[2018-10-12 23:38:05] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:38:05] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:38:05] Checking for Bowtie index files (genome)..
[2018-10-12 23:38:05] Checking for reference FASTA file
[2018-10-12 23:38:05] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:38:09] Reading known junctions from GTF file
[2018-10-12 23:38:14] Preparing reads
	 left reads: min. length=100, max. length=100, 359951 kept reads (213 discarded)
	right reads: min. length=100, max. length=100, 359651 kept reads (513 discarded)
[2018-10-12 23:38:31] Building transcriptome data files /scratch/8792844.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:38:50] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:47:27] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:48:06] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:48:41] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:48:41] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:49:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:49:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:49:40] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:49:50] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:49:59] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:50:39] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:50:49] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:51:03] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:51:15] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:51:25] Searching for junctions via segment mapping
[2018-10-12 23:54:51] Retrieving sequences for splices
[2018-10-12 23:57:13] Indexing splices
[2018-10-12 23:57:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:57:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:57:43] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:57:48] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:57:54] Joining segment hits
[2018-10-13 00:00:12] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:00:16] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:00:20] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:00:24] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:00:28] Joining segment hits
[2018-10-13 00:03:07] Reporting output tracks
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[2018-10-13 00:06:47] A summary of the alignment counts can be found in /scratch/8792844.1.linga/tophat2/align_summary.txt
[2018-10-13 00:06:47] Run complete: 00:28:41 elapsed