Tophat 2.0.0 strange errors

[EGrassi]

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.

        
$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

In the logs I see:

cat S1_001.th/logs/prep_reads.log 
prep_reads v2.0.0 (3280)
---------------------------
0 out of 0 reads have been filtered out

But if I manually launch prep_reads getting the command line from run.log it seems to run without any problem:

/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

Any idea? Thanks.