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bioinfo-ut / PhenotypeSeeker

Identify phenotype-specific k-mers and predict phenotype using sequenced bacterial strains
GNU General Public License v3.0
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cannot execute binary files of phenotypeseeker #13

Closed philt31 closed 3 years ago

philt31 commented 3 years ago

I'm getting the following errors when I try and run the example scripts on my mac, any ideas why it wont execute the binary files? Generating the k-mer lists for input samples: /bin/sh: /usr/local/bin/glistmaker: cannot execute binary file /bin/sh: /usr/local/bin/glistmaker: cannot execute binary file /bin/sh: /usr/local/bin/glistmaker: cannot execute binary file /bin/sh: /usr/local/bin/glistmaker: cannot execute binary file /bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 1 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file /bin/sh: /usr/local/bin/glistmaker: cannot execute binary file /bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 8 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 9 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 10 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file /bin/sh: /usr/local/bin/glistmaker: cannot execute binary file /bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 11 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 12 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file /bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 16 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 17 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 18 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file /bin/sh: /usr/local/bin/glistmaker: cannot execute binary file /bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 19 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 20 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 22 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 24 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file /bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 25 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 26 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 27 of 30 lists generated./bin/sh: /usr/local/bin/glistmaker: cannot execute binary file /bin/sh: /usr/local/bin/glistmaker: cannot execute binary file 30 of 30 lists generated. Generating the k-mer feature vector. /bin/sh: /usr/local/bin/glistmaker: cannot execute binary file Mapping samples to the feature vector space: /bin/sh: /usr/local/bin/glistquery: cannot execute binary file /bin/sh: /usr/local/bin/glistquery: cannot execute binary file /bin/sh: /usr/local/bin/glistquery: cannot execute binary file /bin/sh: /usr/local/bin/glistquery: cannot execute binary file /bin/sh: /usr/local/bin/glistquery: cannot execute binary file /bin/sh: /usr/local/bin/glistquery: cannot execute binary file /bin/sh: /usr/local/bin/glistquery: cannot execute binary file /bin/sh: /usr/local/bin/glistquery: cannot execute binary file rm: K-mer_lists/VL_0004_13.list: No such file or directory rm: K-mer_lists/VL_0216_13.list: No such file or directory

bioinfo-ut commented 3 years ago

Usually that error message means Linux doesn't recognize the file as a shell script or as an executable file. Typically the cause is running an executable on the wrong architecture.

Which Linux do you use and which CPU?

erkiaun commented 3 years ago

These binary files are compiled for Linux operating systems and can't be executed on macOS at the moment.

philt31 commented 3 years ago

okay thanks, I've installed it now on a unix box, but now when I try and run the ./test_PS_modeling.sh I get the following error below. any ideas?

(kmer) (klmf372@asprd0111) - (08:37) - (~/bin/PhenotypeSeeker/example) -=>>./test_PS_modeling.sh Downloading the folder with example files ...

--2021-04-01 08:37:25-- http://bioinfo.ut.ee/PhenotypeSeeker/PS_modeling_example_files.tar.gz Resolving bioinfo.ut.ee... 193.40.23.25 Connecting to bioinfo.ut.ee|193.40.23.25|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://bioinfo.ut.ee/PhenotypeSeeker/PS_modeling_example_files.tar.gz [following] --2021-04-01 08:37:25-- https://bioinfo.ut.ee/PhenotypeSeeker/PS_modeling_example_files.tar.gz Connecting to bioinfo.ut.ee|193.40.23.25|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 52856987 (50M) [application/x-gzip] Saving to: `PS_modeling_example_files.tar.gz'

100%[====================================================================================================================================================================================================================================>] 52,856,987 1.73M/s in 70s

2021-04-01 08:38:36 (735 KB/s) - `PS_modeling_example_files.tar.gz' saved [52856987/52856987]

Unpacking the folder ...

PS_modeling_example_files/ PS_modeling_example_files/VL_0453.fasta PS_modeling_example_files/VL_0064.fasta PS_modeling_example_files/VL_0040.fasta PS_modeling_example_files/VL_0004.fasta PS_modeling_example_files/VL_0276.fasta PS_modeling_example_files/VL_0216.fasta PS_modeling_example_files/VL_0112.fasta PS_modeling_example_files/VL_0368.fasta PS_modeling_example_files/VL_0378.fasta PS_modeling_example_files/VL_0369.fasta PS_modeling_example_files/VL_0065.fasta PS_modeling_example_files/VL_0091.fasta PS_modeling_example_files/VL_0303.fasta PS_modeling_example_files/VL_0233.fasta PS_modeling_example_files/VL_0073.fasta PS_modeling_example_files/VL_0464.fasta PS_modeling_example_files/VL_0098.fasta PS_modeling_example_files/VL_0159.fasta PS_modeling_example_files/VL_0442.fasta PS_modeling_example_files/VL_0377.fasta PS_modeling_example_files/VL_0198.fasta PS_modeling_example_files/VL_0456.fasta PS_modeling_example_files/VL_0088.fasta PS_modeling_example_files/VL_0137.fasta PS_modeling_example_files/VL_0302.fasta PS_modeling_example_files/VL_0288.fasta PS_modeling_example_files/VL_0047.fasta PS_modeling_example_files/VL_0346.fasta PS_modeling_example_files/VL_0252.fasta PS_modeling_example_files/VL_0296.fasta PS_modeling_example_files/VL_0373.fasta PS_modeling_example_files/VL_0208.fasta PS_modeling_example_files/VL_0191.fasta PS_modeling_example_files/VL_0194.fasta PS_modeling_example_files/VL_0069.fasta PS_modeling_example_files/VL_0348.fasta PS_modeling_example_files/VL_0029.fasta PS_modeling_example_files/VL_0111.fasta PS_modeling_example_files/VL_0140.fasta PS_modeling_example_files/VL_0367.fasta PS_modeling_example_files/data.pheno

