[2019-06-24 20:59:46] Beginning TopHat run (v2.1.1)
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[2019-06-24 20:59:46] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 20:59:46] Checking for Bowtie index files (genome)..
[2019-06-24 20:59:46] Checking for reference FASTA file
[2019-06-24 20:59:46] Generating SAM header for Bowtie2Index/genome
[2019-06-24 20:59:49] Reading known junctions from GTF file
[2019-06-24 20:59:53] Preparing reads
	 left reads: min. length=32, max. length=36, 19694520 kept reads (35801 discarded)
	right reads: min. length=32, max. length=36, 19531246 kept reads (199075 discarded)
[2019-06-24 21:08:14] Building transcriptome data files /scratch/7056802.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 21:08:33] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 21:15:31] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 21:22:14] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 21:29:08] 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 21:29:08] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 21:30:28] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 21:32:59] Searching for junctions via segment mapping
[2019-06-24 21:35:33] Retrieving sequences for splices
[2019-06-24 21:38:00] Indexing splices
[2019-06-24 21:38:14] 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/7056802.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 21:38:17] Joining segment hits
[2019-06-24 21:42:45] 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/7056802.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 21:42:48] Joining segment hits
[2019-06-24 21:47:25] Reporting output tracks
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[2019-06-24 22:13:23] A summary of the alignment counts can be found in /scratch/7056802.1.linga/tophat2/align_summary.txt
[2019-06-24 22:13:23] Run complete: 01:13:36 elapsed