[2018-10-13 03:16:46] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 03:16:46] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:16:46] Checking for Bowtie index files (genome)..
[2018-10-13 03:16:46] Checking for reference FASTA file
[2018-10-13 03:16:46] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:16:52] Reading known junctions from GTF file
[2018-10-13 03:16:56] Preparing reads
	 left reads: min. length=100, max. length=100, 464177 kept reads (329 discarded)
	right reads: min. length=100, max. length=100, 463926 kept reads (580 discarded)
[2018-10-13 03:17:16] Building transcriptome data files /scratch/8792950.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:17:36] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:26:19] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:27:07] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:27:56] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:27:56] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:28:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:29:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:29:15] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:29:27] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:29:39] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:30:31] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:30:43] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:31:00] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:31:12] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:31:24] Searching for junctions via segment mapping
[2018-10-13 03:34:17] Retrieving sequences for splices
[2018-10-13 03:36:26] Indexing splices
[2018-10-13 03:36:45] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:36:50] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:36:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:36:59] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:37:04] Joining segment hits
[2018-10-13 03:39:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:39:23] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:39:29] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:39:33] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:39:38] Joining segment hits
[2018-10-13 03:41:55] Reporting output tracks
-----------------------------------------------
[2018-10-13 03:45:51] A summary of the alignment counts can be found in /scratch/8792950.1.linga/tophat2/align_summary.txt
[2018-10-13 03:45:51] Run complete: 00:29:04 elapsed