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


[2019-06-24 17:41:57] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-06-24 17:41:57] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 17:41:57] Checking for Bowtie index files (genome)..
[2019-06-24 17:41:57] Checking for reference FASTA file
[2019-06-24 17:41:57] Generating SAM header for Bowtie2Index/genome
[2019-06-24 17:42:02] Reading known junctions from GTF file
[2019-06-24 17:42:06] Preparing reads
	 left reads: min. length=150, max. length=150, 31183217 kept reads (1050 discarded)
	right reads: min. length=150, max. length=150, 31180855 kept reads (3412 discarded)
[2019-06-24 18:19:28] Building transcriptome data files /scratch/7056751.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 18:19:47] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 18:26:41] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 18:55:14] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:24:42] Resuming TopHat pipeline with unmapped reads
[2019-06-24 19:24:43] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 20:04:26] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-24 20:09:57] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-24 20:15:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-24 20:21:48] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-24 20:27:35] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-24 20:32:18] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-24 20:34:32] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 21:25:34] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-24 21:33:12] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-24 21:40:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-24 21:49:30] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-24 21:57:11] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-24 22:04:15] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-24 22:08:09] Searching for junctions via segment mapping
[2019-06-25 02:52:27] Retrieving sequences for splices
[2019-06-25 02:54:44] Indexing splices
Building a SMALL index
[2019-06-25 02:55:25] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-25 02:59:10] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-25 03:02:58] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-25 03:06:49] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-25 03:10:33] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-25 03:13:11] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-25 03:13:58] Joining segment hits
[2019-06-25 03:23:42] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-25 03:28:29] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-25 03:33:05] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-25 03:37:33] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-25 03:41:48] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-25 03:44:54] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-25 03:46:04] Joining segment hits
[2019-06-25 03:56:19] Reporting output tracks
-----------------------------------------------
[2019-06-25 05:13:03] A summary of the alignment counts can be found in /scratch/7056751.1.linga/tophat2/align_summary.txt
[2019-06-25 05:13:03] Run complete: 11:31:05 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 29 files...