[2019-04-24 14:54:36] Beginning TopHat run (v2.1.1)
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[2019-04-24 14:54:36] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-24 14:54:37] Checking for Bowtie index files (genome)..
[2019-04-24 14:54:37] Checking for reference FASTA file
[2019-04-24 14:54:37] Generating SAM header for Bowtie2Index/genome
[2019-04-24 14:54:41] Reading known junctions from GTF file
[2019-04-24 14:54:44] Preparing reads
	 left reads: min. length=32, max. length=36, 13355729 kept reads (77135 discarded)
	right reads: min. length=32, max. length=36, 12996020 kept reads (436844 discarded)
[2019-04-24 14:59:37] Building transcriptome data files /scratch/5555367.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-24 14:59:56] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-24 15:08:05] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:14:46] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:21:32] 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 15:21:32] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:23:45] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:32:29] Searching for junctions via segment mapping
[2019-04-24 15:34:32] Retrieving sequences for splices
[2019-04-24 15:36:29] Indexing splices
[2019-04-24 15:36:47] 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/5555367.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:36:50] Joining segment hits
[2019-04-24 15:40:22] 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/5555367.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:40:25] Joining segment hits
[2019-04-24 15:44:01] Reporting output tracks
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[2019-04-24 15:56:49] A summary of the alignment counts can be found in /scratch/5555367.1.linga/tophat2/align_summary.txt
[2019-04-24 15:56:49] Run complete: 01:02:12 elapsed