merged.gtf file is missing

[Ashnada]

Dear all,

I tried to create a denovo annotation,

but after running cuffmerge I recieved only the following files in my output folder:

merge_denovo/logs/run.log
merge_denovo/tmp/gtf2sam_fileMU1yNJ

what has happened? I used the command:

cuffmerge -p 2 -o merge_denovo -g ref_Amel_4.5_top_level_edited.gff3 -s Amel3/Amel_genome.fa assemblies.txt

In assemblies.txt I have the PATHs to all my .gtf files that should be merged.

Thanks for your help,

Ash

[jwfoley]

Maybe your run failed? This is why programs output error messages. What's in run.log?

[Ashnada]

I did not get an error message.

This is in the run.log:

/software/cufflinks/2.1.1/uv2000/bin/cuffmerge -p 8 -o merge_denovo -g /scratch_gs/chsch049/data/F_vs_M/Amel3/ref_Amel_4.5_top_level_edited.gff3 -s /scratch_gs/chsch049/data/F_vs_M/Amel3/Amel_genome.fa assemblies.txt
gtf_to_sam -F /scratch_gs/chsch049/data/Female1_cufflinks_denovo/transcripts.gtf merge_denovo/tmp/gtf2sam_file5g3GIT