Open MostafaYA opened 4 years ago
MoggoB
commented
4 years ago Hello, I came across the same mistake, so I changed line 54 like this:
if not os.path.isfile(ref_dict_fpath):
command("picard CreateSequenceDictionary REFERENCE={} OUTPUT {}".format(REF_FASTA,re.findall("(.*?).fa",REF_FASTA)[0]+".dict")).run_comm(0) I don't get any error messages now. I installed picard using conda. I hope this can help you.
MostafaYA
commented
4 years ago Hi, thanks for your answer, I installed picard using conda and changed line 54 as indicated. still I am getting this error (2nd error above)
ERROR: picard CreateSequenceDictionary REFERENCE=/home/mostafa.abdel/aProjects/cryptosporidium/ebi-parasite/working_dir/simone/ref/cryptosporidium_hominis.fasta OUTPUT=/home/most.dict FAILED!!! I feel that picard want to write an output file most.dict directly in/home/ which I am not allowed to, becuase of write privilages.
This is the full error
properties_file: /home/mostafa.abdel/aProjects/cryptosporidium/ebi-parasite/properties.txt
genome_name: cryptosporidium_hominis
Properties attributes:
{'propertyf': '/home/mostafa.abdel/aProjects/cryptosporidium/ebi-parasite/properties.txt', 'available_genomes': '/home/mostafa.abdel/aProjects/cryptosporidium/ebi-parasite/genome_list.txt', 'workdir': '/home/mostafa.abdel/aProjects/cryptosporidium/ebi-parasite/working_dir/simone', 'snpeff_dir': '/home/software/snpEff/', 'snpeff_config': '/home/software/snpEff/snpEff.config', 'r_script': '/home/mostafa.abdel/aProjects/cryptosporidium/ebi-parasite/create_all_images.R', 'r_snp_dist_on_chr': '/home/mostafa.abdel/aProjects/cryptosporidium/ebi-parasite/SNP_dist_on_chrom.R'}
initiating...
executing...
cmd=curl -s https://cryptodb.org/common/downloads/Current_Release/ChominisUdeA01//gff/data/ | grep buildNumber | awk '{split($0,a,"\"");print a[2]}'
curl -s https://cryptodb.org/common/downloads/Current_Release/ChominisUdeA01//gff/data/ | grep buildNumber | awk '{split($0,a,"\"");print a[2]}'
version=46
curl https://cryptodb.org/common/downloads/Current_Release/ChominisUdeA01//fasta/data/CryptoDB-46_ChominisUdeA01_Genome.fasta -o /home/mostafa.abdel/aProjects/cryptosporidium/ebi-parasite/working_dir/simone/ref/cryptosporidium_hominis.fasta
cmd=curl -s https://cryptodb.org/common/downloads/Current_Release/ChominisUdeA01//gff/data/ | grep buildNumber | awk '{split($0,a,"\"");print a[2]}'
curl -s https://cryptodb.org/common/downloads/Current_Release/ChominisUdeA01//gff/data/ | grep buildNumber | awk '{split($0,a,"\"");print a[2]}'
version=46
curl https://cryptodb.org/common/downloads/Current_Release/ChominisUdeA01//gff/data/CryptoDB-46_ChominisUdeA01.gff -o /home/mostafa.abdel/aProjects/cryptosporidium/ebi-parasite/working_dir/simone/ref/cryptosporidium_hominis.gff3
samtools faidx /home/mostafa.abdel/aProjects/cryptosporidium/ebi-parasite/working_dir/simone/ref/cryptosporidium_hominis.fasta
bwa index /home/mostafa.abdel/aProjects/cryptosporidium/ebi-parasite/working_dir/simone/ref/cryptosporidium_hominis.fasta
bowtie2-build /home/mostafa.abdel/aProjects/cryptosporidium/ebi-parasite/working_dir/simone/ref/cryptosporidium_hominis.fasta cryptosporidium_hominis
picard CreateSequenceDictionary REFERENCE=/home/mostafa.abdel/aProjects/cryptosporidium/ebi-parasite/working_dir/simone/ref/cryptosporidium_hominis.fasta OUTPUT /home/most.dict
ERROR: picard CreateSequenceDictionary REFERENCE=/home/mostafa.abdel/aProjects/cryptosporidium/ebi-parasite/working_dir/simone/ref/cryptosporidium_hominis.fasta OUTPUT /home/most.dict FAILED!!!
