polyactis / accucopy Goto Github PK

Dear author,

I built the singularity environment from the Docker image recently. I got this errror as mentioned in the title when I run it. The detailed error information is as follows:
[2020-11-17T17:07:15.734560] [node127.cm.cluster] [68840_1] [WorkflowRunner] [ERROR] Worklow terminated due to the following task errors:
[2020-11-17T17:07:15.735768] [node127.cm.cluster] [68840_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'rm_individual_seg_files' launched from master workflow, error code: 1, command: 'rm'
[2020-11-17T17:07:15.736237] [node127.cm.cluster] [68840_1] [WorkflowRunner] [ERROR] [rm_individual_seg_files] Error Message:
[2020-11-17T17:07:15.736848] [node127.cm.cluster] [68840_1] [WorkflowRunner] [ERROR] [rm_individual_seg_files] Last 2 stderr lines from task (of 2 total lines):
[2020-11-17T17:07:15.736848] [node127.cm.cluster] [68840_1] [WorkflowRunner] [ERROR] [2020-11-17T15:50:23.975587] [node127.cm.cluster] [68840_1] [rm_individual_seg_files] rm: missing operand
[2020-11-17T17:07:15.736848] [node127.cm.cluster] [68840_1] [WorkflowRunner] [ERROR] [2020-11-17T15:50:23.975877] [node127.cm.cluster] [68840_1] [rm_individual_seg_files] Try 'rm --help' for more information.

Do you have any clue why this error happened? Can you please help me to solve it?

Additional information: I was implementing the program on a pair of WGS of canine tumour and normal tissue. The required reference files were properly made, except the snp_sites.gz file. But, I removed the option --callRegions of the SNP calling step using the Strelka from the main.py file. So the program can still work without the snp_sites file.

Regards,
Yun

Hi,

Great tool and documentation! I've read on your documentation page that the tool might work with whole exome data - could you please provide more information on that? Is possible and is it recommended?

Thank you a lot in advance!

probalica

The web site https://www.yfish.org/display/PUB/Accucopy referenced here is broken

Hi there, thank you for developing accucopy. it was relatively straight forward to run and fast! How do we prepare input for pyclone-vi (example: https://github.com/Roth-Lab/pyclone-vi/blob/master/examples/tracerx.tsv) from cnv.output.tsv? Specifically, how do we get major_cn and minor_cn? I think pyclone-vi only accepts integer values for both.
Thanks

Hi,
I tried the new mode "--period" option and found small bug in the main.py script at line 540.
It shows "period" parameter not defind.
To fix this, I just removed Line 540-543, and the script works!

if (ap.period < 0):
msg = (f"Argument period is non-negative integer-value, but you have "
f"specified {ap.period}. O will be used instead.")
sys.stderr.write(msg)

Thank you for your nice tool.
Apiwat

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!

Dear author,
I am running Accucopy on a batch of low-coverage WGS data. All raw-data were mapped with BWA(grch37 provided on document chapter 3.7), and marked with picard.
Some of the bams have ideal results, while the others have empty output in infer.out.tsv and infer.out.details.tsv.

the last 20 lines of infer.status.txt are shown below,
_segment_stddev_divider=20 _snp_maf_stddev_divider=20 _snp_covearge_min=2 _snp_coverage_var_vs_mean_ratio=10 _no_of_peaks_for_logL=3 Reading SNPs from /gpfs/share/home/1601111669/WGS_15/accucopy_result//MLPS_ZJW_C/het_snp.tsv.gz ... 22 chromosomes, 423742 SNPs, 570146 lines. Reading in segments from /gpfs/share/home/1601111669/WGS_15/accucopy_result//MLPS_ZJW_C/all_segments.tsv.gz ... Outputting segment ratio data to /gpfs/share/home/1601111669/WGS_15/accucopy_result//MLPS_ZJW_C/rc_ratio_window_count_smoothed.tsv...Done. Outputting segment ratio data to /gpfs/share/home/1601111669/WGS_15/accucopy_result//MLPS_ZJW_C/rc_ratio_no_of_windows_by_chr.tsv...Done. 32 segments. 32 segments used. 423717 SNPs used. Calculating auto correlation ...Done. Outputting SNP logORs by segments to /gpfs/share/home/1601111669/WGS_15/accucopy_result//MLPS_ZJW_C/snp_logOR_by_segment.tsv ... 32 segments. Calculating auto correlation shift-1 difference ... #mean is: 0, sigma is: 0.0010521 Done. Inferring candidate periods through GADA, run_type=1, left_x=-0.000266546, right_x=0.000266546 ... Initiating GADA instance ...GADA done Found 0 candidate periods. ERROR: No candidate period discovered.

