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Segmentation fault error using filter bam
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