I'm just starting out with RNA-seq, and I'm trying to get the installation of Tophat to work. I'm following the "Getting started" instructions on the site, and am currently testing the installation. When I run
... this is what I get:
... and I don't really understand the error. It doesn't say what type of error it is, just says [FAILED] and give the long string of whatever caused the error, which I don't understand.
Any help would be greatly appreciated!
Erik
Code:
tophat -r 20 test_ref reads_1.fq reads_2.fq
Code:
[2014-06-20 13:01:22] Beginning TopHat run (v2.0.11) ----------------------------------------------- [2014-06-20 13:01:22] Checking for Bowtie Bowtie version: 2.2.3.0 [2014-06-20 13:01:22] Checking for Samtools Samtools version: 0.1.19.0 [2014-06-20 13:01:22] Checking for Bowtie index files (genome).. Found both Bowtie1 and Bowtie2 indexes. [2014-06-20 13:01:22] Checking for reference FASTA file [2014-06-20 13:01:22] Generating SAM header for test_ref [2014-06-20 13:01:22] Preparing reads left reads: min. length=75, max. length=75, 100 kept reads (0 discarded) right reads: min. length=75, max. length=75, 100 kept reads (0 discarded) [2014-06-20 13:01:22] Mapping left_kept_reads to genome test_ref with Bowtie2 [FAILED] Error running: /Users/erikfasterius/bin/bam2fastx --all ./tophat_out/tmp/left_kept_reads.bam|/Users/erikfasterius/bin/bowtie2 -k 20 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 1 --sam-no-hd -x test_ref -|/Users/erikfasterius/bin/fix_map_ordering --bowtie2-min-score 15 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --index-outfile ./tophat_out/tmp/left_kept_reads.mapped.bam.index --sam-header ./tophat_out/tmp/test_ref_genome.bwt.samheader.sam - ./tophat_out/tmp/left_kept_reads.mapped.bam ./tophat_out/tmp/left_kept_reads_unmapped.bam
Any help would be greatly appreciated!
Erik
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