[2018-10-13 18:26:08] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:26:08] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:26:08] Checking for Bowtie index files (genome)..
[2018-10-13 18:26:08] Checking for reference FASTA file
[2018-10-13 18:26:08] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:26:12] Reading known junctions from GTF file
[2018-10-13 18:26:18] Preparing reads
	 left reads: min. length=100, max. length=100, 546886 kept reads (271 discarded)
	right reads: min. length=100, max. length=100, 546449 kept reads (708 discarded)
[2018-10-13 18:26:43] Building transcriptome data files /scratch/8793438.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:27:03] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:35:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:36:31] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:37:17] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:37:17] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:38:02] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:38:12] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:38:25] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:38:36] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:38:46] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:39:34] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:39:44] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:39:59] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:40:11] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:40:21] Searching for junctions via segment mapping
[2018-10-13 18:43:26] Retrieving sequences for splices
[2018-10-13 18:45:26] Indexing splices
[2018-10-13 18:45:47] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:45:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:45:56] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:46:01] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:46:06] Joining segment hits
[2018-10-13 18:48:33] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:48:38] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:48:44] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:48:48] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:48:53] Joining segment hits
[2018-10-13 18:51:17] Reporting output tracks
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[2018-10-13 18:55:04] A summary of the alignment counts can be found in /scratch/8793438.1.linga/tophat2/align_summary.txt
[2018-10-13 18:55:04] Run complete: 00:28:56 elapsed