THetA2 does not end

[starz77]

Hello,

I'm doing copy number analysis using CNVkit and THeTA2

I ran THetA2 using 43 samples on April 23rd, 40 samples were completed in about a day,

but work on the 3 samples is still running (May 19th)

here's my log

---

Reading in query file...
Frac with potential copy numbers: 0.876086346237
Reading SNP file at /bio/scratch/starz77/sylee/CNV_TP/P7/P7_T.bwamem.sorted.dedup.realn.recal.dedup.tumor.snp_formatted.txt
Reading SNP file at /bio/scratch/starz77/sylee/CNV_TP/P7/P7_T.bwamem.sorted.dedup.realn.recal.dedup.normal.snp_formatted.txt
Reading interval file at /bio/scratch/starz77/sylee/CNV_TP/P7/P7.theta.interval_count
Calculating BAFs
Determining heterozygosity.
Calculating BAFs.
First round of clustering...
Begin meta clustering...
Classifying clusters...
Plotting classifications...
Determining copy number bounds...
Plotting clusters...
WARNING: Was unable to remove bnpy output. This can be manually removed after THetA has completed. bnpy output has been stored in ./P7_2_cluster_data/
Selecting meta-intervals...
Selected 13 intervals for analysis.
Preprocessing data...
Writing bounds file to ./P7.n2.withBounds
Estimating time...
Estimated Total Time: 88 hour(s)
Performing optimization...

thank you.