Open almutwerner opened 2 years ago
Alexander-Mitrofanov
commented
2 years ago Yes it seems that the problem exactly with the Casboundary module. It seems that the output is empty and therefore the error is occurring.
Can I kindly ask you to provide the labled intervals for the given input sequence if you know that certain cassettes are missing?
almutwerner
commented
2 years ago Hello, thank you for your reply! I have no idea whether the sequence contains anything or not. That was just my guess based on the HMM output. I will attach the whole output folder, maybe that is helpful to you.
NODE_457_length_14276_cov_6173406__bin10_BGR2_DNA_150204_S0.zip
Hello everyone!
I am running CRISPRloci in dna mode over a multi fasta and get the following error: ` /work_beegfs/sunam157/CRISPRloci/CRISPRloci-1.0.0/Casboundary Running Prodigal on input Fasta file. Generating Genome DataFrame Searching for potential signature proteins Extracting potential regions. Traceback (most recent call last): File "Casboundary.py", line 384, in
regions_fasta_file = extract_regions_sequences(proteins_fasta_file, regions_dataframes, args.output_dir)
File "Casboundary.py", line 125, in extract_regions_sequences
proteins_ids_regions = set.union(*regions_prot_ids)
TypeError: descriptor 'union' of 'set' object needs an argument
################################################################################### ########## CRISPR: Master Script ######### ###################################################################################
mkdir /work_dagan/sunam157/BGR_2013_2015/CRISPRloci/output/NODE_457_length_14276_cov_6173406bin10_BGR2_DNA_150204_S0 res local folder /work_dagan/sunam157/BGR_2013_2015/CRISPRloci/output/NODE_457_length_14276_cov_6173406bin10_BGR2_DNA_150204_S0 input file /work_dagan/sunam157/BGR_2013_2015/CRISPRloci/output/NODE_457_length_14276_cov_6173406bin10_BGR2_DNA_150204_S0.fasta Traceback (most recent call last): File "/work_beegfs/sunam157/CRISPRloci/CRISPRloci-1.0.0/CRISPRloci_standalone.py", line 1447, in
if len(os.listdir(dirname_cas + '/predictions/raw_cassettes/')) != 0:
FileNotFoundError: [Errno 2] No such file or directory: '/work_dagan/sunam157/BGR_2013_2015/CRISPRloci/output/NODE_457_length_14276_cov_6173406 bin10_BGR2_DNA_150204_S0/tmp/output-Casboundary/predictions/raw_cassettes/'
`
I briefly checked the output-Casboundary/hmmsearch_output_dir/Sig_HMM/ contents and didn't see any hits in the files. So I maybe, Casboundary was confused because there were no hits? I also ran it on the example data. There it completed that step without issues. I will add the failed fasta to this issue, so you can better trace the error.
NODE_457_length_14276_cov_6173406__bin10_BGR2_DNA_150204_S0.zip