========================================================== Start date : Fri Aug 2 11:16:45 EDT 2019 Job name : cuffmerge_all Job ID : 8205158 undefined ========================================================== [Fri Aug 2 11:16:55 2019] Beginning transcriptome assembly merge ------------------------------------------- [Fri Aug 2 11:16:55 2019] Preparing output location /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/results/ Traceback (most recent call last): File "/share/pkg.7/cufflinks/2.2.1/install/bin/cuffmerge", line 580, in sys.exit(main()) File "/share/pkg.7/cufflinks/2.2.1/install/bin/cuffmerge", line 538, in main gtf_input_files = test_input_files(transfrag_list_file) File "/share/pkg.7/cufflinks/2.2.1/install/bin/cuffmerge", line 268, in test_input_files g = open(line,"r") IOError: [Errno 2] No such file or directory: '/restricted/projectnb/waxmanlab/varsha/cufflinks/KI13_cufflinks/transcripts.gtf' ========================================================== Start date : Fri Aug 2 11:26:15 EDT 2019 Job name : cuffmerge_all Job ID : 8207260 undefined ========================================================== [Fri Aug 2 11:26:17 2019] Beginning transcriptome assembly merge ------------------------------------------- [Fri Aug 2 11:26:17 2019] Preparing output location /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/results/ [Fri Aug 2 11:47:49 2019] Converting GTF files to SAM [11:47:50] Loading reference annotation. 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Command line: cufflinks -o /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/results/ -F 0.05 -g /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/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/results/tmp/mergeSam_fileWCVyU2 [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/results/tmp/mergeSam_fileWCVyU2 doesn't appear to be a valid BAM file, trying SAM... [12:18:41] Loading reference annotation. [12:18:45] Inspecting reads and determining fragment length distribution. Processed 31698 loci. > Map Properties: > Normalized Map Mass: 12656892.00 > Raw Map Mass: 12656892.00 > Fragment Length Distribution: Truncated Gaussian (default) > Default Mean: 200 > Default Std Dev: 80 [12:22:42] Assembling transcripts and estimating abundances. Processed 31698 loci. [Fri Aug 2 15:24:38 2019] Comparing against reference file /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/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/genomeWithRandom.fa. Rebuilding, please wait.. Fasta index rebuilt. [Fri Aug 2 15:27:24 2019] Comparing against reference file /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/genes.gtf Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).