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 17:04:10] Beginning TopHat run (v2.1.1) ----------------------------------------------- [2019-06-26 17:04:10] Checking for Bowtie Bowtie version: 2.3.4.1 [2019-06-26 17:04:11] Checking for Bowtie index files (genome).. [2019-06-26 17:04:11] Checking for reference FASTA file [2019-06-26 17:04:11] Generating SAM header for Bowtie2Index/genome [2019-06-26 17:04:15] Reading known junctions from GTF file [2019-06-26 17:04:19] Preparing reads left reads: min. length=35, max. length=76, 25171825 kept reads (412286 discarded) right reads: min. length=35, max. length=76, 25507846 kept reads (76265 discarded) [2019-06-26 17:22:27] Building transcriptome data files /scratch/7076177.1.linga/tophat2/tmp/RefSeq_GeneBody [2019-06-26 17:22:47] Building Bowtie index from RefSeq_GeneBody.fa [2019-06-26 17:29:39] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 [2019-06-26 17:44:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 [2019-06-26 17:58:40] Resuming TopHat pipeline with unmapped reads [2019-06-26 17:58:40] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 [2019-06-26 18:06:55] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3) [2019-06-26 18:08:36] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3) [2019-06-26 18:10:26] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3) [2019-06-26 18:12:15] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 [2019-06-26 18:21:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3) [2019-06-26 18:24:06] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3) [2019-06-26 18:26:37] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3) [2019-06-26 18:29:13] Searching for junctions via segment mapping [2019-06-26 18:37:16] Retrieving sequences for splices [2019-06-26 18:39:37] Indexing splices Building a SMALL index [2019-06-26 18:40:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3) [2019-06-26 18:40:21] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3) [2019-06-26 18:41:22] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3) [2019-06-26 18:42:26] Joining segment hits [2019-06-26 18:46:26] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3) [2019-06-26 18:46:43] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3) [2019-06-26 18:47:39] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3) [2019-06-26 18:49:03] Joining segment hits [2019-06-26 18:53:48] Reporting output tracks ----------------------------------------------- [2019-06-26 22:19:40] A summary of the alignment counts can be found in /scratch/7076177.1.linga/tophat2/align_summary.txt [2019-06-26 22:19:40] Run complete: 05:15:29 elapsed [samopen] SAM header is present: 22 sequences. [bam_sort_core] merging from 18 files...