[2018-10-13 07:37:03] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:37:03] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:37:04] Checking for Bowtie index files (genome)..
[2018-10-13 07:37:04] Checking for reference FASTA file
[2018-10-13 07:37:04] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:37:07] Reading known junctions from GTF file
[2018-10-13 07:37:11] Preparing reads
	 left reads: min. length=100, max. length=100, 1241551 kept reads (132 discarded)
	right reads: min. length=100, max. length=100, 1241094 kept reads (589 discarded)
[2018-10-13 07:37:59] Building transcriptome data files /scratch/8793090.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:38:17] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:45:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:46:34] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:47:30] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:47:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:48:08] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:48:17] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:48:32] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:48:43] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:48:54] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:49:34] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:49:44] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:50:00] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:50:12] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:50:24] Searching for junctions via segment mapping
[2018-10-13 07:54:11] Retrieving sequences for splices
[2018-10-13 07:56:21] Indexing splices
[2018-10-13 07:56:42] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:56:48] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:56:54] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:57:00] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:57:05] Joining segment hits
[2018-10-13 07:59:38] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:59:44] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:59:50] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:59:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:00:02] Joining segment hits
[2018-10-13 08:02:47] Reporting output tracks
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[2018-10-13 08:11:25] A summary of the alignment counts can be found in /scratch/8793090.1.linga/tophat2/align_summary.txt
[2018-10-13 08:11:25] Run complete: 00:34:21 elapsed