Question: error: segment-based junction search failed with err =-5 Reason: image not found
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gravatar for jolin0701-dy
3.1 years ago by
jolin0701-dy70
jolin0701-dy70 wrote:

tophat2 mapping error

I always use this command and mapping is successfully end.

tophat2 --max-multihits 1 --b2-very-sensitive --GTF mm10_genes.gtf --output-dir sample_thout Bowtie2Index_mm10/genome sample.fastq &

But, Today, I got an error message .. and can't making accepted_hits.bam

Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2016-06-01 15:16:50] Checking for Bowtie
Bowtie version:  2.2.6.0
[2016-06-01 15:16:50] Checking for Bowtie index files (genome)..
[2016-06-01 15:16:50] Checking for reference FASTA file
    Warning: Could not find FASTA file Bowtie2Index_mm10/genome.fa
[2016-06-01 15:16:50] Reconstituting reference FASTA file from Bowtie index
  Executing: bowtie2-inspect Bowtie2Index_mm10/genome > Sample_thout/tmp/genome.fa
[2016-06-01 15:20:22] Generating SAM header for Bowtie2Index_mm10/genome
[2016-06-01 15:21:40] Reading known junctions from GTF file
[2016-06-01 15:21:43] Preparing reads
left reads: min. length=20, max. length=76, 31820980 kept reads (29069 discarded)
[2016-06-01 15:32:37] Building transcriptome data files Tu1-3_thout/tmp/mm10_genes
[2016-06-01 15:37:10] Building Bowtie index from mm10_genes.fa
[2016-06-01 15:45:15] Mapping left_kept_reads to transcriptome mm10_genes with Bowtie2 
[2016-06-01 16:55:42] Resuming TopHat pipeline with unmapped reads
[2016-06-01 16:55:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2016-06-01 17:23:25] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2016-06-01 17:28:18] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2016-06-01 17:33:11] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2016-06-01 17:37:10] Searching for junctions via segment mapping
    [FAILED]
Error: segment-based junction search failed with err =-5
  Reason: image not found

Last week, I did something to my laptop. so maybe some of Program files are deleted in that process. Any help would be appreciated.

rna-seq • 1.6k views
ADD COMMENTlink modified 3.1 years ago by genomax68k • written 3.1 years ago by jolin0701-dy70

Are you getting this error on a Mac?

ADD REPLYlink written 3.1 years ago by genomax68k

yes, it is on mac. OS X 10.8.5

ADD REPLYlink written 3.1 years ago by jolin0701-dy70

Assume you are using the pre-compiled version. Have you tried a newly downloaded copy?

ADD REPLYlink written 3.1 years ago by genomax68k

Do you think a newly downloaded copy work? I'll try it. thanks.

ADD REPLYlink written 3.1 years ago by jolin0701-dy70

For those also on Mac and stumbling upon this, check out this thread that has more recent updates.

ADD REPLYlink written 2.3 years ago by Wayne320
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