EOF marker is absent - Githubissues

deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

http://deweylab.biostat.wisc.edu/rsem/

GNU General Public License v3.0

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Open ckr123tw opened 7 years ago

ckr123tw commented 7 years ago

Hi, I was running the following command:

rsem-calculate-expression --paired-end --alignments Aligned.toTranscriptome.out.bam GCA_000001405.15_GRCh38_no_alt sample1

And an error message popped out: [W::bam_hdr_read] EOF marker is absent. The input is probably truncated.

I checked the integrity of Aligned.toTranscriptome.out.bam by samtools quickcheck, but it seemed intact. Should I worry about the error message?

RSEM version: 1.2.31 samtools version: 1.4 STAR version: 2.5.2b

wangyugui commented 7 years ago

There seems problems in Aligned.toTranscriptome.out.bam output by STAR when gff file is used.