[2019-04-24 14:54:52] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-04-24 14:54:52] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-24 14:54:53] Checking for Bowtie index files (genome)..
[2019-04-24 14:54:53] Checking for reference FASTA file
[2019-04-24 14:54:53] Generating SAM header for Bowtie2Index/genome
[2019-04-24 14:54:57] Reading known junctions from GTF file
[2019-04-24 14:55:02] Preparing reads
	 left reads: min. length=32, max. length=36, 24145578 kept reads (44096 discarded)
	right reads: min. length=32, max. length=36, 23847178 kept reads (342496 discarded)
[2019-04-24 15:04:06] Building transcriptome data files /scratch/5555368.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-24 15:04:26] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-24 15:12:31] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:24:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:35:50] 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 15:35:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:38:56] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:44:04] Searching for junctions via segment mapping
[2019-04-24 15:46:05] Retrieving sequences for splices
[2019-04-24 15:48:14] Indexing splices
[2019-04-24 15:48:35] 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/5555368.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:48:39] Joining segment hits
[2019-04-24 15:53:05] 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/5555368.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:53:09] Joining segment hits
[2019-04-24 15:57:34] Reporting output tracks
-----------------------------------------------
[2019-04-24 16:16:04] A summary of the alignment counts can be found in /scratch/5555368.1.linga/tophat2/align_summary.txt
[2019-04-24 16:16:04] Run complete: 01:21:11 elapsed