Closed HoneeeyBee closed 2 years ago
I solved the problem with a change of my reference .fasta file headers, like '>chr1 1' into '>1'.
I re-made an index file (.fai) of the changed fasta file using "samtools faidx", and ran GTCtoVCF, and it worked!
Yes the fasta headers cannot have 'chr' if you use the download script it should remove them. Glad you fixed the issue.
Hello, I met an error with GTCtoVCF running.
I ran GTCtoVCF in my Ubuntu VM on Windows 10 (Anaconda, python v2.7) and it gave me an error like this:
"GTC converter - ERROR - Reference is missing entry for chromosome 3"
I tried three times to run the GTCtoVCF tool with the same error, and in the error message, the chromosome number changed at each try.
And the last log file said:
2021-11-29 12:09:20,695 - GTC converter - WARNING - Skipping indel X:2836035 2021-11-29 12:09:20,695 - GTC converter - WARNING - Skipping indel X:77387141 2021-11-29 12:09:22,464 - GTC converter - ERROR - Reference is missing entry for chromosome 3 2021-11-29 12:09:22,465 - GTC converter - DEBUG - Traceback (most recent call last): File "/home/moirai/Tools/GTCtoVCF-develop/gtc_to_vcf.py", line 309, in main driver(gtc_paths, manifest_reader, genome_reader, output_vcf_files, args.expand_identifiers, args.unsquash_duplicates, auxiliary_records, args.include_attributes, logger) File "/home/moirai/Tools/GTCtoVCF-develop/gtc_to_vcf.py", line 141, in driver locus_entries = LocusEntryFactory(vcf_record_factory, genome_reader.get_contig_order(), unsquash_duplicates, logger).create_locus_entries(manifest_reader) File "/home/moirai/Tools/GTCtoVCF-develop/LocusEntryFactory.py", line 38, in create_locus_entries result.append(self._generate_locus_entry(record_group)) File "/home/moirai/Tools/GTCtoVCF-develop/LocusEntryFactory.py", line 81, in _generate_locus_entry return LocusEntry(bpm_record_group, self._vcf_record_factory.create_vcf_record(bpm_record_group)) File "/home/moirai/Tools/GTCtoVCF-develop/VcfRecordFactory.py", line 78, in create_vcf_record return self._get_record_for_snv(bpm_record_group) File "/home/moirai/Tools/GTCtoVCF-develop/VcfRecordFactory.py", line 179, in _get_record_for_snv chrom, start_index, start_index + 1) File "/home/moirai/Tools/GTCtoVCF-develop/ReferenceGenome.py", line 178, in get_reference_bases "Reference is missing entry for chromosome " + str(chrom)) ValueError: Reference is missing entry for chromosome 3
My command was:
/home/MyUserID/Tools/GTCtoVCF-develop/gtc_to_vcf.py --gtc-paths /MyGTCFilePath/ --manifest-file /IlluminaBPMFile --genome-fasta-file /MyRefGenomeFile(GrCh38) --output-vcf-path /home/MyUserID/VCF --skip-indels --log-file /home/MyUserID/VCF/log.txt
Can you help me with this issue?
Thanks.