GKR3-wt2early
[bam_sort_core] merging from 24 files...
Command line:
/data/results/tools/align/cufflinks-2.2.0.Linux_x86_64/cufflinks --no-effective-length-correction -G /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -L GKR3-wt2early --no-update-check --library-type fr-secondstrand --num-threads 8 -q -o GKR3-wt2early/accepted_hits www/GKR3-wt2early.bam 
[18:22:46] Loading reference annotation.
[18:22:53] Inspecting reads and determining fragment length distribution.
Processed 21125 loci.                       
> Map Properties:
>	Normalized Map Mass: 43532953.40
>	Raw Map Mass: 43532953.40
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
[18:28:04] Estimating transcript abundances.
Processed 21125 loci.                       
GKR4-DARE2early
[bam_sort_core] merging from 32 files...
Command line:
/data/results/tools/align/cufflinks-2.2.0.Linux_x86_64/cufflinks --no-effective-length-correction -G /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -L GKR4-DARE2early --no-update-check --library-type fr-secondstrand --num-threads 8 -q -o GKR4-DARE2early/accepted_hits www/GKR4-DARE2early.bam 
[18:46:15] Loading reference annotation.
[18:46:19] Inspecting reads and determining fragment length distribution.
Processed 21125 loci.                       
> Map Properties:
>	Normalized Map Mass: 43567577.79
>	Raw Map Mass: 43567577.79
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
[18:52:36] Estimating transcript abundances.
Processed 21125 loci.                       
GKR9-wt2late
[bam_sort_core] merging from 32 files...
Command line:
/data/results/tools/align/cufflinks-2.2.0.Linux_x86_64/cufflinks --no-effective-length-correction -G /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -L GKR9-wt2late --no-update-check --library-type fr-secondstrand --num-threads 8 -q -o GKR9-wt2late/accepted_hits www/GKR9-wt2late.bam 
[19:11:58] Loading reference annotation.
[19:12:03] Inspecting reads and determining fragment length distribution.
Processed 21125 loci.                       
> Map Properties:
>	Normalized Map Mass: 41538041.54
>	Raw Map Mass: 41538041.54
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
[19:17:47] Estimating transcript abundances.
Processed 21125 loci.                       
GKR10-DARE2late
[bam_sort_core] merging from 16 files...
Command line:
/data/results/tools/align/cufflinks-2.2.0.Linux_x86_64/cufflinks --no-effective-length-correction -G /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -L GKR10-DARE2late --no-update-check --library-type fr-secondstrand --num-threads 8 -q -o GKR10-DARE2late/accepted_hits www/GKR10-DARE2late.bam 
[19:31:37] Loading reference annotation.
[19:31:43] Inspecting reads and determining fragment length distribution.
Processed 21125 loci.                       
> Map Properties:
>	Normalized Map Mass: 31094370.29
>	Raw Map Mass: 31094370.29
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
[19:35:12] Estimating transcript abundances.
Processed 21125 loci.                       
GKR5-wt3early
[bam_sort_core] merging from 40 files...
Command line:
/data/results/tools/align/cufflinks-2.2.0.Linux_x86_64/cufflinks --no-effective-length-correction -G /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -L GKR5-wt3early --no-update-check --library-type fr-secondstrand --num-threads 8 -q -o GKR5-wt3early/accepted_hits www/GKR5-wt3early.bam 
[19:58:58] Loading reference annotation.
[19:59:02] Inspecting reads and determining fragment length distribution.
Processed 21125 loci.                       
> Map Properties:
>	Normalized Map Mass: 56862897.39
>	Raw Map Mass: 56862897.39
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
[20:06:25] Estimating transcript abundances.
Processed 21125 loci.                       
GKR6-DARE3early
[bam_sort_core] merging from 24 files...
Command line:
/data/results/tools/align/cufflinks-2.2.0.Linux_x86_64/cufflinks --no-effective-length-correction -G /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf -L GKR6-DARE3early --no-update-check --library-type fr-secondstrand --num-threads 8 -q -o GKR6-DARE3early/accepted_hits www/GKR6-DARE3early.bam 
[20:23:49] Loading reference annotation.
[20:23:54] Inspecting reads and determining fragment length distribution.
Processed 21125 loci.                       
> Map Properties:
>	Normalized Map Mass: 36243003.48
>	Raw Map Mass: 36243003.48
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
[20:28:13] Estimating transcript abundances.
Processed 21125 loci.                       
GKR3-wt2early
GKR4-DARE2early