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secastel / phaser

phasing and Allele Specific Expression from RNA-seq
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phaser_gene_ae only compatible with v1.0.0+, I'm using v1.0.0 #33

Closed npklein closed 6 years ago

npklein commented 6 years ago

Hi Secastel,

When I try to run phaser_gene_ae.py on my haplotypic counts I get the error

ERROR - this version of phaser_gene_ae is only compatible with results from phASER v1.0.0+

However, I am using https://github.com/secastel/phaser/archive/cd7daba.zip for the code, and when I look in the log-files of the jobs that got the phASER output it says

################################################## Welcome to phASER v1.0.0 Author: Stephane Castel (scastel@nygenome.org) ##################################################

This is the command I used for phASER:

python /apps/software/phASER/20170714-cd7daba/phaser/phaser.py \ --paired_end 1 \ --bam $BAM \ --vcf $VCF \ --mapq 255 \ --sample $SAMPLE \ --baseq 10 \ --o $phaserOutPrefix \ --temp_dir $TMPDIR \ --threads 1 \ --gw_phase_method 1 \ --gw_phase_vcf 1 \ --show_warning 1 \ --debug 1 \ --unphased_vars 1

and the command for phaser_ae:

python /apps/software/phASER/20170714-cd7daba/phaser_gene_ae/phaser_gene_ae.py \ --haplotypic_counts $haplotype_count \ --features hg19_ensembl.bed \ --o results/gene_ae/$SAMPLENAME.geneAE.txt

Any ideas what could cause this?

Thanks!

npklein commented 6 years ago

Oops, fixed it already, the output was not written correctly.