[2018-10-13 02:41:03] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:41:03] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:41:03] Checking for Bowtie index files (genome)..
[2018-10-13 02:41:03] Checking for reference FASTA file
[2018-10-13 02:41:03] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:41:07] Reading known junctions from GTF file
[2018-10-13 02:41:12] Preparing reads
	 left reads: min. length=100, max. length=100, 511136 kept reads (427 discarded)
	right reads: min. length=100, max. length=100, 511140 kept reads (423 discarded)
[2018-10-13 02:41:37] Building transcriptome data files /scratch/8792923.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:41:56] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:50:30] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:51:13] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:51:57] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:51:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:52:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:53:01] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:53:14] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:53:24] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:53:34] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:54:26] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:54:37] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:54:52] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:55:03] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:55:14] Searching for junctions via segment mapping
[2018-10-13 02:57:57] Retrieving sequences for splices
[2018-10-13 03:00:22] Indexing splices
[2018-10-13 03:00:43] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:00:48] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:00:53] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:00:57] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:01:01] Joining segment hits
[2018-10-13 03:03:34] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:03:38] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:03:43] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:03:48] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:03:52] Joining segment hits
[2018-10-13 03:06:28] Reporting output tracks
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[2018-10-13 03:10:24] A summary of the alignment counts can be found in /scratch/8792923.1.linga/tophat2/align_summary.txt
[2018-10-13 03:10:24] Run complete: 00:29:21 elapsed