[2019-04-29 17:13:09] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-04-29 17:13:09] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 17:13:11] Checking for Bowtie index files (genome)..
[2019-04-29 17:13:11] Checking for reference FASTA file
[2019-04-29 17:13:11] Generating SAM header for Bowtie2Index/genome
[2019-04-29 17:13:13] Reading known junctions from GTF file
[2019-04-29 17:13:15] Preparing reads
	 left reads: min. length=35, max. length=43, 5642137 kept reads (21179 discarded)
	right reads: min. length=35, max. length=43, 5632062 kept reads (31254 discarded)
[2019-04-29 17:14:58] Building transcriptome data files /scratch/5765347.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 17:15:07] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 17:20:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:21:53] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:23:14] 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
[2019-04-29 17:23:14] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:24:03] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:24:36] Searching for junctions via segment mapping
[2019-04-29 17:25:35] Retrieving sequences for splices
[2019-04-29 17:26:35] Indexing splices
[2019-04-29 17:26:47] 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/5765347.1.p16/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-29 17:26:49] Joining segment hits
[2019-04-29 17:28:23] 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/5765347.1.p16/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-29 17:28:26] Joining segment hits
[2019-04-29 17:29:53] Reporting output tracks
-----------------------------------------------
[2019-04-29 17:33:48] A summary of the alignment counts can be found in /scratch/5765347.1.p16/tophat2/align_summary.txt
[2019-04-29 17:33:48] Run complete: 00:20:38 elapsed