[2018-10-13 01:16:47] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 01:16:47] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:16:47] Checking for Bowtie index files (genome)..
[2018-10-13 01:16:47] Checking for reference FASTA file
[2018-10-13 01:16:47] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:16:50] Reading known junctions from GTF file
[2018-10-13 01:16:55] Preparing reads
	 left reads: min. length=100, max. length=100, 418398 kept reads (205 discarded)
	right reads: min. length=100, max. length=100, 418135 kept reads (468 discarded)
[2018-10-13 01:17:13] Building transcriptome data files /scratch/8792879.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:17:33] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:26:12] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:26:48] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:27:24] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:27:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:28:02] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:28:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:28:23] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:28:33] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:28:42] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:29:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:29:32] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:29:45] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:29:56] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:30:06] Searching for junctions via segment mapping
[2018-10-13 01:32:51] Retrieving sequences for splices
[2018-10-13 01:35:00] Indexing splices
[2018-10-13 01:35:19] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:35:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:35:28] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:35:32] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:35:37] Joining segment hits
[2018-10-13 01:38:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:38:07] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:38:11] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:38:15] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:38:19] Joining segment hits
[2018-10-13 01:40:38] Reporting output tracks
-----------------------------------------------
[2018-10-13 01:44:26] A summary of the alignment counts can be found in /scratch/8792879.1.linga/tophat2/align_summary.txt
[2018-10-13 01:44:26] Run complete: 00:27:39 elapsed