[2018-10-13 03:46:03] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:46:03] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:46:03] Checking for Bowtie index files (genome)..
[2018-10-13 03:46:03] Checking for reference FASTA file
[2018-10-13 03:46:03] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:46:07] Reading known junctions from GTF file
[2018-10-13 03:46:11] Preparing reads
	 left reads: min. length=100, max. length=100, 71495 kept reads (153 discarded)
	right reads: min. length=100, max. length=100, 71381 kept reads (267 discarded)
[2018-10-13 03:46:15] Building transcriptome data files /scratch/8792971.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:46:34] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:55:34] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:55:51] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:56:09] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:56:09] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:56:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:56:36] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:56:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:56:55] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:57:03] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:57:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:57:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:57:40] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:57:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:57:58] Searching for junctions via segment mapping
[2018-10-13 04:00:12] Retrieving sequences for splices
[2018-10-13 04:02:22] Indexing splices
[2018-10-13 04:02:39] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:02:43] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:02:48] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:02:52] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:02:56] Joining segment hits
[2018-10-13 04:05:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:05:21] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:05:25] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:05:29] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:05:33] Joining segment hits
[2018-10-13 04:07:46] Reporting output tracks
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[2018-10-13 04:10:09] A summary of the alignment counts can be found in /scratch/8792971.1.linga/tophat2/align_summary.txt
[2018-10-13 04:10:09] Run complete: 00:24:05 elapsed