unable to open file: name = '/data/modif_genome_test1/model_selection_l og/model_selection.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0

Hi,

I'm getting the following error while trying to run accucopy with various samples :

_" 5_1] [plot_model_select] IOError: Unable to open file (unable to open file: name = '/data/modif_genome_test1/model_selection_l og/model_selection.h5', errno = 2, error message = 'No such file or directory', flags = 0, oflags = 0) "

Below is the TRE ratio histogram image for reference :

I would really appreciate it if you could kindly help me troubleshoot the error.

Thanks, Sreejita

Can you show more log messages before the screenshot?

The screenshot is the plotting program complaining about the missing input file (model selection result). But this is usually due to prior errors.

-- Yu S. Huang http://www.yfish.org/ https://sites.google.com/site/polyactis/

On Tue, May 16, 2023 at 1:15 PM csreej27 @.***> wrote:

Hi,

I'm getting the following error while trying to run accucopy with various samples :

" 5_1] [plot_model_select] IOError: Unable to open file (unable to open file: name = '/data/modif_genome_test1/model_selection_l og/model_selection.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) " [image: image] https://user-images.githubusercontent.com/119156694/238537700-df98b22d-5e52-4246-b33b-743aa7010d38.png

Below is the TRE ratio histogram image for reference : [image: image] https://user-images.githubusercontent.com/119156694/238539588-b07c1853-ded5-476f-b952-55b989fb611e.png

I would really appreciate it if you could kindly help me troubleshoot the error.

Thanks, Sreejita

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Sure,

I've attached below the three log files that got generated in the folder pyflow.data/logs , for you to have a closer look : pyflow_log.txt pyflow_tasks_stderr_log.txt pyflow_tasks_stdout_log.txt

The purity/ploidy/CNA inference part failed (log below), but without apparent reason.

Can you send me /data/test_out1/all_segments.tsv.gz, /data/test_out1/het_snp.tsv.gz , /data/refData/genome.dict?

... Inferring the best period by log likelihood from 2 candidates ...

candidate period_int: 80

Finding first peak, period_int: 80, within bounds of (10-1070)... best_first_peak center: 626 sum of window count at all periodic peaks: 59785.5 half_width_int: 21 Find_first_peak_ab_init() for period: 80 first peak: 626 lower bound: 605 upper bound: 647 Tallest peak index=0, peak_center_int=626, no_of_windows=244912. First peak's peak_index=0, peak_center_int=626, no_of_windows=244912. no_of_copy_nos_bf_1st_peak_prior=2 max_no_of_copy_nos_bf_1st_peak=2 best_logL_snp: -1e+99 no_of_peaks_for_logL: 3 purity: -1 ploidy: -1 logL: -1e+99

candidate period_int: 119

Finding first peak, period_int: 119, within bounds of (10-1079)... best_first_peak center: 627 sum of window count at all periodic peaks: 53024.6 half_width_int: 21 Find_first_peak_ab_init() for period: 119 first peak: 627 lower bound: 606 upper bound: 648 Tallest peak index=0, peak_center_int=626, no_of_windows=244912. First peak's peak_index=0, peak_center_int=626, no_of_windows=244912. no_of_copy_nos_bf_1st_peak_prior=2 max_no_of_copy_nos_bf_1st_peak=2 best_logL_snp: -1e+99 no_of_peaks_for_logL: 3 purity: -1 ploidy: -1 logL: -1e+99

Best period from likelihood: 0

best_purity: -1 best_ploidy: -1 Q: -1 logL: 0 best_no_of_copy_nos_bf_1st_peak: 0 first_peak_center: -1 first_peak_half_width: -1 ERROR: logL 0<=0 or best_purity -1 <=0!

-- Yu S. Huang http://www.yfish.org/ https://sites.google.com/site/polyactis/

On Tue, May 16, 2023 at 2:12 PM csreej27 @.***> wrote:

Sure,

I've attached below the three log files that got generated in the folder pyflow.data/logs , for you to have a closer look : pyflow_log.txt https://github.com/polyactis/Accucopy/files/11484540/pyflow_log.txt pyflow_tasks_stderr_log.txt https://github.com/polyactis/Accucopy/files/11484541/pyflow_tasks_stderr_log.txt pyflow_tasks_stdout_log.txt https://github.com/polyactis/Accucopy/files/11484542/pyflow_tasks_stdout_log.txt

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Sure ,

Here are the files :

all_segments.tsv.gz het_snp.tsv.gz

Genome.dict file is not supported to be sent in this github thread - I shall email it to you.

Hi ,

I have attached the three files you asked for below .

Thanks, Sreejita

On Fri, May 19, 2023 at 11:26 AM Yu S. Huang @.***> wrote:

The purity/ploidy/CNA inference part failed (log below), but without apparent reason.

Can you send me /data/test_out1/all_segments.tsv.gz, /data/test_out1/het_snp.tsv.gz , /data/refData/genome.dict?

