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Object has no attribute 'length' in the last step, Output final VCF file #105

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wjaratlerdsiri opened this issue Feb 28, 2016 · 9 comments
Open

Object has no attribute 'length' in the last step, Output final VCF file #105

wjaratlerdsiri opened this issue Feb 28, 2016 · 9 comments

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@wjaratlerdsiri
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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
@marghoob
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Contributor

This is most likely a problem due to using the latest version of pyvcf.
Please try using version 0.6.7 (https://pypi.python.org/pypi/PyVCF) and let
me know how it goes.

Thanks
Marghoob.

On Sun, Feb 28, 2016 at 1:41 PM, wjaratlerdsiri [email protected]
wrote:

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- 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- 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- 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- 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

—
Reply to this email directly or view it on GitHub
#105.

@wjaratlerdsiri
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Author

Got a new problem?

wget https://pypi.python.org/packages/source/P/PyVCF/PyVCF-0.6.7.tar.gz
tar -zxvf PyVCF-0.6.7.tar.gz
$ /bcbiometasv/miniconda/bin/python2.7 setup.py build
/bcbiometasv/miniconda/bin/python2.7 setup.py install --prefix /bcbiometasv/miniconda
creating /bcbiometasv/miniconda/lib/python2.7/site-packages/PyVCF-0.6.7-py2.7-linux-x86_64.egg
Extracting PyVCF-0.6.7-py2.7-linux-x86_64.egg to /bcbiometasv/miniconda/lib/python2.7/site-packages
Adding PyVCF 0.6.7 to easy-install.pth file
Installing vcf_melt script to /bcbiometasv/miniconda/bin
Installing vcf_filter.py script to/bcbiometasv/miniconda/bin

Installed /bcbiometasv/miniconda/lib/python2.7/site-packages/PyVCF-0.6.7-py2.7-linux-x86_64.egg
Processing dependencies for PyVCF==0.6.7
Searching for distribute==0.6.28
Best match: distribute 0.6.28
Processing distribute-0.6.28-py2.7.egg
distribute 0.6.28 is already the active version in easy-install.pth
Installing easy_install script to /bcbiometasv/miniconda/bin
Installing easy_install-2.7 script to /bcbiometasv/miniconda/bin

Using /usr/local/python/2.7.9/lib/python2.7/site-packages/distribute-0.6.28-py2.7.egg
Finished processing dependencies for PyVCF==0.6.7

So, I got 2 versions

drwxr-sr-x 4096 Mar 1 17:35 PyVCF-0.6.7-py2.7-linux-x86_64.egg
drwxr-sr-x 4096 Jan 19 09:01 PyVCF-0.6.8.dev0-py2.7.egg-info

I ran the same command as above and stopped so quick.

WARNING 2016-03-01 17:55:46,800 metasv.sv_interval Skipping Record(CHROM=chrX, POS=84663964, REF=T, ALT=[TCCCCCC]) due to small size
INFO 2016-03-01 17:55:46,800 metasv.sv_interval Loading SV intervals from 3.tumorFR07887821.gt.lumpy.svtyper.PRECISE.N0.PTonly.filtered.somatic.142.recode.vcf
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 150, in run_metasv
svs_to_report=args.svs_to_report, maxsvlen=args.maxsvlen)
File "/scratch/RDS-SMS-PCaGenomes-RW/weejar/bcbiometasv/miniconda/lib/python2.7/site-packages/MetaSV-0.5-py2.7.egg/metasv/vcf_utils.py", line 71, in load_intervals
vcf_reader = vcf.Reader(open(in_vcf))
File "/scratch/RDS-SMS-PCaGenomes-RW/weejar/bcbiometasv/miniconda/lib/python2.7/site-packages/PyVCF-0.6.7-py2.7-linux-x86_64.egg/vcf/parser.py", line 288, in init
self._parse_metainfo()
File "/scratch/RDS-SMS-PCaGenomes-RW/weejar/bcbiometasv/miniconda/lib/python2.7/site-packages/PyVCF-0.6.7-py2.7-linux-x86_64.egg/vcf/parser.py", line 329, in _parse_metainfo
key, val = parser.read_meta(line)
File "/scratch/RDS-SMS-PCaGenomes-RW/weejar/bcbiometasv/miniconda/lib/python2.7/site-packages/PyVCF-0.6.7-py2.7-linux-x86_64.egg/vcf/parser.py", line 224, in read_meta
return match.group('key'), match.group('val')
AttributeError: 'NoneType' object has no attribute 'group'

I go back to reinstall MetaSV v0.5.