Could you please kindly suggest the reason GADA found 0 candidate and if there's sth I can done?

Best Regards,
Junyi

Hi there,
Hope you're well! I am running accucopy on multiple paired tumour-normal WGS samples. It has worked perfectly on most of them, except for in one sample where the infer_out.txt file is empty. I have checked the infer.status.txt file and the last line shows this error: ### 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_int: 0
ERROR: logL 0<=0 or best_purity -1 <=0!

Please could you let me know what this means? I am reading it as it is returning the purity to be 0%, but this would be impossible.

Thanks very much

Hi,

I ran Accucopy with WGS data and got minus copy number and "na" for major_allele_cp as shown below.
What is the meaning of this number?

chr start end cp major_allele_cp copy_no_float cumu_start cumu_end
7 142652501 142797500 14 10 14.0741 1374656804 1374801803
7 38299501 38337500 17 12 17 1270303804 1270341803
14 22177501 22352000 21 16 20.9444 2213584811 2213759310
17 22999501 26574500 -6.66667 NA -6.66667 2513780063 2517355062
2 92732501 93811000 -6.61111 NA -6.61111 341688923 342767422
7 63674501 63726000 -5.16667 NA -5.16667 1295678804 1295730303
14 18605501 19241000 1.25926 NA 1.25926 2210012811 2210648310
15 17009001 20739000 1.44444 NA 1.44444 2315460029 2319190028

Thank you very much,
Apiwat

thanks a lot

I've ran into some errors with the docker (build in Singularity). The plotting steps require matplotlib. However, plot_cnv errors out when importing matplotlib. Interestingly, plotCPandMCP.py is written in Python3. I suspect the docker only installed matplotlib for python2.

log:

[15_1] [TaskRunner:plot_cnv] Task initiated on local node
[15_1] [TaskManager] [ERROR] Failed to complete command task: 'plot_cnv' launched from master workflow, error code: 1, command: '/usr/local/Accucopy/plotCPandMCP.py -i /.../accucopy/results/cnv.output.tsv -r /mnt/refData/genome.dict --no_of_autosomes 22 -o /.../accucopy/results/plot.cnv.png'
[15_1] [TaskManager] [ERROR] [plot_cnv] Error Message:
[15_1] [TaskManager] [ERROR] [plot_cnv] Last 27 stderr lines from task (of 27 total lines):
[15_1] [TaskManager] [ERROR] [plot_cnv] Error processing line 1 of /usr/local/lib/python3.6/dist-packages/matplotlib-3.3.4-py3.6-nspkg.pth:
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]   Traceback (most recent call last):
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]     File "/usr/lib/python3.6/site.py", line 174, in addpackage
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]     exec(line)
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]     File "<string>", line 1, in <module>
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]     File "<frozen importlib._bootstrap>", line 568, in module_from_spec
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]   AttributeError: 'NoneType' object has no attribute 'loader'
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] Remainder of file ignored
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] Matplotlib created a temporary config/cache directory at /tmp/matplotlib-pql0p325 because the default path (/root/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] Traceback (most recent call last):
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]   File "/usr/local/Accucopy/plotCPandMCP.py", line 7, in <module>
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]     from matplotlib import pyplot as plt
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]   File "/usr/local/lib/python3.6/dist-packages/matplotlib/pyplot.py", line 36, in <module>
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]     import matplotlib.colorbar
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]   File "/usr/local/lib/python3.6/dist-packages/matplotlib/colorbar.py", line 44, in <module>
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]     import matplotlib.contour as contour
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]   File "/usr/local/lib/python3.6/dist-packages/matplotlib/contour.py", line 21, in <module>
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]     import matplotlib.texmanager as texmanager
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]   File "<frozen importlib._bootstrap>", line 971, in _find_and_load
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]   File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]   File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]   File "<frozen importlib._bootstrap_external>", line 674, in exec_module
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]   File "<frozen importlib._bootstrap_external>", line 779, in get_code
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv]   File "<frozen importlib._bootstrap_external>", line 487, in _compile_bytecode
[15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] EOFError: marshal data too short
[15_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.

