[2019-06-24 21:41:23] Beginning TopHat run (v2.1.1)
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[2019-06-24 21:41:23] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 21:41:23] Checking for Bowtie index files (genome)..
[2019-06-24 21:41:23] Checking for reference FASTA file
[2019-06-24 21:41:23] Generating SAM header for Bowtie2Index/genome
[2019-06-24 21:41:25] Reading known junctions from GTF file
[2019-06-24 21:41:28] Preparing reads
	 left reads: min. length=32, max. length=36, 23963312 kept reads (114772 discarded)
	right reads: min. length=32, max. length=36, 23648689 kept reads (429395 discarded)
[2019-06-24 21:50:16] Building transcriptome data files /scratch/7056806.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 21:50:31] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 21:56:26] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 22:04:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 22:12:20] 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 22:12:20] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 22:14:18] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 22:18:48] Searching for junctions via segment mapping
[2019-06-24 22:20:47] Retrieving sequences for splices
[2019-06-24 22:22:55] Indexing splices
[2019-06-24 22:23:06] 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/7056806.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 22:23:09] Joining segment hits
[2019-06-24 22:27:43] 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/7056806.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 22:27:46] Joining segment hits
[2019-06-24 22:32:35] Reporting output tracks
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[2019-06-24 22:59:43] A summary of the alignment counts can be found in /scratch/7056806.1.linga/tophat2/align_summary.txt
[2019-06-24 22:59:43] Run complete: 01:18:20 elapsed