TopHat error during aligning reads

Question

[lingling]

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.

[karl.stamm]

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Answer 1

[lingling]

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

[WouterDeCoster]

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

[lingling]

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