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sequana / pacbio_qc

QC on pacbio data
BSD 3-Clause "New" or "Revised" License
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Input Dir /BAM Error #5

Open kiranpatil222 opened 1 year ago

kiranpatil222 commented 1 year ago

Hi,

I installed pacbio_qc with pip install and ran below two commands sequana_pacbio_qc --input-directory /data/shared/clinical/LongRead/Data/

input dir where i have one of BAM file GIAB Trio sample i got below error ERROR [sequana_pipetools.sequana_manager:205]: package provided (pacbio_qc) not installed.

I tried to give full path of BAM file sequana_pacbio_qc /data/shared/clinical/LongRead/Data/m84011_220902_175841_s1.hifi_reads.bam then got below error pacbio_qc: error: unrecognized arguments: /data/shared/clinical/LongRead/Data/m84011_220902_175841_s1.hifi_reads.bam

Kindly help how do i pass input bam for pacbio_qc

cokelaer commented 1 year ago

dear @kiranpatil222 thanks for using this pipeline. The first command should be correct.

sequana_pacbio_qc --input-directory /data/shared/clinical/LongRead/Data/

What version of python are you using. What platform ? How did you install the tool ? with pip or conda ?

Best

kiranpatil222 commented 1 year ago

Hi, Python : Python 3.8.10 I installed using pip, and Platform is Revivo (https://downloads.pacbcloud.com/public/revio/2022Q4/