[2018-10-13 02:38:04] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 02:38:04] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:38:04] Checking for Bowtie index files (genome)..
[2018-10-13 02:38:04] Checking for reference FASTA file
[2018-10-13 02:38:04] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:38:08] Reading known junctions from GTF file
[2018-10-13 02:38:12] Preparing reads
	 left reads: min. length=100, max. length=100, 448100 kept reads (283 discarded)
	right reads: min. length=100, max. length=100, 447688 kept reads (695 discarded)
[2018-10-13 02:38:31] Building transcriptome data files /scratch/8792921.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:38:50] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:47:10] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:47:50] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:48:31] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:48:31] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:49:16] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:49:26] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:49:40] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:49:51] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:50:02] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:50:48] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:50:59] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:51:14] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:51:25] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:51:37] Searching for junctions via segment mapping
[2018-10-13 02:54:19] Retrieving sequences for splices
[2018-10-13 02:56:21] Indexing splices
[2018-10-13 02:56:39] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:56:43] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:56:48] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:56:53] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:56:57] Joining segment hits
[2018-10-13 02:59:20] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:59:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:59:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:59:34] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:59:39] Joining segment hits
[2018-10-13 03:02:15] Reporting output tracks
-----------------------------------------------
[2018-10-13 03:05:57] A summary of the alignment counts can be found in /scratch/8792921.1.linga/tophat2/align_summary.txt
[2018-10-13 03:05:57] Run complete: 00:27:52 elapsed