[2018-10-13 02:43:25] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:43:25] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:43:26] Checking for Bowtie index files (genome)..
[2018-10-13 02:43:26] Checking for reference FASTA file
[2018-10-13 02:43:26] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:43:30] Reading known junctions from GTF file
[2018-10-13 02:43:34] Preparing reads
	 left reads: min. length=100, max. length=100, 442664 kept reads (263 discarded)
	right reads: min. length=100, max. length=100, 442320 kept reads (607 discarded)
[2018-10-13 02:43:53] Building transcriptome data files /scratch/8792926.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:44:13] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:52:44] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:53:27] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:54:10] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:54:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:54:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:55:06] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:55:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:55:32] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:55:44] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:56:31] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:56:42] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:56:57] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:57:10] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:57:21] Searching for junctions via segment mapping
[2018-10-13 03:00:10] Retrieving sequences for splices
[2018-10-13 03:02:20] Indexing splices
[2018-10-13 03:02:41] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:02:45] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:02:50] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:02:55] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:02:59] Joining segment hits
[2018-10-13 03:05:14] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:05:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:05:23] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:05:27] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:05:31] Joining segment hits
[2018-10-13 03:07:47] Reporting output tracks
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[2018-10-13 03:11:24] A summary of the alignment counts can be found in /scratch/8792926.1.linga/tophat2/align_summary.txt
[2018-10-13 03:11:24] Run complete: 00:27:58 elapsed