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TrinityCTAT / ctat-mutations

Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
https://github.com/TrinityCTAT/ctat-mutations
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KeyError: u'Mutation ID' #34

Closed maojn closed 4 years ago

maojn commented 5 years ago

Hi,

I ran into problem during Genome lib setup step.

$ export PICARD_HOME=/usr/local/Anaconda/envs_app/ctatmutaions/2.0.1/share/picard-2.18.14-0/

$ python /usr/local/Anaconda/envs_app/ctatmutaions/2.0.1/share/ctat-mutations-2.0.1-5/mutation_lib_prep/ctat-mutation-lib-integration.py \ --CosmicCodingMuts /usr/local/apps/ctatmutations/GRCh37/CosmicCodingMuts.vcf.gz \ --CosmicMutantExport /usr/local/apps/ctatmutations/GRCh37/CosmicMutantExport.tsv.gz \ --genome_lib_dir /usr/local/apps/ctatmutations/GRCh37/GRCh37_gencode_v19_CTAT_lib_Aug152019.plug-n-play/ctat_genome_lib_build_dir/

2019-09-11 14:59:46,738: Uncompressing mutation lib in genome_lib_dir ctat_mutation_lib/ ctat_mutation_lib/rediportal.txt ctat_mutation_lib/header/ ctat_mutation_lib/header/cravat_annotation.txt ctat_mutation_lib/dbsnp_138.vcf.gz.tbi ctat_mutation_lib/dbsnp_138.vcf.gz ctat_mutation_lib/radar.txt ctat_mutation_lib/refGene.sort.bed ctat_mutation_lib/dbsnp_138.vcf.gz.csi ctat_mutation_lib/properties.json 2019-09-11 15:00:09,081: Generating /usr/local/apps/ctatmutations/GRCh37/GRCh37_gencode_v19_CTAT_lib_Aug152019.plug-n-play/ctat_genome_l ib_build_dir/ref_genome.dict INFO 2019-09-11 15:00:10 CreateSequenceDictionary

** NOTE: Picard's command line syntax is changing.

** For more information, please see: ** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)

** The command line looks like this in the new syntax:

** CreateSequenceDictionary -R /usr/local/apps/ctatmutations/GRCh37/GRCh37_gencode_v19_CTAT_lib_Aug152019.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa -O /usr/local/apps/ctatmutations/GRCh37/GRCh37_gencode_v19_CTAT_lib_Aug152019.plug-n-play/ctat_genome_lib_build_dir/ref_genome.dict -VALIDATION_STRINGENCY LENIENT

15:00:10.932 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/Anaconda/envs_app/ctatmutaions/2.0.1/share/picard-2.18.14-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Wed Sep 11 15:00:10 EDT 2019] CreateSequenceDictionary OUTPUT=/usr/local/apps/ctatmutations/GRCh37/GRCh37_gencode_v19_CTAT_lib_Aug152019.plug-n-play/ctat_genome_lib_build_dir/ref_genome.dict VALIDATION_STRINGENCY=LENIENT REFERENCE=/usr/local/apps/ctatmutations/GRCh37/GRCh37_gencode_v19_CTAT_lib_Aug152019.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed Sep 11 15:00:10 EDT 2019] Executing as maoj@cn3097 on Linux 3.10.0-862.14.4.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT [Wed Sep 11 15:00:35 EDT 2019] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.41 minutes. Runtime.totalMemory()=3670540288 2019-09-11 15:00:35,463: ref dict created for gatk use in pipe 2019-09-11 15:00:35,464: Capturing info from: /usr/local/apps/ctatmutations/GRCh37/CosmicMutantExport.tsv.gz Traceback (most recent call last): File "/usr/local/Anaconda/envs_app/ctatmutaions/2.0.1/share/ctat-mutations-2.0.1-5/mutation_lib_prep/ctat-mutation-lib-integration.py", line 116, in mutant_dict_necessary_info[row["Mutation ID"]]=info KeyError: u'Mutation ID'

Can someone help?

peter-yufan-zeng commented 4 years ago

Also running into the same problem while trying to set up my genome lib. Any luck?

brianjohnhaas commented 4 years ago

Hi,

It may be that the cosmic data formatting has changed. We'll look into this and aim to have a new software release out by the end of the week.

