[2019-06-24 18:05:18] Beginning TopHat run (v2.1.1)
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[2019-06-24 18:05:18] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 18:05:18] Checking for Bowtie index files (genome)..
[2019-06-24 18:05:18] Checking for reference FASTA file
[2019-06-24 18:05:18] Generating SAM header for Bowtie2Index/genome
[2019-06-24 18:05:20] Reading known junctions from GTF file
[2019-06-24 18:05:23] Preparing reads
	 left reads: min. length=101, max. length=101, 32275886 kept reads (1365 discarded)
	right reads: min. length=101, max. length=101, 32260035 kept reads (17216 discarded)
[2019-06-24 18:38:54] Building transcriptome data files /scratch/7056788.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 18:39:10] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 18:45:04] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:08:55] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:34:09] Resuming TopHat pipeline with unmapped reads
[2019-06-24 19:34:09] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 19:46:07] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 19:48:01] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 19:50:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 19:52:11] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 19:54:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 20:06:43] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 20:08:52] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 20:11:16] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 20:13:37] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 20:15:44] Searching for junctions via segment mapping
[2019-06-24 20:45:50] Retrieving sequences for splices
[2019-06-24 20:48:18] Indexing splices
[2019-06-24 20:49:06] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 20:50:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 20:51:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 20:52:52] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 20:53:55] Joining segment hits
[2019-06-24 20:58:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 21:00:02] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 21:01:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 21:02:54] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 21:04:00] Joining segment hits
[2019-06-24 21:09:10] Reporting output tracks
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[2019-06-24 23:04:08] A summary of the alignment counts can be found in /scratch/7056788.1.linga/tophat2/align_summary.txt
[2019-06-24 23:04:08] Run complete: 04:58:50 elapsed