[2018-10-13 09:58:21] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:58:21] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:58:21] Checking for Bowtie index files (genome)..
[2018-10-13 09:58:21] Checking for reference FASTA file
[2018-10-13 09:58:21] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:58:26] Reading known junctions from GTF file
[2018-10-13 09:58:30] Preparing reads
	 left reads: min. length=100, max. length=100, 1001494 kept reads (92 discarded)
	right reads: min. length=100, max. length=100, 1001257 kept reads (329 discarded)
[2018-10-13 09:59:08] Building transcriptome data files /scratch/8793162.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:59:27] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 10:07:05] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:07:54] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:08:42] Resuming TopHat pipeline with unmapped reads
[2018-10-13 10:08:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:09:16] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:09:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:09:40] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:09:50] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:10:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:10:41] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:10:52] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:11:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:11:18] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:11:28] Searching for junctions via segment mapping
[2018-10-13 10:15:03] Retrieving sequences for splices
[2018-10-13 10:17:08] Indexing splices
[2018-10-13 10:17:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:17:31] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:17:37] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:17:41] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:17:46] Joining segment hits
[2018-10-13 10:20:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:20:06] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:20:12] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:20:17] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:20:22] Joining segment hits
[2018-10-13 10:23:01] Reporting output tracks
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[2018-10-13 10:29:16] A summary of the alignment counts can be found in /scratch/8793162.1.linga/tophat2/align_summary.txt
[2018-10-13 10:29:16] Run complete: 00:30:55 elapsed