========================================================== Start date : Wed Jul 24 13:01:09 EDT 2019 Job name : cuffmerge_all Job ID : 7985706 undefined ========================================================== [Wed Jul 24 13:01:11 2019] Beginning transcriptome assembly merge ------------------------------------------- [Wed Jul 24 13:01:11 2019] Preparing output location /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/ [Wed Jul 24 13:15:43 2019] Converting GTF files to SAM [13:15:43] Loading reference annotation. [13:15:49] Loading reference annotation. [13:15:57] Loading reference annotation. [13:16:03] Loading reference annotation. [13:16:09] Loading reference annotation. [13:16:16] Loading reference annotation. [13:16:23] Loading reference annotation. [13:16:29] Loading reference annotation. [13:16:36] Loading reference annotation. [13:16:42] Loading reference annotation. [13:16:49] Loading reference annotation. 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Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu). Command line: cufflinks -o /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/ -F 0.05 -g /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/genes.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 1 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/mergeSam_fileMbdoJg [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 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/mergeSam_fileMbdoJg doesn't appear to be a valid BAM file, trying SAM... [13:36:07] Loading reference annotation. [13:36:12] Inspecting reads and determining fragment length distribution. Processed 31809 loci. > Map Properties: > Normalized Map Mass: 8363161.00 > Raw Map Mass: 8363161.00 > Fragment Length Distribution: Truncated Gaussian (default) > Default Mean: 200 > Default Std Dev: 80 [13:38:45] Assembling transcripts and estimating abundances. Processed 31809 loci. [Wed Jul 24 15:37:56 2019] Comparing against reference file /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/genes.gtf Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu). [Wed Jul 24 15:39:59 2019] Comparing against reference file /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/genes.gtf Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).