TypeError: iter_gmap_sam() got an unexpected keyword argument 'type' using collapse_isoforms_by_sam.py

[gyorkeia]

Hi, I'm trying to use collapse_isoforms_by_sam.py as a part of a pipeline according to this paper: https://www.frontiersin.org/articles/10.3389/fgene.2021.683408/full

...with the following arguments:

python /cluster/projects/nn9244k/for_adam/lophius/cDNA_Cupcake/cupcake/tofu/collapse_isoforms_by_sam.py \ --cpus 6 -b ../mapping/minimap2_mapping/all_samples_polished.hq.highQual.mapped.bam --dun-merge-5-shorter -o all_samples_polished.hq.highQual.mapped

I get the following error however and despite searching for a solution I couldn't find none. What should I look at next or try? Thanks. Adam

WARNING: input fasta not given. Will use query sequence in the BAM file. Process Process-2: Traceback (most recent call last): File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/cluster/projects/nn9244k/for_adam/lophius/cDNA_Cupcake/cupcake/tofu/collapse_isoforms_by_sam.py", line 215, in multiprocess_helper max_3_diff=args.max_3_diff) File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/site-packages/cupcake/tofu/branch/branch_simple2.py", line 40, in init self.transfrag_len_dict = dict((r.id.split()[0], len(r.seq)) for r in SeqIO.parse(open(transfrag_filename), 'fastq' if is_fq else 'fasta')) TypeError: expected str, bytes or os.PathLike object, not NoneType Process Process-1: Traceback (most recent call last): File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/cluster/projects/nn9244k/for_adam/lophius/cDNA_Cupcake/cupcake/tofu/collapse_isoforms_by_sam.py", line 215, in multiprocess_helper max_3_diff=args.max_3_diff) File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/site-packages/cupcake/tofu/branch/branch_simple2.py", line 40, in init self.transfrag_len_dict = dict((r.id.split()[0], len(r.seq)) for r in SeqIO.parse(open(transfrag_filename), 'fastq' if is_fq else 'fasta')) TypeError: expected str, bytes or os.PathLike object, not NoneType Process Process-3: Traceback (most recent call last): File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/cluster/projects/nn9244k/for_adam/lophius/cDNA_Cupcake/cupcake/tofu/collapse_isoforms_by_sam.py", line 215, in multiprocess_helper max_3_diff=args.max_3_diff) File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/site-packages/cupcake/tofu/branch/branch_simple2.py", line 40, in init self.transfrag_len_dict = dict((r.id.split()[0], len(r.seq)) for r in SeqIO.parse(open(transfrag_filename), 'fastq' if is_fq else 'fasta')) TypeError: expected str, bytes or os.PathLike object, not NoneType Process Process-4: Traceback (most recent call last): File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/cluster/projects/nn9244k/for_adam/lophius/cDNA_Cupcake/cupcake/tofu/collapse_isoforms_by_sam.py", line 215, in multiprocess_helper max_3_diff=args.max_3_diff) File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/site-packages/cupcake/tofu/branch/branch_simple2.py", line 40, in init self.transfrag_len_dict = dict((r.id.split()[0], len(r.seq)) for r in SeqIO.parse(open(transfrag_filename), 'fastq' if is_fq else 'fasta')) TypeError: expected str, bytes or os.PathLike object, not NoneType Process Process-5: Traceback (most recent call last): File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/cluster/projects/nn9244k/for_adam/lophius/cDNA_Cupcake/cupcake/tofu/collapse_isoforms_by_sam.py", line 215, in multiprocess_helper max_3_diff=args.max_3_diff) File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/site-packages/cupcake/tofu/branch/branch_simple2.py", line 40, in init self.transfrag_len_dict = dict((r.id.split()[0], len(r.seq)) for r in SeqIO.parse(open(transfrag_filename), 'fastq' if is_fq else 'fasta')) TypeError: expected str, bytes or os.PathLike object, not NoneType Process Process-6: Traceback (most recent call last): File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/cluster/projects/nn9244k/for_adam/lophius/cDNA_Cupcake/cupcake/tofu/collapse_isoforms_by_sam.py", line 215, in multiprocess_helper max_3_diff=args.max_3_diff) File "/cluster/projects/nn9244k/for_adam/lophius/preanalysis/cupcake/lib/python3.7/site-packages/cupcake/tofu/branch/branch_simple2.py", line 40, in init self.transfrag_len_dict = dict((r.id.split()[0], len(r.seq)) for r in SeqIO.parse(open(transfrag_filename), 'fastq' if is_fq else 'fasta')) TypeError: expected str, bytes or os.PathLike object, not NoneType ERROR:Sanity checking all_samples_polished.hq.highQual.mapped.collapsed.gff0 is GFF3 format: expected 9 tab-delimited fields but saw 1! Abort!