[2018-10-13 08:20:46] Beginning TopHat run (v2.1.1)
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[2018-10-13 08:20:46] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:20:46] Checking for Bowtie index files (genome)..
[2018-10-13 08:20:46] Checking for reference FASTA file
[2018-10-13 08:20:46] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:20:50] Reading known junctions from GTF file
[2018-10-13 08:20:54] Preparing reads
	 left reads: min. length=100, max. length=100, 1122712 kept reads (129 discarded)
	right reads: min. length=100, max. length=100, 1122342 kept reads (499 discarded)
[2018-10-13 08:21:41] Building transcriptome data files /scratch/8793111.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:22:00] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:30:15] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:31:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:32:15] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:32:15] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:32:59] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:33:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:33:27] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:33:40] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:33:52] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:34:35] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:34:47] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:35:03] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:35:17] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:35:30] Searching for junctions via segment mapping
[2018-10-13 08:41:05] Retrieving sequences for splices
[2018-10-13 08:43:19] Indexing splices
[2018-10-13 08:43:42] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:43:50] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:43:59] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:44:06] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:44:13] Joining segment hits
[2018-10-13 08:46:54] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:47:02] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:47:10] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:47:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:47:25] Joining segment hits
[2018-10-13 08:49:52] Reporting output tracks
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[2018-10-13 09:00:14] A summary of the alignment counts can be found in /scratch/8793111.1.linga/tophat2/align_summary.txt
[2018-10-13 09:00:14] Run complete: 00:39:28 elapsed