[2019-04-24 15:10:21] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-04-24 15:10:21] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-24 15:10:21] Checking for Bowtie index files (genome)..
[2019-04-24 15:10:21] Checking for reference FASTA file
[2019-04-24 15:10:21] Generating SAM header for Bowtie2Index/genome
[2019-04-24 15:10:25] Reading known junctions from GTF file
[2019-04-24 15:10:28] Preparing reads
	 left reads: min. length=32, max. length=36, 18042185 kept reads (45969 discarded)
	right reads: min. length=32, max. length=36, 17936885 kept reads (151269 discarded)
[2019-04-24 15:16:46] Building transcriptome data files /scratch/5555373.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-24 15:17:02] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-24 15:24:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:34:11] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:44:20] 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 15:44:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:46:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:48:26] Searching for junctions via segment mapping
[2019-04-24 15:50:14] Retrieving sequences for splices
[2019-04-24 15:52:04] Indexing splices
[2019-04-24 15:52:22] 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/5555373.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:52:26] Joining segment hits
[2019-04-24 15:55:46] 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/5555373.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:55:50] Joining segment hits
[2019-04-24 15:59:15] Reporting output tracks
-----------------------------------------------
[2019-04-24 16:15:51] A summary of the alignment counts can be found in /scratch/5555373.1.linga/tophat2/align_summary.txt
[2019-04-24 16:15:51] Run complete: 01:05:29 elapsed