In the singularity container i couldn't import matplotlib, pandas or numpy for python3 (but could for python2).

Hi @polyactis,

First, thank you for this great tool.

I aligned my reads to the reference genome included in hs38d1 provided by Accucopy and sorted the bam files with duplicates marked. However, I am having the error as shown below when trying to run the main.py file.

Please let me know if you have any suggestions! Thank you very much!

[2022-04-28T20:45:05.792488] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr4' to master workflow
  [2022-04-28T20:45:05.792738] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr5' to master workflow
  [2022-04-28T20:45:05.792866] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr6' to master workflow
  [2022-04-28T20:45:05.792992] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr7' to master workflow
  [2022-04-28T20:45:05.793113] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr8' to master workflow
  [2022-04-28T20:45:05.793232] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr9' to master workflow
  [2022-04-28T20:45:05.793362] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr10' to master workflow
  [2022-04-28T20:45:05.793481] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr11' to master workflow
  [2022-04-28T20:45:05.793596] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr12' to master workflow
  [2022-04-28T20:45:05.794122] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr13' to mast' to master workflow
  [2022-04-28T20:45:05.793481] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr11' to master workflow
  [2022-04-28T20:45:05.793596] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr12' to master workflow
  [2022-04-28T20:45:05.794122] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr13' to master workflow
  [2022-04-28T20:45:05.794601] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr14' to master workflow
  [2022-04-28T20:45:05.795005] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr15' to master workflow
  [2022-04-28T20:45:05.795131] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr16' to master workflow
  [2022-04-28T20:45:05.795248] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr17' to master workflow
  [2022-04-28T20:45:05.795368] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr18' to master workflow
  [2022-04-28T20:45:05.795483] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr19' to master workflow
  [2022-04-28T20:45:05.795597] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr20' to master workflow
  [2022-04-28T20:45:05.795710] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr21' to master workflow
  [2022-04-28T20:45:05.795840] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr22' to master workflow
  [2022-04-28T20:45:05.795961] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'reduce_all_segments' to master workflow
  [2022-04-28T20:45:05.796443] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'rm_individual_seg_files' to master workflow
  Last step time span: 0:00:00.007164
  step 5: Infer tumor purity and ploidy.
  	start time: 2022-04-29 04:45:05.796882
  [2022-04-28T20:45:05.797097] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'infer' to master workflow
  Last step time span: 0:00:00.000715
  step 6: Make plots.
  	start time: 2022-04-29 04:45:05.797597
  [2022-04-28T20:45:05.797682] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'plot_cnv' to master workflow
  Last step time span: 0:00:00.000146
  End time: 2022-04-29 04:45:05.797743
  [2022-04-28T20:45:05.797779] [1d46eeca3e55] [8_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
  [2022-04-28T20:45:59.922904] [1d46eeca3e55] [8_1] [TaskManager] Completed command task: 'indexTumorBam' launched from master workflow
  [2022-04-28T20:46:00.087241] [1d46eeca3e55] [8_1] [TaskManager] Completed command task: 'indexNormalBam' launched from master workflow
  [2022-04-28T20:46:00.087753] [1d46eeca3e55] [8_1] [TaskManager] Launching command task: 'strelka_prepare' from master workflow
  [2022-04-28T20:46:00.088045] [1d46eeca3e55] [8_1] [TaskManager] Launching command task: 'normalize' from master workflow
  [2022-04-28T20:46:00.090603] [1d46eeca3e55] [8_1] [TaskRunner:strelka_prepare] Task initiated on local node
  [2022-04-28T20:46:00.091298] [1d46eeca3e55] [8_1] [TaskRunner:normalize] Task initiated on local node
  [2022-04-28T20:46:00.151922] [1d46eeca3e55] [8_1] [TaskManager] [ERROR] Failed to complete command task: 'normalize' launched from master workflow, error code: 101, command: 
  [2022-04-28T20:46:00.151960] [1d46eeca3e55] [8_1] [TaskManager] [ERROR] [normalize] Error Message:
  [2022-04-28T20:46:00.151972] [1d46eeca3e55] [8_1] [TaskManager] [ERROR] [normalize] Last 0 stderr lines from task (of 0 total lines):
  [2022-04-28T20:46:00.151983] [1d46eeca3e55] [8_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
  [2022-04-28T20:46:00.366062] [1d46eeca3e55] [8_1] [TaskManager] Completed command task: 'strelka_prepare' launched from master workflow
  [2022-04-28T20:46:08.952897] [1d46eeca3e55] [8_1] [WorkflowRunner] [ERROR] Worklow terminated due to the following task errors:
  [2022-04-28T20:46:08.952995] [1d46eeca3e55] [8_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'normalize' launched from master workflow, error code: 101, command: 
  [2022-04-28T20:46:08.953010] [1d46eeca3e55] [8_1] [WorkflowRunner] [ERROR] [normalize] Error Message:
  [2022-04-28T20:46:08.953019] [1d46eeca3e55] [8_1] [WorkflowRunner] [ERROR] [normalize] Last 0 stderr lines from task (of 0 total lines):

