[2019-04-29 17:07:55] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-04-29 17:07:55] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 17:07:55] Checking for Bowtie index files (genome)..
[2019-04-29 17:07:55] Checking for reference FASTA file
[2019-04-29 17:07:55] Generating SAM header for Bowtie2Index/genome
[2019-04-29 17:07:57] Reading known junctions from GTF file
[2019-04-29 17:07:59] Preparing reads
	 left reads: min. length=35, max. length=43, 5075104 kept reads (23825 discarded)
	right reads: min. length=35, max. length=43, 5078001 kept reads (20928 discarded)
[2019-04-29 17:09:39] Building transcriptome data files /scratch/5765342.1.c/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 17:09:49] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 17:15:32] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:17:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:18:18] 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 17:18:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:19:02] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:19:37] Searching for junctions via segment mapping
[2019-04-29 17:20:41] Retrieving sequences for splices
[2019-04-29 17:21:46] Indexing splices
[2019-04-29 17:21:58] 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/5765342.1.c/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-29 17:22:00] Joining segment hits
[2019-04-29 17:23:39] 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/5765342.1.c/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-29 17:23:40] Joining segment hits
[2019-04-29 17:25:15] Reporting output tracks
-----------------------------------------------
[2019-04-29 17:29:00] A summary of the alignment counts can be found in /scratch/5765342.1.c/tophat2/align_summary.txt
[2019-04-29 17:29:00] Run complete: 00:21:05 elapsed