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Starting on : Mon Jul 15 11:45:08 EDT 2019
Running on node : scc-wl3
Current directory : /restricted/projectnb/waxmanlab/varsha/cufflinks
Current job ID : 7712700
Current job name : cuffGFP_1343
Task index number : 
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/scratch/7712700.1.w
Running on host scc-wl3

Directory is /scratch/7712700.1.w

Start time is Mon Jul 15 11:45:08 EDT 2019

copying...
cp: cannot stat '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/GFP_1343/fastq/tophat2/GFP_1343_primary_unique.bam': No such file or directory
Current dir:
/scratch/7712700.1.w

running commands...

genes.gtf
genomeWithRandom.fa
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
open: No such file or directory
File mapped.bam doesn't appear to be a valid BAM file, trying SAM...
Error: cannot open alignment file mapped.bam for reading
cufflinks -o GFP_1343_cufflinks -p 4 -g genes.gtf -b genomeWithRandom.fa -u --library-type fr-secondstrand mapped.bam
done running. copying...
List of files in scratch
genes.gtf
genomeWithRandom.fa

GFP_1343_cufflinks:
Size of files in scratch
4.0K	GFP_1343_cufflinks
89M	genes.gtf
2.6G	genomeWithRandom.fa
2.7G	total
Stop time is Mon Jul 15 11:45:40 EDT 2019