The number of PBID records disagree

[gabbycoffing]

Hi Liz,

I keep getting this error when trying to run filter_away_subset.py:
The number of PBID records in the files disagree! Sanity check failed.
num of PBIDs in polished.hq.fastq.sorted.sam.merge.collapsed.rep.fq: 42573
num of PBIDs in polished.hq.fastq.sorted.sam.merge.collapsed.gff: 42573
num of PBIDs in polished.hq.fastq.sorted.sam.merge.collapsed.abundance.txt: 41858

I'm not having problems with any of the other scripts. I updated to the latest cDNA_Cupcake version and I am using minimap2 to map reads to the genome. This seems to be similar to #15, but I have not found that I have the same issue with IDs not matching up between the cluster report and group txt. Do you have an idea of what could be going wrong?

Thank you!
Gabby

[Magdoll]

Hi @gabbycoffing ,

Well the error is exactly what the error is saying....in polished.hq.fastq.sorted.sam.merge.collapsed.abundance.txt somehow you have fewer number of PBIDs than the GFF and FASTQ files.

Can you show the first 20 lines of polished.hq.fastq.sorted.sam.merge.collapsed.abundance.txt with head -n 20 polished.hq.fastq.sorted.sam.merge.collapsed.abundance.txt as a first step sanity check?
--Liz

[gabbycoffing]

Yes, here it is:

Field explanation

count_fl: Number of associated FL reads
norm_fl: count_fl / total number of FL reads, mapped or unmapped
Total Number of FL reads: 693004

pbid count_fl norm_fl
PB.1.1 3 4.3290e-06
PB.1.2 2 2.8860e-06
PB.1.3 2 2.8860e-06
PB.1.4 3 4.3290e-06
PB.1.5 2 2.8860e-06
PB.1.6 2 2.8860e-06
PB.2.1 4 5.7720e-06
PB.2.2 32 4.6176e-05
PB.3.1 18 2.5974e-05
PB.4.1 2 2.8860e-06
PB.5.1 19 2.7417e-05