[2019-04-29 16:50:02] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-04-29 16:50:02] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 16:50:02] Checking for Bowtie index files (genome)..
[2019-04-29 16:50:02] Checking for reference FASTA file
[2019-04-29 16:50:02] Generating SAM header for Bowtie2Index/genome
[2019-04-29 16:50:07] Reading known junctions from GTF file
[2019-04-29 16:50:10] Preparing reads
	 left reads: min. length=35, max. length=43, 5154197 kept reads (23060 discarded)
	right reads: min. length=35, max. length=43, 5155349 kept reads (21908 discarded)
[2019-04-29 16:52:21] Building transcriptome data files /scratch/5765330.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 16:52:37] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 16:59:53] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:02:32] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:05:15] 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
[2019-04-29 17:05:15] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:06:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:07:36] Searching for junctions via segment mapping
[2019-04-29 17:09:29] Retrieving sequences for splices
[2019-04-29 17:11:26] Indexing splices
[2019-04-29 17:11:47] 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/5765330.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-29 17:11:50] Joining segment hits
[2019-04-29 17:14:45] 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/5765330.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-29 17:14:50] Joining segment hits
[2019-04-29 17:17:30] Reporting output tracks
-----------------------------------------------
[2019-04-29 17:24:40] A summary of the alignment counts can be found in /scratch/5765330.1.linga/tophat2/align_summary.txt
[2019-04-29 17:24:40] Run complete: 00:34:37 elapsed