========================================================== Start date : Mon Jul 22 14:35:12 EDT 2019 Job name : cuff_test Job ID : 7911008 undefined ========================================================== /var/spool/sge/scc-ka3/job_scripts/7911008: line 33: ad: command not found [Mon Jul 22 14:35:15 2019] Beginning transcriptome assembly merge ------------------------------------------- [Mon Jul 22 14:35:15 2019] Preparing output location /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/ 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: '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/HJ-0001 _cufflinks/transcripts.gtf' ========================================================== Start date : Mon Jul 22 14:48:50 EDT 2019 Job name : cuff_test Job ID : 7911085 undefined ========================================================== [Mon Jul 22 14:48:52 2019] Beginning transcriptome assembly merge ------------------------------------------- [Mon Jul 22 14:48:52 2019] Preparing output location /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/ 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: '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/HJ-0001 _cufflinks/transcripts.gtf' ========================================================== Start date : Tue Jul 23 11:05:13 EDT 2019 Job name : cuff_test Job ID : 7923005 undefined ========================================================== [Tue Jul 23 11:05:14 2019] Beginning transcriptome assembly merge ------------------------------------------- [Tue Jul 23 11:05:14 2019] Preparing output location /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/ [Tue Jul 23 11:16:50 2019] Converting GTF files to SAM [11:16:51] Loading reference annotation. 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[11:33:08] Loading reference annotation. [11:33:14] Loading reference annotation. [11:33:20] Loading reference annotation. [11:33:27] Loading reference annotation. [11:33:33] Loading reference annotation. [Tue Jul 23 11:34:26 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/cuffmer_test/ -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/cuffmer_test/tmp/mergeSam_fileqx1T4B [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/cuffmer_test/tmp/mergeSam_fileqx1T4B doesn't appear to be a valid BAM file, trying SAM... [11:34:26] Loading reference annotation. [11:34:30] Inspecting reads and determining fragment length distribution. Processed 29584 loci. > Map Properties: > Normalized Map Mass: 7332947.00 > Raw Map Mass: 7332947.00 > Fragment Length Distribution: Truncated Gaussian (default) > Default Mean: 200 > Default Std Dev: 80 [11:36:44] Assembling transcripts and estimating abundances. Processed 29584 loci. [Tue Jul 23 13:05:24 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). No fasta index found for /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/genomeWithRandom.fa. Rebuilding, please wait.. Fasta index rebuilt. [Tue Jul 23 13:07:30 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).