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polyactis / Accucopy

Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data.
https://www.yfish.org/software/Accucopy
GNU General Public License v3.0
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Stuck at reduce_all_segments #8

Closed NikdAK closed 3 years ago

NikdAK commented 3 years ago

Hi, I am trying to get results for purity and ploidy using your pipeline. But somehow the tool is stuck for 2 days at this step:

[2020-12-18T09:03:35.706978] [713099f5307d] [135_1] [WorkflowRunner] [StatusUpdate] ===== MainFlow StatusUpdate =====
[2020-12-18T09:03:35.707082] [713099f5307d] [135_1] [WorkflowRunner] [StatusUpdate] Workflow specification is complete?: True
[2020-12-18T09:03:35.707112] [713099f5307d] [135_1] [WorkflowRunner] [StatusUpdate] Task status (waiting/queued/running/complete/error): 3/0/1/6/0
[2020-12-18T09:03:35.707137] [713099f5307d] [135_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task time (hrs): 0.0000
[2020-12-18T09:03:35.707163] [713099f5307d] [135_1] [WorkflowRunner] [StatusUpdate] Longest ongoing queued task name: ''
[2020-12-18T09:03:35.707189] [713099f5307d] [135_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task time (hrs): 46.0008
[2020-12-18T09:03:35.707215] [713099f5307d] [135_1] [WorkflowRunner] [StatusUpdate] Longest ongoing running task name: 'reduce_all_segments'

I called it like this: './main.py -c configure -t /mnt/Tumor.bam -n /mnt/Normal.bam -o /mnt/accucopy_output/ --nCores 30' Any suggestions?

What would be the fastest way to get just purity/ploidy results, based on either FASTQ, BAM or copynumer files. Thanks!

polyactis commented 3 years ago

"reduce_all_segments" (combining CNV segments from all chromosomes together) should finish in seconds. It may be a filesystem issue or your data was in a format that the segmentation algorithm did not like and thus failed to produce any segments. Please check our online help on how to check those files.