[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 19:24:35] Reading known junctions from GTF file
[2019-06-24 19:24:39] Preparing reads
	 left reads: min. length=32, max. length=36, 15675963 kept reads (52290 discarded)
	right reads: min. length=32, max. length=36, 15507079 kept reads (221174 discarded)
[2019-06-24 19:30:27] Building transcriptome data files /scratch/7056794.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 19:30:43] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 19:36:47] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:42:50] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:49:04] 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 19:49:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 19:50:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 19:53:58] Searching for junctions via segment mapping
[2019-06-24 19:56:12] Retrieving sequences for splices
[2019-06-24 19:58:28] Indexing splices
[2019-06-24 19:58:40] 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/7056794.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 19:58:43] Joining segment hits
[2019-06-24 20:02:18] 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/7056794.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 20:02:21] Joining segment hits
[2019-06-24 20:06:15] Reporting output tracks
-----------------------------------------------
[2019-06-24 20:30:30] A summary of the alignment counts can be found in /scratch/7056794.1.linga/tophat2/align_summary.txt
[2019-06-24 20:30:30] Run complete: 01:05:57 elapsed