[2018-10-13 07:23:43] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:23:43] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:23:43] Checking for Bowtie index files (genome)..
[2018-10-13 07:23:43] Checking for reference FASTA file
[2018-10-13 07:23:43] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:23:47] Reading known junctions from GTF file
[2018-10-13 07:23:51] Preparing reads
	 left reads: min. length=100, max. length=100, 1270757 kept reads (97 discarded)
	right reads: min. length=100, max. length=100, 1270460 kept reads (394 discarded)
[2018-10-13 07:24:44] Building transcriptome data files /scratch/8793085.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:25:04] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:33:05] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:34:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:35:05] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:35:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:35:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:35:50] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:36:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:36:14] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:36:24] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:37:02] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:37:11] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:37:24] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:37:35] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:37:46] Searching for junctions via segment mapping
[2018-10-13 07:41:39] Retrieving sequences for splices
[2018-10-13 07:43:51] Indexing splices
[2018-10-13 07:44:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:44:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:44:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:44:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:44:35] Joining segment hits
[2018-10-13 07:47:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:47:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:47:16] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:47:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:47:28] Joining segment hits
[2018-10-13 07:50:01] Reporting output tracks
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[2018-10-13 07:59:35] A summary of the alignment counts can be found in /scratch/8793085.1.linga/tophat2/align_summary.txt
[2018-10-13 07:59:35] Run complete: 00:35:51 elapsed