[2019-04-24 14:44:12] Beginning TopHat run (v2.1.1)
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[2019-04-24 14:44:12] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-24 14:44:12] Checking for Bowtie index files (genome)..
[2019-04-24 14:44:12] Checking for reference FASTA file
[2019-04-24 14:44:12] Generating SAM header for Bowtie2Index/genome
[2019-04-24 14:44:19] Reading known junctions from GTF file
[2019-04-24 14:44:24] Preparing reads
	 left reads: min. length=32, max. length=36, 16492384 kept reads (72949 discarded)
	right reads: min. length=32, max. length=36, 16221461 kept reads (343872 discarded)
[2019-04-24 14:53:59] Building transcriptome data files /scratch/5555355.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-24 14:54:19] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-24 15:06:06] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:19:34] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:33:28] 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 15:33:28] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:35:38] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:40:11] Searching for junctions via segment mapping
[2019-04-24 15:43:04] Retrieving sequences for splices
[2019-04-24 15:45:14] Indexing splices
[2019-04-24 15:45:51] 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/5555355.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:45:56] Joining segment hits
[2019-04-24 15:51:11] 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/5555355.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:51:15] Joining segment hits
[2019-04-24 15:56:35] Reporting output tracks
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[2019-04-24 16:19:58] A summary of the alignment counts can be found in /scratch/5555355.1.linga/tophat2/align_summary.txt
[2019-04-24 16:19:58] Run complete: 01:35:46 elapsed