On Sun, Oct 13, 2019 at 10:30 PM peter-yufan-zeng notifications@github.com wrote:

Also running into the same problem while trying to set up my genome lib. Any luck?

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brianjohnhaas commented 4 years ago

Hi - the system is fully revised now and has a simpler setup. Please let me know if the new release gives you any trouble. The wiki is updated w/ pointers to the new ctat genome lib supplement for mutation calling too.

peter-yufan-zeng commented 4 years ago

Hi Brian - thanks so much for your help.

After updating all my files, now I am getting an this error

Code $ python mutation_lib_prep/ctat-mutation-lib-integration.py --genome_lib_dir GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir/ --CosmicCodingMuts GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/cosmic.vcf.gz --CosmicMutantExport GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/CosmicMutantExport.tsv.gz

Error 2019-10-22 11:04:27,337: ref dict created for gatk use in pipe 2019-10-22 11:04:27,337: Capturing info from: GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/CosmicMutantExport.tsv.gz Traceback (most recent call last): File "mutation_lib_prep/ctat-mutation-lib-integration.py", line 104, in <module> for row in mutant_reader: File "/home/ionadmin/anaconda3/lib/python3.7/csv.py", line 111, in __next__ self.fieldnames File "/home/ionadmin/anaconda3/lib/python3.7/csv.py", line 98, in fieldnames self._fieldnames = next(self.reader) _csv.Error: iterator should return strings, not bytes (did you open the file in text mode?)

brianjohnhaas commented 4 years ago

Hi Peter,

In the latest release, you don't need to run that step. The new ctat mutation lib supplement comes with what you need.

best,

~brian

On Tue, Oct 22, 2019 at 11:22 AM Peter Zeng notifications@github.com wrote:

Hi Brian - thanks so much for your help.

After updating all my files, now I am getting an this error

Code $ python mutation_lib_prep/ctat-mutation-lib-integration.py --genome_lib_dir GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir/ --CosmicCodingMuts GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/cosmic.vcf.gz --CosmicMutantExport GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/CosmicMutantExport.tsv.gz

Error 2019-10-22 11:04:27,337: ref dict created for gatk use in pipe 2019-10-22 11:04:27,337: Capturing info from: GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/CosmicMutantExport.tsv.gz Traceback (most recent call last): File "mutation_lib_prep/ctat-mutation-lib-integration.py", line 104, in for row in mutant_reader: File "/home/ionadmin/anaconda3/lib/python3.7/csv.py", line 111, in next self.fieldnames File "/home/ionadmin/anaconda3/lib/python3.7/csv.py", line 98, in fieldnames self._fieldnames = next(self.reader) _csv.Error: iterator should return strings, not bytes (did you open the file in text mode?)

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peter-yufan-zeng commented 4 years ago

Hi Brian, Thanks again for your help. I have tried running ctat-mutation again, and it seems the folder now is lacking dbsnp_138.vcf.gz and radar.txt. I renamed dbsbp.vcf.gz to dbsnp_138.vcf.fz in the ctat_mutation_lib, but I am still missing the radar file.

Error code FileNotFoundError: [Errno 2] No such file or directory: '/media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/radar.txt' Traceback (most recent call last): File "/media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/ctat_mutations", line 1649, in <module> pipeliner.run() File "/media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/PyLib/Pipeliner.py", line 53, in run run_cmd(cmd.get_cmd()) File "/media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/PyLib/Pipeliner.py", line 17, in run_cmd subprocess.check_call(cmd, shell=True) File "/home/ionadmin/anaconda3/lib/python3.7/subprocess.py", line 347, in check_call raise CalledProcessError(retcode, cmd)

brianjohnhaas commented 4 years ago

Hi Peter,

Can you pull down the latest software: v2.3.0b https://github.com/NCIP/ctat-mutations/releases

I had to cut a new release recently, in case that's part of the problem you're experiencing here.

