[2019-04-24 14:48:47] Beginning TopHat run (v2.1.1)
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[2019-04-24 14:48:47] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-24 14:48:49] Checking for Bowtie index files (genome)..
[2019-04-24 14:48:49] Checking for reference FASTA file
[2019-04-24 14:48:49] Generating SAM header for Bowtie2Index/genome
[2019-04-24 14:48:59] Reading known junctions from GTF file
[2019-04-24 14:49:05] Preparing reads
	 left reads: min. length=32, max. length=36, 22942893 kept reads (56938 discarded)
	right reads: min. length=32, max. length=36, 22605116 kept reads (394715 discarded)
[2019-04-24 14:57:38] Building transcriptome data files /scratch/5555361.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-24 14:57:54] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-24 15:10:40] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:37:21] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:55:04] 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 15:55:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 16:01:29] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 16:15:01] Searching for junctions via segment mapping
[2019-04-24 16:17:33] Retrieving sequences for splices
[2019-04-24 16:19:51] Indexing splices
[2019-04-24 16:20:35] 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/5555361.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-24 16:20:59] Joining segment hits
[2019-04-24 16:27:09] 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/5555361.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-24 16:27:16] Joining segment hits
[2019-04-24 16:34:28] Reporting output tracks
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[2019-04-24 17:04:49] A summary of the alignment counts can be found in /scratch/5555361.1.linga/tophat2/align_summary.txt
[2019-04-24 17:04:49] Run complete: 02:16:01 elapsed