[2018-10-13 18:24:17] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 18:24:17] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:24:17] Checking for Bowtie index files (genome)..
[2018-10-13 18:24:17] Checking for reference FASTA file
[2018-10-13 18:24:17] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:24:21] Reading known junctions from GTF file
[2018-10-13 18:24:26] Preparing reads
	 left reads: min. length=100, max. length=100, 177432 kept reads (13 discarded)
	right reads: min. length=100, max. length=100, 177029 kept reads (416 discarded)
[2018-10-13 18:24:33] Building transcriptome data files /scratch/8793435.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:24:52] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:33:04] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:33:20] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:33:35] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:33:35] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:33:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:33:58] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:34:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:34:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:34:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:34:39] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:34:47] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:34:56] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:35:04] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:35:11] Searching for junctions via segment mapping
[2018-10-13 18:37:35] Retrieving sequences for splices
[2018-10-13 18:39:47] Indexing splices
[2018-10-13 18:40:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:40:12] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:40:16] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:40:20] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:40:24] Joining segment hits
[2018-10-13 18:42:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:42:35] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:42:39] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:42:43] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:42:47] Joining segment hits
[2018-10-13 18:44:56] Reporting output tracks
-----------------------------------------------
[2018-10-13 18:47:33] A summary of the alignment counts can be found in /scratch/8793435.1.linga/tophat2/align_summary.txt
[2018-10-13 18:47:33] Run complete: 00:23:15 elapsed