STDERR: b'INFO\t2020-04-21 13:07:01\tCreateSequenceDictionary\t\n\n********** NOTE: Picard\'s command line syntax is changing.\n**********\n********** For more information, please see:\n********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\n**********\n********** The command line looks like this in the new syntax:\n**********\n********** CreateSequenceDictionary -REFERENCE /home/mostafa.abdel/aProjects/cryptosporidium/ebi-parasite/working_dir/simone/ref/cryptosporidium_hominis.fasta OUTPUT /home/most.dict\n**********\n\n\nERROR: Invalid argument \'OUTPUT\'.\n\nUSAGE: CreateSequenceDictionary [options]\n\nDocumentation: http://broadinstitute.github.io/picard/command-line-overview.html#CreateSequenceDictionary\n\nCreates a sequence dictionary for a reference sequence. This tool creates a sequence dictionary file (with ".dict"\nextension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools.\nThe output file contains a header but no SAMRecords, and the header contains only sequence records.\n\nThe reference sequence can be gzipped (both .fasta and .fasta.gz are supported).\nUsage example:\n\njava -jar picard.jar CreateSequenceDictionary \\ \nR=reference.fasta \\ \nO=reference.dict\n\n\nVersion: 2.22.3\n\n\nOptions:\n\n--help\n-h Displays options specific to this tool.\n\n--stdhelp\n-H Displays options specific to this tool AND options common to all Picard command line\n tools.\n\n--version Displays program version.\n\nOUTPUT=File\nO=File Output SAM file containing only the sequence dictionary. By default it will use the base\n name of the input reference with the .dict extension Default value: null. \n\nGENOME_ASSEMBLY=String\nAS=String Put into AS field of sequence dictionary entry if supplied Default value: null. \n\nURI=String\nUR=String Put into UR field of sequence dictionary entry. If not supplied, input reference file is\n used Default value: null. \n\nSPECIES=String\nSP=String Put into SP field of sequence dictionary entry Default value: null. \n\nTRUNCATE_NAMES_AT_WHITESPACE=Boolean\n Make sequence name the first word from the > line in the fasta file. By default the\n entire contents of the > line is used, excluding leading and trailing whitespace. Default\n value: true. This option can be set to \'null\' to clear the default value. Possible values:\n {true, false} \n\nNUM_SEQUENCES=Integer Stop after writing this many sequences. For testing. Default value: 2147483647. This\n option can be set to \'null\' to clear the default value. \n\nALT_NAMES=File\nAN=File Optional file containing the alternative names for the contigs. Tools may use this\n information to consider different contig notations as identical (e.g: \'chr1\' and \'1\'). The\n alternative names will be put into the appropriate @AN annotation for each contig. No\n header. First column is the original name, the second column is an alternative name. One\n contig may have more than one alternative name. Default value: null. \n\nREFERENCE=File\nR=File Input reference fasta or fasta.gz Required. \n\n'
STDOUT: b''
Hi, thanks for this great work. I tried to reproduce the results using the README instructions. However I got this error.
NameError: name 'picard' is not definedHere what I have done (after adjusting paths in the file "properties.txt" )
./download_and_index_genome_files.py -p ~/ebi-parasite/properties.txt -g cryptosporidium_hoministhis is the outputI have picard installed
java -jar /home/software/picard/picard.jar. Therfore I tried to replcepicardin the script with"java -jar /home/software/picard/picard.jar"Dont know if it was a good idea, but finally I got a different error