[2019-04-24 15:27:26] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-04-24 15:27:26] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-24 15:27:26] Checking for Bowtie index files (genome)..
[2019-04-24 15:27:26] Checking for reference FASTA file
[2019-04-24 15:27:26] Generating SAM header for Bowtie2Index/genome
[2019-04-24 15:27:29] Reading known junctions from GTF file
[2019-04-24 15:27:32] Preparing reads
	 left reads: min. length=32, max. length=36, 15374662 kept reads (110608 discarded)
	right reads: min. length=32, max. length=36, 15043845 kept reads (441425 discarded)
[2019-04-24 15:30:58] Building transcriptome data files /scratch/5555374.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-24 15:31:07] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-24 15:36:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:39:54] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:43:23] 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 15:43:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:44:13] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:47:08] Searching for junctions via segment mapping
[2019-04-24 15:48:44] Retrieving sequences for splices
[2019-04-24 15:50:15] Indexing splices
[2019-04-24 15:50:31] 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/5555374.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:50:34] Joining segment hits
[2019-04-24 15:53:02] 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/5555374.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:53:04] Joining segment hits
[2019-04-24 15:55:02] Reporting output tracks
-----------------------------------------------
[2019-04-24 16:02:50] A summary of the alignment counts can be found in /scratch/5555374.1.linga/tophat2/align_summary.txt
[2019-04-24 16:02:50] Run complete: 00:35:23 elapsed