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aquaskyline / Clairvoyante

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
BSD 3-Clause "New" or "Revised" License
171 stars 27 forks source link

zsh: no such option #15

Closed ghost closed 5 years ago

ghost commented 5 years ago

Hello,

That might be a python/bash issue more than one related to Clairvoyante, but I am unable to launch clairvoyante.py callVarBamParallel. I installed via conda.

Here is my commands.sh script

clairvoyante.py callVarBamParallel \
--chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3-illumina-novoalign-hg002-hg38/learningRate1e-3.epoch999 \
--ref_fn final.genome.scf.fasta \
--bam_fn arc.sorted.bam \
--sampleName ARC_ancestor \
--output_prefix ARC_ancestor_clairvoyante \
--threshold 0.125 \
--minCoverage 4 \
--includingAllContigs \
--tensorflowThreads 4

Then I ran export CUDA_VISIBLE_DEVICES="" And cat commands.sh | parallel -j4 which returns 

zsh: no such option: chkpnt_fn /media/urbe/MyBDrive/masurca_assembly_analysis/trainedModels/fullv3_illumina_novoalign_hg002_hg38/learningRate1e_3.epoch999 \
zsh: no such option: ref_fn final.genome.scf.fasta \
zsh: no such option: bam_fn arc.sorted.bam \
zsh: no such option: sampleName ARC_ancestor \
zsh: no such option: output_prefix ARC_ancestor_clairvoyante \
zsh: no such option: threshold 0.125 \
zsh: no such option: minCoverage 4 \
zsh: no such option: includingAllContigs \
zsh: no such option: tensorflowThreads 4
usage: callVarBamParallel.py [-h] [--chkpnt_fn CHKPNT_FN] [--ref_fn REF_FN]
                             [--bed_fn BED_FN] [--refChunkSize REFCHUNKSIZE]
                             [--bam_fn BAM_FN] [--vcf_fn VCF_FN]
                             [--output_prefix OUTPUT_PREFIX]
                             [--includingAllContigs [INCLUDINGALLCONTIGS]]
                             [--tensorflowThreads TENSORFLOWTHREADS]
                             [--threshold THRESHOLD]
                             [--minCoverage MINCOVERAGE] [--qual QUAL]
                             [--sampleName SAMPLENAME]
                             [--considerleftedge [CONSIDERLEFTEDGE]]
                             [--samtools SAMTOOLS] [--pypy PYPY]
                             [--delay DELAY]
callVarBamParallel.py: error: unrecognized arguments:

Thanks for your help

ghost commented 5 years ago

ahah ok I got you need to launch the callVarBamParallel in the command prompt to get the commands.sh sorry!

aquaskyline commented 5 years ago

No problem.