Segmentation fault error using filter bam

[El-Castor]

Hi,

As recommanded by mehlan, I open an issue related to filterbam script use.

I have aligned the RNA-seq paired reads using tophat following this command:

# Running TopHat:
tophat -o $outputDIR1/ -p 16 $index_DIR/dgl_COI_bwt_index $RNAseq_leaves_interleave

# convert junction bed file from the first run:
junction_bedFile_PATH=$outputDIR1/junctions.bed
cat $junction_bedFile_PATH | python2 /NetScratch/cpichot/.conda/envs/tophat/bin/bed_to_juncs > $outputDIR1/junctions_parsed.bed

RNAseq_roots_interleave=$RNAseq_files_DIR/SRR1664818_Pisum_sativum_cv_Cameor_Root_system_paired_end_library_stage_A_High-nitrate_Hydroponics_readNameChanged_interleave.fastq.gz

tophat -j $outputDIR1/junctions_parsed.bed -o $outputDIR2/ -p 16 $index_DIR/dgl_COI_bwt_index $RNAseq_roots_interleave

After Alignment I sort the bam file from topHat using samtools following this command:

conda activate samtools

align_results_bam_leaves_PATH=$outputDIR1/accepted_hits.bam
align_results_bam_root_PATH=$outputDIR2/accepted_hits.bam

samtools sort -n $align_results_bam_leaves_PATH > $outputDIR1/accepted_hits.s

samtools sort -n $align_results_bam_root_PATH > $outputDIR2/accepted_hits.s
conda deactivate

And then I try to filtered the bam files using filterBam script following this command:

conda activate Augustus
#samtools sort -n -o $outputDIR1/accepted_hits.s.bam $outputDIR1/accepted_hits.bam # recommandation of mehlan
filterBam --verbose --uniq --paired --in $outputDIR1/accepted_hits.s.bam --out $outputDIR1/accepted_hits.sf.bam --pairwiseAlignments

filterBam --uniq --paired --in $outputDIR2/accepted_hits.s --out $outputDIR2/accepted_hits.sf.bam --pairwiseAlignments
conda deactivate

Unfortunatly I have segmentation fault error as you can see bellow :

filterBam --verbose --uniq --paired --in $outputDIR1/accepted_hits.s.bam --out $outputDIR1/accepted_hits.sf.bam
------------------------------------------------
Selected options are: 
best=0
help=0
noIntrons=0
paired=1
uniq=1
verbose=1
pairwiseAlignments=0
Input file: /NetScratch/FLOCAD/cpichot/genome_assembling/2-geneAnnotation/topHat_out_leaves/accepted_hits.s.bam
Output file: /NetScratch/FLOCAD/cpichot/genome_assembling/2-geneAnnotation/topHat_out_leaves/accepted_hits.sf.bam
insertLimit=10
maxIntronLen=500000
minCover=80
minId=92
minIntronLen=35
uniqThresh=0.96
commonGeneFile=
pairBedFile=
------------------------------------------------
Erreur de segmentation

I dragged the bam file so you can check it
bamfiles.zip

Do you have any recommendation, or see what I am doing wrong ?

Thanks in advance

[El-Castor]

up ?