[2019-04-24 14:47:59] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-04-24 14:47:59] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-24 14:48:00] Checking for Bowtie index files (genome)..
[2019-04-24 14:48:00] Checking for reference FASTA file
[2019-04-24 14:48:00] Generating SAM header for Bowtie2Index/genome
[2019-04-24 14:48:05] Reading known junctions from GTF file
[2019-04-24 14:48:09] Preparing reads
	 left reads: min. length=32, max. length=36, 15675963 kept reads (52290 discarded)
	right reads: min. length=32, max. length=36, 15507079 kept reads (221174 discarded)
[2019-04-24 14:54:26] Building transcriptome data files /scratch/5555357.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-24 14:54:44] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-24 15:02:07] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:11:42] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:20:34] 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
[2019-04-24 15:20:35] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:22:35] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:26:36] Searching for junctions via segment mapping
[2019-04-24 15:28:51] Retrieving sequences for splices
[2019-04-24 15:31:03] Indexing splices
[2019-04-24 15:31:24] 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/5555357.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:31:28] Joining segment hits
[2019-04-24 15:35:35] 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/5555357.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:35:39] Joining segment hits
[2019-04-24 15:39:32] Reporting output tracks
-----------------------------------------------
[2019-04-24 15:54:53] A summary of the alignment counts can be found in /scratch/5555357.1.linga/tophat2/align_summary.txt
[2019-04-24 15:54:53] Run complete: 01:06:53 elapsed