$ /weejar/bcbiometasv/miniconda/metasv27jan/python2.7 setup0.5.py build
0.5
running build
running build_py
running build_scripts
copying and adjusting scripts/run_metasv.py -> build/scripts-2.7
copying and adjusting scripts/svtool_to_vcf.py -> build/scripts-2.7
copying and adjusting scripts/annotate_vcf_bam.py -> build/scripts-2.7
changing mode of build/scripts-2.7/run_metasv.py from 644 to 755
changing mode of build/scripts-2.7/svtool_to_vcf.py from 644 to 755
changing mode of build/scripts-2.7/annotate_vcf_bam.py from 644 to 755

$/bcbiometasv/miniconda/metasv27jan/python2.7 setup0.5.py install --prefix /bcbiometasv/miniconda/
0.5
running install
running bdist_egg
running egg_info
creating MetaSV.egg-info
...
Installed /scratch/RDS-SMS-PCaGenomes-RW/weejar/bcbiometasv/miniconda/lib/python2.7/site-packages/MetaSV-0.5-py2.7.egg
Processing dependencies for MetaSV==0.5
Searching for PyVCF==0.6.8.dev0
Best match: PyVCF 0.6.8.dev0
Removing PyVCF 0.6.7 from easy-install.pth file
Adding PyVCF 0.6.8.dev0 to easy-install.pth file

And I run MetaSV again. It runs fine until merging. I think it would end up with my original error in the last step.

WARNING 2016-03-01 18:03:53,128 metasv.sv_interval Skipping Record(CHROM=chrX, POS=84663964, REF=T, ALT=[TCCCCCC]) due to small size
INFO 2016-03-01 18:03:53,128 metasv.sv_interval Loading SV intervals from 3.tumorFR07887821.gt.lumpy.svtyper.PRECISE.N0.PTonly.filtered.somatic.142.recode.vcf
ERROR 2016-03-01 18:03:53,134 metasv.sv_interval Ignoring record due to missing SVTYPE or INFO field in Record(CHROM=chr7, POS=14327396, REF=N, ALT=[[CHR7:14695592[N])
ERROR 2016-03-01 18:03:53,134 metasv.sv_interval Ignoring record due to missing SVTYPE or
...
ERROR 2016-03-01 18:03:53,173 metasv.sv_interval Ignoring record due to missing SVTYPE or INFO field in Record(CHROM=chr14, POS=68967382, REF=G, ALT=[[CHR6:130257583[G])
ERROR 2016-03-01 18:03:53,173 metasv.sv_interval Ignoring record due to missing SVTYPE or INFO field in Record(CHROM=chr14, POS=69025435, REF=A, ALT=[A]CHR8:81396417]])
INFO 2016-03-01 18:03:53,175 metasv.main SV types are set(['DEL', 'DUP', 'INV', 'INS'])
INFO 2016-03-01 18:03:53,175 metasv.main Do merging
INFO 2016-03-01 18:03:53,175 metasv.main Processing SVs of type DEL
INFO 2016-03-01 18:03:53,176 metasv.main Intra-tool Merging SVs of type DEL
INFO 2016-03-01 18:03:53,176 metasv.main First level merging for DEL for tool BreakDancer

Did I do anything wrong? Thankyou again.

James

@wjaratlerdsiri
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Hang on Marghoob!

When I submitted my job via qsub, the job above is still running until now, March 2nd 8am. I am sure because I have checked spades.log file. I am not sure maybe because the command above is for qsub, not for running directly.

