[2019-04-24 14:49:30] Beginning TopHat run (v2.1.1)
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[2019-04-24 14:49:30] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-24 14:49:30] Checking for Bowtie index files (genome)..
[2019-04-24 14:49:30] Checking for reference FASTA file
[2019-04-24 14:49:30] Generating SAM header for Bowtie2Index/genome
[2019-04-24 14:49:35] Reading known junctions from GTF file
[2019-04-24 14:49:40] Preparing reads
	 left reads: min. length=32, max. length=36, 21100610 kept reads (25510 discarded)
	right reads: min. length=32, max. length=36, 20963743 kept reads (162377 discarded)
[2019-04-24 14:57:22] Building transcriptome data files /scratch/5555363.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-24 14:57:40] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-24 15:06:07] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:20:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:34:57] 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 15:34:58] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:37:37] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:41:18] Searching for junctions via segment mapping
[2019-04-24 15:43:21] Retrieving sequences for splices
[2019-04-24 15:45:18] Indexing splices
[2019-04-24 15:45:40] 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/5555363.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:45:43] Joining segment hits
[2019-04-24 15:50:30] 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/5555363.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:50:35] Joining segment hits
[2019-04-24 15:55:01] Reporting output tracks
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[2019-04-24 16:17:42] A summary of the alignment counts can be found in /scratch/5555363.1.linga/tophat2/align_summary.txt
[2019-04-24 16:17:42] Run complete: 01:28:12 elapsed