[2019-04-29 17:13:58] Beginning TopHat run (v2.1.1)
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[2019-04-29 17:13:58] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 17:13:59] Checking for Bowtie index files (genome)..
[2019-04-29 17:13:59] Checking for reference FASTA file
[2019-04-29 17:13:59] Generating SAM header for Bowtie2Index/genome
[2019-04-29 17:15:24] Reading known junctions from GTF file
[2019-04-29 17:15:31] Preparing reads
	 left reads: min. length=35, max. length=43, 5542813 kept reads (21533 discarded)
	right reads: min. length=35, max. length=43, 5529718 kept reads (34628 discarded)
[2019-04-29 17:18:18] Building transcriptome data files /scratch/5765344.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 17:19:00] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 17:27:06] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:30:24] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:34:00] 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 17:34:00] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:35:51] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:37:19] Searching for junctions via segment mapping
[2019-04-29 17:39:25] Retrieving sequences for splices
[2019-04-29 17:41:27] Indexing splices
[2019-04-29 17:41:48] 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/5765344.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-29 17:41:52] Joining segment hits
[2019-04-29 17:45:20] 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/5765344.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-29 17:45:25] Joining segment hits
[2019-04-29 17:48:41] Reporting output tracks
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[2019-04-29 17:57:06] A summary of the alignment counts can be found in /scratch/5765344.1.linga/tophat2/align_summary.txt
[2019-04-29 17:57:06] Run complete: 00:43:07 elapsed