[2019-04-29 17:07:54] Beginning TopHat run (v2.1.1)
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[2019-04-29 17:07:54] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 17:07:55] Checking for Bowtie index files (genome)..
[2019-04-29 17:07:55] Checking for reference FASTA file
[2019-04-29 17:07:55] Generating SAM header for Bowtie2Index/genome
[2019-04-29 17:07:57] Reading known junctions from GTF file
[2019-04-29 17:07:59] Preparing reads
	 left reads: min. length=35, max. length=43, 5121294 kept reads (19083 discarded)
	right reads: min. length=35, max. length=43, 5114823 kept reads (25554 discarded)
[2019-04-29 17:09:41] Building transcriptome data files /scratch/5765341.1.c/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 17:09:51] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 17:15:20] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:16:48] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:18:02] 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 17:18:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:18:49] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:19:24] Searching for junctions via segment mapping
[2019-04-29 17:20:29] Retrieving sequences for splices
[2019-04-29 17:21:34] Indexing splices
[2019-04-29 17:21:46] 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/5765341.1.c/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-29 17:21:48] Joining segment hits
[2019-04-29 17:23:27] 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/5765341.1.c/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-29 17:23:29] Joining segment hits
[2019-04-29 17:25:05] Reporting output tracks
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[2019-04-29 17:28:51] A summary of the alignment counts can be found in /scratch/5765341.1.c/tophat2/align_summary.txt
[2019-04-29 17:28:51] Run complete: 00:20:56 elapsed