[2018-10-13 04:35:30] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 04:35:30] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:35:30] Checking for Bowtie index files (genome)..
[2018-10-13 04:35:30] Checking for reference FASTA file
[2018-10-13 04:35:30] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:35:35] Reading known junctions from GTF file
[2018-10-13 04:35:39] Preparing reads
	 left reads: min. length=100, max. length=100, 1141006 kept reads (111 discarded)
	right reads: min. length=100, max. length=100, 1140674 kept reads (443 discarded)
[2018-10-13 04:36:24] Building transcriptome data files /scratch/8792997.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:36:42] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:44:25] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:45:43] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:46:58] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:46:58] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:47:32] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:47:41] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:47:54] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:48:05] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:48:17] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:48:52] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:49:03] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:49:17] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:49:29] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:49:42] Searching for junctions via segment mapping
[2018-10-13 04:54:33] Retrieving sequences for splices
[2018-10-13 04:56:42] Indexing splices
[2018-10-13 04:57:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:57:10] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:57:18] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:57:24] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:57:31] Joining segment hits
[2018-10-13 05:00:03] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:00:09] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:00:17] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:00:24] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:00:32] Joining segment hits
[2018-10-13 05:03:05] Reporting output tracks
-----------------------------------------------
[2018-10-13 05:19:16] A summary of the alignment counts can be found in /scratch/8792997.1.linga/tophat2/align_summary.txt
[2018-10-13 05:19:16] Run complete: 00:43:45 elapsed