Empty cycles, graph , and SV view files

[Tina04021997]

Hi,

I'm running PrepareAA with sorted .bam file and in the summary file I do obtain 1 amplicon, however, the cycles.txt and graph.txt are empty (I didn't get the SV view file). I was running the PrepareAA commends with all the default settings and there's no error message shown in the log (the log file stops at "INFO:root:#TIME 6045.110 Optimizing graph copy number flow"). And the version I used for AmpliconArchitect is version 1.2.

The CNV_GAIN.bed looks fine: chr2 91427532 91602683 CNVkit 5.1621783983230305 chr10 70980394 72100395 CNVkit 6.357722290579679 chr10 73090396 74025397 CNVkit 7.466644275167549 chr10 74025397 74605398 CNVkit 12.793685333852864 chr10 74605398 74660398 CNVkit 11.100094085953696 chr10 74660398 80505405 CNVkit 7.2586940063270475 chr14 19631713 19696714 CNVkit 4.555154539026766

But I do get empty .out files for 2 chr intervals: chr10:70980394-72100395.out is empty chr10:73090396-80505405.out is also empty --> For chr10:70980394-72100395.cnseg.txt

chrom start end cn start_refined end_refined

chr10 70960394 72100395 6.350560204545149 False False

--> For 72990396_80605405_cnseg.txt

chrom start end cn start_refined end_refined

chr10 72990000 73097399 2.7839369792454893 False True chr10 73097400 74021099 7.445366587668969 True True chr10 74021100 74665199 12.460291280653006 True True chr10 74665200 80517599 7.337669214443177 True True chr10 80517600 80610000 3.8547943500404847 True False

And the summary.txt is as follows: [amplicon1] AmpliconID = 1 [amplicon1] #Intervals = 3 [amplicon1] Intervals = chr10:70960394-72100395,chr10:72990396-80605405,chr17:34336389-34347157 [amplicon1] OncogenesAmplified = KAT6B,NUTM2B,

I wonder what might caused the empty output files and how can i fix it. Thank you so much!!

[jluebeck]

Hi,

Thanks for reaching out about this. If I understand correctly, AA terminated prior to expected completion and the last message in the log file was related to optimizing copy number flow, which is a step handled by the Mosek library. Was there any message in the stdout related to Mosek or the Mosek license file? I am thinking this was caused by one of the following:

• Incorrect Mosek version. Version 8 is required, there should be a printed warning about version mismatch in the logs or stdout. If this is the case, there is a link to the location where Mosek 8 can be downloaded in the AA Readme.
• Mosek license not present or out of date (academic license is valid for one year before re-downloading - which is still free, link in Readme)
• Mosek not installed correctly or the Mosek paths are not set in the .bashrc file (see AA Readme)

Please let me know though if the issues continue after considering these possibilities!

Thanks, Jens

[Tina04021997]

Hi Jens,

Thank you so much for the timely reply! I re-downloaded the Mosek package and it worked!!

Best, Tina