Comments (7)
ksahlin
commented on July 1, 2024
Hi @unique379r,
Glad you got it installed through conda! The fasta/q parser is complaining. This is a well-tested function, so my bet is that there is something wrong with the fasta file.
Perhaps you can manually check the first lines with
zcat reads/alz.polished.hq.fasta.gz | head -n 10
does everything look as expected for fasta format?
the problem is some unicode character seen from the line
**UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte**
It seems to be at the very beginning of the file.
Second idea is to try uLTRA with the unzipped reads file reads/alz.polished.hq.fasta
Let me know how it goes.
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ksahlin
commented on July 1, 2024
On second thought, I don't think the readfq parser handles .gz files, so I would try idea 2 first. It is probably what is causing the error.
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unique379r
commented on July 1, 2024
Hey Kristoffer
You are correct, your fq parser was not able to deal with gz file, so i tried simple fasta. however i got the error about 'mummer' step.
Please take a look error log:
Traceback (most recent call last):
File "/scratch/rupesh/Apps/envs/ultra/lib/python3.9/site-packages/modules/mem_wrapper.py", line 31, in find_mems_slamem
subprocess.check_call([ 'slaMEM', '-l' , str(min_mem), refs_path, read_path, '-o', out_path ], stdout=stdout_file, stderr=stderr_file)
File "/scratch/rupesh/Apps/envs/ultra/lib/python3.9/subprocess.py", line 368, in check_call
retcode = call(*popenargs, **kwargs)
File "/scratch/rupesh/Apps/envs/ultra/lib/python3.9/subprocess.py", line 349, in call
with Popen(*popenargs, **kwargs) as p:
File "/scratch/rupesh/Apps/envs/ultra/lib/python3.9/subprocess.py", line 951, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/scratch/rupesh/Apps/envs/ultra/lib/python3.9/subprocess.py", line 1821, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'slaMEM'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/scratch/rupesh/Apps/envs/ultra/bin/uLTRA", line 722, in <module>
align_reads(args)
File "/scratch/rupesh/Apps/envs/ultra/bin/uLTRA", line 395, in align_reads
mem_wrapper.find_mems_slamem(args.outfolder, args.reads_tmp, ref_path, mummer_out_path, args.min_mem)
File "/scratch/rupesh/Apps/envs/ultra/lib/python3.9/site-packages/modules/mem_wrapper.py", line 34, in find_mems_slamem
find_mems_mummer(outfolder, read_path, refs_path, out_path, min_mem)
File "/scratch/rupesh/Apps/envs/ultra/lib/python3.9/site-packages/modules/mem_wrapper.py", line 16, in find_mems_mummer
subprocess.check_call([ 'mummer', '-maxmatch', '-l' , str(min_mem), refs_path, read_path], stdout=output_file, stderr=null)
File "/scratch/rupesh/Apps/envs/ultra/lib/python3.9/subprocess.py", line 368, in check_call
retcode = call(*popenargs, **kwargs)
File "/scratch/rupesh/Apps/envs/ultra/lib/python3.9/subprocess.py", line 349, in call
with Popen(*popenargs, **kwargs) as p:
File "/scratch/rupesh/Apps/envs/ultra/lib/python3.9/subprocess.py", line 951, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/scratch/rupesh/Apps/envs/ultra/lib/python3.9/subprocess.py", line 1821, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'mummer'
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ksahlin
commented on July 1, 2024
The conda installation should install slaMEM for you, but it seems slaMEM is not installed, or at least it is not found on your machine.
Did you run conda activate [name of your ultra env] after the conda installation?
Otherwise, you can manually install slaMEM easily by:
git clone [email protected]:fjdf/slaMEM.git
cd slaMEM
make
and then put the resulting binary file slaMEM in your path.
Best,
/K
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ksahlin
commented on July 1, 2024
You don't need to worry about the mummer. It's a fall-back call if slaMEM returns an error. In this case the error was that slaMEM is not found. If you followed the bioconda installation it should have installed it for you. My bet is that you, perhaps, followed only some of the steps in the manual installation.
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unique379r
commented on July 1, 2024
Hi there,
I guess, i got it and its running now...
Few more Q:
- Can uLTRA accepts CCS bam (HIFI pacbio) reads as input ? Since help says its required fasta/fastq which i dont have though i have HQ fasta and fastq from isoseq3. is this uLTRA expect from isoseq ? or bam2fastq of CCS reads can be used as input?
- The gtf input i am guessing its exons only not the genecode fully gtf with gene, exons etc, right ?
- After the mapping or pipeline output as bam, do you suggest to go isoseq clustering ?
Rupesh Kesharwani
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ksahlin
commented on July 1, 2024
Great that you got it running!
- No, but HQ fastq from isoseq3 is fine, or alternatively, simply get the fastq reads from the bam as you write (e.g., with bam2fastq).
- No, uLTRA assumes it is the "full" gtf with gene, transcript, and exon information (such as for the gencode gtfs).
- Depends on what you want to do after mapping, but in general no. isoseq clustering is usually a reference-free analysis step. You are mapping to a reference, and can therefore use a reference based software (depending on what you want to do). TAMA, FLAIR, SQANTI, talon comes to mind. There are more tools though.
Best,
K
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Related Issues (20)
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