Launching the phenotypeseeker modeling: phenotypeseeker modeling PS_modeling_example_files/data.pheno

PhenotypeSeeker
modeling

Generating the k-mer lists for input samples: 30 of 30 lists generated. Generating the k-mer feature vector. Mapping samples to the feature vector space: 30 of 30 samples mapped. Estimating the Mash distances between samples... Calculating the GSC weights from mash distance matrix... Conducting the k-mer specific chi-square tests: split: invalid option -- 'n' Try split --help' for more information. split: invalid option -- 'n' Trysplit --help' for more information. split: invalid option -- 'n' Try split --help' for more information. split: invalid option -- 'n' Trysplit --help' for more information. split: invalid option -- 'n' Try split --help' for more information. split: invalid option -- 'n' Trysplit --help' for more information. split: invalid option -- 'n' Try split --help' for more information. split: invalid option -- 'n' Trysplit --help' for more information. split: invalid option -- 'n' Try split --help' for more information. split: invalid option -- 'n' Trysplit --help' for more information. split: invalid option -- 'n' Try split --help' for more information. split: invalid option -- 'n' Trysplit --help' for more information. split: invalid option -- 'n' Try split --help' for more information. split: invalid option -- 'n' Trysplit --help' for more information. split: invalid option -- 'n' Try split --help' for more information. split: invalid option -- 'n' Trysplit --help' for more information. split: invalid option -- 'n' Try split --help' for more information. split: invalid option -- 'n' Trysplit --help' for more information. split: invalid option -- 'n' Try split --help' for more information. split: invalid option -- 'n' Trysplit --help' for more information. split: invalid option -- 'n' Try split --help' for more information. split: invalid option -- 'n' Trysplit --help' for more information. split: invalid option -- 'n' Try split --help' for more information. split: invalid option -- 'n' Trysplit --help' for more information. split: invalid option -- 'n' Try split --help' for more information. split: invalid option -- 'n' Trysplit --help' for more information. split: invalid option -- 'n' Try split --help' for more information. split: invalid option -- 'n' Trysplit --help' for more information. split: invalid option -- 'n' Try split --help' for more information. split: invalid option -- 'n' Trysplit --help' for more information. multiprocess.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/klmf372/.local/lib/python3.8/site-packages/multiprocess/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/home/klmf372/.local/lib/python3.8/site-packages/multiprocess/pool.py", line 48, in mapstar return list(map(args)) File "/home/klmf372/.local/lib/python3.8/site-packages/PhenotypeSeeker/modeling.py", line 638, in get_kmers_tested for line in zip([open(item) for item in split_of_kmer_lists]): File "/home/klmf372/.local/lib/python3.8/site-packages/PhenotypeSeeker/modeling.py", line 638, in for line in zip([open(item) for item in split_of_kmer_lists]): FileNotFoundError: [Errno 2] No such file or directory: 'K-mer_lists/VL_0004_mapped_00000' """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/klmf372/.local/bin/phenotypeseeker", line 307, in Main() File "/home/klmf372/.local/bin/phenotypeseeker", line 296, in Main func = args.func(args) File "/home/klmf372/.local/lib/python3.8/site-packages/PhenotypeSeeker/modeling.py", line 1651, in modeling list(map( File "/home/klmf372/.local/lib/python3.8/site-packages/PhenotypeSeeker/modeling.py", line 1652, in lambda x: x.test_kmers_association_with_phenotype(), File "/home/klmf372/.local/lib/python3.8/site-packages/PhenotypeSeeker/modeling.py", line 574, in test_kmers_association_with_phenotype pvalues_from_all_threads = Input.pool.map( File "/home/klmf372/.local/lib/python3.8/site-packages/multiprocess/pool.py", line 364, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/home/klmf372/.local/lib/python3.8/site-packages/multiprocess/pool.py", line 768, in get raise self._value FileNotFoundError: [Errno 2] No such file or directory: 'K-mer_lists/VL_0004_mapped_00000'