[2019-06-24 19:43:57] Beginning TopHat run (v2.1.1)
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[2019-06-24 19:43:57] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 19:43:59] Checking for Bowtie index files (genome)..
[2019-06-24 19:43:59] Checking for reference FASTA file
[2019-06-24 19:43:59] Generating SAM header for Bowtie2Index/genome
[2019-06-24 19:44:01] Reading known junctions from GTF file
[2019-06-24 19:44:04] Preparing reads
	 left reads: min. length=32, max. length=36, 21256592 kept reads (52962 discarded)
	right reads: min. length=32, max. length=36, 20996406 kept reads (313148 discarded)
[2019-06-24 19:51:54] Building transcriptome data files /scratch/7056797.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 19:52:09] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 19:58:01] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 20:05:39] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 20:13:30] 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
[2019-06-24 20:13:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 20:16:08] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 20:20:36] Searching for junctions via segment mapping
[2019-06-24 20:22:35] Retrieving sequences for splices
[2019-06-24 20:24:37] Indexing splices
[2019-06-24 20:24:49] 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/7056797.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 20:24:51] Joining segment hits
[2019-06-24 20:30:43] 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/7056797.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 20:30:46] Joining segment hits
[2019-06-24 20:36:27] Reporting output tracks
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[2019-06-24 21:09:27] A summary of the alignment counts can be found in /scratch/7056797.1.linga/tophat2/align_summary.txt
[2019-06-24 21:09:27] Run complete: 01:25:29 elapsed