[2018-10-13 06:01:10] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:01:10] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:01:10] Checking for Bowtie index files (genome)..
[2018-10-13 06:01:10] Checking for reference FASTA file
[2018-10-13 06:01:10] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:01:14] Reading known junctions from GTF file
[2018-10-13 06:01:18] Preparing reads
	 left reads: min. length=100, max. length=100, 1049473 kept reads (262 discarded)
	right reads: min. length=100, max. length=100, 1049204 kept reads (531 discarded)
[2018-10-13 06:02:00] Building transcriptome data files /scratch/8793040.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:02:18] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:11:03] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:12:50] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:14:39] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:14:40] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:15:22] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:15:34] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:15:57] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:16:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:16:26] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:17:10] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:17:22] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:17:47] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:18:03] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:18:18] Searching for junctions via segment mapping
[2018-10-13 06:28:04] Retrieving sequences for splices
[2018-10-13 06:30:07] Indexing splices
[2018-10-13 06:30:31] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:30:43] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:31:00] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:31:15] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:31:29] Joining segment hits
[2018-10-13 06:34:06] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:34:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:34:37] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:34:53] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:35:06] Joining segment hits
[2018-10-13 06:37:34] Reporting output tracks
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[2018-10-13 07:04:42] A summary of the alignment counts can be found in /scratch/8793040.1.linga/tophat2/align_summary.txt
[2018-10-13 07:04:42] Run complete: 01:03:31 elapsed