I will let you know more about this job.

James

@marghoob
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@wjaratlerdsiri just checking if the suggestion worked for you.

@wjaratlerdsiri
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THX for the follow-up,

I have to do other projects, so I moved BAM file away. I will try soon.

However, if performing only merging, it worked well. I am thinking that because I used Lumpy VCF modified by SVtyper (adding more columns in the format). This might cause errors in the last VCF output.

I will try again without that Lumpy-SVtyper vcf file.

James,

@wjaratlerdsiri
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wjaratlerdsiri commented Apr 15, 2016 •
edited
Loading

Sample file of Lumpy+SVtyper:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT UP
chr1 569387 6 N 0.00 .

SVTYPE=DEL;SVLEN=-457;END=569844;STRANDS=+-:7;CIPOS=-5,4;CIEND=-6,4;CIPOS95=0,0;CIEND95=0,0;SU=7;PE=0;SR=7 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:RP:AP:AB 0/0:7:0:7:134.86:0.00:-84,-27765,-94585:96182:95754:428:95753:427:37686:14:58067:413:0.0044 0/0:0:0:0:200:0.00:-8,-3339,-11423:11654:11589:64:11589:63:0:0:11589:63:0.0054
chr1 991719 9 N 12.39 .

SVTYPE=DEL;SVLEN=-383;END=992102;STRANDS=+-:7;CIPOS=-5,4;CIEND=-5,4;CIPOS95=0,0;CIEND95=0,0;SU=7;PE=0;SR=7 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:RP:AP:AB 0/0:3:0:3:200:0.00:-2,-26,-101:115:109:6:109:5:109:5:0:0:0.044

James

@justin-mbca
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The following resolved the MetaSV issue "Object has no attribute 'length' in the last step, Output final VCF file"

python/2.2.0-anaconda/lib/python2.7/site-packages/vcf/parser.py
Change Line: 670
From
if line.length:
to
if len(line):

-Justin :)

@marghoob
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Thanks @justin-mbca . Was this a change in the pyvcf package?

@justin-mbca
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It should be.
The beginning of the file "parser.py" is:

import codecs
import collections
import csv
import gzip
import itertools
import os
import re
import sys

try:
from collections import OrderedDict
except ImportError:
from ordereddict import OrderedDict

try:
import pysam
except ImportError:
pysam = None

try:
import cparse
except ImportError:
cparse = None

from model import _Call, _Record, make_calldata_tuple
from model import _Substitution, _Breakend, _SingleBreakend, _SV

Metadata parsers/constants

RESERVED_INFO = {
'AA': 'String', 'AC': 'Integer', 'AF': 'Float', 'AN': 'Integer',
'BQ': 'Float', 'CIGAR': 'String', 'DB': 'Flag', 'DP': 'Integer',
'END': 'Integer', 'H2': 'Flag', 'H3': 'Flag', 'MQ': 'Float',
'MQ0': 'Integer', 'NS': 'Integer', 'SB': 'String', 'SOMATIC': 'Flag',
'VALIDATED': 'Flag', '1000G': 'Flag',

# Keys used for structural variants
'IMPRECISE': 'Flag', 'NOVEL': 'Flag', 'SVTYPE': 'String',
'SVLEN': 'Integer', 'CIPOS': 'Integer', 'CIEND': 'Integer',
'HOMLEN': 'Integer', 'HOMSEQ': 'String', 'BKPTID': 'String',
'MEINFO': 'String', 'METRANS': 'String', 'DGVID': 'String',
'DBVARID': 'String', 'DBRIPID': 'String', 'MATEID': 'String',
'PARID': 'String', 'EVENT': 'String', 'CILEN': 'Integer',
'DPADJ': 'Integer', 'CN': 'Integer', 'CNADJ': 'Integer',
'CICN': 'Integer', 'CICNADJ': 'Integer'

}

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@marghoob @justin-mbca @wjaratlerdsiri