[2019-06-24 22:54:56] Beginning TopHat run (v2.1.1)
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[2019-06-24 22:54:56] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 22:54:56] Checking for Bowtie index files (genome)..
[2019-06-24 22:54:56] Checking for reference FASTA file
[2019-06-24 22:54:56] Generating SAM header for Bowtie2Index/genome
[2019-06-24 22:54:57] Reading known junctions from GTF file
[2019-06-24 22:54:59] Preparing reads
	 left reads: min. length=32, max. length=36, 17264626 kept reads (54852 discarded)
	right reads: min. length=32, max. length=36, 17161605 kept reads (157873 discarded)
[2019-06-24 22:59:05] Building transcriptome data files /scratch/7056814.1.c/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 22:59:15] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 23:03:44] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 23:07:43] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 23:11:50] 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 23:11:51] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 23:12:28] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 23:13:52] Searching for junctions via segment mapping
[2019-06-24 23:15:08] Retrieving sequences for splices
[2019-06-24 23:16:20] Indexing splices
[2019-06-24 23:16:27] 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/7056814.1.c/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-06-24 23:16:29] Joining segment hits
[2019-06-24 23:18:36] 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/7056814.1.c/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-06-24 23:18:38] Joining segment hits
[2019-06-24 23:20:45] Reporting output tracks
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[2019-06-24 23:33:16] A summary of the alignment counts can be found in /scratch/7056814.1.c/tophat2/align_summary.txt
[2019-06-24 23:33:16] Run complete: 00:38:19 elapsed