[2018-10-13 01:56:16] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:56:16] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:56:16] Checking for Bowtie index files (genome)..
[2018-10-13 01:56:16] Checking for reference FASTA file
[2018-10-13 01:56:16] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:56:20] Reading known junctions from GTF file
[2018-10-13 01:56:24] Preparing reads
	 left reads: min. length=100, max. length=100, 399890 kept reads (251 discarded)
	right reads: min. length=100, max. length=100, 399485 kept reads (656 discarded)
[2018-10-13 01:56:41] Building transcriptome data files /scratch/8792900.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:56:59] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:04:49] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:05:26] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:06:03] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:06:03] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:06:47] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:06:56] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:07:08] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:07:18] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:07:28] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:08:13] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:08:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:08:36] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:08:46] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:08:56] Searching for junctions via segment mapping
[2018-10-13 02:11:33] Retrieving sequences for splices
[2018-10-13 02:13:39] Indexing splices
[2018-10-13 02:13:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:14:03] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:14:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:14:12] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:14:16] Joining segment hits
[2018-10-13 02:16:37] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:16:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:16:46] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:16:50] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:16:54] Joining segment hits
[2018-10-13 02:19:06] Reporting output tracks
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[2018-10-13 02:22:28] A summary of the alignment counts can be found in /scratch/8792900.1.linga/tophat2/align_summary.txt
[2018-10-13 02:22:28] Run complete: 00:26:12 elapsed