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) "

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

Hi @polyactis,
First of all, thanks for your great work of Accucopy. It really helps a lot in my low-coverage WGS project.
And I wonder which kind of bam files you would like to suggest as input bams? Such as raw bams after bwa, or sorted bams, or sorted bams with picard-MarkDuplicate procedure?

Thanks,
Junyi

Hi
Thanks for this excellent tool. caller_path the path of the 3rd-party variant calling program; in demo, Strelka2 was used. could gatk be uesd as caller?

Dear professor,
thansk for such a accurate software.

when I am using it, it raise errors like follows. MAYbe caused by chrM and chrMT.

what is more, since your genome.dict has many patch chromosome names, like

SN:GL000207.1
SN:GL000226.1
SN:GL000229.1
SN:GL000231.1
, but when users input bam, they may use a different version of genome, even for hg19, the patch chromosome seems to be different, so why not the input is a fastq, but a bam? ,can you give me some suggestions

ERRORS screenshot like following

Dear author,

Thanks for developing this software. I re-aligned my bam files with the provided reference genome, then ran Accucopy docker image with Singularity following the instructions, but I always get the following errors:

Exception in thread TaskFileWriter-Thread:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner
self.run()
File "/usr/local/lib/python2.7/dist-packages/pyflow/pyflow.py", line 1650, in run
self._writeIfSet()
File "/usr/local/lib/python2.7/dist-packages/pyflow/pyflow.py", line 1660, in _writeIfSet
self.writeFunc()
File "/usr/local/lib/python2.7/dist-packages/pyflow/pyflow.py", line 537, in wrapped
return f(self, *args, **kw)
File "/usr/local/lib/python2.7/dist-packages/pyflow/pyflow.py", line 2717, in writeTaskInfo
fp = open(self.taskInfoFile, "a")
IOError: [Errno 2] No such file or directory: 'output/pyflow.data/state/pyflow_tasks_info.txt'
Exception in thread TaskFileWriter-Thread:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner
self.run()
File "/usr/local/lib/python2.7/dist-packages/pyflow/pyflow.py", line 1650, in run
self._writeIfSet()
File "/usr/local/lib/python2.7/dist-packages/pyflow/pyflow.py", line 1660, in _writeIfSet
self.writeFunc()
File "/usr/local/lib/python2.7/dist-packages/pyflow/pyflow.py", line 537, in wrapped
return f(self, *args, **kw)
File "/usr/local/lib/python2.7/dist-packages/pyflow/pyflow.py", line 2618, in writeTaskStatus
tmpFp = open(tmpFile, "w")
IOError: [Errno 2] No such file or directory: 'output/pyflow.data/state/pyflow_tasks_runstate.txt.update.incomplete'

I might have missed something. Any suggestions? Thanks.

Jack

Hello working with several samples, all but 1 sample output the cnv.output.tsv. Have ran accucopy on this single sample many times, however no CNV output. Accucopy finishes with no error. Job finishes but the cnv.output file is not written. What are the reasons this woud happen?

Hi! I am running into a segmentation fault. Why might this be happening?

