Singularity & GATK 4.4.0.0. CreateSequenceDictionary

Question

I ran the following code in bash (I added print statements for ease):

# Module loading

echo "I am loading the specified modules"

module load Singularity/version_number

# Define the path to the singularity:

singularity_image="/path/to/folder/GATK/gatk_latest.sif"

echo "I am going to make the `.dict ` file"

singularity exec $singularity_image /gatk/gatk --java-options -Xms8000m \
  CreateSequenceDictionary \
  -R /path/to/my/primary_assembly.fa \
  -O /path/to/the/primary_assembly.dict

echo "I am all done"

However, I get the following out file:

I am loading the specified modules
job_scripts_number: line 23:
.dict: command not found I am going to make the  file 
INFO  NativeLibraryLoader - Loading libgkl_compression.so from
jar:file:/gatk/gatk-package-4.4.0.0-local.jar!/path/to/libgkl_compression.so [Today's date] CreateSequenceDictionary --OUTPUT
path/to/my/primary_assembly.dict
--REFERENCE /path/to/my/primary_assembly.fa
--TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 999999 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Today's date] Executing as user@node_number on Linux version
; OpenJDK 64-Bit Server VM version;
Deflater: A; Inflater: A; Provider is available; Picard
version: Version:4.4.0.0 [Today's date]
picard.sam.CreateSequenceDictionary done. Elapsed time: 0.53 minutes.
Runtime.totalMemory()=8388608000 Tool returned: 0 Using GATK jar
/gatk/gatk-package-4.4.0.0-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 -Xms8000m -jar /gatk/gatk-package-4.4.0.0-local.jar CreateSequenceDictionary -R
/path/to/primary_assembly.fa
-O /path/to/primary_assembly.dict
I am all done

Why would I get the error ".dict: command not found I am going to make the file " especially when I look at the head of the .dict file and it seems to look the way it should?

Answer 1

This has nothing to do with Singularity/Docker or GATK. You get the error .dict: command not found because you've used backticks to perform a command substitution in a prior echo command:

echo "I am going to make the `.dict ` file"

Backticks are legacy syntax, you could have also written:

echo "I am going to make the $(.dict) file"

But neither of these makes any sense - there is no .dict command. Of course single quotes would prevent the command substitution:

echo 'I am going to make the `.dict` file'

But this might cause some confusion when the output is displayed. A better choice would be to use double quotes, but without the backticks. For example:

echo "I am going to make the '.dict' file"