[2018-10-13 01:56:17] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:56:17] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:56:17] Checking for Bowtie index files (genome)..
[2018-10-13 01:56:17] Checking for reference FASTA file
[2018-10-13 01:56:17] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:56:22] Reading known junctions from GTF file
[2018-10-13 01:56:26] Preparing reads
	 left reads: min. length=100, max. length=100, 379600 kept reads (265 discarded)
	right reads: min. length=100, max. length=100, 379255 kept reads (610 discarded)
[2018-10-13 01:56:43] Building transcriptome data files /scratch/8792901.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:57:03] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:05:15] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:05:55] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:06:36] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:06:36] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:07:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:07:29] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:07:43] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:07:54] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:08:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:08:49] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:09:01] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:09:15] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:09:27] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:09:38] Searching for junctions via segment mapping
[2018-10-13 02:12:25] Retrieving sequences for splices
[2018-10-13 02:14:34] Indexing splices
[2018-10-13 02:14:57] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:15:01] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:15:06] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:15:10] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:15:14] Joining segment hits
[2018-10-13 02:18:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:18:21] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:18:26] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:18:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:18:34] Joining segment hits
[2018-10-13 02:21:03] Reporting output tracks
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[2018-10-13 02:24:47] A summary of the alignment counts can be found in /scratch/8792901.1.linga/tophat2/align_summary.txt
[2018-10-13 02:24:47] Run complete: 00:28:30 elapsed