[2018-10-13 04:49:04] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:49:04] 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, 551527 kept reads (365 discarded)
	right reads: min. length=100, max. length=100, 551105 kept reads (787 discarded)
[2018-10-13 04:49:35] Building transcriptome data files /scratch/8793005.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:49:56] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:58:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:59:58] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:01:13] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:01:13] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:01:52] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:02:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:02:18] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:02:31] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:02:44] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:03:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:03:32] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:03:49] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:04:01] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:04:14] Searching for junctions via segment mapping
[2018-10-13 05:10:22] Retrieving sequences for splices
[2018-10-13 05:12:28] Indexing splices
[2018-10-13 05:12:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:12:57] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:13:06] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:13:14] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:13:22] Joining segment hits
[2018-10-13 05:15:44] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:15:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:15:59] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:16:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:16:16] Joining segment hits
[2018-10-13 05:18:37] Reporting output tracks
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[2018-10-13 05:34:34] A summary of the alignment counts can be found in /scratch/8793005.1.linga/tophat2/align_summary.txt
[2018-10-13 05:34:34] Run complete: 00:45:29 elapsed