[2019-04-24 14:51:42] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-04-24 14:51:42] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-24 14:51:42] Checking for Bowtie index files (genome)..
[2019-04-24 14:51:42] Checking for reference FASTA file
[2019-04-24 14:51:42] Generating SAM header for Bowtie2Index/genome
[2019-04-24 14:51:47] Reading known junctions from GTF file
[2019-04-24 14:51:51] Preparing reads
	 left reads: min. length=32, max. length=36, 22083167 kept reads (52972 discarded)
	right reads: min. length=32, max. length=36, 21860410 kept reads (275729 discarded)
[2019-04-24 15:00:14] Building transcriptome data files /scratch/5555364.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-24 15:00:32] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-24 15:09:15] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:22:34] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:37:38] 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 15:37:38] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:41:12] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:46:17] Searching for junctions via segment mapping
[2019-04-24 15:49:06] Retrieving sequences for splices
[2019-04-24 15:51:20] Indexing splices
[2019-04-24 15:51:43] 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/5555364.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:51:55] Joining segment hits
[2019-04-24 15:56:30] 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/5555364.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:56:34] Joining segment hits
[2019-04-24 16:01:20] Reporting output tracks
-----------------------------------------------
[2019-04-24 16:27:15] A summary of the alignment counts can be found in /scratch/5555364.1.linga/tophat2/align_summary.txt
[2019-04-24 16:27:15] Run complete: 01:35:32 elapsed