bgzf_read error during samtools run

when i used following command on my bam file:

samtools view -F 4 myfile.bam | perl -lane 'print "$F[2]\t$F[3]"' > myfile.hits

i got this message:

[E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes

[main_samview] truncated file.

anybody can help me to resolve it.

software error samtools cnv-seq bgzf

• 4,390 views • link

updated 8.7 years ago by Devon Ryan

• written 8.7 years ago by kk.mahsa

1 answer

Somehow your BAM file got corrupted. You'll want to remake it.

• 0 views • link

written 8.7 years ago by Devon Ryan

More posts like this

samtools BGZF block error
written 1.8 years ago by Novice •

Hi all, I tried to run samtools depth on my bam file to generate average depth using samtools depth input.bam | awk '{sum+=$3} END { …
samtools produces truncated error during merging the bam files
written 2.8 years ago by rj.rezwan •

Hi, I am using the merge function of `samtools` to merge all the available bam files produced after `HISAT alignment`. Every file has `>85%` alignment …
Problem with using flagstat after bowtie2 alignment
written 4.7 years ago by Ivan •

I'm running `bowtie2` to align multiple samples to one reference genome, and then run `samtools flagstats` to output the results. All but two samples have …
multiBamSummary for unpaired end read?
written 4.7 years ago by adR

Hello everyone, I am using `multiBamSummary` to computes read coverages for many bam files. multiBamSummary bins --bamfiles *.bam -out readCounts.npz --outRawCounts readCounts.tab However, I got …
Samtools error -1
written 5.8 years ago by rin •

Hi all, I am analyzing some data from [GSE156255][1] and I keep getting an error when ordering the bam files. I tried to look it …
freebayes error for SNP calling
written 5.9 years ago by evafinegan •

Hello, I am using freebayes for SNP calling using multiple input bam files: fasta_generate_regions.py genome.fasta.fai 100000 > genome.txt export TMPDIR=. freebayes-parallel genome.txt 8 \ -f …
Freebayes error message
written 6.0 years ago by ocortes •

Hi all, I am running freebayes with 42 .bam files and after several minutes running the instruction I got an error message: [E::bgzf_read] Read block …
"[E::bgzf_read] Read block operation failed" error - possible truncation/corruption of BAM file
written 6.8 years ago by gordo2b •

Hey! I am trying to run velocyto on my BAM file, however I was getting some errors that implied a truncation or corruption of the …
EOF Marker absent .bam.pbi files
written 7.2 years ago by selplat21 •

I received a series of subreads.bam.pbi files from my sequencing facility and I unzipped each file. When I try to samtools merge all of the …
bgzf_blocked error when using samtools
written 8.7 years ago by milanlove •

when i used samtools sort for sorting .bam file, following error was appeared. any body know that how i can solve it? [E::bgzf_read] Read block …