itmat / camparee Goto Github PK

Hello ITMAT Bioinformatics Laboratory team,

I have been trying to use CAMPAREE to generate transcripts from an RNA sample. I would like the resulting transcripts to be equal to the reference genome, without any variants. This is so I can introduce specific variants later on and perform benchmarking on variant-calling tools.

In the template.config.yaml file, I found the following description of the "pooled" parameter:
Setting this to 'True' will skip all variant-calling, phasing, parental genome construction, and allele-specific quantification operations in the CAMPAREE pipeline. Simulated transcripts will effectively be generated from the haploid reference genome.

However, even when setting "pooled" to True, the variant calling and phasing are being executed. In my case, during the beagle step, an error occurs which stops the execution. The log is not very descriptive of the problem:

beagle.28Sep18.793.jar (version 5.0)
Copyright (C) 2014-2018 Brian L. Browning
Enter "java -jar beagle.28Sep18.793.jar" to list command line argument
Start time: 01:18 PM CET on 08 Feb 2023

Command line: java -Xmx16080m -jar beagle.28Sep18.793.jar
gt=/media/scratch/rnaseq_read_simulation/analysis/camparee/run_prueba/CAMPAREE/data/all_variants.vcf
out=/media/scratch/rnaseq_read_simulation/analysis/camparee/run_prueba/CAMPAREE/data/beagle
seed=1273642419
nthreads=1

No genetic map is specified: using 1 cM = 1 Mb

Reference samples: 0
Study samples: 1

Window 1 (chr1:16242-39963300)
Study markers: 26,508

When running CAMPAREE, I get an error from BEAGLE.

It looks like beagle is complaining that "ERROR: there is only one sample". I got this by using a newer version of beagle. How can I run CAMPAREE on single sample RNA-seq data (only one pair of fastq files)?

Here are the err messages:

BeagleStep.log (exit code 1):

No genetic map is specified: using 1 cM = 1 Mb

Reference samples:           0
Study samples:               1

Window 1 (chr1:14498-39975388)
Study markers:          36,017

Burnin  iteration 1:           1 second
Burnin  iteration 2:           1 second
Burnin  iteration 3:           1 second
Burnin  iteration 4:           1 second
Burnin  iteration 5:           2 seconds
Exception in thread "main" java.lang.IllegalArgumentException: NaN
	at phase.PhaseData.<init>(PhaseData.java:76)
	at main.MainHelper.lsPhaseSingles(MainHelper.java:94)
	at main.MainHelper.phase(MainHelper.java:72)
	at main.Main.phaseData(Main.java:166)
	at main.Main.main(Main.java:116)


*****STDERR:
None

and BeagleStep.serial.err :

Traceback (most recent call last):
  File "/home/mrasekh/git/BEERS2/CAMPAREE/camparee/beagle.py", line 79, in execute
    beagle_result = subprocess.run(command, shell=True, check=True,
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mrasekh/.install/mamba/envs/beers2/lib/python3.11/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'java -jar ~/git/BEERS2/CAMPAREE/third_party_software/beagle.28Sep18.793.jar gt=/data/camparee/run_
1/CAMPAREE/data/all_variants.vcf out=/data/output/camparee/run_1/CAMPAREE/data/beagle seed=1890316565 nthreads=36' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "~/git/BEERS2/CAMPAREE/camparee/beagle.py", line 231, in <module>
    sys.exit(BeagleStep.main())
             ^^^^^^^^^^^^^^^^^
  File "/home/mrasekh/git/BEERS2/CAMPAREE/camparee/beagle.py", line 188, in main
    beagle_step.execute(beagle_jar_path=args.beagle_jar_path,
  File "/home/mrasekh/git/BEERS2/CAMPAREE/camparee/beagle.py", line 90, in execute
    raise CampareeException(f"\nBeagle process failed. "
camparee.camparee_utils.CampareeException: 
Beagle process failed. For full details see /illumina-isi07/scratch/dragen_team_share2/users/mrasekh/RNA_benchmarking/data/Human/real/giab_HG005/camparee/run_1/CAMPAREE/logs/BeagleStep.log

This error appears to be separate from the original issue in which it was discussed. I moved it into its own issue.

I had been running CAMPAREE with only one sample. After reading your comment, I introduced another sample to see if the error would be solved. However, now I am getting a different error, also at the Beagle step.
BeagleStep.log
BeagleStep.serial.err.txt
BeagleStep.serial.out.txt

Originally posted by @Argonvi in #3 (comment)

Can we generate the synthetic miRNA-seq data for the human genome?