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gatk CreateSequenceDictionary command issue #86

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readline opened this issue Mar 25, 2021 · 10 comments
Closed

gatk CreateSequenceDictionary command issue #86

readline opened this issue Mar 25, 2021 · 10 comments

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@readline
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I'm prep the ctat mutation library with official singularity image. However an error happened:

`>singularity exec -e -B /gs9,/data,/home,/lscratch /path/to/ctat_mutations.v3.0.0.simg /usr/local/src/ctat-mutations/mutation_lib_prep/ctat-mutation-lib-integration.py --genome_lib_dir /path/to/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_bui
ld_dir
2021-03-24 22:53:13,315: Generating /path/to/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.dict
Using GATK jar /usr/local/src/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /usr/local/src/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar CreateSequenceDictionary -R /path/to/GRCh38_gencode_v37_CTAT_
lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa -O /path/to/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.dict VALIDATION_STRINGENCY=LENIENT
INFO 2021-03-25 02:53:15 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 /path/to/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa -O /path/to/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.dict -
VALIDATION_STRINGENCY LENIENT

ERROR: Invalid argument '-R'.

USAGE: CreateSequenceDictionary [options]

Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CreateSequenceDictionary

Creates a sequence dictionary for a reference sequence. This tool creates a sequence dictionary file (with ".dict"
extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools.
The output file contains a header but no SAMRecords, and the header contains only sequence records.

The reference sequence can be gzipped (both .fasta and .fasta.gz are supported).
Usage example:

java -jar picard.jar CreateSequenceDictionary \
R=reference.fasta \
O=reference.dict`

After I modified the source code of ctat-mutation-lib-integration.py to meet the format of "R=reference.fasta O=reference.dict", it will work.
@joshua-gould
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joshua-gould commented Mar 25, 2021 via email

@joshua-gould
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I updated the singularity image. Please re-download. Thanks for reporting.

@ConcettaDe4
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Hi! I am building the "mutation lib integration utility" using the singularity image ctat_mutations.v3.0.0.simg with the command:

singularity exec -e -B /path/to/your/ctat_genome_lib_build_dir \
     ctat-mutations.simg \
     /usr/local/src/ctat-mutations/mutation_lib_prep/ctat-mutation-lib-integration.py \
     --genome_lib_dir /path/to/your/ctat_genome_lib_build_dir

Unfortunately I got the error ERROR: Invalid argument '-R'.

Do you have any suggestion to fix the problem?
Thank you.

Concetta

@brianjohnhaas
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brianjohnhaas commented May 13, 2021 via email

@ConcettaDe4
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Here the error message:

INFO:    Converting SIF file to temporary sandbox...
2021-05-13 15:28:14,332: Generating /home/stefania/RNAseq_project/test_ctat_mutations/GRCh38_gencode_v22_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ref_genome.dict
Using GATK jar /usr/local/src/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /usr/local/src/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar CreateSequenceDictionary -R /home/stefania/RNAseq_project/test_ctat_mutations/GRCh38_gencode_v22_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ref_genome.fa -O /home/stefania/RNAseq_project/test_ctat_mutations/GRCh38_gencode_v22_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ref_genome.dict VALIDATION_STRINGENCY=LENIENT
INFO    2021-05-13 15:28:20     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 /home/stefania/RNAseq_project/test_ctat_mutations/GRCh38_gencode_v22_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ref_genome.fa -O /home/stefania/RNAseq_project/test_ctat_mutations/GRCh38_gencode_v22_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ref_genome.dict -VALIDATION_STRINGENCY LENIENT
**********


ERROR: Invalid argument '-R'.

USAGE: CreateSequenceDictionary [options]

Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CreateSequenceDictionary

Creates a sequence dictionary for a reference sequence.  This tool creates a sequence dictionary file (with ".dict"
extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools.
The output file contains a header but no SAMRecords, and the header contains only sequence records.

The reference sequence can be gzipped (both .fasta and .fasta.gz are supported).
Usage example:

java -jar picard.jar CreateSequenceDictionary \
R=reference.fasta \
O=reference.dict


Version: 4.1.9.0


Options:

--help
-h                            Displays options specific to this tool.

--stdhelp
-H                            Displays options specific to this tool AND options common to all Picard command line
                              tools.

--version                     Displays program version.

OUTPUT=File
O=File                        Output SAM file containing only the sequence dictionary. By default it will use the base
                              name of the input reference with the .dict extension  Default value: null.

GENOME_ASSEMBLY=String
AS=String                     Put into AS field of sequence dictionary entry if supplied  Default value: null.

URI=String
UR=String                     Put into UR field of sequence dictionary entry.  If not supplied, input reference file is
                              used  Default value: null.

SPECIES=String
SP=String                     Put into SP field of sequence dictionary entry  Default value: null.

TRUNCATE_NAMES_AT_WHITESPACE=Boolean
                              Make sequence name the first word from the > line in the fasta file.  By default the
                              entire contents of the > line is used, excluding leading and trailing whitespace.  Default
                              value: true. This option can be set to 'null' to clear the default value. Possible values:
                              {true, false}

NUM_SEQUENCES=Integer         Stop after writing this many sequences.  For testing.  Default value: 2147483647. This
                              option can be set to 'null' to clear the default value.

ALT_NAMES=File
AN=File                       Optional file containing the alternative names for the contigs. Tools may use this
                              information to consider different contig notations as identical (e.g: 'chr1' and '1'). The
                              alternative names will be put into the appropriate @AN annotation for each contig. No
                              header. First column is the original name, the second column is an alternative name. One
                              contig may have more than one alternative name.  Default value: null.

REFERENCE=File
R=File                        Input reference fasta or fasta.gz  Required.

Tool returned:
1
Traceback (most recent call last):
  File "/usr/local/src/ctat-mutations/mutation_lib_prep/ctat-mutation-lib-integration.py", line 66, in <module>
    subprocess.check_call(cmd)
  File "/opt/conda/lib/python3.7/subprocess.py", line 347, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['gatk', 'CreateSequenceDictionary', '-R', '/home/stefania/RNAseq_project/test_ctat_mutations/GRCh38_gencode_v22_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ref_genome.fa', '-O', '/home/stefania/RNAseq_project/test_ctat_mutations/GRCh38_gencode_v22_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ref_genome.dict', 'VALIDATION_STRINGENCY=LENIENT']' returned non-zero exit status 4.
INFO:    Cleaning up image...

@brianjohnhaas
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brianjohnhaas commented May 13, 2021 via email

@brianjohnhaas
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brianjohnhaas commented May 13, 2021 via email

@brianjohnhaas
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brianjohnhaas commented May 13, 2021 via email

@ConcettaDe4
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Hi!
Sorry for my late reply. Now it works!

Thank you for your help.

Best,

Concetta

@brianjohnhaas
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brianjohnhaas commented May 18, 2021 via email

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@joshua-gould @brianjohnhaas @readline @ConcettaDe4