[2019-06-24 21:45:07] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-06-24 21:45:07] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 21:45:07] Checking for Bowtie index files (genome)..
[2019-06-24 21:45:07] Checking for reference FASTA file
[2019-06-24 21:45:07] Generating SAM header for Bowtie2Index/genome
[2019-06-24 21:45:14] Reading known junctions from GTF file
[2019-06-24 21:45:22] Preparing reads
	 left reads: min. length=32, max. length=36, 12915523 kept reads (80942 discarded)
	right reads: min. length=32, max. length=36, 12689107 kept reads (307358 discarded)
[2019-06-24 21:55:24] Building transcriptome data files /scratch/7056807.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 21:55:58] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 22:07:27] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 22:16:20] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 22:25:19] Resuming TopHat pipeline with unmapped reads
Warning: you have only one segment per read.
	If the read length is greater than or equal to 45bp,
	we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segments
[2019-06-24 22:25:19] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 22:27:24] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 22:31:05] Searching for junctions via segment mapping
[2019-06-24 22:35:30] Retrieving sequences for splices
[2019-06-24 22:40:23] Indexing splices
[2019-06-24 22:40:48] Mapping left_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
open: No such file or directory
Error: bam2fastx failed to open BAM file /scratch/7056807.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 22:40:54] Joining segment hits
[2019-06-24 22:48:45] Mapping right_kept_reads.m2g_um_unmapped to genome segment_juncs with Bowtie2 (1/1)
open: No such file or directory
Error: bam2fastx failed to open BAM file /scratch/7056807.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 22:48:50] Joining segment hits
[2019-06-24 22:56:37] Reporting output tracks
-----------------------------------------------
[2019-06-24 23:32:50] A summary of the alignment counts can be found in /scratch/7056807.1.linga/tophat2/align_summary.txt
[2019-06-24 23:32:50] Run complete: 01:47:43 elapsed