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Starting on : Mon Jul 15 11:43:21 EDT 2019
Running on node : scc-tm1
Current directory : /restricted/projectnb/waxmanlab/varsha/cufflinks
Current job ID : 7712553
Current job name : cuffHJ-0001
Task index number : 
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/scratch/7712553.1.linga
Running on host scc-tm1

Directory is /scratch/7712553.1.linga

Start time is Mon Jul 15 11:43:21 EDT 2019

copying...
cp: target 'mapped.bam' is not a directory
Current dir:
/scratch/7712553.1.linga

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 HJ-0001_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

HJ-0001_cufflinks:
Size of files in scratch
4.0K	HJ-0001_cufflinks
89M	genes.gtf
2.6G	genomeWithRandom.fa
2.7G	total
Stop time is Mon Jul 15 11:43:28 EDT 2019