[2018-10-13 07:27:30] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:27:30] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:27:30] Checking for Bowtie index files (genome)..
[2018-10-13 07:27:30] Checking for reference FASTA file
[2018-10-13 07:27:30] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:27:34] Reading known junctions from GTF file
[2018-10-13 07:27:38] Preparing reads
	 left reads: min. length=100, max. length=100, 1383972 kept reads (203 discarded)
	right reads: min. length=100, max. length=100, 1383671 kept reads (504 discarded)
[2018-10-13 07:28:32] Building transcriptome data files /scratch/8793086.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:28:50] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:36:30] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:38:27] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:40:21] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:40:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:41:14] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:41:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:41:51] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:42:05] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:42:20] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:43:15] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:43:27] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:43:52] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:44:07] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:44:23] Searching for junctions via segment mapping
[2018-10-13 07:52:55] Retrieving sequences for splices
[2018-10-13 07:54:55] Indexing splices
[2018-10-13 07:55:18] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:55:30] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:55:47] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:56:00] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:56:11] Joining segment hits
[2018-10-13 07:58:49] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:59:01] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:59:17] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:59:29] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:59:40] Joining segment hits
[2018-10-13 08:02:09] Reporting output tracks
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[2018-10-13 08:24:30] A summary of the alignment counts can be found in /scratch/8793086.1.linga/tophat2/align_summary.txt
[2018-10-13 08:24:30] Run complete: 00:56:59 elapsed