[2018-10-13 03:28:26] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:28:26] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:28:26] Checking for Bowtie index files (genome)..
[2018-10-13 03:28:26] Checking for reference FASTA file
[2018-10-13 03:28:26] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:28:30] Reading known junctions from GTF file
[2018-10-13 03:28:34] Preparing reads
	 left reads: min. length=100, max. length=100, 117993 kept reads (69 discarded)
	right reads: min. length=100, max. length=100, 117828 kept reads (234 discarded)
[2018-10-13 03:28:39] Building transcriptome data files /scratch/8792959.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:28:59] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:37:23] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:37:42] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:38:00] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:38:00] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:38:21] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:38:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:38:38] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:38:46] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:38:54] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:39:15] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:39:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:39:32] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:39:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:39:49] Searching for junctions via segment mapping
[2018-10-13 03:42:10] Retrieving sequences for splices
[2018-10-13 03:44:15] Indexing splices
[2018-10-13 03:44:35] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:44:39] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:44:43] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:44:47] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:44:51] Joining segment hits
[2018-10-13 03:47:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:47:08] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:47:12] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:47:16] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:47:20] Joining segment hits
[2018-10-13 03:49:31] Reporting output tracks
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[2018-10-13 03:52:05] A summary of the alignment counts can be found in /scratch/8792959.1.linga/tophat2/align_summary.txt
[2018-10-13 03:52:05] Run complete: 00:23:39 elapsed