Can't locate object method "qstring" via package "Bio::DB::Bam::AlignWrapper" at epiTEome.pl line 2275."

[yq342]

Dear Professor:
I meet a error when I run the test program in step 2. I hope you can give me some advice and the computer operating system for me is ubuntu 16.04.
the issue is that:
"yangqing@yangqing-Lenovo-G480:~/epiTEome-master/test$ perl epiTEome.pl -gff tair10TEs.gff3 -ref Chr2.epiTEome.masked.fasta -un unmapped.fastq -t teid.lst
Possible precedence issue with control flow operator at epiTEome.pl line 482.
INFO epiTEome.pl Sun May 20 09:29:55 2018 Start program!
INFO epiTEome.pl Sun May 20 09:29:55 2018 Run Module: readGffFile!

INFO epiTEome.pl Sun May 20 09:29:58 2018 STEP 1: read ends mapping.
INFO epiTEome.pl: --> Skiping Step 1: unmapped.step1.sort.bam allready exist.
INFO epiTEome.pl Sun May 20 09:29:58 2018 Run Module: splitFastq!

INFO epiTEome.pl Sun May 20 09:29:58 2018 STEP 2: split-reads mapping.

INFO epiTEome.pl Sun May 20 09:29:58 2018 BATCH #1.
INFO epiTEome.pl Sun May 20 09:29:58 2018 Run Module: selectPairedEndReads !
AT2TE41090 284
INFO epiTEome.pl Sun May 20 09:29:58 2018 Run Module: pairedEndGrab !
/home/yangqing/miniconda2/bin/bamutils filter unmapped.step1.sort.bam unmapped.matePairedEnd.bam -whitelist unmapped.fishReads.list
Done! (0:00)
208 kept
775 failed
/home/yangqing/miniconda2/bin/samtools index unmapped.matePairedEnd.bam
INFO epiTEome.pl Sun May 20 09:29:58 2018 Run Module: checkPairedEndPosition !
/home/yangqing/miniconda2/bin/fastqutils filter -whitelist unmapped.step1.list unmapped.fastq > unmapped.step1.fastq
112 reads in whitelist
Done! (0:00)
Criteria Kept Altered Removed
FASTQReader 121 0 0
WhitelistFilter 112 0 9
INFO epiTEome.pl Sun May 20 09:29:58 2018 Run Module: splitFastq!
INFO epiTEome.pl Sun May 20 09:29:58 2018 Run Module: Segemehl mapping !
/usr/bin/segemehl.x --silent -t 1 -D 1 -E 5 -i Chr2.epiTEome.masked.fasta.ctidx -j Chr2.epiTEome.masked.fasta.gaidx -d Chr2.epiTEome.masked.fasta -q unmapped.step1.sr.fastq -o unmapped.step2.sam -F 1 2>log
/home/yangqing/miniconda2/bin/samtools view -b unmapped.step2.sam | /home/yangqing/miniconda2/bin/samtools sort - -o unmapped.step2.sort.bam
/home/yangqing/miniconda2/bin/samtools index unmapped.step2.sort.bam
INFO epiTEome.pl Sun May 20 09:30:02 2018 Run Module: selectSplitReads !
INFO epiTEome.pl Sun May 20 09:30:02 2018 Run Module: splitReadsGrab !
/home/yangqing/miniconda2/bin/bamutils filter unmapped.step2.sort.bam unmapped.mateSplitReads.bam -whitelist unmapped.fishReads.list
Done! (0:00)
759 kept
3411 failed
/home/yangqing/miniconda2/bin/samtools index unmapped.mateSplitReads.bam
INFO epiTEome.pl Sun May 20 09:30:03 2018 Run Module: groupOverlapingmNeoReads, 103 to process.
INFO epiTEome.pl Sun May 20 09:30:03 2018 Run Module: neoInsertionFinder !
INFO epiTEome.pl: Cleaning file: /bin/rm unmapped.fishReads.list unmapped.matePairedEnd.bam unmapped.matePairedEnd.bam.bai unmapped.mateSplitReads.bam unmapped.mateSplitReads.bam.bai unmapped.pe.fastq unmapped.step1.fastq unmapped.step1.list unmapped.step1.sr.fastq unmapped.step2.sort.bam unmapped.step2.sort.bam.bai
Can't locate object method "qstring" via package "Bio::DB::Bam::AlignWrapper" at epiTEome.pl line 2275."
thank you very much!

[KRotemD]

Hi,
I run into similar issue, any help would be greatly appreciated!

[yq342]

Hi, KRotemD
I done some recompose for epiTEome.pl at line 2274 and the program run successfully. as follow:

 	# $self->{printBam}->{reads}->{$kr}->mtid,
$self->{printBam}->{reads}->{$seqid}->{$pos}->{$readId}->mpos,
$self->{printBam}->{reads}->{$seqid}->{$pos}->{$readId}->isize,
$self->{printBam}->{reads}->{$seqid}->{$pos}->{$readId}->query->dna,
#$self->{printBam}->{reads}->{$seqid}->{$pos}->{$readId}->qstring,
$self->{printBam}->{reads}->{$seqid}->{$pos}->{$readId}->aux

[KRotemD]

Thanks yq342, it worked