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SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
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error using GFF or converted GTF #71

Open noor-albader opened 3 years ago

noor-albader commented 3 years ago

Hi I am using sqanti3 with the following parameters :

Version 2.0.0
Input   all_samples.chained.gff
Annotation      OcoaRS1.PZYT01.fa.all.maker.functional_ipr.gff
Genome  OcoaRS1.PZYT01.fa.masked
Aligner minimap2
FLCount all_samples.chained_count.txt
Expression      transcript_tpms_all_samples.tsv
Junction        *SJ.tab.out
CagePeak        NA
PolyA   NA
PolyAPeak       NA
IsFusion        False

The script I am running: 

sqanti3_qc.py --gtf /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/chain_filtered_isoseq_3/all_samples.chained.gff \
/home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.all.maker.functional_ipr.gff \
/home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked \
--fl_count /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/chain_filtered_isoseq_3/all_samples.chained_count.txt \
-c star/*SJ.tab.out --expression rsem_exp/GeneMat.txt --isoAnnotLite -t 128 -n 8

But get this error (a directory named splits/, with subdirectories 0/ to 7/, are created, however the contents of the subdirectory are unequal (not all contain a *.faa) and all other output files are empty) :

R scripting front-end version 3.6.1 (2019-07-05)
Write arguments to /ibex/scratch/projects/c2042/analysis/sqanti3/all_samples.chained.params.txt...
**** Running SQANTI3...
launching worker on on splits/0/all_samples.chained.gff.split0....
launching worker on on splits/1/all_samples.chained.gff.split1....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
launching worker on on splits/2/all_samples.chained.gff.split2....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
launching worker on on splits/3/all_samples.chained.gff.split3....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
launching worker on on splits/4/all_samples.chained.gff.split4....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
launching worker on on splits/5/all_samples.chained.gff.split5....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
launching worker on on splits/6/all_samples.chained.gff.split6....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
launching worker on on splits/7/all_samples.chained.gff.split7....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
**** Parsing provided files....
Reading genome fasta /home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.masked....
Skipping aligning of sequences because GTF file was provided.
Skipping aligning of sequences because GTF file was provided.
Skipping aligning of sequences because GTF file was provided.
Skipping aligning of sequences because GTF file was provided.
Skipping aligning of sequences because GTF file was provided.
Skipping aligning of sequences because GTF file was provided.
Skipping aligning of sequences because GTF file was provided.
Skipping aligning of sequences because GTF file was provided.

Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).

Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).

Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).

Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").

Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").

Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").

Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").

Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
**** Predicting ORF sequences...
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LC_CTYPE = "UTF-8",
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
error: data input empty 
GeneMarkS: error on last system call, error code 256
Abort program!!!
Process Process-1:
Traceback (most recent call last):
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1748, in run
    orfDict = correctionPlusORFpred(args, genome_dict)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 583, in correctionPlusORFpred
    if subprocess.check_call(cmd, shell=True, cwd=gmst_dir)!=0:
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/subprocess.py", line 363, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'perl /ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/utilities/gmst/gmst.pl -faa --strand direct --fnn --output /ibex/scratch/projects/c2042/analysis/sqanti3/splits/0/GMST/GMST_tmp /ibex/scratch/projects/c2042/analysis/sqanti3/splits/0/all_samples.chained_corrected.fasta' returned non-zero exit status 1.
**** Parsing Reference Transcriptome....
/home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.all.maker.functional_ipr.gff doesn't appear to be a GTF file (GFF not supported by this program)
Process Process-8:
Traceback (most recent call last):
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1751, in run
    refs_1exon_by_chr, refs_exons_by_chr, junctions_by_chr, junctions_by_gene, start_ends_by_gene = reference_parser(args, list(genome_dict.keys()))
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 653, in reference_parser
    for r in genePredReader(referenceFiles):
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 134, in __init__
    self.f = open(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/ibex/scratch/projects/c2042/analysis/sqanti3/splits/7/refAnnotation_all_samples.chained.genePred'
**** Parsing Reference Transcriptome....
/home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.all.maker.functional_ipr.gff doesn't appear to be a GTF file (GFF not supported by this program)
Process Process-3:
Traceback (most recent call last):
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1751, in run
    refs_1exon_by_chr, refs_exons_by_chr, junctions_by_chr, junctions_by_gene, start_ends_by_gene = reference_parser(args, list(genome_dict.keys()))
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 653, in reference_parser
    for r in genePredReader(referenceFiles):
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 134, in __init__
    self.f = open(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/ibex/scratch/projects/c2042/analysis/sqanti3/splits/2/refAnnotation_all_samples.chained.genePred'
**** Parsing Reference Transcriptome....
/home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.all.maker.functional_ipr.gff doesn't appear to be a GTF file (GFF not supported by this program)
Process Process-3:
Traceback (most recent call last):
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1751, in run
    refs_1exon_by_chr, refs_exons_by_chr, junctions_by_chr, junctions_by_gene, start_ends_by_gene = reference_parser(args, list(genome_dict.keys()))
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 653, in reference_parser
    for r in genePredReader(referenceFiles):
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 134, in __init__
    self.f = open(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/ibex/scratch/projects/c2042/analysis/sqanti3/splits/2/refAnnotation_all_samples.chained.genePred'
^[[B**** Parsing Reference Transcriptome....
/home/albadenm/c2042/analysis/IsoSeq_Ocoarcata/maker/OcoaRS1.PZYT01.fa.maker.output/round4/OcoaRS1.PZYT01.fa.all.maker.functional_ipr.gff doesn't appear to be a GTF file (GFF not supported by this program)
Process Process-4:
Traceback (most recent call last):
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1751, in run
    refs_1exon_by_chr, refs_exons_by_chr, junctions_by_chr, junctions_by_gene, start_ends_by_gene = reference_parser(args, list(genome_dict.keys()))
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 653, in reference_parser
    for r in genePredReader(referenceFiles):
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 134, in __init__
    self.f = open(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/ibex/scratch/projects/c2042/analysis/sqanti3/splits/3/refAnnotation_all_samples.chained.genePred'
error: data input empty 
GeneMarkS: error on last system call, error code 256
Abort program!!!
Process Process-7:
Traceback (most recent call last):
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1748, in run
    orfDict = correctionPlusORFpred(args, genome_dict)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 583, in correctionPlusORFpred
    if subprocess.check_call(cmd, shell=True, cwd=gmst_dir)!=0:
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/subprocess.py", line 363, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'perl /ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/utilities/gmst/gmst.pl -faa --strand direct --fnn --output /ibex/scratch/projects/c2042/analysis/sqanti3/splits/6/GMST/GMST_tmp /ibex/scratch/projects/c2042/analysis/sqanti3/splits/6/all_samples.chained_corrected.fasta' returned non-zero exit status 1.
error: data input empty 
GeneMarkS: error on last system call, error code 256
Abort program!!!
Process Process-5:
Traceback (most recent call last):
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1748, in run
    orfDict = correctionPlusORFpred(args, genome_dict)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 583, in correctionPlusORFpred
    if subprocess.check_call(cmd, shell=True, cwd=gmst_dir)!=0:
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/subprocess.py", line 363, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'perl /ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/utilities/gmst/gmst.pl -faa --strand direct --fnn --output /ibex/scratch/projects/c2042/analysis/sqanti3/splits/4/GMST/GMST_tmp /ibex/scratch/projects/c2042/analysis/sqanti3/splits/4/all_samples.chained_corrected.fasta' returned non-zero exit status 1.
error: data input empty 
GeneMarkS: error on last system call, error code 256
Abort program!!!
Process Process-6:
Traceback (most recent call last):
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1748, in run
    orfDict = correctionPlusORFpred(args, genome_dict)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 583, in correctionPlusORFpred
    if subprocess.check_call(cmd, shell=True, cwd=gmst_dir)!=0:
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/subprocess.py", line 363, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'perl /ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/utilities/gmst/gmst.pl -faa --strand direct --fnn --output /ibex/scratch/projects/c2042/analysis/sqanti3/splits/5/GMST/GMST_tmp /ibex/scratch/projects/c2042/analysis/sqanti3/splits/5/all_samples.chained_corrected.fasta' returned non-zero exit status 1.
error: data input empty 
GeneMarkS: error on last system call, error code 256
Abort program!!!
Process Process-2:
Traceback (most recent call last):
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 1748, in run
    orfDict = correctionPlusORFpred(args, genome_dict)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 583, in correctionPlusORFpred
    if subprocess.check_call(cmd, shell=True, cwd=gmst_dir)!=0:
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/subprocess.py", line 363, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'perl /ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/utilities/gmst/gmst.pl -faa --strand direct --fnn --output /ibex/scratch/projects/c2042/analysis/sqanti3/splits/1/GMST/GMST_tmp /ibex/scratch/projects/c2042/analysis/sqanti3/splits/1/all_samples.chained_corrected.fasta' returned non-zero exit status 1.
Traceback (most recent call last):
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 2337, in <module>
    main()
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 2328, in main
    combine_split_runs(args, split_dirs)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 2151, in combine_split_runs
    with open(_orf) as h: f_faa.write(h.read())
FileNotFoundError: [Errno 2] No such file or directory: '/ibex/scratch/projects/c2042/analysis/sqanti3/splits/0/all_samples.chained_corrected.faa'

Any help or insight would be greatly appreciated :)

noor-albader commented 3 years ago

OH! and I also tried converting my gff to gtf using gffread all_samples.chained.gff -T -o all_samples.gtfand then running sqanti3 on the gtf instead of the gff output of cupcake collapse but get a similar errors as others (i.e. ticket #35 ):

Loading module for SQANTI3
SQANTI3 1.6 is now loaded
R scripting front-end version 3.6.1 (2019-07-05)
Traceback (most recent call last):
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 2337, in <module>
    main()
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 2327, in main
    split_dirs = split_input_run(args)
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 2085, in split_input_run
    recs = [r for r in collapseGFFReader(args.isoforms)]
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/SQANTI3/sqanti3_qc.py", line 2085, in <listcomp>
    recs = [r for r in collapseGFFReader(args.isoforms)]
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/site-packages/cupcake-19.0.0-py3.7-linux-x86_64.egg/cupcake/io/GFF.py", line 408, in __next__
    return self.read()
  File "/ibex/sw/csi/sqanti3/1.6/el7.9_conda3/miniconda3/envs/SQANTI3.env/lib/python3.7/site-packages/cupcake-19.0.0-py3.7-linux-x86_64.egg/cupcake/io/GFF.py", line 579, in read
    assert raw[2] == 'transcript'
AssertionError