Could not parse threshold

[csb5]

Could not parse threshold

[zipho]

lofreq call -f "/galaxy/database/files/000/dataset_131.fasta" -o "/galaxy/database/files/000/dataset_132.vcf" --force-overwrite "/galaxy/database/files/000/dataset_129.bam"

A simple basic call command is returning the following:

[fai_fetch_seq] The sequence "seq1" not found
FATAL(plp.c|mplp_func:651):
Couldn't fetch sequence 'seq1'.

[andreas-wilm]

Hi Zipho,

the first command contains two syntax errors and has a few other problems:

• "--sig" takes an argument but none is given
• same for "--bon f", which should be "--bonf"
• "--src-qual", "--use-orphan" and "--no-default-filter" should be considered special, non-default cases.
• "--plp-summary-only" is for debugging and prevents the program from actually calling variants.

The syntax for the second command is okay, but seq1, which is present in the BAM file, cannot be found in the reference fasta file. This happens when the BAM file was produced with a different reference file than used for calling.

Hope this helps,
Andreas

[zipho]

Excellent. Thank you so much for the above @andreas-wilm .

[andreas-wilm]

Sorry about the typos. Should be fixed now