[bam_header_read] EOF marker is absent. The input is probably truncated.

[Giorgio Casaburi]

Hi all,

I have been generating a few .bam files using bowtie in paired-end mode with parameters that are default in Trinity  (i.e., --all --best --strata -m 300 --chunkmbs 512). 

When I try to run CORSET on the bam file I have this error:

Running Corset Version 1.06

Setting read alignments to be output to file.

Corset will exit after reading bam files.

Reading bam file : lo_sab.bam

[bam_header_read] EOF marker is absent. The input is probably truncated.

[bam_header_read] invalid BAM binary header (this is not a BAM file).

fail to open lo_sab.bam for reading.

Any clue on what's happening?

Thanks,

Giorgio

[Giorgio Casaburi]

Nevermind,  I found the issue, the output from bowtie was in legacy format. I had to re-run wiht the -S option and then convert the sam to bam and did not have error.

 

[cgiaco...@gmail.com]

Hello Giorgio,

I'm totally a newbie at this and I'm struggling with this problem for almost a week. Could you help me?

Where did you add the -S option, running bowtie or samtools?

I'm getting the same error message with the following script:

samtools flagstat map.fastq.sam > flagstat
samtools view -b map.fastq.sam > mapped.bam
samtools sort -O SAM mapped.bam > sorted.sam

python -m HTSeq.scripts.count -s yes -r pos -m intersection-nonempty -q sorted.sam /home/carolgs/Cpapaya/annotation/Cpapaya_113_ASGPBv0.4.gene.gff3 > counts_b.txt

Can you see what's the problem?

Thanks in advance,
Carol