[2018-10-13 04:49:03] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:49:03] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:49:04] Checking for Bowtie index files (genome)..
[2018-10-13 04:49:04] Checking for reference FASTA file
[2018-10-13 04:49:04] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:49:08] Reading known junctions from GTF file
[2018-10-13 04:49:13] Preparing reads
	 left reads: min. length=100, max. length=100, 532458 kept reads (178 discarded)
	right reads: min. length=100, max. length=100, 532165 kept reads (471 discarded)
[2018-10-13 04:49:42] Building transcriptome data files /scratch/8793007.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:50:02] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:58:54] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:59:35] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:00:16] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:00:16] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:00:46] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:00:55] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:01:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:01:18] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:01:28] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:01:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:02:08] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:02:20] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:02:31] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:02:42] Searching for junctions via segment mapping
[2018-10-13 05:06:52] Retrieving sequences for splices
[2018-10-13 05:09:03] Indexing splices
[2018-10-13 05:09:23] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:09:28] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:09:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:09:39] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:09:45] Joining segment hits
[2018-10-13 05:12:14] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:12:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:12:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:12:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:12:35] Joining segment hits
[2018-10-13 05:15:03] Reporting output tracks
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[2018-10-13 05:21:45] A summary of the alignment counts can be found in /scratch/8793007.1.linga/tophat2/align_summary.txt
[2018-10-13 05:21:45] Run complete: 00:32:41 elapsed