[2019-04-24 16:09:56] Beginning TopHat run (v2.1.1)
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[2019-04-24 16:09:56] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-24 16:09:56] Checking for Bowtie index files (genome)..
[2019-04-24 16:09:56] Checking for reference FASTA file
[2019-04-24 16:09:56] Generating SAM header for Bowtie2Index/genome
[2019-04-24 16:09:58] Reading known junctions from GTF file
[2019-04-24 16:10:00] Preparing reads
	 left reads: min. length=32, max. length=36, 17264626 kept reads (54852 discarded)
	right reads: min. length=32, max. length=36, 17161605 kept reads (157873 discarded)
[2019-04-24 16:14:21] Building transcriptome data files /scratch/5555377.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-04-24 16:14:30] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-24 16:19:27] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 16:23:12] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 16:26:56] 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 16:26:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 16:27:36] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 16:28:52] Searching for junctions via segment mapping
[2019-04-24 16:29:51] Retrieving sequences for splices
[2019-04-24 16:30:50] Indexing splices
[2019-04-24 16:31:02] 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/5555377.1.p16/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-24 16:31:04] Joining segment hits
[2019-04-24 16:32:49] 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/5555377.1.p16/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-24 16:32:51] Joining segment hits
[2019-04-24 16:34:38] Reporting output tracks
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[2019-04-24 16:42:58] A summary of the alignment counts can be found in /scratch/5555377.1.p16/tophat2/align_summary.txt
[2019-04-24 16:42:58] Run complete: 00:33:02 elapsed