Hello,

I used cuffmerge to merge all assemblies to create a single merged transcriptome annotation.

cufflinks version 2.2.1

cuffmerge -g Homo_sapiens.GRCh37.82.chr_patch_hapl_scaff.gtf -s human_g1k_v37_decoy_bowtie2 -p 8 assemblies.txt

Output:

[Thu Jun  1 17:56:10 2017] Beginning transcriptome assembly merge
-------------------------------------------

[Thu Jun  1 17:56:10 2017] Preparing output location ./merged_asm/
[Thu Jun  1 17:56:22 2017] Converting GTF files to SAM
[17:56:22] Loading reference annotation.
[17:56:25] Loading reference annotation.
[17:56:27] Loading reference annotation.
[17:56:30] Loading reference annotation.
[17:56:33] Loading reference annotation.
[17:56:36] Loading reference annotation.
[Thu Jun  1 17:56:39 2017] Quantitating transcripts
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
Command line:
cufflinks -o ./merged_asm/ -F 0.05 -g Homo_sapiens.GRCh37.82.chr_patch_hapl_scaff.gtf -q --overhang-tolerance 200   --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 8 ./merged_asm/tmp/mergeSam_fileckgq08 
[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).
File ./merged_asm/tmp/mergeSam_fileckgq08 doesn't appear to be a valid BAM file, trying SAM...
[17:56:39] Loading reference annotation.
[17:57:07] Inspecting reads and determining fragment length distribution.
Processed 57942 loci.                       
> Map Properties:
>       Normalized Map Mass: 405038.00
>       Raw Map Mass: 405038.00
>       Fragment Length Distribution: Truncated Gaussian (default)
>                     Default Mean: 200
>                  Default Std Dev: 80
[17:57:11] Assembling transcripts and estimating abundances.
Processed 57942 loci.                       
[Thu Jun  1 18:02:31 2017] Comparing against reference file Homo_sapiens.GRCh37.82.chr_patch_hapl_scaff.gtf
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
Error: file/directory human_g1k_v37_decoy_bowtie2 does not exist!
    [FAILED]
Error: could not execute cuffcompare

There is no merged.gtf file in merged_asm. It has genes.fpkm_tracking, isoforms.fpkm_tracking, skipped.gtf, transcripts.gtf and logs, tmp folders. Why there is no merged.gtf file and what about cuff compare?