[2018-10-13 01:16:48] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:16:48] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:16:48] Checking for Bowtie index files (genome)..
[2018-10-13 01:16:48] Checking for reference FASTA file
[2018-10-13 01:16:48] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:16:52] Reading known junctions from GTF file
[2018-10-13 01:16:58] Preparing reads
	 left reads: min. length=100, max. length=100, 393524 kept reads (139 discarded)
	right reads: min. length=100, max. length=100, 393244 kept reads (419 discarded)
[2018-10-13 01:17:15] Building transcriptome data files /scratch/8792882.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:17:35] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:25:49] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:26:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:26:58] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:26:58] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:27:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:27:52] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:28:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:28:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:28:21] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:29:04] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:29:13] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:29:24] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:29:34] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:29:43] Searching for junctions via segment mapping
[2018-10-13 01:32:15] Retrieving sequences for splices
[2018-10-13 01:34:27] Indexing splices
[2018-10-13 01:34:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:34:56] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:35:01] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:35:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:35:11] Joining segment hits
[2018-10-13 01:37:30] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:37:35] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:37:40] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:37:44] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:37:49] Joining segment hits
[2018-10-13 01:40:16] Reporting output tracks
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[2018-10-13 01:43:59] A summary of the alignment counts can be found in /scratch/8792882.1.linga/tophat2/align_summary.txt
[2018-10-13 01:43:59] Run complete: 00:27:11 elapsed