Here is the infer.status.txt file:

Reading in genome coverage from "/mnt/CT432.bam" ...
New chromosome chr1, length=248956422, window size=500, no_of_windows=497913.
59661040 reads so far for "/mnt/CT432.bam". Chromosome chr1 contains 0 valid fragments.
New chromosome chr10, length=133797422, window size=500, no_of_windows=267595.
81042310 reads so far for "/mnt/CT432.bam". Chromosome chr10 contains 0 valid fragments.
New chromosome chr11, length=135086622, window size=500, no_of_windows=270174.
110417527 reads so far for "/mnt/CT432.bam". Chromosome chr11 contains 0 valid fragments.
New chromosome chr12, length=133275309, window size=500, no_of_windows=266551.
139816736 reads so far for "/mnt/CT432.bam". Chromosome chr12 contains 0 valid fragments.
New chromosome chr13, length=114364328, window size=500, no_of_windows=228729.
161439829 reads so far for "/mnt/CT432.bam". Chromosome chr13 contains 0 valid fragments.
New chromosome chr14, length=107043718, window size=500, no_of_windows=214088.
181255065 reads so far for "/mnt/CT432.bam". Chromosome chr14 contains 0 valid fragments.
New chromosome chr15, length=101991189, window size=500, no_of_windows=203983.
199363069 reads so far for "/mnt/CT432.bam". Chromosome chr15 contains 0 valid fragments.
New chromosome chr16, length=90338345, window size=500, no_of_windows=180677.
218150818 reads so far for "/mnt/CT432.bam". Chromosome chr16 contains 0 valid fragments.
New chromosome chr17, length=83257441, window size=500, no_of_windows=166515.
235637677 reads so far for "/mnt/CT432.bam". Chromosome chr17 contains 0 valid fragments.
New chromosome chr18, length=80373285, window size=500, no_of_windows=160747.
253134738 reads so far for "/mnt/CT432.bam". Chromosome chr18 contains 0 valid fragments.
New chromosome chr19, length=58617616, window size=500, no_of_windows=117236.
265860905 reads so far for "/mnt/CT432.bam". Chromosome chr19 contains 0 valid fragments.
New chromosome chr2, length=242193529, window size=500, no_of_windows=484388.
319870334 reads so far for "/mnt/CT432.bam". Chromosome chr2 contains 0 valid fragments.
New chromosome chr20, length=64444167, window size=500, no_of_windows=128889.
333674604 reads so far for "/mnt/CT432.bam". Chromosome chr20 contains 0 valid fragments.
New chromosome chr21, length=46709983, window size=500, no_of_windows=93420.
343433771 reads so far for "/mnt/CT432.bam". Chromosome chr21 contains 0 valid fragments.
New chromosome chr22, length=50818468, window size=500, no_of_windows=101637.
351723849 reads so far for "/mnt/CT432.bam". Chromosome chr22 contains 0 valid fragments.
New chromosome chr3, length=198295559, window size=500, no_of_windows=396592.
396184917 reads so far for "/mnt/CT432.bam". Chromosome chr3 contains 0 valid fragments.
New chromosome chr4, length=190214555, window size=500, no_of_windows=380430.
441143709 reads so far for "/mnt/CT432.bam". Chromosome chr4 contains 0 valid fragments.
New chromosome chr5, length=181538259, window size=500, no_of_windows=363077.
482509996 reads so far for "/mnt/CT432.bam". Chromosome chr5 contains 0 valid fragments.
New chromosome chr6, length=170805979, window size=500, no_of_windows=341612.
518332470 reads so far for "/mnt/CT432.bam". Chromosome chr6 contains 0 valid fragments.
New chromosome chr7, length=159345973, window size=500, no_of_windows=318692.
562631614 reads so far for "/mnt/CT432.bam". Chromosome chr7 contains 0 valid fragments.
New chromosome chr8, length=145138636, window size=500, no_of_windows=290278.
594804392 reads so far for "/mnt/CT432.bam". Chromosome chr8 contains 0 valid fragments.
New chromosome chr9, length=138394717, window size=500, no_of_windows=276790.
653668784 reads so far for "/mnt/CT432.bam". Chromosome chr9 contains 0 valid fragments.
Reading and smoothing of coverage from "/mnt/CT432.bam" is Done. 22 unique chromosomes, 653668784 reads.
Genome wide mean coverage is 0
Reading in genome coverage from "/mnt/CT434.bam" ...
New chromosome chr1, length=248956422, window size=500, no_of_windows=497913.
21543443 reads so far for "/mnt/CT434.bam". Chromosome chr1 contains 0 valid fragments.
New chromosome chr10, length=133797422, window size=500, no_of_windows=267595.
33519753 reads so far for "/mnt/CT434.bam". Chromosome chr10 contains 0 valid fragments.
New chromosome chr11, length=135086622, window size=500, no_of_windows=270174.
45224913 reads so far for "/mnt/CT434.bam". Chromosome chr11 contains 0 valid fragments.
New chromosome chr12, length=133275309, window size=500, no_of_windows=266551.
57193479 reads so far for "/mnt/CT434.bam". Chromosome chr12 contains 0 valid fragments.
New chromosome chr13, length=114364328, window size=500, no_of_windows=228729.
