[2019-04-24 14:51:56] Beginning TopHat run (v2.1.1)
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[2019-04-24 14:51:56] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-24 14:51:57] Checking for Bowtie index files (genome)..
[2019-04-24 14:51:57] Checking for reference FASTA file
[2019-04-24 14:51:57] Generating SAM header for Bowtie2Index/genome
[2019-04-24 14:52:03] Reading known junctions from GTF file
[2019-04-24 14:52:07] 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)
[2019-04-24 14:59:34] Building transcriptome data files /scratch/5555365.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-24 14:59:53] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-24 15:08:31] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:18:35] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-24 15:27:57] 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 15:27:58] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:30:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-24 15:33:12] Searching for junctions via segment mapping
[2019-04-24 15:35:09] Retrieving sequences for splices
[2019-04-24 15:37:08] Indexing splices
[2019-04-24 15:37:27] 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/5555365.1.linga/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:37:31] Joining segment hits
[2019-04-24 15:41:27] 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/5555365.1.linga/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-24 15:41:31] Joining segment hits
[2019-04-24 15:45:34] Reporting output tracks
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[2019-04-24 16:02:01] A summary of the alignment counts can be found in /scratch/5555365.1.linga/tophat2/align_summary.txt
[2019-04-24 16:02:01] Run complete: 01:10:05 elapsed