[2018-10-13 07:20:25] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:20:25] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:20:25] Checking for Bowtie index files (genome)..
[2018-10-13 07:20:25] Checking for reference FASTA file
[2018-10-13 07:20:25] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:20:29] Reading known junctions from GTF file
[2018-10-13 07:20:33] Preparing reads
	 left reads: min. length=100, max. length=100, 1232489 kept reads (348 discarded)
	right reads: min. length=100, max. length=100, 1232178 kept reads (659 discarded)
[2018-10-13 07:21:22] Building transcriptome data files /scratch/8793082.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:21:42] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:30:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:32:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:34:38] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:34:38] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:35:23] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:35:33] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:35:55] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:36:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:36:26] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:37:11] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:37:21] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:37:43] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:37:59] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:38:15] Searching for junctions via segment mapping
[2018-10-13 07:48:31] Retrieving sequences for splices
[2018-10-13 07:50:35] Indexing splices
[2018-10-13 07:50:57] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:51:05] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:51:18] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:51:31] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:51:43] Joining segment hits
[2018-10-13 07:54:09] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:54:17] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:54:31] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:54:44] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:54:57] Joining segment hits
[2018-10-13 07:57:26] Reporting output tracks
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[2018-10-13 08:27:16] A summary of the alignment counts can be found in /scratch/8793082.1.linga/tophat2/align_summary.txt
[2018-10-13 08:27:16] Run complete: 01:06:51 elapsed