[2021-04-15 15:42:31] Beginning TopHat run (v2.1.1)
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[2021-04-15 15:42:31] Checking for Bowtie
		  Bowtie version:	 2.4.2.0
[2021-04-15 15:42:31] Checking for Bowtie index files (genome)..
[2021-04-15 15:42:31] Checking for reference FASTA file
[2021-04-15 15:42:31] Generating SAM header for ref/test_ref
[2021-04-15 15:42:31] Preparing reads
	 left reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
	right reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
[2021-04-15 15:42:31] Mapping left_kept_reads to genome test_ref with Bowtie2 
[2021-04-15 15:42:31] Mapping left_kept_reads_seg1 to genome test_ref with Bowtie2 (1/3)
[2021-04-15 15:42:31] Mapping left_kept_reads_seg2 to genome test_ref with Bowtie2 (2/3)
[2021-04-15 15:42:31] Mapping left_kept_reads_seg3 to genome test_ref with Bowtie2 (3/3)
[2021-04-15 15:42:31] Mapping right_kept_reads to genome test_ref with Bowtie2 
[2021-04-15 15:42:31] Mapping right_kept_reads_seg1 to genome test_ref with Bowtie2 (1/3)
[2021-04-15 15:42:31] Mapping right_kept_reads_seg2 to genome test_ref with Bowtie2 (2/3)
[2021-04-15 15:42:31] Mapping right_kept_reads_seg3 to genome test_ref with Bowtie2 (3/3)
[2021-04-15 15:42:31] Searching for junctions via segment mapping
[2021-04-15 15:42:31] Retrieving sequences for splices
[2021-04-15 15:42:31] Indexing splices
[2021-04-15 15:42:32] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2021-04-15 15:42:32] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2021-04-15 15:42:32] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2021-04-15 15:42:32] Joining segment hits
[2021-04-15 15:42:32] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2021-04-15 15:42:32] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2021-04-15 15:42:32] Mapping right_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2021-04-15 15:42:32] Joining segment hits
[2021-04-15 15:42:32] Reporting output tracks
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[2021-04-15 15:42:32] A summary of the alignment counts can be found in out/tophat_pe/align_summary.txt
[2021-04-15 15:42:32] Run complete: 00:00:01 elapsed