[2018-10-13 06:58:23] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 06:58:23] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:58:23] Checking for Bowtie index files (genome)..
[2018-10-13 06:58:23] Checking for reference FASTA file
[2018-10-13 06:58:23] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:58:28] Reading known junctions from GTF file
[2018-10-13 06:58:32] Preparing reads
	 left reads: min. length=100, max. length=100, 1396519 kept reads (186 discarded)
	right reads: min. length=100, max. length=100, 1396206 kept reads (499 discarded)
[2018-10-13 06:59:31] Building transcriptome data files /scratch/8793073.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:59:51] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:08:17] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:09:27] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:10:38] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:10:38] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:11:22] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:11:32] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:11:48] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:12:00] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:12:12] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:13:00] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:13:11] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:13:28] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:13:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:13:54] Searching for junctions via segment mapping
[2018-10-13 07:18:24] Retrieving sequences for splices
[2018-10-13 07:20:34] Indexing splices
[2018-10-13 07:20:58] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:21:05] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:21:13] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:21:19] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:21:27] Joining segment hits
[2018-10-13 07:23:59] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:24:06] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:24:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:24:21] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:24:28] Joining segment hits
[2018-10-13 07:27:01] Reporting output tracks
-----------------------------------------------
[2018-10-13 07:41:11] A summary of the alignment counts can be found in /scratch/8793073.1.linga/tophat2/align_summary.txt
[2018-10-13 07:41:11] Run complete: 00:42:47 elapsed