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kovaltsuk1 / saab_plus

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No output.txt #4

Open robbinxiaochen opened 3 years ago

robbinxiaochen commented 3 years ago

I have tried to run the example file in EXAMPLE using; SAAB_PLUS -f example_H.fa -n 20 -s human However, I got the error as:

SAAB_PLUS -f Light_chain.fasta -c L -n 20 FILE: Light_chain.fasta CORES: 20 ORGANISM: human CHAIN: L OutputName: output.txt OutputDir: . SAAB plus log is found in saab_plus.log Diagnostics log is found in diagnostics.log

    Initiating anarci parsing

    anarci parsing is done

    Initiating SAAB plus

gzip: output.txt: No such file or directory Traceback (most recent call last): File "/home/lvxiaochen/anaconda3/envs/saab_plus/bin/SAAB_PLUS", line 255, in STUDY.convert_fasta_to_frame().run() File "/home/lvxiaochen/anaconda3/envs/saab_plus/bin/SAAB_PLUS", line 178, in run saab_instance.initiate_SAAB() File "/home/lvxiaochen/.local/lib/python2.7/site-packages/saab_plus/RunSAAB.py", line 138, in initiate_SAAB os.rename("{0}.gz".format( self.output_name ), os.path.join( self.output_dir,"{0}.gz".format( self.output_name ))) OSError: [Errno 2] No such file or directory

And the saab_plus.log is like: 2021-03-04 16:42:04 INFO Initiating structural annotation pipeline 2021-03-04 16:42:04 INFO FILE: vloupe_clonotype1_consensus_2_reference_aa.fasta 2021-03-04 16:42:04 INFO CORES: 20 2021-03-04 16:42:04 INFO ORGANISM: human 2021-03-04 16:42:04 INFO CHAIN: H 2021-03-04 16:42:04 INFO OutputName: output.txt 2021-03-04 16:42:04 INFO OutputDir: . 2021-03-04 16:42:04 INFO Writing DIAGNOSTICS log

2021-03-04 16:42:04 INFO Successfully imported: anarci 2021-03-04 16:42:04 INFO Successfully imported: anarci germlines 2021-03-04 16:42:04 INFO Successfully imported: anarci Accept 2021-03-04 16:42:04 INFO Successfully imported: scalop 2021-03-04 16:42:04 INFO Successfully imported: scalop assing 2021-03-04 16:42:04 INFO Successfully imported: FREAD 2021-03-04 16:42:04 INFO Successfully imported: FREAD ESS table 2021-03-04 16:42:04 INFO Successfully imported: prosci module 2021-03-04 16:42:04 INFO Successfully imported: Common module 2021-03-04 16:42:04 INFO PDB template info file for H3 loop is located: OK 2021-03-04 16:42:04 INFO PDB template info file for L3 loop is located: OK 2021-03-04 16:42:04 INFO CDR-H3 cluster mapping file is located: OK 2021-03-04 16:42:04 INFO CDR-L3 cluster mapping file is located: OK 2021-03-04 16:42:04 INFO Directory with PDB frameworks for H3 loop is located: OK 2021-03-04 16:42:04 INFO Directory with PDB frameworks for L3 loop is located: OK 2021-03-04 16:42:04 INFO Directory with FREAD templates for H3 loop is located: OK 2021-03-04 16:42:04 INFO Number of FREAD templates found: 3759 2021-03-04 16:42:04 INFO Directory with FREAD templates for L3 loop is located: OK 2021-03-04 16:42:04 INFO Number of FREAD templates found: 3606 2021-03-04 16:42:04 INFO Imported pandas, Version 0.24.2 2021-03-04 16:42:04 INFO Imported Bio, Version 1.70 2021-03-04 16:42:04 INFO Starting ANARCI parsing

2021-03-04 16:42:04 INFO checking version of anarci used 2021-03-04 16:42:04 INFO ANARCI version 1.3 is used 2021-03-04 16:42:04 INFO Total number of sequences: 35 2021-03-04 16:42:04 ERROR ANARCI parsing failed to parse this chunk of sequences 2021-03-04 16:42:04 INFO ANARCI parsing is finished 2021-03-04 16:42:04 INFO Removing intermediate: vloupe_clonotype1_consensus_2_reference_aa.fasta_df.txt.gz 2021-03-04 16:42:04 INFO Starting SAAB plus pipeline

2021-03-04 16:42:04 INFO Loading Structures chunk: numbered_sabdab_imgt_fread.pkl 2021-03-04 16:42:05 INFO ################ 2021-03-04 16:42:05 INFO Numbered PDBs have been loaded into memory 2021-03-04 16:42:05 INFO Output Directory already exists

Could you please help me out? Thanks!

krishnaroskin commented 2 years ago

I'm having the same issue.

LiCanhui-Huyi commented 1 year ago

Hello, I want to ask you a question unrelated to this question. How do you match saab Plus and ANARCi? saab Plus is based on Python 2, while ANARCI is based on Python 3. When I run "SAAB_PLUS_DIAG", an error will occur: File "/usr/lib/python2.7/site-packages/anarci/anarci.py", line 123 print(">%s"%name, file=f) ^ SyntaxError: invalid syntax "File" is a parameter only available in Python 3's print. Obviously, Python 2 cannot run this command. I want to know how you solve this problem? Because I see this problem in issue, but no one provides a solution. So I came to ask you for advice. I'm sorry to bother you.