... Inferring the best period by log likelihood from 2 candidates ...

candidate period_int: 80

Finding first peak, period_int: 80, within bounds of (10-1070)... best_first_peak center: 626 sum of window count at all periodic peaks: 59785.5 half_width_int: 21 Find_first_peak_ab_init() for period: 80 first peak: 626 lower bound: 605 upper bound: 647 Tallest peak index=0, peak_center_int=626, no_of_windows=244912. First peak's peak_index=0, peak_center_int=626, no_of_windows=244912. no_of_copy_nos_bf_1st_peak_prior=2 max_no_of_copy_nos_bf_1st_peak=2 best_logL_snp: -1e+99 no_of_peaks_for_logL: 3 purity: -1 ploidy: -1 logL: -1e+99

candidate period_int: 119

Finding first peak, period_int: 119, within bounds of (10-1079)... best_first_peak center: 627 sum of window count at all periodic peaks: 53024.6 half_width_int: 21 Find_first_peak_ab_init() for period: 119 first peak: 627 lower bound: 606 upper bound: 648 Tallest peak index=0, peak_center_int=626, no_of_windows=244912. First peak's peak_index=0, peak_center_int=626, no_of_windows=244912. no_of_copy_nos_bf_1st_peak_prior=2 max_no_of_copy_nos_bf_1st_peak=2 best_logL_snp: -1e+99 no_of_peaks_for_logL: 3 purity: -1 ploidy: -1 logL: -1e+99

Best period from likelihood: 0

best_purity: -1 best_ploidy: -1 Q: -1 logL: 0 best_no_of_copy_nos_bf_1st_peak: 0 first_peak_center: -1 first_peak_half_width: -1 ERROR: logL 0<=0 or best_purity -1 <=0!

-- Yu S. Huang http://www.yfish.org/ https://sites.google.com/site/polyactis/

On Tue, May 16, 2023 at 2:12 PM csreej27 @.***> wrote:

Sure,

I've attached below the three log files that got generated in the folder pyflow.data/logs , for you to have a closer look : pyflow_log.txt https://github.com/polyactis/Accucopy/files/11484540/pyflow_log.txt pyflow_tasks_stderr_log.txt < https://github.com/polyactis/Accucopy/files/11484541/pyflow_tasks_stderr_log.txt

pyflow_tasks_stdout_log.txt < https://github.com/polyactis/Accucopy/files/11484542/pyflow_tasks_stdout_log.txt

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Hi ,

Thai is just to remind you that I have sent you the files you asked for and I am awaiting your response.

I would really appreciate it if you could get back ot me as soon as possible.

Thank you, Sreejita

On Fri, May 19, 2023 at 11:26 AM Yu S. Huang @.***> wrote:

The purity/ploidy/CNA inference part failed (log below), but without apparent reason.

Can you send me /data/test_out1/all_segments.tsv.gz, /data/test_out1/het_snp.tsv.gz , /data/refData/genome.dict?

... Inferring the best period by log likelihood from 2 candidates ...

candidate period_int: 80

Finding first peak, period_int: 80, within bounds of (10-1070)... best_first_peak center: 626 sum of window count at all periodic peaks: 59785.5 half_width_int: 21 Find_first_peak_ab_init() for period: 80 first peak: 626 lower bound: 605 upper bound: 647 Tallest peak index=0, peak_center_int=626, no_of_windows=244912. First peak's peak_index=0, peak_center_int=626, no_of_windows=244912. no_of_copy_nos_bf_1st_peak_prior=2 max_no_of_copy_nos_bf_1st_peak=2 best_logL_snp: -1e+99 no_of_peaks_for_logL: 3 purity: -1 ploidy: -1 logL: -1e+99

candidate period_int: 119

Finding first peak, period_int: 119, within bounds of (10-1079)... best_first_peak center: 627 sum of window count at all periodic peaks: 53024.6 half_width_int: 21 Find_first_peak_ab_init() for period: 119 first peak: 627 lower bound: 606 upper bound: 648 Tallest peak index=0, peak_center_int=626, no_of_windows=244912. First peak's peak_index=0, peak_center_int=626, no_of_windows=244912. no_of_copy_nos_bf_1st_peak_prior=2 max_no_of_copy_nos_bf_1st_peak=2 best_logL_snp: -1e+99 no_of_peaks_for_logL: 3 purity: -1 ploidy: -1 logL: -1e+99

Best period from likelihood: 0

best_purity: -1 best_ploidy: -1 Q: -1 logL: 0 best_no_of_copy_nos_bf_1st_peak: 0 first_peak_center: -1 first_peak_half_width: -1 ERROR: logL 0<=0 or best_purity -1 <=0!

-- Yu S. Huang http://www.yfish.org/ https://sites.google.com/site/polyactis/

On Tue, May 16, 2023 at 2:12 PM csreej27 @.***> wrote:

Sure,

I've attached below the three log files that got generated in the folder pyflow.data/logs , for you to have a closer look : pyflow_log.txt https://github.com/polyactis/Accucopy/files/11484540/pyflow_log.txt pyflow_tasks_stderr_log.txt < https://github.com/polyactis/Accucopy/files/11484541/pyflow_tasks_stderr_log.txt

pyflow_tasks_stdout_log.txt < https://github.com/polyactis/Accucopy/files/11484542/pyflow_tasks_stdout_log.txt

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Apologies for the late reply! Was only able to check this email a few days ago :)

There was a stupid bug in our program that puts a limit on the maximum ploidy possible (4). I removed it and re-made the docker image. Please pull the latest docker image.