65967040 reads so far for "/mnt/CT434.bam". Chromosome chr13 contains 0 valid fragments.
New chromosome chr14, length=107043718, window size=500, no_of_windows=214088.
73940039 reads so far for "/mnt/CT434.bam". Chromosome chr14 contains 0 valid fragments.
New chromosome chr15, length=101991189, window size=500, no_of_windows=203983.
81214655 reads so far for "/mnt/CT434.bam". Chromosome chr15 contains 0 valid fragments.
New chromosome chr16, length=90338345, window size=500, no_of_windows=180677.
88145461 reads so far for "/mnt/CT434.bam". Chromosome chr16 contains 0 valid fragments.
New chromosome chr17, length=83257441, window size=500, no_of_windows=166515.
95287511 reads so far for "/mnt/CT434.bam". Chromosome chr17 contains 0 valid fragments.
New chromosome chr18, length=80373285, window size=500, no_of_windows=160747.
102166467 reads so far for "/mnt/CT434.bam". Chromosome chr18 contains 0 valid fragments.
New chromosome chr19, length=58617616, window size=500, no_of_windows=117236.
106899655 reads so far for "/mnt/CT434.bam". Chromosome chr19 contains 0 valid fragments.
New chromosome chr2, length=242193529, window size=500, no_of_windows=484388.
128578844 reads so far for "/mnt/CT434.bam". Chromosome chr2 contains 0 valid fragments.
New chromosome chr20, length=64444167, window size=500, no_of_windows=128889.
133963433 reads so far for "/mnt/CT434.bam". Chromosome chr20 contains 0 valid fragments.
New chromosome chr21, length=46709983, window size=500, no_of_windows=93420.
137937298 reads so far for "/mnt/CT434.bam". Chromosome chr21 contains 0 valid fragments.
New chromosome chr22, length=50818468, window size=500, no_of_windows=101637.
141126722 reads so far for "/mnt/CT434.bam". Chromosome chr22 contains 0 valid fragments.
New chromosome chr3, length=198295559, window size=500, no_of_windows=396592.
159234832 reads so far for "/mnt/CT434.bam". Chromosome chr3 contains 0 valid fragments.
New chromosome chr4, length=190214555, window size=500, no_of_windows=380430.
177053732 reads so far for "/mnt/CT434.bam". Chromosome chr4 contains 0 valid fragments.
New chromosome chr5, length=181538259, window size=500, no_of_windows=363077.
193446228 reads so far for "/mnt/CT434.bam". Chromosome chr5 contains 0 valid fragments.
New chromosome chr6, length=170805979, window size=500, no_of_windows=341612.
209476810 reads so far for "/mnt/CT434.bam". Chromosome chr6 contains 0 valid fragments.
New chromosome chr7, length=159345973, window size=500, no_of_windows=318692.
223320566 reads so far for "/mnt/CT434.bam". Chromosome chr7 contains 0 valid fragments.
New chromosome chr8, length=145138636, window size=500, no_of_windows=290278.
236709378 reads so far for "/mnt/CT434.bam". Chromosome chr8 contains 0 valid fragments.
New chromosome chr9, length=138394717, window size=500, no_of_windows=276790.
263020395 reads so far for "/mnt/CT434.bam". Chromosome chr9 contains 0 valid fragments.
Reading and smoothing of coverage from "/mnt/CT434.bam" is Done. 22 unique chromosomes, 263020395 reads.
Genome wide mean coverage is 0
Outputting normalized coverage ratio of chr1 ... Output done.
Outputting normalized coverage ratio of chr2 ... Output done.
Outputting normalized coverage ratio of chr3 ... Output done.
Outputting normalized coverage ratio of chr4 ... Output done.
Outputting normalized coverage ratio of chr5 ... Output done.
Outputting normalized coverage ratio of chr6 ... Output done.
Outputting normalized coverage ratio of chr7 ... Output done.
Outputting normalized coverage ratio of chr8 ... Output done.
Outputting normalized coverage ratio of chr9 ... Output done.
Outputting normalized coverage ratio of chr10 ... Output done.
Outputting normalized coverage ratio of chr11 ... Output done.
Outputting normalized coverage ratio of chr12 ... Output done.
Outputting normalized coverage ratio of chr13 ... Output done.
Outputting normalized coverage ratio of chr14 ... Output done.
Outputting normalized coverage ratio of chr15 ... Output done.
Outputting normalized coverage ratio of chr16 ... Output done.
Outputting normalized coverage ratio of chr17 ... Output done.
Outputting normalized coverage ratio of chr18 ... Output done.
Outputting normalized coverage ratio of chr19 ... Output done.
Outputting normalized coverage ratio of chr20 ... Output done.
Outputting normalized coverage ratio of chr21 ... Output done.
Outputting normalized coverage ratio of chr22 ... Output done.
program name is /usr/local/Accucopy/GADA.
Reading data from /mnt/output_CT432_CT434/chr14.ratio.w500.csv.gz ... program name is /usr/local/Accucopy/GADA.
Reading data from /mnt/output_CT432_CT434/chr22.ratio.w500.csv.gz ... 0 data points for chromosome chr14.
Running SBLandBE ...
0 data points for chromosome chr22.
Running SBLandBE ...

