txt awk: /var/work/gene-is/scripts/extractSClip.awk: line 29: illegal reference to array vect awk: /var/work/gene-is/scripts/extractSClip.awk: line 37: illegal reference to array vect awk: /var/work/gene-is/scripts/extractSClip.awk: line 43: illegal reference to array vect awk: /var/work/gene-is/scripts/extractSClip.awk: line 52: illegal reference to array vect

Any insights would be appreciated!

Hi, one cause could be that you are not using a GNU version of awk. Try to install it and rerun the pipeline

best rf

szsctt commented 3 years ago

Thanks! I've installed GNU awk and rerun, but I still get some errors:

1) Targeted Sequencing Pair BWA  4) All
2) Targeted Sequencing Single    5) Clear
3) LAM-PCR           6) Quit
Please enter your choice: 1
......................................................
Mon Nov 23 23:33:36 Australia 2020
###################################################################
Pre-proceesing (Quality Filtering and Adapter Trimming) in progress...

perl /var/work/gene-is/scripts/filteringTrimming.pl  -f /var/work/gene-is/test/targetedSequencing/testData.TS.pair1.fastq.gz  -r /var/work/gene-is/test/targetedSequencing/testData.TS.pair2.fastq.gz -qual 20  -adaptF GATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -adaptR AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT    -sOut filtTrim -o /var/work/gene-is/test/targetedSequencing/results/pairedEnd -sk /var/work/gene-is/tools/bin/skewer

Quality value is 20.

Results will be stored in  /var/work/gene-is/test/targetedSequencing/results/pairedEnd
/var/work/gene-is/tools/bin/skewer -x GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -y AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 20 -l 50 -o /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtTrim /var/work/gene-is/test/targetedSequencing/testData.TS.pair1.fastq.gz /var/work/gene-is/test/targetedSequencing/testData.TS.pair2.fastq.gz
Parameters used:
-- 3' end adapter sequence (-x):    GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
-- maximum error ratio allowed (-r):    0.100
-- maximum indel error ratio allowed (-d):  0.030
-- end quality threshold (-q):      20
-- minimum read length allowed after trimming (-l): 20
-- file format (-f):        Sanger/Illumina 1.8+ FASTQ (auto detected)
Mon Nov 23 23:33:36 2020 >> started
|>                                                 | (0.66%)
Mon Nov 23 23:33:40 2020 >> done (4.250s)
50000 read pairs processed; of these:
   57 ( 0.11%) short read pairs filtered out after trimming by size control
10927 (21.85%) empty read pairs filtered out after trimming by size control
39016 (78.03%) read pairs available; of these:
35612 (91.28%) trimmed read pairs available after processing
 3404 ( 8.72%) untrimmed read pairs available after processing
log has been saved to "/var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtTrim.log".

###################################################################
Alignment in process...

=======>>>>>>>>>>>> 1
perl -I /var/work/gene-is/lib /var/work/gene-is/scripts/alignment.pl  -p 2 -f filtTrim-pair1.fastq -r filtTrim-pair2.fastq  -gv /var/work/gene-is/test/datasets/testGenomeVector.fa   -a /var/work/gene-is/tools/bin/bwa  -aOut completAlignment  -o /var/work/gene-is/test/targetedSequencing/results/pairedEnd -t AGILENT -s /var/work/gene-is/scripts -sam /var/work/gene-is/tools/bin/samtools 
Alignemnt type AGILENT
BWA is used as Aligner

/var/work/gene-is/tools/bin/bwa mem -M -t 2 /var/work/gene-is/test/datasets/testGenomeVector.fa  /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtTrim-pair1.fastq  /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtTrim-pair2.fastq  > /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sam 
[M::main_mem] read 78032 sequences (14192295 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 2490, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (76, 130, 202)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 454)
[M::mem_pestat] mean and std.dev: (147.89, 92.35)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 580)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::worker2@1] performed mate-SW for 14830 reads
[M::worker2@0] performed mate-SW for 14710 reads
[main] Version: 0.7.4-r385
[main] CMD: /var/work/gene-is/tools/bin/bwa mem -M -t 2 /var/work/gene-is/test/datasets/testGenomeVector.fa /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtTrim-pair1.fastq /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtTrim-pair2.fastq
[main] Real time: 8.429 sec; CPU: 16.152 sec
[samopen] SAM header is present: 6 sequences.
[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.
[bam_rmdup_core] processing reference VECTOR...
[bam_rmdup_core] processing reference chr1...
[bam_rmdup_core] 0 / 2 = 0.0000 in library '    '
[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.
###################################################################
IS extraction and post-processing in progress...

perl -I /var/work/gene-is/lib /var/work/gene-is/scripts/extractIS.pl -l /var/work/gene-is/lib -p -aIn completAlignment.sorted.bam -o /var/work/gene-is/test/targetedSequencing/results/pairedEnd -s /var/work/gene-is/scripts -r /var/work/gene-is/test/datasets/VECTOR.fa -i /var/work/gene-is/test/datasets/testGenomeVector.fa.2bit -v VECTOR -t AGILENT   -bla /var/work/gene-is/tools/bin/blat -minIden 95 -range 3 -samtools /var/work/gene-is/tools/bin/samtools -specificity 0 

