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 14:59:22] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-06-24 14:59:22] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 14:59:22] Checking for Bowtie index files (genome)..
[2019-06-24 14:59:22] Checking for reference FASTA file
[2019-06-24 14:59:22] Generating SAM header for Bowtie2Index/genome
[2019-06-24 14:59:24] Reading known junctions from GTF file
[2019-06-24 14:59:28] Preparing reads
	 left reads: min. length=50, max. length=50, 60568281 kept reads (93095 discarded)
	right reads: min. length=50, max. length=50, 60390423 kept reads (270953 discarded)
[2019-06-24 15:23:47] Building transcriptome data files /scratch/7052574.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 15:24:02] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 15:30:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 15:44:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 15:57:44] Resuming TopHat pipeline with unmapped reads
[2019-06-24 15:57:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 16:18:52] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-24 16:21:32] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-24 16:25:37] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 16:48:43] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-24 16:52:04] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-24 16:57:55] Searching for junctions via segment mapping
[2019-06-24 17:06:07] Retrieving sequences for splices
[2019-06-24 17:08:13] Indexing splices
Building a SMALL index
[2019-06-24 17:08:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-24 17:08:50] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-24 17:09:28] Joining segment hits
[2019-06-24 17:12:52] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-24 17:13:24] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-24 17:14:12] Joining segment hits
[2019-06-24 17:17:51] Reporting output tracks
-----------------------------------------------
[2019-06-24 18:14:06] A summary of the alignment counts can be found in /scratch/7052574.1.linga/tophat2/align_summary.txt
[2019-06-24 18:14:06] Run complete: 03:14:43 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 41 files...