Hello, I've been running some test with fake data with tophat (in order to compare results from different tools like cufflink/cuffdiff/deseq/MISO/...) and I've stumbled in a strange error.
In the logs I see:
But if I manually launch prep_reads getting the command line from run.log it seems to run without any problem:
Any idea? Thanks.
Code:
$tophat -p 5 -G /rogue/bioinfotree/prj/rnaseq_test/local/share/data/fake.gtf --transcriptome-index=transcriptome -o S1_001.th ../alignment/expanded_genome2 <(zcat /rogue/bioinfotree/prj/rnaseq_test/dataset/0.1/reads//S1_blah_R1_001.fastq.gz) <(zcat /rogue/bioinfotree/prj/rnaseq_test/dataset/0.1/reads//S1_blah_R2_001.fastq.gz) [2012-09-04 14:12:39] Beginning TopHat run (v2.0.0) ----------------------------------------------- [2012-09-04 14:12:39] Checking for Bowtie Bowtie version: 2.0.0.6 [2012-09-04 14:12:39] Checking for Samtools Samtools version: 0.1.18.0 [2012-09-04 14:12:39] Checking for Bowtie index files [2012-09-04 14:12:39] Checking for reference FASTA file [2012-09-04 14:12:39] Generating SAM header for ../alignment/expanded_genome2 format: fastq quality scale: phred33 (default) [2012-09-04 14:13:09] Reading known junctions from GTF file [2012-09-04 14:13:09] Preparing reads [FAILED] Error retrieving prep_reads info. make: *** [S1_001.th] Error 1
Code:
cat S1_001.th/logs/prep_reads.log prep_reads v2.0.0 (3280) --------------------------- 0 out of 0 reads have been filtered out
Code:
/home/data/rnaseq/bin/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir S1_001.th/ --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 --max-mismatches 2 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p5 --inner-dist-mean 50 --inner-dist-std-dev 20 --gtf-annotations transcriptome/fake.gff --gtf-juncs S1_001.th/tmp/fake.juncs --no-closure-search --no-coverage-search --no-microexon-search --fastq --aux-outfile=S1_001.th/left_kept_reads.info --index-outfile=S1_001.th/tmp/left_kept_reads.bam.index --sam-header=S1_001.th/tmp/expanded_genome2.bwt.samheader.sam --outfile=S1_001.th/tmp/left_kept_reads.bam <(zcat /rogue/bioinfotree/prj/rnaseq_test/dataset/0.1/reads//S1_blah_R1_001.fastq.gz) prep_reads v2.0.0 (3280) --------------------------- 0 out of 3 reads have been filtered out