[2018-10-13 01:52:04] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:52:04] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:52:04] Checking for Bowtie index files (genome)..
[2018-10-13 01:52:04] Checking for reference FASTA file
[2018-10-13 01:52:04] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:52:08] Reading known junctions from GTF file
[2018-10-13 01:52:12] Preparing reads
	 left reads: min. length=100, max. length=100, 281591 kept reads (210 discarded)
	right reads: min. length=100, max. length=100, 281200 kept reads (601 discarded)
[2018-10-13 01:52:25] Building transcriptome data files /scratch/8792899.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:52:44] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:01:14] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:01:42] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:02:10] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:02:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:02:42] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:02:50] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:03:00] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:03:08] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:03:16] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:03:47] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:03:56] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:04:07] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:04:15] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:04:24] Searching for junctions via segment mapping
[2018-10-13 02:06:51] Retrieving sequences for splices
[2018-10-13 02:09:02] Indexing splices
[2018-10-13 02:09:23] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:09:27] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:09:31] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:09:35] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:09:39] Joining segment hits
[2018-10-13 02:12:07] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:12:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:12:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:12:19] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:12:23] Joining segment hits
[2018-10-13 02:14:42] Reporting output tracks
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[2018-10-13 02:17:49] A summary of the alignment counts can be found in /scratch/8792899.1.linga/tophat2/align_summary.txt
[2018-10-13 02:17:49] Run complete: 00:25:45 elapsed