Results will be stored in  /var/work/gene-is/test/targetedSequencing/results/pairedEnd
bash /var/work/gene-is/scripts/extractIS.sh /var/work/gene-is/test/targetedSequencing/results/pairedEnd completAlignment.sorted.bam /var/work/gene-is/scripts /var/work/gene-is/test/datasets/VECTOR.fa VECTOR /var/work/gene-is/tools/bin/blat  /var/work/gene-is/lib /var/work/gene-is/test/datasets/testGenomeVector.fa.2bit 95 3 /var/work/gene-is/tools/bin/samtools 0 
mv: cannot stat '/var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.nodup.bam.bai': No such file or directory
/var/work/gene-is/tools/bin/samtools view /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sorted.bam | awk -v thr=20 -v specific=0 -f /var/work/gene-is/scripts/extractSClip.awk > /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sorted.bam.sclip.txt
Processing whole alignment
sort -k1,1 -k2,2n -k5,5 /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sorted.bam.sclip.txt > /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sorted.bam.sclip.txt.app; mv /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sorted.bam.sclip.txt.app /var/work/gene-is/test/targetedSequencing/results/pairedEnd/completAlignment.sorted.bam.sclip.txt

BLAT alignment in process... 
/var/work/gene-is/tools/bin/blat /var/work/gene-is/test/datasets/testGenomeVector.fa.2bit /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.fa -out=blast8 -minIdentity=95 /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.bst
/var/work/gene-is/tools/bin/blat: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory
sort -k1,1 -k12,12nr /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.bst > /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.sort.bst
sort: cannot read: /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.bst: No such file or directory
awk -F"\t" -v vectorStr=VECTOR -f /var/work/gene-is/scripts/extractIS.awk /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.sort.bst |grep VECTOR > /var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDup.csv
sort -k1,1 -u /var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDup.csv > /var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDupSingle.csv

Clustering in process...
cut -d " " -f 1,2,3,4,5,6,7 /var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDupSingle.csv |awk -v vectorName=VECTOR -f /var/work/gene-is/scripts/formatIS.awk |sort -k4nr >/var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDup.csv.total
sort -k1,1 -k2,2n /var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDup.csv.total| awk -v range=3  -f /var/work/gene-is/scripts/solveIS.awk > /var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDup.csv.total.results

No extra filtering...
###################################################################
Multiple aligned reads processing TS ...

bash /var/work/gene-is/scripts/repeatsExtractTS.sh VECTOR /var/work/gene-is/test/targetedSequencing/results/pairedEnd /var/work/gene-is/scripts 0.95 /var/work/gene-is/tools/bin/blat /var/work/gene-is/test/datasets/testGenomeVector.fa.2bit 95 3
awk: fatal: cannot open file `/var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.bst' for reading (No such file or directory)
cut: /var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.bst: No such file or directory
/var/work/gene-is/tools/bin/blat: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory
awk: fatal: cannot open file `/var/work/gene-is/test/targetedSequencing/results/pairedEnd/filtered.temp.bst' for reading (No such file or directory)
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IS annotation TS...

perl -I /var/work/gene-is/lib /var/work/gene-is/scripts/annotation.pl -o /var/work/gene-is/test/targetedSequencing/results/pairedEnd -s /var/work/gene-is/scripts -t /var/work/gene-is/tools/bin/bedtools -a1 /var/work/gene-is/test/datasets/UCSC.anno.table_hg38.txt  -r1 /var/work/gene-is/test/targetedSequencing/results/pairedEnd/resultsNoDup.csv.total.results
perl -I /var/work/gene-is/lib /var/work/gene-is/scripts/annotation.pl -o /var/work/gene-is/test/targetedSequencing/results/pairedEnd -s /var/work/gene-is/scripts -t /var/work/gene-is/tools/bin/bedtools -a1 /var/work/gene-is/test/datasets/UCSC.anno.table_hg38.txt  -r1 /var/work/gene-is/test/targetedSequencing/results/pairedEnd/repeats.resultsNoDup.csv.total.results
Error: The requested bed file (/var/work/gene-is/test/targetedSequencing/results/pairedEnd/ISFileMod1.bed) could not be opened. Exiting!
/var/work/gene-is/test/targetedSequencing/results/pairedEnd
Error: The requested bed file (/var/work/gene-is/test/targetedSequencing/results/pairedEnd/anno9.bed) could not be opened. Exiting!
Error: The requested bed file (/var/work/gene-is/test/targetedSequencing/results/pairedEnd/anno9.bed) could not be opened. Exiting!
Error: The requested bed file (/var/work/gene-is/test/targetedSequencing/results/pairedEnd/ISFileMod1.bed) could not be opened. Exiting!
/var/work/gene-is/test/targetedSequencing/results/pairedEnd
Error: The requested bed file (/var/work/gene-is/test/targetedSequencing/results/pairedEnd/anno9.bed) could not be opened. Exiting!
Error: The requested bed file (/var/work/gene-is/test/targetedSequencing/results/pairedEnd/anno9.bed) could not be opened. Exiting!
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Generating General Statistics ...

Finished.
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##################### Testing Pair-ends Output #########################
Generated Output File /var/work/gene-is/test/targetedSequencing/results/testDataTS.pair.csv
Template Output File /var/work/gene-is/test/targetedSequencing/results/pairedEnd/testDataTS.ResultsClusteredAnnotated.csv
!!! Assertion failed !!!
Output File /var/work/gene-is/test/targetedSequencing/results/testDataTS.pair.csv is not the same as expected
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