Here the output after bugfix. Inferred purity is 0.25. The ploidy 6.67 is a bit wonky because in the end, the ploidy based on all segments's inferred copy number status is ploidy_cnv_all=2.53699 (in the last lines of the cnv output file). Is your sample an exome or a panel?

Best period from likelihood: 80

best_purity: 0.255591 best_ploidy: 6.675 Q: 626 logL: 1.37095e+06 best_no_of_copy_nos_bf_1st_peak: 2 first_peak_center: 626 first_peak_half_width: 21 Outputting copy number to output/cnv.output.tsv copy number: 2 copy number: 3 copy number: 4 copy number: 5 copy number: 6 copy number: 7 copy number: 8 copy number: 9 copy number: 10 copy number: 11 copy number: 12 copy number: 13 copy number: 14 copy number: 15 copy number: 16 copy number: 17 copy number: 18 copy number: 19 copy number: 20 copy number: 21 copy number: 22 copy number: 23 copy number: 24 copy number: 25 copy number: 26 copy number: 27 copy number: 28 copy number: 29 copy number: 30 copy number: 31 For subclone regions CNV output done. ploidy_cnv_all=2.53699 ploidy_clonal=2.37565 Outputting logL ...Done. Outputting SNP logORs by peaks to output/snp_logOR_by_peak.tsv ... 7 peaks with valid data. Outputting RC ratio of peaks to output/rc_ratios_of_peaks_of_best_period.tsv ... 1284 segments. Outputting peak bounds to output/peak_bounds.tsv ... 30 peaks.

-- Yu S. Huang http://www.yfish.org/ https://sites.google.com/site/polyactis/

On Thu, May 25, 2023 at 11:48 AM csreej27 @.***> wrote:

Hi ,

Thai is just to remind you that I have sent you the files you asked for and I am awaiting your response.

I would really appreciate it if you could get back ot me as soon as possible.

Thank you, Sreejita

On Fri, May 19, 2023 at 11:26 AM Yu S. Huang @.***> wrote:

The purity/ploidy/CNA inference part failed (log below), but without apparent reason.

Can you send me /data/test_out1/all_segments.tsv.gz, /data/test_out1/het_snp.tsv.gz , /data/refData/genome.dict?

... Inferring the best period by log likelihood from 2 candidates ...

candidate period_int: 80

Finding first peak, period_int: 80, within bounds of (10-1070)... best_first_peak center: 626 sum of window count at all periodic peaks: 59785.5 half_width_int: 21 Find_first_peak_ab_init() for period: 80 first peak: 626 lower bound: 605 upper bound: 647 Tallest peak index=0, peak_center_int=626, no_of_windows=244912. First peak's peak_index=0, peak_center_int=626, no_of_windows=244912. no_of_copy_nos_bf_1st_peak_prior=2 max_no_of_copy_nos_bf_1st_peak=2 best_logL_snp: -1e+99 no_of_peaks_for_logL: 3 purity: -1 ploidy: -1 logL: -1e+99

candidate period_int: 119

Finding first peak, period_int: 119, within bounds of (10-1079)... best_first_peak center: 627 sum of window count at all periodic peaks: 53024.6 half_width_int: 21 Find_first_peak_ab_init() for period: 119 first peak: 627 lower bound: 606 upper bound: 648 Tallest peak index=0, peak_center_int=626, no_of_windows=244912. First peak's peak_index=0, peak_center_int=626, no_of_windows=244912. no_of_copy_nos_bf_1st_peak_prior=2 max_no_of_copy_nos_bf_1st_peak=2 best_logL_snp: -1e+99 no_of_peaks_for_logL: 3 purity: -1 ploidy: -1 logL: -1e+99

Best period from likelihood: 0

best_purity: -1 best_ploidy: -1 Q: -1 logL: 0 best_no_of_copy_nos_bf_1st_peak: 0 first_peak_center: -1 first_peak_half_width: -1 ERROR: logL 0<=0 or best_purity -1 <=0!

-- Yu S. Huang http://www.yfish.org/ https://sites.google.com/site/polyactis/

On Tue, May 16, 2023 at 2:12 PM csreej27 @.***> wrote:

Sure,

I've attached below the three log files that got generated in the folder pyflow.data/logs , for you to have a closer look : pyflow_log.txt https://github.com/polyactis/Accucopy/files/11484540/pyflow_log.txt pyflow_tasks_stderr_log.txt <

https://github.com/polyactis/Accucopy/files/11484541/pyflow_tasks_stderr_log.txt

pyflow_tasks_stdout_log.txt <

https://github.com/polyactis/Accucopy/files/11484542/pyflow_tasks_stdout_log.txt

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