anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 [2019-06-26 15:03:44] Beginning TopHat run (v2.1.1) ----------------------------------------------- [2019-06-26 15:03:44] Checking for Bowtie Bowtie version: 2.3.4.1 [2019-06-26 15:03:44] Checking for Bowtie index files (genome).. [2019-06-26 15:03:44] Checking for reference FASTA file [2019-06-26 15:03:44] Generating SAM header for Bowtie2Index/genome [2019-06-26 15:03:50] Reading known junctions from GTF file [2019-06-26 15:03:55] Preparing reads left reads: min. length=35, max. length=76, 26113823 kept reads (662982 discarded) right reads: min. length=35, max. length=76, 26645609 kept reads (131196 discarded) [2019-06-26 15:25:44] Building transcriptome data files /scratch/7076170.1.linga/tophat2/tmp/RefSeq_GeneBody [2019-06-26 15:26:32] Building Bowtie index from RefSeq_GeneBody.fa [2019-06-26 15:34:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 [2019-06-26 15:55:21] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 [2019-06-26 16:16:31] Resuming TopHat pipeline with unmapped reads [2019-06-26 16:16:31] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 [2019-06-26 16:27:57] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3) [2019-06-26 16:30:40] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3) [2019-06-26 16:33:48] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3) [2019-06-26 16:36:50] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 [2019-06-26 16:49:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3) [2019-06-26 16:54:35] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3) [2019-06-26 16:58:19] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3) [2019-06-26 17:02:14] Searching for junctions via segment mapping [2019-06-26 17:14:26] Retrieving sequences for splices [2019-06-26 17:17:05] Indexing splices Building a SMALL index [2019-06-26 17:17:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3) [2019-06-26 17:17:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3) [2019-06-26 17:19:43] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3) [2019-06-26 17:21:23] Joining segment hits [2019-06-26 17:25:42] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3) [2019-06-26 17:26:05] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3) [2019-06-26 17:27:49] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3) [2019-06-26 17:30:09] Joining segment hits [2019-06-26 17:34:53] Reporting output tracks ----------------------------------------------- [2019-06-26 22:40:00] A summary of the alignment counts can be found in /scratch/7076170.1.linga/tophat2/align_summary.txt [2019-06-26 22:40:00] Run complete: 07:36:16 elapsed [samopen] SAM header is present: 22 sequences. [bam_sort_core] merging from 18 files...