Indel filtering using default filter at the last step failed

[masterrite]

I'm trying to call indel with lofreq. Everything was fine until the filtering stage. I ran the command:

lofreq call-parallel --pp-threads 8 --verbose -f ce11.fasta -o "WU2093 Called Variants.vcf" --call-indels --min-cov 5 --max-depth 1000 --min-alt-bq 6 --min-mq 0 --max-mq 255 --min-jq 0 --min-alt-jq 0 --sig 0.01 --bonf dynamic WU2093.bam
and received a fatal error:

INFO [2025-02-26 16:55:56,414]: Adding 25 commands to mp-pool Checking the headers and starting positions of 25 files Number of substitution tests performed: 89856936 Number of indel tests performed: 570883 INFO [2025-02-26 20:55:30,905]: Executing lofreq filter -i /tmp/lofreq2_call_parallel7dyj8lhz/concat.vcf.gz -o WU2093 Called Variants.vcf --snvqual-thresh 100 --indelqual-thresh 78

FATAL(lofreq_filter.c|main_filter:1104): Unrecognized argument found. Exiting...

CRITICAL [2025-02-26 20:55:30,913]: Final filtering command failed. Commmand was lofreq filter -i /tmp/lofreq2_call_parallel7dyj8lhz/concat.vcf.gz -o WU2093 Called Variants.vcf --snvqual-thresh 100 --indelqual-thresh 78

I'm using 2.1.5 built on Dec 15, 2024. Also, is there a source or documentation on the parameters that can be used? I can't seem to find it.

[andreas-wilm]

Hi there, the problem is likely the vcf file name, which contains spaces. It seems this is not properly handled/escape in some system calls that LoFreq makes. This should work if you remove the spaces from the name. I'm afraid LoFreq is not actively supported anymore.

[masterrite]

Hi there, the problem is likely the vcf file name, which contains spaces. It seems this is not properly handled/escape in some system calls that LoFreq makes. This should work if you remove the spaces from the name. I'm afraid LoFreq is not actively supported anymore.

Thanks! I'll try that.