collapse_isoforms_by_sam.py error TypeError: expected str, bytes or os.PathLike object, not NoneType

[khandaud15]

Hi,
I am using collapse_isoforms_by_sam.py to collapse into unique Transcript using command,
collapse_isoforms_by_sam.py --input 3k.dedup.fasta -s 3k.dedup.fasta.sorted.sam -c 0.99 -i 0.95 --gen_mol_count -o 3k.5merge --cpus 10 .

I am getting an error, not sure whats going wrong

Traceback (most recent call last):
File "/usr/local/anaconda3-2020/envs/anaCogent/bin/collapse_isoforms_by_sam.py", line 4, in
import('pkg_resources').run_script('cupcake==28.0.0', 'collapse_isoforms_by_sam.py')
File "/usr/local/anaconda3-2020/envs/anaCogent/lib/python3.7/site-packages/pkg_resources/init.py", line 656, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/local/anaconda3-2020/envs/anaCogent/lib/python3.7/site-packages/pkg_resources/init.py", line 1453, in run_script
exec(code, namespace, namespace)
File "/usr/local/anaconda3/envs/anaCogent/lib/python3.7/site-packages/cupcake-28.0.0-py3.7-linux-x86_64.egg/EGG-INFO/scripts/collapse_isoforms_by_sam.py", line 444, in
main(args)
File "/usr/local/anaconda3/envs/anaCogent/lib/python3.7/site-packages/cupcake-28.0.0-py3.7-linux-x86_64.egg/EGG-INFO/scripts/collapse_isoforms_by_sam.py", line 322, in main
region_list_ignore, chunk_regions_list = multiprocess_predefine_regions(args.bam, args.cpus)
File "/usr/local/anaconda3/envs/anaCogent/lib/python3.7/site-packages/cupcake-28.0.0-py3.7-linux-x86_64.egg/EGG-INFO/scripts/collapse_isoforms_by_sam.py", line 167, in multiprocess_predefine_regions
reader = pysam.AlignmentFile(open(aligned_bam_filename), 'rb', check_sq=False)
TypeError: expected str, bytes or os.PathLike object, not NoneType

can you please let me know, how can I fix it

[Magdoll]

Hmm that’s weird. Something might be wrong w chunking the file? Can you change —CPU’s to 1 and see what happens?

On Thu, Dec 2, 2021 at 1:12 PM Daud Khan ***@***.***> wrote: Hi, I am using collapse_isoforms_by_sam.py to collapse into unique Transcript using command, collapse_isoforms_by_sam.py --input 3k.dedup.fasta -s 3k.dedup.fasta.sorted.sam -c 0.99 -i 0.95 --gen_mol_count -o 3k.5merge --cpus 10 . I am getting an error, not sure whats going wrong Traceback (most recent call last): File "/usr/local/anaconda3-2020/envs/anaCogent/bin/collapse_isoforms_by_sam.py", line 4, in *import*('pkg_resources').run_script('cupcake==28.0.0', 'collapse_isoforms_by_sam.py') File "/usr/local/anaconda3-2020/envs/anaCogent/lib/python3.7/site-packages/pkg_resources/ *init*.py", line 656, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/local/anaconda3-2020/envs/anaCogent/lib/python3.7/site-packages/pkg_resources/ *init*.py", line 1453, in run_script exec(code, namespace, namespace) File "/usr/local/anaconda3/envs/anaCogent/lib/python3.7/site-packages/cupcake-28.0.0-py3.7-linux-x86_64.egg/EGG-INFO/scripts/collapse_isoforms_by_sam.py", line 444, in main(args) File "/usr/local/anaconda3/envs/anaCogent/lib/python3.7/site-packages/cupcake-28.0.0-py3.7-linux-x86_64.egg/EGG-INFO/scripts/collapse_isoforms_by_sam.py", line 322, in main region_list_ignore, chunk_regions_list = multiprocess_predefine_regions(args.bam, args.cpus) File "/usr/local/anaconda3/envs/anaCogent/lib/python3.7/site-packages/cupcake-28.0.0-py3.7-linux-x86_64.egg/EGG-INFO/scripts/collapse_isoforms_by_sam.py", line 167, in multiprocess_predefine_regions reader = pysam.AlignmentFile(open(aligned_bam_filename), 'rb', check_sq=False) TypeError: expected str, bytes or os.PathLike object, not NoneType can you please let me know, how can I fix it — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#180>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAEQE356UT6RYHTZGVR52TLUO7ONJANCNFSM5JIEZJ6A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

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[arslan9732]

Is this issue resolved? How we can use multi-CPU for collapse_isoforms_by_sam.py? I am facing the same problem.

[Magdoll]

Hi @arslan9732 - cupcake is getting obsoleted. Please use isoseq3 collapse from https://isoseq.how/classification/isoseq-collapse.html instead.