[2019-06-24 22:49:38] Beginning TopHat run (v2.1.1)
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[2019-06-24 22:49:38] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 22:49:38] Checking for Bowtie index files (genome)..
[2019-06-24 22:49:38] Checking for reference FASTA file
[2019-06-24 22:49:38] Generating SAM header for Bowtie2Index/genome
[2019-06-24 22:49:40] Reading known junctions from GTF file
[2019-06-24 22:49:43] Preparing reads
	 left reads: min. length=32, max. length=36, 21491809 kept reads (90849 discarded)
	right reads: min. length=32, max. length=36, 21315070 kept reads (267588 discarded)
[2019-06-24 22:57:50] Building transcriptome data files /scratch/7056813.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 22:58:05] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 23:04:06] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 23:12:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 23:20:35] 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 23:20:35] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 23:22:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 23:24:28] Searching for junctions via segment mapping
[2019-06-24 23:26:25] Retrieving sequences for splices
[2019-06-24 23:28:54] Indexing splices
[2019-06-24 23:29:06] 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/7056813.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 23:29:09] Joining segment hits
[2019-06-24 23:33:34] 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/7056813.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 23:33:36] Joining segment hits
[2019-06-24 23:37:49] Reporting output tracks
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[2019-06-25 00:08:51] A summary of the alignment counts can be found in /scratch/7056813.1.linga/tophat2/align_summary.txt
[2019-06-25 00:08:51] Run complete: 01:19:12 elapsed