chain_samples.py Exception: Sanity check failed!

[tabeariepe]

Hi,

I am trying to chain 3 samples. However, I keep getting the following error:

Exception: Sanity check failed! Please make sure the PBIDs listed in collapsed.gff are also in collapsed.group.txt and collapsed.abundance.txt

I analysed the three samples separately and run collapse_isoforms_by_sam.py and get_abundance_post_collapse.py . After this, I run chain_samples.py. I checked the different files and it seems that PB.1 is in the group.txt and gff file but missing from the abundance file.

group.txt

PB.1.1  transcript/65862
PB.1.2  transcript/222686
PB.1.3  transcript/230257
PB.2.1  transcript/75062
PB.2.2  transcript/220217
PB.2.3  transcript/200435
PB.2.4  transcript/216715
PB.2.5  transcript/128338
PB.2.6  transcript/175013
PB.2.7  transcript/961

abundance.txt
#
# -----------------
# 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: 1962754
#
pbid    count_fl        norm_fl
PB.2.2  4       2.0380e-06
PB.2.3  2       1.0190e-06
PB.2.4  2       1.0190e-06
PB.2.6  3       1.5285e-06
PB.2.7  3       1.5285e-06
PB.2.8  3       1.5285e-06
PB.2.10 4       2.0380e-06
PB.2.11 4       2.0380e-06
PB.2.13 3       1.5285e-06
PB.2.14 3       1.5285e-06
PB.2.16 3       1.5285e-06

collapsed.gff
chr1    PacBio  transcript      29393   33449   .       +       .       transcript_id "PB.1.1"; gene_id "PB.1";
chr1    PacBio  exon    29393   30667   .       +       .       transcript_id "PB.1.1"; gene_id "PB.1";
chr1    PacBio  exon    30976   33449   .       +       .       transcript_id "PB.1.1"; gene_id "PB.1";
chr1    PacBio  transcript      29403   31109   .       +       .       transcript_id "PB.1.2"; gene_id "PB.1";
chr1    PacBio  exon    29403   31109   .       +       .       transcript_id "PB.1.2"; gene_id "PB.1";
chr1    PacBio  transcript      29408   31109   .       +       .       transcript_id "PB.1.3"; gene_id "PB.1";
chr1    PacBio  exon    29408   30667   .       +       .       transcript_id "PB.1.3"; gene_id "PB.1";
chr1    PacBio  exon    30976   31109   .       +       .       transcript_id "PB.1.3"; gene_id "PB.1";
chr1    PacBio  transcript      14361   24891   .       -       .       transcript_id "PB.2.1"; gene_id "PB.2";
chr1    PacBio  exon    14361   16765   .       -       .       transcript_id "PB.2.1"; gene_id "PB.2";