chain_samples.py does not work!

[unique379r]

Hi
I am trying to use "chain_samples.py" from your package script after post collapsed step of cDNA. Here i am using three different mappers out from cDNA and the config looks like:

**# sample.config2**
SAMPLE=HG002;../MMCupcake
SAMPLE=HG002;../ultraCupcake
SAMPLE=HG002;../saltCupcake

GROUP_FILENAME=HG002.collapsed.group.txt
GFF_FILENAME=HG002.collapsed.gff
COUNT_FILENAME=HG002.collapsed.abundance.txt
FASTQ_FILENAME=HG002.collapsed.rep.fq

Command:
chain_samples.py sample.config2 count_fl --dun-merge-5-shorter

ERROR

Traceback (most recent call last):
  File "/stornext/snfs5/next-gen/scratch/rupesh/Apps/envs/cupcake/bin/chain_samples.py", line 528, in <module>
    chain_samples_multithread(sample_dirs, sample_names, group_filename, gff_filename, count_filename, args.field_to_use, args.fuzzy_junction, args.allow_5merge, args.max_3_diff, fastq_filename, cpus=args.cpus)
  File "/stornext/snfs5/next-gen/scratch/rupesh/Apps/envs/cupcake/bin/chain_samples.py", line 386, in chain_samples_multithread
    sample_sanity_check(os.path.join(d, group_filename),\
  File "/stornext/snfs5/next-gen/scratch/rupesh/Apps/envs/cupcake/bin/chain_samples.py", line 32, in sample_sanity_check
    raise Exception("Sanity check failed! Please make sure the PBIDs listed in {1} are also in {0} and {2}".format(\
Exception: Sanity check failed! Please make sure the PBIDs listed in ../saltCupcake/HG002.collapsed.gff are also in ../saltCupcake/HG002.collapsed.group.txt and ../saltCupcake/HG002.collapsed.abundance.txt

I am not sure why i should not have same PBID in gff, txt and in abundance, since the output comes from cupcake.