soroushsamadian
commented
6 years ago Hi just to double check, do you provide "splitbams" directory where the input.bam is split by individual chromosome(also sorted by name) or do you let Bamgineer do it for you?
If you provide "splitbams" folder Bamgineer assumes you already have your input split by chromosome and hence skips " pool1.map_async(split_bam_by_chr, chromosome_event)..." function. However, in the folder is empty, you will get an exception later in the run.
vipuljain222
Hi, I am getting error while running run_example1.sh using example data set. I have recreated exons.bed as explained in input_preparation.md file and modified config file with appropriate path.
File structure:
|-- inputs | |-- cnv.bed | |-- config.cfg | |-- config_ORI.cfg | |-- exons.bed | |-- exons_ORI.bed | |-- normal_het.vcf | -- normal_het.vcf.gz |-- outputs | |-- cnv_dir | |-- gain.bed | |-- finalbams | |-- haplotypedir | | |-- bedtool.log | | |-- chr21_exons_in_roigain.bed | | |-- chr21_het_snpgain.bed | | |-- exons_in_roigain.bed | | -- het_snpgain.bed | |-- logs | |-- debug.log | |-- phasedvcfdir | | |-- hap1_het_filtered.bed | | |-- hap1_het_filtered.log | | |-- hap1_het_filtered.recode.vcf | | |-- hap1_het.vcf | | |-- hap2_het_filtered.bed | | |-- hap2_het_filtered.log | | |-- hap2_het_filtered.recode.vcf | | |-- hap2_het.vcf | | |-- normal_het_phased.log | | |-- normal_het_phased.vcf.gz | | |-- normal_het_phased.warnings | | -- PHASED.BED |-- tmpbams |-- scripts | |-- beagle.log | -- run_example1.sh |-- splitbams | |-- chr21.bam | |-- chr21.bam.bai | |-- chr21.byname.bam | |-- chr22.bam | |-- chr22.bam.bai |-- chr22.byname.bam
Here is the output:
/opt/installers/bamgineer/examples/outputs phasing vcf file beagle.09Nov15.d2a.jar Copyright (C) 2014-2015 Brian L. Browning Enter "java -jar beagle.jar" for a summary of command line arguments. Start time: 01:04 PM IST on 25 Apr 2018
Command line: java -Xmx3641m -jar beagle.jar gt=/opt/installers/bamgineer/examples/inputs/normal_het.vcf.gz out=/opt/installers/bamgineer/examples/outputs/phasedvcfdir/normal_het_phased
No genetic map is specified: using 1 cM = 1 Mb
reference samples: 0 target samples: 1
Window 1 [ chr21:9414112-48119669 ] target markers: 10225
Starting burn-in iterations
Window=1 Iteration=1 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 2.000 mean count/edge: 1
Window=1 Iteration=2 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 2.000 mean count/edge: 1
Window=1 Iteration=3 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 2.000 mean count/edge: 1
Window=1 Iteration=4 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 2.000 mean count/edge: 1
Window=1 Iteration=5 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 2.000 mean count/edge: 1
Window=1 Iteration=6 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 2.000 mean count/edge: 1
Window=1 Iteration=7 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 2.000 mean count/edge: 1
Window=1 Iteration=8 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 2.000 mean count/edge: 1
Window=1 Iteration=9 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 2.000 mean count/edge: 1
Window=1 Iteration=10 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 2.000 mean count/edge: 1
Starting phasing iterations
Window=1 Iteration=11 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 2.000 mean count/edge: 1
states/marker: 1.0
Window=1 Iteration=12 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 2.000 mean count/edge: 1
states/marker: 1.0
Window=1 Iteration=13 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 2.000 mean count/edge: 1
states/marker: 1.0
Window=1 Iteration=14 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 2.000 mean count/edge: 1
states/marker: 1.0
Window=1 Iteration=15 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 2.000 mean count/edge: 1
states/marker: 1.0
Window 2 [ chr22:16066867-51239065 ] target markers: 3455
Starting burn-in iterations
Window=2 Iteration=1 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 1.999 mean count/edge: 1
Window=2 Iteration=2 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 1.999 mean count/edge: 1
Window=2 Iteration=3 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 1.999 mean count/edge: 1
Window=2 Iteration=4 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 1.999 mean count/edge: 1
Window=2 Iteration=5 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 1.999 mean count/edge: 1
Window=2 Iteration=6 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 1.999 mean count/edge: 1
Window=2 Iteration=7 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 1.999 mean count/edge: 1
Window=2 Iteration=8 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 1.999 mean count/edge: 1
Window=2 Iteration=9 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 1.999 mean count/edge: 1
Window=2 Iteration=10 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 1.999 mean count/edge: 1
Starting phasing iterations
Window=2 Iteration=11 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 1.999 mean count/edge: 1
states/marker: 1.0
Window=2 Iteration=12 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 1.999 mean count/edge: 1
states/marker: 1.0
Window=2 Iteration=13 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 1.999 mean count/edge: 1
states/marker: 1.0
Window=2 Iteration=14 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 1.999 mean count/edge: 1
states/marker: 1.0
Window=2 Iteration=15 Time for building model: 0 seconds Time for sampling (singles): 0 seconds DAG statistics mean edges/level: 2 max edges/level: 2 mean edges/node: 1.999 mean count/edge: 1
states/marker: 1.0
Number of markers: 13680 Total time for building model: 1 second Total time for sampling: 1 second Total run time: 2 seconds
End time: 01:04 PM IST on 25 Apr 2018 beagle.09Nov15.d2a.jar finished
VCFtools - v0.1.12a (C) Adam Auton and Anthony Marcketta 2009
Parameters as interpreted: --vcf /opt/installers/bamgineer/examples/outputs/phasedvcfdir/hap1_het.vcf --thin 50 --out /opt/installers/bamgineer/examples/outputs/phasedvcfdir/hap1_het_filtered --recode
After filtering, kept 0 out of 0 Individuals Outputting VCF file... After filtering, kept 5324 out of a possible 6773 Sites Run Time = 0.00 seconds
VCFtools - v0.1.12a (C) Adam Auton and Anthony Marcketta 2009
Parameters as interpreted: --vcf /opt/installers/bamgineer/examples/outputs/phasedvcfdir/hap2_het.vcf --thin 50 --out /opt/installers/bamgineer/examples/outputs/phasedvcfdir/hap2_het_filtered --recode
After filtering, kept 0 out of 0 Individuals Outputting VCF file... After filtering, kept 5424 out of a possible 6905 Sites Run Time = 0.00 seconds [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [main_samview] fail to read the header from "/opt/installers/bamgineer/examples/outputs/tmpbams/chr21_r Exception in thread Thread-1: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner self.run() File "/usr/lib/python2.7/threading.py", line 763, in run self.target(*self.args, **self.__kwargs) File "/opt/installers/bamgineer/src/helpers/handlers.py", line 76, in receive record = self.queue.get(True, self.polltime) File "/usr/lib/python2.7/multiprocessing/queues.py", line 135, in get res = self._recv() TypeError: ('init() takes exactly 2 arguments (1 given)', <class 'pysam.utils.SamtoolsError'>, ())