[2018-10-13 03:43:09] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:43:09] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:43:09] Checking for Bowtie index files (genome)..
[2018-10-13 03:43:09] Checking for reference FASTA file
[2018-10-13 03:43:09] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:43:13] Reading known junctions from GTF file
[2018-10-13 03:43:18] Preparing reads
	 left reads: min. length=100, max. length=100, 865482 kept reads (164 discarded)
	right reads: min. length=100, max. length=100, 865273 kept reads (373 discarded)
[2018-10-13 03:43:57] Building transcriptome data files /scratch/8792965.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:44:16] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:52:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:53:51] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:55:03] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:55:03] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:55:39] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:55:48] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:56:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:56:15] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:56:27] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:57:04] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:57:14] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:57:29] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:57:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:57:54] Searching for junctions via segment mapping
[2018-10-13 04:03:37] Retrieving sequences for splices
[2018-10-13 04:05:43] Indexing splices
[2018-10-13 04:06:09] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:06:15] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:06:22] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:06:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:06:37] Joining segment hits
[2018-10-13 04:09:07] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:09:13] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:09:22] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:09:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:09:39] Joining segment hits
[2018-10-13 04:12:10] Reporting output tracks
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[2018-10-13 04:26:48] A summary of the alignment counts can be found in /scratch/8792965.1.linga/tophat2/align_summary.txt
[2018-10-13 04:26:48] Run complete: 00:43:38 elapsed