[2019-04-29 16:59:09] Beginning TopHat run (v2.1.1)
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[2019-04-29 16:59:09] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 16:59:10] Checking for Bowtie index files (genome)..
[2019-04-29 16:59:10] Checking for reference FASTA file
[2019-04-29 16:59:10] Generating SAM header for Bowtie2Index/genome
[2019-04-29 16:59:13] Reading known junctions from GTF file
[2019-04-29 16:59:15] Preparing reads
	 left reads: min. length=35, max. length=43, 5076193 kept reads (19272 discarded)
	right reads: min. length=35, max. length=43, 5067126 kept reads (28339 discarded)
[2019-04-29 17:00:51] Building transcriptome data files /scratch/5765338.1.p/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 17:01:00] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 17:05:56] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:07:25] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 17:08:36] 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
[2019-04-29 17:08:37] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:09:20] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 17:09:53] Searching for junctions via segment mapping
[2019-04-29 17:10:52] Retrieving sequences for splices
[2019-04-29 17:11:51] Indexing splices
[2019-04-29 17:12:02] 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/5765338.1.p/tophat2/tmp/left_kept_reads.m2g_um_unmapped.bam
[2019-04-29 17:12:04] Joining segment hits
[2019-04-29 17:13:34] 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/5765338.1.p/tophat2/tmp/right_kept_reads.m2g_um_unmapped.bam
[2019-04-29 17:13:37] Joining segment hits
[2019-04-29 17:15:03] Reporting output tracks
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[2019-04-29 17:18:36] A summary of the alignment counts can be found in /scratch/5765338.1.p/tophat2/align_summary.txt
[2019-04-29 17:18:36] Run complete: 00:19:28 elapsed