[2018-10-13 04:55:27] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 04:55:27] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:55:27] Checking for Bowtie index files (genome)..
[2018-10-13 04:55:27] Checking for reference FASTA file
[2018-10-13 04:55:27] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:55:31] Reading known junctions from GTF file
[2018-10-13 04:55:36] Preparing reads
	 left reads: min. length=100, max. length=100, 1140435 kept reads (144 discarded)
	right reads: min. length=100, max. length=100, 1140147 kept reads (432 discarded)
[2018-10-13 04:56:23] Building transcriptome data files /scratch/8793010.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:56:43] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:05:25] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:07:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:09:52] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:09:52] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:10:23] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:10:33] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:10:47] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:10:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:11:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:11:45] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:11:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:12:11] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:12:24] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:12:38] Searching for junctions via segment mapping
[2018-10-13 05:20:36] Retrieving sequences for splices
[2018-10-13 05:22:46] Indexing splices
[2018-10-13 05:23:13] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:23:21] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:23:33] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:23:44] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:23:54] Joining segment hits
[2018-10-13 05:27:05] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:27:15] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:27:26] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:27:37] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:27:48] Joining segment hits
[2018-10-13 05:30:22] Reporting output tracks
-----------------------------------------------
[2018-10-13 05:59:15] A summary of the alignment counts can be found in /scratch/8793010.1.linga/tophat2/align_summary.txt
[2018-10-13 05:59:15] Run complete: 01:03:48 elapsed