...
Code Block |
---|
[INFO] I am collecting information on the run. [INFO] Checking GTF file *[WARN] Unsorted in line 27 - chr/strand Chr1 + already read. ********* OK (371481371580:1394828662:5909) [GTF FILE] The GTF reference file given is not sorted, but we found a sorted version. [GTF FILE] The Simulator will use /Users/micha/Desktop/TAIR9_GFF3_genes_sorted.gtf [GTF FILE] You might want to update your parameters file [PROFILING] I am assigning the expression profile ********** OK (371481371580:1394828662:5909) Reading reference annotation **[WARN] merging exon (-21073927,-21073974) with exon (-21073898,-21073924) in transcript AT1G56280.1 because intervening intron has 4 or less nt. ********[WARN] skipped chromosome ChrM OK (00:00:03) found 38564 transcripts [PROFILING] Parameters NB_MOLECULES 5000000 EXPRESSION_K -0.6 EXPRESSION_X0 5.0E7 EXPRESSION_X1 9500.0 PRO_FILE_NAME /Users/micha/Desktop/t9_nebulization.pro profiling ********** OK (00:00:00) Updating .pro file ********** OK (00:00:00) molecules 4999389 [LIBRARY] creating the cDNA libary Initializing Fragmentation File ********** OK (00:00:06) 4999389 mol initialized [LIBRARY] Reverse Transcription [LIBRARY] Configuration Mode: PDT PWM: No RT MIN: 400 RT MAX: 2600 Processing Fragments ********** OK (00:00:17) 4999389 mol: in 4999389, new 0, out 4999389 avg Len 1148.562, maxLen 2600 [LIBRARY] Nebulization [LIBRARY] Configuration Lambda: 600.0 M: 5.0 Max Length: 2600.0 Recursions: 5 Processing Fragments ********** OK (00:00:32) 8804186 mol: in 4999389, new 3804797, out 8804186 avg Len 652.202, maxLen 2427 start amplification [LIBRARY] PCR disabled, skipping amplification Copied results to /Users/micha/Desktop/t9_nebulization.lib Updating .pro file ********** OK (00:00:00) [SEQUENCING] getting the reads Initializing Fragment Index Indexing ********** OK (00:00:10) 8804186 lines indexed (8804186 fragments, 18951 entries) sequencing ***[WARN] merging exon (-21073927,-21073974) with exon (-21073898,-21073924) in transcript AT1G56280.1 because intervening intron has 4 or less nt. *******[WARN] skipped chromosome ChrM OK (00:10:22) found 38564 transcripts [PROFILING] Parameters NB_MOLECULES 5000000 EXPRESSION_K -0.6 EXPRESSION_X0 5.0E7 EXPRESSION_X1 9500.0 PRO_FILE_NAME /Users/micha/Desktop/t9_nebulization.pro profiling ********** OK (00:00:00) Updating .pro file ********** OK (00:00:00) molecules 49993894999395 [LIBRARY] creating the cDNA libary Initializing Fragmentation File ********** OK (00:00:0604) 4999395 4999389 mol initialized [LIBRARY] Reverse Transcription [LIBRARY] Configuration Mode: PDT PWM: No RT MIN: 400 RT MAX: 2600 Processing Fragments ********** OK (00:00:1718) 4999389 4999395 mol: in 49993894999395, new 0, out 4999389 4999395 avg Len 11481039.5627405, maxLen 2600 [LIBRARY] Nebulization [LIBRARY] Configuration Lambda: 600.0 M: 5.0 Max Length: 2600.0 Recursions: 53 Processing Fragments ********** OK (00:00:3223) 8804186 7498699 mol: in 49993894999395, new 38047972499304, out 88041867498699 avg Len 652693.2021967, maxLen 2427 2590 start amplification [LIBRARY] PCR disabled, skipping amplification Copied results to /Users/micha/Desktop/t9_nebulization.lib Updating .pro file ********** OK (00:00:00) [SEQUENCING] getting the reads Initializing Fragment Index Indexing ********** OK (00:00:1009) 88041867498699 lines indexed (88041867498699 fragments, 1895118849 entries) sequencing ***[WARN] merging exon (-21073927,-21073974) with exon (-21073898,-21073924) in transcript AT1G56280.1 because intervening intron has 4 or less nt. *******[WARN] skipped chromosome ChrM OK (00:1008:2237) 7498699 8804186 fragments found (88041867498699 without PCR duplicates) 2001148 3995704 reads sequenced 0 1251847 reads fall in poly-A tail 42854 3770 truncated reads Moving temporary BED file Updating .pro file ********** OK (00:00:00) Updating .pro file ********** OK (00:00:00) Updating .pro file ********** OK (00:00:00) Updating .pro file ********** OK (00:00:00) [END] I finished, took me 695579 sec. |
...