The CTAT mutation supplement https://github.com/NCIP/ctat-mutations/wiki/CTAT-mutations-installation

is the same as from the earlier faulty v2.3.0 release.

I'll put out a broader announcement about this.

Let me know if the latest gives you any trouble.

best,

~brian

On Thu, Oct 31, 2019 at 9:53 AM Peter Zeng notifications@github.com wrote:

Hi Brian, Thanks again for your help. I have tried running ctat-mutation again, and it seems the folder now is lacking dbsnp_138.vcf.gz and radar.txt. I renamed dbsbp.vcf.gz to dbsnp_138.vcf.fz in the ctat_mutation_lib, but I am still missing the radar file.

Error code FileNotFoundError: [Errno 2] No such file or directory: '/media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/radar.txt' Traceback (most recent call last): File "/media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/ctat_mutations", line 1649, in pipeliner.run() File "/media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/PyLib/Pipeliner.py", line 53, in run run_cmd(cmd.get_cmd()) File "/media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/PyLib/Pipeliner.py", line 17, in run_cmd subprocess.check_call(cmd, shell=True) File "/home/ionadmin/anaconda3/lib/python3.7/subprocess.py", line 347, in check_call raise CalledProcessError(retcode, cmd)

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peter-yufan-zeng commented 4 years ago

Hi Brian, After updating ctat-mutation to the newest version, I no longer get an error like above.

However, I now encounter an error below. It seems to be missing the file ref_annot.splice_adj.bed.gz, which I cannot find in the mutation_lib file that I downloaded (the oct 18th version)

thanks in advance again for your help! I really appreciate it

CRITICAL:__main__:cannot locate required file: /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/ref_annot.splice_adj.bed.gz 2019-11-02 17:57:26,400: ERROR Pipeliner.Pipeliner.run_cmd Error: Command '/media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/src/annotate_exon_splice_proximity.py --input_vcf /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/Peter/20190916_OICR_Data/190718_D00430_0371_ACDPHCANXX/104R/test/work_dir/HaplotypeCaller.raw_variants.vcf_snpeff.vcf_adj.vcf_RNAedit.vcf_PASSreads.vcf_Repeats.vcf_homopolymers.vcf.gz --ctat_mutation_lib_dir /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib --output_vcf /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/Peter/20190916_OICR_Data/190718_D00430_0371_ACDPHCANXX/104R/test/work_dir/HaplotypeCaller.raw_variants.vcf_snpeff.vcf_adj.vcf_RNAedit.vcf_PASSreads.vcf_Repeats.vcf_homopolymers.vcf_SpliceDist.vcf --tmpdir /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/Peter/20190916_OICR_Data/190718_D00430_0371_ACDPHCANXX/104R/test/work_dir' returned non-zero exit status 1., exit val: 1 2019-11-02 17:57:26,401: ERROR Pipeliner.Pipeliner.run Error, command: [ /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/src/annotate_exon_splice_proximity.py --input_vcf /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/Peter/20190916_OICR_Data/190718_D00430_0371_ACDPHCANXX/104R/test/work_dir/HaplotypeCaller.raw_variants.vcf_snpeff.vcf_adj.vcf_RNAedit.vcf_PASSreads.vcf_Repeats.vcf_homopolymers.vcf.gz --ctat_mutation_lib_dir /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib --output_vcf /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/Peter/20190916_OICR_Data/190718_D00430_0371_ACDPHCANXX/104R/test/work_dir/HaplotypeCaller.raw_variants.vcf_snpeff.vcf_adj.vcf_RNAedit.vcf_PASSreads.vcf_Repeats.vcf_homopolymers.vcf_SpliceDist.vcf --tmpdir /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/Peter/20190916_OICR_Data/190718_D00430_0371_ACDPHCANXX/104R/test/work_dir ] failed, stack trace: [ st: file:/media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/PyLib/Pipeliner.py, lineno:86

brianjohnhaas commented 4 years ago

Hi Peter,

The ctat mutation lib integration step should be generating that file. Did you run through the full installation procedure for the latest release?

