stuck in SV plotting even set--runmode as - CYCLES

[Serene0503]

I already use --AA_runmode to stop create the output for SV visualization. But still show process of SV View and stuck here for 5days. :

[MOSEK:INFO]    Beginning MOSEK call
[root:INFO]     #TIME 654.764    Plotting SV View

Here is my code:

AmpliconSuite-pipeline.py -s SRR3124856 -t 30 -o /home/data/sdb/cj/GR_CTCdata/3x_PrimaryTC/AA_results --cnvkit_dir /home/cj/miniconda3/envs/ecDNA/bin/cnvkit.py --fastqs SRR3124856_1.fastq SRR3124856_2.fastq --ref GRCh38 --run_AA --AA_runmode CYCLES  --run_AC

[jluebeck]

Hi, thanks for reaching out. Are you able to share the complete AA log file? If you re-run it do you encounter the same error?

Also, is this data single-cell sequencing or bulk?

Thanks,
Jens

[Serene0503]

Hi, thanks for reaching out. Are you able to share the complete AA log file? If you re-run it do you encounter the same error?

Also, is this data single-cell sequencing or bulk?

Thanks, Jens

Thanks for your reply！
Here's my log file:
testAA.log
I have rerun my previous code serval times, but still stuck in Plotting SV View. According to the optional arguments in AA, using the --AA_runmode CYCLES argument can reconstruct the breakpoint graph and cycles, but do not create the output for SV visualization. Can the 'do not create the output for SV visualization' here be understood as no longer plotting the SV view? If not, can other argument be set here to turn off plotting the SV view?
In addition, my data is 3X single cell WGS.

[jluebeck]

Thanks - I will look into reproducing this issue using that SRA dataset.

Unfortunately we do not yet know how well AmpliconArchitect will perform on single-cell WGS data. It was not designed with that use case in mind. Are you able to share the _graph.txt and _cycles.txt files from the run as well?

Thanks,
Jens

[Serene0503]

Thanks - I will look into reproducing this issue using that SRA dataset.

Unfortunately we do not yet know how well AmpliconArchitect will perform on single-cell WGS data. It was not designed with that use case in mind. Are you able to share the _graph.txt and _cycles.txt files from the run as well?

Thanks, Jens

Thanks a lot.
Here are my _graph.txtand _cycles.txtfiles
SRR3124856_amplicon1_cycles.txt
SRR3124856_amplicon1_graph.txt

[jluebeck]

Can you try running AmpliconSuite-pipeline again (you can re-use the bam file for --bam and AA_CNV_SEEDS.bed for --bed), but please set --AA_insert_sdevs 9. This will help remove sequencing artifacts.

Thanks,
Jens

[Serene0503]

Can you try running AmpliconSuite-pipeline again (you can re-use the bam file for --bam and AA_CNV_SEEDS.bed for --bed), but please set --AA_insert_sdevs 9. This will help remove sequencing artifacts.

Thanks, Jens

Thank you so much! After I set --AA_insert_sdevs 9, the running time of "Plotting SV view "was reduced to 30 minutes.

Thanks again for your advice, AA is an excellent work!