Question: TopHat error during aligning reads
0
gravatar for lingling
3.4 years ago by
lingling0
lingling0 wrote:

I use tophat to analyze RNA-seq DATA on my Macbook Pro(RAM, 8GB) ,but there is an error:

2016-07-25 12:00:56] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2016-07-25 12:00:56] Checking for Bowtie
          Bowtie version:    2.2.9.0
[2016-07-25 12:00:56] Checking for Bowtie index files (genome)..
[2016-07-25 12:00:56] Checking for reference FASTA file
[2016-07-25 12:00:56] Generating SAM header for genome
[2016-07-25 12:00:56] Reading known junctions from GTF file
[2016-07-25 12:00:59] Preparing reads
     left reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded)
    right reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded)
[2016-07-25 12:05:32] Building transcriptome data files C1_R1_thout/tmp/genes
[2016-07-25 12:05:37] Building Bowtie index from genes.fa
[2016-07-25 12:09:58] Mapping left_kept_reads to transcriptome genes with Bowtie2 
[2016-07-25 14:24:11] Mapping right_kept_reads to transcriptome genes with Bowtie2 
[2016-07-25 14:38:39] Resuming TopHat pipeline with unmapped reads
[2016-07-25 14:38:39] Reporting output tracks
    [FAILED]
Error running /Users/lingling/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir C1_R1_thout/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip --inner-dist-mean 50 --inner-dist-std-dev 20 --gtf-annotations genes.gtf --gtf-juncs C1_R1_thout/tmp/genes.juncs --no-closure-search --no-coverage-search --no-microexon-search --sam-header C1_R1_thout/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/Users/lingling/bin/samtools_0.1.18 --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 genome.fa C1_R1_thout/junctions.bed C1_R1_thout/insertions.bed C1_R1_thout/deletions.bed C1_R1_thout/fusions.out C1_R1_thout/tmp/accepted_hits C1_R1_thout/tmp/left_kept_reads.m2g.bam C1_R1_thout/tmp/left_kept_reads.bam C1_R1_thout/tmp/right_kept_reads.m2g.bam C1_R1_thout/tmp/right_kept_reads.bam
  Reason: image not found

any help would be appreciated.

rna-seq • 1.2k views
ADD COMMENTlink modified 3.4 years ago by geek_y10k • written 3.4 years ago by lingling0

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ADD REPLYlink written 3.4 years ago by karl.stamm3.6k
0
gravatar for lingling
3.4 years ago by
lingling0
lingling0 wrote:

/Users/lingling/Desktop/Screen Shot 2016-07-25 at 15.51.42.png

ADD COMMENTlink written 3.4 years ago by lingling0

Seriously? There is no way that we can access that link, you know that?

ADD REPLYlink written 3.4 years ago by WouterDeCoster42k

I am sorry about that, that is a screenshot of the Terminal, I don't know how to remove it.

ADD REPLYlink written 3.4 years ago by lingling0
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