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AmpliconSuite / AmpliconSuite-pipeline

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
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AA error in insert_sdevs #27

Closed Tina04021997 closed 1 year ago

Tina04021997 commented 1 year ago

Hi,

Thank you for your work! While I was trying to run AA by applying PAA, I ran into the error message: AmpliconArchitect.py: error: unrecognized arguments: --insert_sdevs 3.0

I used the following commend: $PAA/PrepareAA.py -s $sample -t 20 -o $outputfile --ref GRCh38 --python3_path /home/tiy002/anaconda3/envs/pAA/bin/python3 --aa_python_interpreter /home/tiy002/anaconda3/envs/AA/bin/python2.7 --cnv_bed $CNV_CALLS.bed --sorted_bam $sample.bam --cngain 4.3 --cnsize_min 50000 --run_AA

When I tried to add the parameter --AA_insert_sdevs 3.0 and ran PAA again, the same error still occurs. I have upgraded all AA, PAA, AC before sending the job to the latest version and I wonder what else do you suggest me to adjust. Thank you!

jluebeck commented 1 year ago

Hi Tina,

Thanks for reaching out about this. This error could happen for a couple of reasons:

1) Not using the jluebeck AA fork. (Also check your $AA_SRC variable to ensure it is pointing to the correct place). 2) The version of AA is outdated (1.2 or earlier). Once you've confirmed that you are using the jluebeck fork, please pull the latest version and try running PAA again. If issues persist, please let me know!

Jens

Tina04021997 commented 1 year ago

Problem solved! Thank you, Jens. Also, I would like to ask: I was working on creating union seeds across all relevant samples in the same patient, and I realized the CNV_CALLS.bed were not been filtered (the cngain threshold has not been applied). The CNV_SEEDS.bed was filtered. I wonder if I have to apply additional filtering steps. Thank you.

jluebeck commented 1 year ago

Hi Tina,

To create a set of union seeds, please merge from the AA_CNV_SEEDS.bed files, and assign an arbitrary copy-number in the last column, then feed into PrepareAA when running each individual sample from that group. Note that the merged file should still end with "_AA_CNV_SEEDS.bed". I have added a brief explanation of the multi-sample merging procedure to the GUIDE.md file in the latest update.

Thanks, Jens

Tina04021997 commented 1 year ago

Understood! Thank you!