[2019-06-24 19:24:33] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-06-24 19:24:33] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 19:24:33] Checking for Bowtie index files (genome)..
[2019-06-24 19:24:33] Checking for reference FASTA file
[2019-06-24 19:24:33] Generating SAM header for Bowtie2Index/genome
[2019-06-24 19:24:37] Reading known junctions from GTF file
[2019-06-24 19:24:40] Preparing reads
	 left reads: min. length=32, max. length=36, 16378253 kept reads (101919 discarded)
	right reads: min. length=32, max. length=36, 16027698 kept reads (452474 discarded)
[2019-06-24 19:30:48] Building transcriptome data files /scratch/7056795.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 19:31:04] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 19:37:05] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:45:52] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:54:16] 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
[2019-06-24 19:54:17] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 19:55:25] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 19:58:06] Searching for junctions via segment mapping
[2019-06-24 20:00:10] Retrieving sequences for splices
[2019-06-24 20:02:13] Indexing splices
[2019-06-24 20:02:25] 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/7056795.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 20:02:28] Joining segment hits
[2019-06-24 20:06:02] 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/7056795.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 20:06:05] Joining segment hits
[2019-06-24 20:10:06] Reporting output tracks
-----------------------------------------------
[2019-06-24 20:51:12] A summary of the alignment counts can be found in /scratch/7056795.1.linga/tophat2/align_summary.txt
[2019-06-24 20:51:12] Run complete: 01:26:39 elapsed