[2018-10-13 09:05:54] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 09:05:54] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:05:54] Checking for Bowtie index files (genome)..
[2018-10-13 09:05:54] Checking for reference FASTA file
[2018-10-13 09:05:54] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:05:59] Reading known junctions from GTF file
[2018-10-13 09:06:03] Preparing reads
	 left reads: min. length=100, max. length=100, 1243138 kept reads (80 discarded)
	right reads: min. length=100, max. length=100, 1242739 kept reads (479 discarded)
[2018-10-13 09:06:54] Building transcriptome data files /scratch/8793135.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:07:13] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:15:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:16:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:17:06] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:17:06] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:17:39] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:17:48] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:18:00] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:18:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:18:21] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:18:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:19:06] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:19:19] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:19:30] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:19:42] Searching for junctions via segment mapping
[2018-10-13 09:24:22] Retrieving sequences for splices
[2018-10-13 09:26:35] Indexing splices
[2018-10-13 09:26:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:27:04] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:27:10] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:27:16] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:27:22] Joining segment hits
[2018-10-13 09:29:50] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:29:56] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:30:02] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:30:09] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:30:16] Joining segment hits
[2018-10-13 09:32:50] Reporting output tracks
-----------------------------------------------
[2018-10-13 09:42:33] A summary of the alignment counts can be found in /scratch/8793135.1.linga/tophat2/align_summary.txt
[2018-10-13 09:42:33] Run complete: 00:36:38 elapsed