[2018-10-13 12:35:34] Beginning TopHat run (v2.1.1)
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[2018-10-13 12:35:34] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 12:35:34] Checking for Bowtie index files (genome)..
[2018-10-13 12:35:34] Checking for reference FASTA file
[2018-10-13 12:35:34] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:35:39] Reading known junctions from GTF file
[2018-10-13 12:35:44] Preparing reads
	 left reads: min. length=100, max. length=100, 1499097 kept reads (109 discarded)
	right reads: min. length=100, max. length=100, 1498488 kept reads (718 discarded)
[2018-10-13 12:36:49] Building transcriptome data files /scratch/8793239.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:37:09] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:45:42] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:46:56] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:48:10] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:48:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:49:04] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:49:14] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:49:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:49:43] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:49:55] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:50:47] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:51:00] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:51:18] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:51:32] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:51:47] Searching for junctions via segment mapping
[2018-10-13 12:56:10] Retrieving sequences for splices
[2018-10-13 12:58:28] Indexing splices
[2018-10-13 12:58:55] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:59:02] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:59:09] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:59:16] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:59:22] Joining segment hits
[2018-10-13 13:02:00] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:02:06] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:02:13] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:02:20] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:02:27] Joining segment hits
[2018-10-13 13:05:03] Reporting output tracks
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[2018-10-13 13:15:22] A summary of the alignment counts can be found in /scratch/8793239.1.linga/tophat2/align_summary.txt
[2018-10-13 13:15:22] Run complete: 00:39:47 elapsed