[2018-10-13 11:46:24] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:46:24] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:46:24] Checking for Bowtie index files (genome)..
[2018-10-13 11:46:24] Checking for reference FASTA file
[2018-10-13 11:46:24] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:46:29] Reading known junctions from GTF file
[2018-10-13 11:46:34] Preparing reads
	 left reads: min. length=100, max. length=100, 2622455 kept reads (507 discarded)
	right reads: min. length=100, max. length=100, 2621787 kept reads (1175 discarded)
[2018-10-13 11:48:26] Building transcriptome data files /scratch/8793215.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:48:48] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:57:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:06:44] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:16:33] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:16:33] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:18:01] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:18:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:19:28] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:20:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:21:01] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:22:32] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:22:51] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:23:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:24:28] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:25:13] Searching for junctions via segment mapping
[2018-10-13 12:55:51] Retrieving sequences for splices
[2018-10-13 12:58:15] Indexing splices
[2018-10-13 12:58:47] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:59:27] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:00:28] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:01:17] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:02:14] Joining segment hits
[2018-10-13 13:05:27] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:05:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:06:51] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:07:42] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:08:35] Joining segment hits
[2018-10-13 13:11:34] Reporting output tracks
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[2018-10-13 15:23:52] A summary of the alignment counts can be found in /scratch/8793215.1.linga/tophat2/align_summary.txt
[2018-10-13 15:23:52] Run complete: 03:37:27 elapsed