[2019-04-24 14:47:06] Beginning TopHat run (v2.1.1)
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[2019-04-24 14:47:06] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-24 14:47:07] Checking for Bowtie index files (genome)..
[2019-04-24 14:47:07] Checking for reference FASTA file
[2019-04-24 14:47:07] Generating SAM header for Bowtie2Index/genome
[2019-04-24 14:47:09] Reading known junctions from GTF file
[2019-04-24 14:47:11] 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)
[2019-04-24 14:51:27] Building transcriptome data files /scratch/5555358.1.p8/tophat2/tmp/RefSeq_GeneBody
[2019-04-24 14:51:36] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-24 14:56:33] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:01:11] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:05:37] 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 15:05:37] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:06:17] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:08:16] Searching for junctions via segment mapping
[2019-04-24 15:09:15] Retrieving sequences for splices
[2019-04-24 15:10:15] Indexing splices
[2019-04-24 15:10:26] 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/5555358.1.p8/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:10:27] Joining segment hits
[2019-04-24 15:12:15] 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/5555358.1.p8/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:12:17] Joining segment hits
[2019-04-24 15:14:05] Reporting output tracks
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[2019-04-24 15:25:24] A summary of the alignment counts can be found in /scratch/5555358.1.p8/tophat2/align_summary.txt
[2019-04-24 15:25:24] Run complete: 00:38:18 elapsed