now that we have tophat2 out the door, i'm sure we'll have bunch of tophat2 related error messages and solutions - hopefully.
thank you to the team for releasing the new version. i'm very excited for the combination of tophat and tophat-fusion.
now my problem. I've downloaded and installed bowtie2 and tophat2. everything started out just fine until tophat tried to search for junctions via segment mapping. I got an error 5
I'm hoping it's an easy solution and am sure it's something i did wrong. anyone has any ideas?
Thanks!
thank you to the team for releasing the new version. i'm very excited for the combination of tophat and tophat-fusion.
now my problem. I've downloaded and installed bowtie2 and tophat2. everything started out just fine until tophat tried to search for junctions via segment mapping. I got an error 5
Code:
tophat2 -o A673_rep1_tophat2 -r 158 --mate-std-dev 44 -p 24 --microexon-search --library-type fr-unstranded --b2-sensitive --fusion-search --fusion-min-dist 50000 --fusion-multireads 5 --fusion-multipairs 5 ~/genome_reference/bowtie_indexed/hg19.bowtie2 A673_rep1_R1.fastq A673_rep1_R2.fastq [2012-04-11 14:16:47] Beginning TopHat run (v2.0.0) ----------------------------------------------- [2012-04-11 14:16:47] Checking for Bowtie Bowtie version: 2.0.0.5 [2012-04-11 14:16:47] Checking for Samtools Samtools version: 0.1.18.0 [2012-04-11 14:16:47] Checking for Bowtie index files [2012-04-11 14:16:47] Checking for reference FASTA file Warning: Could not find FASTA file /Users/zehira/genome_reference/bowtie_indexed/hg19.bowtie2.fa [2012-04-11 14:16:47] Reconstituting reference FASTA file from Bowtie index Executing: /Users/zehira/local/bin/bowtie2-inspect /Users/zehira/genome_reference/bowtie_indexed/hg19.bowtie2 > A673_rep1_tophat2/tmp/hg19.bowtie2.fa [2012-04-11 14:19:57] Generating SAM header for /Users/zehira/genome_reference/bowtie_indexed/hg19.bowtie2 format: fastq quality scale: phred33 (default) [2012-04-11 14:20:00] Preparing reads left reads: min. length=75, count=12942699 right reads: min. length=75, count=12927964 [2012-04-11 14:28:54] Mapping left_kept_reads against hg19.bowtie2 with Bowtie2 [2012-04-11 14:44:43] Mapping left_kept_reads_seg1 against hg19.bowtie2 with Bowtie2 (1/3) [2012-04-11 14:47:28] Mapping left_kept_reads_seg2 against hg19.bowtie2 with Bowtie2 (2/3) [2012-04-11 14:50:06] Mapping left_kept_reads_seg3 against hg19.bowtie2 with Bowtie2 (3/3) [2012-04-11 14:53:27] Mapping right_kept_reads against hg19.bowtie2 with Bowtie2 [2012-04-11 15:09:38] Mapping right_kept_reads_seg1 against hg19.bowtie2 with Bowtie2 (1/3) [2012-04-11 15:12:11] Mapping right_kept_reads_seg2 against hg19.bowtie2 with Bowtie2 (2/3) [2012-04-11 15:14:44] Mapping right_kept_reads_seg3 against hg19.bowtie2 with Bowtie2 (3/3) [2012-04-11 15:17:26] Searching for junctions via segment mapping [FAILED] Error: segment-based junction search failed with err =-5 Reason: image not found
Thanks!
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