Input parameters:
--infile                 T1_transcripts.gtf,T2_transcripts.gtf,U1_transcripts.gtf,U2_transcripts.gtf
--min-isoform-fraction   0.1
--user_annotation        Crassostrea_gigas.GCA_000297895.1.21.gtf
--user_database          Crassostrea_gigas.GCA_000297895.1.21.dna_rm.toplevel.fa
--version                2.1.1
-p                       6
Executing: cuffmerge -o cuffmerge_out -g Crassostrea_gigas.GCA_000297895.1.21.gtf  -s Crassostrea_gigas.GCA_000297895.1.21.dna_rm.toplevel.fa  --min-isoform-fraction 0.1  gtf_to_merge.txt 

[Thu Feb  6 09:55:19 2014] Beginning transcriptome assembly merge
-------------------------------------------

[Thu Feb  6 09:55:19 2014] Preparing output location cuffmerge_out/
[Thu Feb  6 09:55:23 2014] Converting GTF files to SAM
gtf_to_sam: /lib64/libz.so.1: no version information available (required by gtf_to_sam)
[09:55:23] Loading reference annotation.
gtf_to_sam: /lib64/libz.so.1: no version information available (required by gtf_to_sam)
[09:55:26] Loading reference annotation.
gtf_to_sam: /lib64/libz.so.1: no version information available (required by gtf_to_sam)
[09:55:28] Loading reference annotation.
gtf_to_sam: /lib64/libz.so.1: no version information available (required by gtf_to_sam)
[09:55:32] Loading reference annotation.
[Thu Feb  6 09:55:36 2014] Quantitating transcripts
cufflinks: /lib64/libz.so.1: no version information available (required by cufflinks)
You are using Cufflinks v2.1.1, which is the most recent release.
Command line:
cufflinks -o cuffmerge_out/ -F 0.1 -g Crassostrea_gigas.GCA_000297895.1.21.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 1 cuffmerge_out/tmp/mergeSam_fileWErbbR 
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File cuffmerge_out/tmp/mergeSam_fileWErbbR doesn't appear to be a valid BAM file, trying SAM...
[09:55:36] Loading reference annotation.
[09:55:39] Inspecting reads and determining fragment length distribution.
Processed 38485 loci.                       
> Map Properties:
>	Normalized Map Mass: 182896.00
>	Raw Map Mass: 182896.00
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
[09:55:41] Assembling transcripts and estimating abundances.
Processed 38485 loci.                       
[Thu Feb  6 10:00:57 2014] Comparing against reference file Crassostrea_gigas.GCA_000297895.1.21.gtf
You are using Cufflinks v2.1.1, which is the most recent release.
No fasta index found for Crassostrea_gigas.GCA_000297895.1.21.dna_rm.toplevel.fa. Rebuilding, please wait..
Fasta index rebuilt.
[Thu Feb  6 10:01:38 2014] Comparing against reference file Crassostrea_gigas.GCA_000297895.1.21.gtf
You are using Cufflinks v2.1.1, which is the most recent release.