[2019-06-24 21:57:54] Beginning TopHat run (v2.1.1)
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[2019-06-24 21:57:54] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 21:57:54] Checking for Bowtie index files (genome)..
[2019-06-24 21:57:54] Checking for reference FASTA file
[2019-06-24 21:57:54] Generating SAM header for Bowtie2Index/genome
[2019-06-24 21:57:56] Reading known junctions from GTF file
[2019-06-24 21:57:58] Preparing reads
	 left reads: min. length=32, max. length=36, 18454581 kept reads (31649 discarded)
	right reads: min. length=32, max. length=36, 18330915 kept reads (155315 discarded)
[2019-06-24 22:02:10] Building transcriptome data files /scratch/7056809.1.p/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 22:02:19] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 22:06:49] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 22:10:54] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 22:15:04] 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 22:15:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 22:15:52] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 22:17:28] Searching for junctions via segment mapping
[2019-06-24 22:18:35] Retrieving sequences for splices
[2019-06-24 22:19:43] Indexing splices
[2019-06-24 22:19:50] 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/7056809.1.p/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 22:19:52] Joining segment hits
[2019-06-24 22:22:03] 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/7056809.1.p/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 22:22:05] Joining segment hits
[2019-06-24 22:24:18] Reporting output tracks
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[2019-06-24 22:37:11] A summary of the alignment counts can be found in /scratch/7056809.1.p/tophat2/align_summary.txt
[2019-06-24 22:37:11] Run complete: 00:39:17 elapsed