# Cuffmerge: EOF marker is absent. The input is probably truncated

I need to merge my all transcripts.gtf from cufflinks output follow this command line :

cuffmerge -o merged_gtf_output -p 15 -s ref.fasta -g anot.gtf assembly.txt


But I have this warning :

[bam_header_read] EOF marker is absent. The input is probably truncated.
File merge_B3//tmp/mergeSam_fileOaNffV doesn't appear to be a valid BAM file, trying SAM...
[21:40:05] Inspecting reads and determining fragment length distribution.
Processed 3921 loci.
> Map Properties:
>       Normalized Map Mass: 33242.00
>       Raw Map Mass: 33242.00
>       Fragment Length Distribution: Truncated Gaussian (default)
>                     Default Mean: 200
>                  Default Std Dev: 80


Can someone tell me what this warning means and how to fix it?

• it looks very weird to me, since you are not reading a bam file, some how samtools is called and it throws this warning, see also biostars.org/p/189139 Mar 29 '20 at 11:26
• Yes it's true that it's weird, but I think it alludes to the files from which the gtf were generated by cufflinks Mar 30 '20 at 12:18