[2018-10-13 03:50:04] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:50:04] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:50:04] Checking for Bowtie index files (genome)..
[2018-10-13 03:50:04] Checking for reference FASTA file
[2018-10-13 03:50:04] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:50:09] Reading known junctions from GTF file
[2018-10-13 03:50:14] Preparing reads
	 left reads: min. length=100, max. length=100, 1181325 kept reads (79 discarded)
	right reads: min. length=100, max. length=100, 1180879 kept reads (525 discarded)
[2018-10-13 03:51:04] Building transcriptome data files /scratch/8792973.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:51:24] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:59:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:00:48] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:01:45] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:01:45] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:02:13] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:02:22] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:02:33] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:02:43] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:02:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:03:25] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:03:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:03:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:03:59] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:04:10] Searching for junctions via segment mapping
[2018-10-13 04:08:12] Retrieving sequences for splices
[2018-10-13 04:10:33] Indexing splices
[2018-10-13 04:10:55] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:11:01] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:11:07] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:11:13] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:11:18] Joining segment hits
[2018-10-13 04:13:50] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:13:55] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:14:01] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:14:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:14:13] Joining segment hits
[2018-10-13 04:16:50] Reporting output tracks
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[2018-10-13 04:26:33] A summary of the alignment counts can be found in /scratch/8792973.1.linga/tophat2/align_summary.txt
[2018-10-13 04:26:33] Run complete: 00:36:28 elapsed