========================================================== Start date : Mon Aug 19 10:48:04 EDT 2019 Job name : cuffmerge_18-8-19 Job ID : 8787389 undefined ========================================================== [Mon Aug 19 10:48:06 2019] Beginning transcriptome assembly merge ------------------------------------------- [Mon Aug 19 10:48:06 2019] Preparing output location /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/ [Mon Aug 19 11:10:45 2019] Converting GTF files to SAM [11:10:45] Loading reference annotation. [11:11:04] Loading reference annotation. [11:11:10] Loading reference annotation. [11:11:18] Loading reference annotation. [11:11:25] Loading reference annotation. [11:11:31] Loading reference annotation. [11:11:38] Loading reference annotation. [11:11:45] Loading reference annotation. [11:11:51] Loading reference annotation. [11:11:58] Loading reference annotation. [11:12:04] Loading reference annotation. 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[11:40:49] Loading reference annotation. [11:40:55] Loading reference annotation. [11:41:01] Loading reference annotation. [11:41:07] Loading reference annotation. [Mon Aug 19 11:42:40 2019] Quantitating transcripts Warning: Could not connect to update server to verify current version. 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_withkk/new/ -F 0.05 -g /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/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_withkk/new/tmp/mergeSam_fileL4XIYl [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_withkk/new/tmp/mergeSam_fileL4XIYl doesn't appear to be a valid BAM file, trying SAM... [11:42:40] Loading reference annotation. [11:42:45] Inspecting reads and determining fragment length distribution. Processed 32247 loci. > Map Properties: > Normalized Map Mass: 12853272.00 > Raw Map Mass: 12853272.00 > Fragment Length Distribution: Truncated Gaussian (default) > Default Mean: 200 > Default Std Dev: 80 [11:46:48] Assembling transcripts and estimating abundances. Processed 32247 loci. [Mon Aug 19 15:19:25 2019] Comparing against reference file /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/genes.gtf Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu). No fasta index found for /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/genomeWithRandom.fa. Rebuilding, please wait.. Fasta index rebuilt. [Mon Aug 19 15:22:48 2019] Comparing against reference file /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/genes.gtf Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).