"ERROR: ': ' is not a valid token in plain flow (unquoted) scalars - While using selective re-mapping

[alisondiazc]

Hello! I was wondering if you could help me to solve an issue that I have while running leviosam2. When I try to make a liftover using the leviosam2.sh file I got this error: "ERROR: ': ' is not a valid token in plain flow (unquoted) scalars". I also notice that the program autocompletes mapq, aln_score & hdist as follow:
Adding rule mapq:30
Adding rule aln_score:-10
Adding rule hdist:100
The code line I used was:
bash leviosam2.sh \ -a minimap2 -g 1000 -H 100 -S -x /mnt/Timina/cgonzaga/adiaz/PacBio_secuencias/PYM007/8.Liftover/pacbio_all.yaml \ -l map-hifi \ -i /mnt/Timina/cgonzaga/adiaz/PacBio_secuencias/PYM007/8.Liftover/PYM007.T2T.pbmm2.bam \ -o PYM007_T2TtoGRCh38_lifted \ -f /mnt/Timina/cgonzaga/adiaz/PacBio_secuencias/PYM007/8.Liftover/Homo_sapiens_GRCh38.p14.noMT.fasta \ -C /mnt/Timina/cgonzaga/adiaz/PacBio_secuencias/PYM007/8.Liftover/chm13v2-hg38.clft \ -t 20
I'm using the 0.2.2 version. I attach the log of the run in a text file
logoftherun_liftover.txt

[milkschen]

Hi @alisondiazc,

I tried your command, but I was not able to reproduce the error you posted.

Could you try to run the pipeline without -x /mnt/Timina/cgonzaga/adiaz/PacBio_secuencias/PYM007/8.Liftover/pacbio_all.yaml and see if that works? The error message looks to be related to YAML parsing. If without -x works, maybe try removing the quotes in pacbio_all.yaml. The realignment specification is important for the accuracy of the long read workflows.

[milkschen]

And by the way, please make sure the FASTA you used if identical to what we provided in the case study. Or re-index it by yourself. A discordant FASTA and leviosam2 index (.clft) could result in errors.