Hi @polyactis,

we considered to package Accucopy for Bioconda to make it easily obtainable for end users.
(When or if this might happen depends on demand, required effort, and chiefly on the outcome of this issue.)

I noticed a few licensing issues which would prevent a distribution, though:

• Depending on the interpretation, https://github.com/polyactis/Accucopy/blob/v1.1/LICENSE#L26 might outright prohibit distribution on our part.
• https://github.com/polyactis/Accucopy/blob/v1.1/LICENSE#L1-L6 and further restrictions in the license text violate the license agreements needed for Accucopy's dependencies:
  • GSL is licensed under the GPL 3.0: http://git.savannah.gnu.org/cgit/gsl.git/tree/COPYING?h=release-2-6
  • Accucopy bundles parts of https://github.com/rpique/GADA which is licensed under GPL 3.0+:
    • https://github.com/polyactis/Accucopy/blob/v1.1/src_o/BaseGADA.h#L11-L14
    • https://github.com/polyactis/Accucopy/blob/v1.1/src_o/BaseGADA.cc#L11-L14
  • Strelka2 also uses GPL 3.0+: https://github.com/Illumina/strelka/blob/v2.9.10/COPYRIGHT.txt
    (This one might not be of interest for the source distribution but if you redistribute Strelka2 in a bundle with your binaries/containers and apply your license restrictions to the whole bundle.)
  • You cannot add additional restrictions like those from https://github.com/polyactis/Accucopy/blob/v1.1/LICENSE (non-commercial, distribution restrictions, etc.) in conjunction with your GPL-licensed dependencies, see: https://www.gnu.org/licenses/gpl-faq.html#NoMilitary

Unrelated to our interest in redistributing Accucopy via Bioconda, I'd like to ask you to review the license conformance of your software with its dependencies. (Considering the nature of the GPL, this would probably mean you would have to relicense Accucopy under the GPL 3.0 and as such have to drop the academic/non-commercial and other restrictions.)
I'm not a lawyer and as such cannot offer further help with this issue, but just wanted to make you aware of it.

Cheers,
Marcel

(cc @dlaehnemann)

maestre does not find the libbz2.so.1.0 and fails with the usual lib not found error message:

/opt/accucopy/maestre: error while loading shared libraries: libbz2.so.1.0: cannot open shared object file: No such file or directory

Even though I installed libbz2 for the current conda environment as well as on the system:

conda install -c conda-forge bzip2
yum install bzip2-libs

Hi,

I tested the accucopy docker with a dataset of 100 samples, but no breakpoints were found for 80 of those. So I tried to use a different window size but it seems that somewhere the window size is hard coded as it tries to find the file 'chr22.ratio.w500.csv.gz' in the next step no matter what the actual window size is. Of course, this file does not exist as for a window size of 250 it's actually 'chr22.ratio.w250.csv.gz' and the computation fails. Is it possible to fix this? Is there anything else i could try to get a Tumor purity value for those 80 samples?

Cheers,
Nicole

Hi, I want to use Accucopy on long read data, such as Pacbio or Nanopore. So I want to ask, whether your model fits long reads data or not. If yes, how can i set parameters like read_length and widow_size?

thanks.