Object has no attribute 'length' in the last step, Output final VCF file

[wjaratlerdsiri]

Hello,

I ran: python2.7 run_metasv.py --version run_metasv.py 0.5

module load bedtools/2.24.0 module load gcc/4.8.4

PATH=$PATH:/bcbiometasv/miniconda/bin PYTHONPATH="${PYTHONPATH}:/bcbiometasv/miniconda:/bcbiometasv/miniconda/lib/python2.7/site-packages"

python2.7 run_metasv.py --reference hg19_chromosome.fa --boost_sc
--age /bcbiometasv/miniconda/bin/AGE-master/age_align
--pindel_vcf 5.realigned.pindelx5_1toY.N0_PTonly_LI.filtered.somatic.142.recode.vcf 6.realigned.pindelx5_1toY_N0.PTonly_TD.filtered.somatic.142.recode.vcf 7.realigned.pindelx5_1toY_N0.PTonly_D.filtered.somatic.142.recode.vcf 8.realigned.pindelx5_1toY_N0.PTonly_INV.filtered.somatic.142.recode.vcf 9.realigned.pindelx5_1toY_N0.PTonly_SI.filtered.somatic.142.recode.vcf
--cnvnator_vcf 4.PTonly.NTrealign.root.cnvnator.N0.filtered.somatic.142.recode.vcf
--lumpy_vcf 3.tumor.gt.lumpy.svtyper.PRECISE.N0.PTonly.filtered.somatic.142.recode.vcf --manta_vcf 1.somaticSV_manta.PASS.N0only.PTonly.filtered.somatic.142.recode.vcf
--breakdancer_native 2.breakdancer.cfg.LIBTN.a.TumorOnly.noCTXITX.somatic.manEdit.out
--sample filter.somatic
--bam Clean3_mergedL7L8_hg19_kmer_q15_TrimN_N0_L70.recal_sort2_dedup2.realigned2.NTrealign.bam
--spades /bcbiometasv/miniconda/bin/SPAdes-3.6.0/bin/spades.py
--spades_options '-k 71'
--num_threads 4
--workdir /bcbiometasv/miniconda/bin/UP53input
--outdir out_somatic --min_support_ins 2 --max_ins_intervals 1000000
--mean_read_length 146 --isize_mean 365 --isize_sd 104

It is in the last step. I can see variant.vcf with only a header. But I also see the following error. Can you advise me the workaround for this?

INFO 2016-02-28 23:00:57,715 genotype_interval-<Process(PoolWorker-16, started daemon)> For interval chrY:22260563-22301084 DEL counts are 36, 142 and normal_frac is 0.253521 gt is 0/1 INFO 2016-02-28 23:00:58,091 genotype_interval-<Process(PoolWorker-16, started daemon)> For interval chrY:28792949-28793380 DEL counts are 296, 4088 and normal_frac is 0.072407 gt is 0/1 INFO 2016-02-28 23:00:58,245 genotype_interval-<Process(PoolWorker-16, started daemon)> For interval chrY:28805583-28814110 DEL counts are 229, 3217 and normal_frac is 0.0711843 gt is 0/1 INFO 2016-02-28 23:00:58,700 genotype_intervals-<Process(PoolWorker-16, started daemon)> Genotyped 351 intervals in 1.00553 minutes INFO 2016-02-28 23:00:58,790 parallel_genotype_intervals-<_MainProcess(MainProcess, started)> Following BED files will be merged: ['/scratch/RDS-SMS-PCaGenomes-RW/weejar/bcbiometasv/miniconda/bin/UP53input/genotyping/0/genotyped.bed', '/scratch/RDS-SMS-PCaGenomes-RW/weejar/bcbiometasv/miniconda/bin/UP53input/genotyping/2/genotyped.bed', '/scratch/RDS-SMS-PCaGenomes-RW/weejar/bcbiometasv/miniconda/bin/UP53input/genotyping/1/genotyped.bed', '/scratch/RDS-SMS-PCaGenomes-RW/weejar/bcbiometasv/miniconda/bin/UP53input/genotyping/3/genotyped.bed'] INFO 2016-02-28 23:00:58,878 parallel_genotype_intervals-<_MainProcess(MainProcess, started)> Finished parallel genotyping of 1410 intervals in 1.08642 minutes INFO 2016-02-28 23:00:58,882 metasv.main Output final VCF file Traceback (most recent call last): File "run_metasv.py", line 5, in pkg_resources.run_script('MetaSV==0.5', 'run_metasv.py') File "/usr/local/python/2.7.9/lib/python2.7/site-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 499, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/local/python/2.7.9/lib/python2.7/site-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 1239, in run_script execfile(script_filename, namespace, namespace) File "/scratch/RDS-SMS-PCaGenomes-RW/weejar/bcbiometasv/miniconda/lib/python2.7/site-packages/MetaSV-0.5-py2.7.egg/EGG-INFO/scripts/run_metasv.py", line 142, in sys.exit(run_metasv(args)) File "/scratch/RDS-SMS-PCaGenomes-RW/weejar/bcbiometasv/miniconda/lib/python2.7/site-packages/MetaSV-0.5-py2.7.egg/metasv/main.py", line 335, in run_metasv convert_metasv_bed_to_vcf(bedfile=genotyped_bed, vcf_out=final_vcf, workdir=args.workdir, sample=args.sample, reference=args.reference, pass_calls=False) File "/scratch/RDS-SMS-PCaGenomes-RW/weejar/bcbiometasv/miniconda/lib/python2.7/site-packages/MetaSV-0.5-py2.7.egg/metasv/generate_final_vcf.py", line 476, in convert_metasv_bed_to_vcf vcf_writer = vcf.Writer(open(vcf_out, "w"), vcf_template_reader) File "/scratch/RDS-SMS-PCaGenomes-RW/weejar/bcbiometasv/miniconda/lib/python2.7/site-packages/vcf/parser.py", line 673, in init if line.length: AttributeError: 'tuple' object has no attribute 'length'

Sorry to bother you with too many questions. Thankyou for your time in helping my research.

James