[2018-10-13 07:27:23] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 07:27:23] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:27:23] Checking for Bowtie index files (genome)..
[2018-10-13 07:27:23] Checking for reference FASTA file
[2018-10-13 07:27:23] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:27:25] Reading known junctions from GTF file
[2018-10-13 07:27:28] Preparing reads
	 left reads: min. length=100, max. length=100, 1241621 kept reads (185 discarded)
	right reads: min. length=100, max. length=100, 1241235 kept reads (571 discarded)
[2018-10-13 07:28:00] Building transcriptome data files /scratch/8793088.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:28:16] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:32:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:34:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:35:21] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:35:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:35:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:35:49] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:35:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:36:05] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:36:12] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:36:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:36:43] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:36:52] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:36:59] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:37:08] Searching for junctions via segment mapping
[2018-10-13 07:42:27] Retrieving sequences for splices
[2018-10-13 07:43:34] Indexing splices
Building a SMALL index
[2018-10-13 07:43:47] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:43:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:43:57] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:44:03] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:44:09] Joining segment hits
[2018-10-13 07:45:26] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:45:30] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:45:37] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:45:43] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:45:49] Joining segment hits
[2018-10-13 07:47:07] Reporting output tracks
-----------------------------------------------
[2018-10-13 08:05:02] A summary of the alignment counts can be found in /scratch/8793088.1.p8/tophat2/align_summary.txt
[2018-10-13 08:05:02] Run complete: 00:37:38 elapsed
[samopen] SAM header is present: 114 sequences.