This involves running: ctat-mutations/mutation_lib_prep/ctat-mutation-lib-integration.py

as part of

https://github.com/NCIP/ctat-mutations/wiki/CTAT-mutations-installation

best,

~b

On Sat, Nov 2, 2019 at 11:16 PM Peter Zeng notifications@github.com wrote:

Hi Brian, After updating ctat-mutation to the newest version, I no longer get an error like above.

However, I now encounter an error below. It seems to be missing the file ref_annot.splice_adj.bed.gz, which I cannot find in the mutation_lib file that I downloaded (the oct 18th version)

thanks in advance again for your help! I really appreciate it

CRITICAL:main:cannot locate required file: /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/ref_annot.splice_adj.bed.gz 2019-11-02 17:57:26,400: ERROR Pipeliner.Pipeliner.run_cmd Error: Command '/media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/src/annotate_exon_splice_proximity.py --input_vcf /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/Peter/20190916_OICR_Data/190718_D00430_0371_ACDPHCANXX/104R/test/work_dir/HaplotypeCaller.raw_variants.vcf_snpeff.vcf_adj.vcf_RNAedit.vcf_PASSreads.vcf_Repeats.vcf_homopolymers.vcf.gz --ctat_mutation_lib_dir /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib --output_vcf /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/Peter/20190916_OICR_Data/190718_D00430_0371_ACDPHCANXX/104R/test/work_dir/HaplotypeCaller.raw_variants.vcf_snpeff.vcf_adj.vcf_RNAedit.vcf_PASSreads.vcf_Repeats.vcf_homopolymers.vcf_SpliceDist.vcf --tmpdir /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/Peter/20190916_OICR_Data/190718_D00430_0371_ACDPHCANXX/104R/test/work_dir' returned non-zero exit status 1., exit val: 1 2019-11-02 17:57:26,401: ERROR Pipeliner.Pipeliner.run Error, command: [ /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/src/annotate_exon_splice_proximity.py --input_vcf /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/Peter/20190916_OICR_Data/190718_D00430_0371_ACDPHCANXX/104R/test/work_dir/HaplotypeCaller.raw_variants.vcf_snpeff.vcf_adj.vcf_RNAedit.vcf_PASSreads.vcf_Repeats.vcf_homopolymers.vcf.gz --ctat_mutation_lib_dir /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/GRCh38_gencode_v31_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib --output_vcf /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/Peter/20190916_OICR_Data/190718_D00430_0371_ACDPHCANXX/104R/test/work_dir/HaplotypeCaller.raw_variants.vcf_snpeff.vcf_adj.vcf_RNAedit.vcf_PASSreads.vcf_Repeats.vcf_homopolymers.vcf_SpliceDist.vcf --tmpdir /media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/Peter/20190916_OICR_Data/190718_D00430_0371_ACDPHCANXX/104R/test/work_dir ] failed, stack trace: [ st: file:/media/ionadmin/b68e1a06-1bb3-442c-bb3c-553aab1edfce/bioinformatics/ctat-mutations/PyLib/Pipeliner.py, lineno:86

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/NCIP/ctat-mutations/issues/34?email_source=notifications&email_token=ABZRKXY3OWMKMJ4SLOM2EY3QRY7CJA5CNFSM4IVX3NBKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEC5J6UI#issuecomment-549101393, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXYNL7LBXUC2MMUMZELQRY7CJANCNFSM4IVX3NBA .

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peter-yufan-zeng commented 4 years ago

Hi Brian it works now! Thanks so much for your help! 👍

brianjohnhaas commented 4 years ago

Great to hear!

We're still making improvements, so stay tuned to our google forum for updates.

best,

~brian

On Tue, Nov 5, 2019 at 12:45 PM Peter Zeng notifications@github.com wrote:

Hi Brian it works now! Thanks so much for your help! 👍

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