[2018-10-13 02:41:03] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:41:03] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:41:03] Checking for Bowtie index files (genome)..
[2018-10-13 02:41:03] Checking for reference FASTA file
[2018-10-13 02:41:03] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:41:07] Reading known junctions from GTF file
[2018-10-13 02:41:12] Preparing reads
	 left reads: min. length=100, max. length=100, 438563 kept reads (293 discarded)
	right reads: min. length=100, max. length=100, 438129 kept reads (727 discarded)
[2018-10-13 02:41:31] Building transcriptome data files /scratch/8792924.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:41:50] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:50:32] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:51:16] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:51:59] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:51:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:52:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:52:54] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:53:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:53:18] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:53:29] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:54:15] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:54:25] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:54:40] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:54:51] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:55:02] Searching for junctions via segment mapping
[2018-10-13 02:58:10] Retrieving sequences for splices
[2018-10-13 03:00:17] Indexing splices
[2018-10-13 03:00:36] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:00:40] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:00:45] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:00:49] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:00:53] Joining segment hits
[2018-10-13 03:03:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:03:21] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:03:26] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:03:31] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:03:35] Joining segment hits
[2018-10-13 03:05:59] Reporting output tracks
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[2018-10-13 03:09:44] A summary of the alignment counts can be found in /scratch/8792924.1.linga/tophat2/align_summary.txt
[2018-10-13 03:09:44] Run complete: 00:28:40 elapsed