[2018-10-13 03:43:09] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:43:09] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:43:09] Checking for Bowtie index files (genome)..
[2018-10-13 03:43:09] Checking for reference FASTA file
[2018-10-13 03:43:09] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:43:14] Reading known junctions from GTF file
[2018-10-13 03:43:18] Preparing reads
	 left reads: min. length=100, max. length=100, 606108 kept reads (39 discarded)
	right reads: min. length=100, max. length=100, 605958 kept reads (189 discarded)
[2018-10-13 03:43:43] Building transcriptome data files /scratch/8792966.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:44:03] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:51:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:52:13] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:52:47] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:52:47] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:53:10] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:53:18] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:53:30] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:53:38] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:53:48] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:54:12] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:54:21] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:54:32] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:54:42] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:54:51] Searching for junctions via segment mapping
[2018-10-13 03:57:58] Retrieving sequences for splices
[2018-10-13 04:00:00] Indexing splices
[2018-10-13 04:00:19] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:00:23] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:00:28] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:00:32] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:00:37] Joining segment hits
[2018-10-13 04:03:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:03:09] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:03:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:03:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:03:23] Joining segment hits
[2018-10-13 04:05:43] Reporting output tracks
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[2018-10-13 04:11:03] A summary of the alignment counts can be found in /scratch/8792966.1.linga/tophat2/align_summary.txt
[2018-10-13 04:11:03] Run complete: 00:27:54 elapsed