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 16:37:35] Beginning TopHat run (v2.1.1) ----------------------------------------------- [2019-06-26 16:37:35] Checking for Bowtie Bowtie version: 2.3.4.1 [2019-06-26 16:37:36] Checking for Bowtie index files (genome).. [2019-06-26 16:37:36] Checking for reference FASTA file [2019-06-26 16:37:36] Generating SAM header for Bowtie2Index/genome [2019-06-26 16:37:46] Reading known junctions from GTF file [2019-06-26 16:37:51] Preparing reads left reads: min. length=35, max. length=76, 23900650 kept reads (782096 discarded) right reads: min. length=35, max. length=76, 24539690 kept reads (143056 discarded) [2019-06-26 16:58:42] Building transcriptome data files /scratch/7076175.1.linga/tophat2/tmp/RefSeq_GeneBody [2019-06-26 16:59:18] Building Bowtie index from RefSeq_GeneBody.fa [2019-06-26 17:07:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 [2019-06-26 17:25:51] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 [2019-06-26 17:46:14] Resuming TopHat pipeline with unmapped reads [2019-06-26 17:46:15] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 [2019-06-26 17:57:54] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3) [2019-06-26 18:00:50] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3) [2019-06-26 18:03:50] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3) [2019-06-26 18:06:47] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 [2019-06-26 18:21:26] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3) [2019-06-26 18:26:12] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3) [2019-06-26 18:30:30] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3) [2019-06-26 18:35:09] Searching for junctions via segment mapping [2019-06-26 18:44:45] Retrieving sequences for splices [2019-06-26 18:47:15] Indexing splices Building a SMALL index [2019-06-26 18:47:36] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3) [2019-06-26 18:47:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3) [2019-06-26 18:49:58] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3) [2019-06-26 18:52:01] Joining segment hits [2019-06-26 18:56:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3) [2019-06-26 18:56:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3) [2019-06-26 18:59:39] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3) [2019-06-26 19:03:08] Joining segment hits [2019-06-26 19:08:30] Reporting output tracks ----------------------------------------------- [2019-06-26 21:34:40] A summary of the alignment counts can be found in /scratch/7076175.1.linga/tophat2/align_summary.txt [2019-06-26 21:34:40] Run complete: 04:57:05 elapsed [samopen] SAM header is present: 22 sequences. [bam_sort_core] merging from 17 files...