[2018-10-12 23:18:06] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:18:06] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:18:06] Checking for Bowtie index files (genome)..
[2018-10-12 23:18:06] Checking for reference FASTA file
[2018-10-12 23:18:06] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:18:11] Reading known junctions from GTF file
[2018-10-12 23:18:16] Preparing reads
	 left reads: min. length=100, max. length=100, 3638746 kept reads (815 discarded)
	right reads: min. length=100, max. length=100, 3637880 kept reads (1681 discarded)
[2018-10-12 23:21:05] Building transcriptome data files /scratch/8792832.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:21:27] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:29:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:38:49] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:47:21] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:47:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:49:08] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:49:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:50:35] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:51:17] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:52:01] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:53:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:54:20] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:55:28] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:56:14] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:57:03] Searching for junctions via segment mapping
[2018-10-13 00:18:59] Retrieving sequences for splices
[2018-10-13 00:21:08] Indexing splices
Building a SMALL index
[2018-10-13 00:21:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:21:56] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:22:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:23:20] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:24:00] Joining segment hits
[2018-10-13 00:27:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:27:29] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:28:25] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:29:06] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:29:50] Joining segment hits
[2018-10-13 00:32:43] Reporting output tracks
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[2018-10-13 02:28:21] A summary of the alignment counts can be found in /scratch/8792832.1.linga/tophat2/align_summary.txt
[2018-10-13 02:28:21] Run complete: 03:10:14 elapsed
[samopen] SAM header is present: 114 sequences.
[bam_sort_core] merging from 2 files...