ValueError: invalid literal for int() with base 10: ','

[ramoseks]

Dear @ReverendCasy

I managed to make TOGA2 run successfully for my assemblies, but for some assemblies I am getting the following error and I can't really tell what is the problem. Could you help me?

This is the error:

INFO:numexpr.utils:Note: NumExpr detected 64 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 16.
INFO:numexpr.utils:NumExpr defaulting to 16 threads.
/bin/TOGA2/src/python/classify_chains.py:280: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  df_se['pred'] = se_pred
/bin/TOGA2/src/python/classify_chains.py:281: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  df_me['pred'] = me_pred
Traceback (most recent call last):
  File "/bin/TOGA2/toga2.py", line 1974, in <module>
    toga2()
    ~~~~~^^
  File "/conda/users/envs/***/toga2/lib/python3.13/site-packages/click/core.py", line 1161, in __call__
    return self.main(*args, **kwargs)
           ~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "/conda/users/envs/***/toga2/lib/python3.13/site-packages/click/core.py", line 1082, in main
    rv = self.invoke(ctx)
  File "/conda/users/envs/***/toga2/lib/python3.13/site-packages/click/core.py", line 1697, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
  File "/conda/users/envs/***/toga2/lib/python3.13/site-packages/click/core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/conda/users/envs/***/toga2/lib/python3.13/site-packages/click/core.py", line 788, in invoke
    return __callback(*args, **kwargs)
  File "/bin/TOGA2/toga2.py", line 1237, in run
    TogaMain(**kwargs)
    ~~~~~~~~^^^^^^^^^^
  File "/bin/TOGA2/src/python/modules/toga_main.py", line 708, in __init__
    self.run()
    ~~~~~~~~^^
  File "/bin/TOGA2/src/python/modules/toga_main.py", line 868, in run
    self.run_alignment_jobs()
    ~~~~~~~~~~~~~~~~~~~~~~~^^
  File "/bin/TOGA2/src/python/modules/toga_main.py", line 2101, in run_alignment_jobs
    job_num: int = int(self.job_nums_per_bin[self.cesar_memory_bins.index(mem)])
                   ~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: invalid literal for int() with base 10: ','

Thank you very much!

[ReverendCasy]

Hello @ramoseks ,
Can you please provide the specified values for --job_nums_per_bin and --memory_bins arguments? I suspect your values might have double commas, like ’10,,20’

Unrelated: Could you please update the status of the other two issues you opened? If those are solved, I would like to close them.

Best,
Yury

[ramoseks]

Hi @ReverendCasy

This is how I ran the command:

toga2.py run "${inputdir}/${ref2bit}" \
     "${inputdir}/${qry2bit}" \
     "${inputdir}/${chain}" \
     "${inputdir}"/GCF_964199755.1_bLarMic1.1_genomic_chr.EDTAsoftmasked_plusMTcurated.filtered.D3.bed \
     -i "${inputdir}"/GCF_964199755.1_bLarMic1.1_genomic_chr.EDTAsoftmasked_plusMTcurated.filtered.isoforms.txt \
     -name "${out}" -o "${out}" -k -knf -b 3,5,7,10,15 -jb 500,20,20,10,5 -nc "${inputdir}"/toga2/nextflow_configs \
     --nextflow_exec_script "${inputdir}"/toga2/nextflow_configs/execute_joblist.nf

There are no double commas in the -b and -jb parameters and I am using the default values. I also tried not setting -b and -jb and letting the program to fill it with the default values itself, but I got the same error. I was able to run it successfully for two species and I can see they have jobs for the bins 3Gb, 5Gb, 7Gb and 10Gb, but for others I am getting this error and they don't pass few jobs with 10Gb. Can't find any errors or extra "," in the Nextflow configs for the bins.

And sure! I will update the other issues. Sorry =)

Best,

[ReverendCasy]

@ramoseks Sorry for the false call. Can you please attach the tmp/cesar_alignment_jobs/joblist_description.tsv file?

[ramoseks]

Hi @ReverendCasy
Here it is, there is no much inside this file. Is it correct?
joblist_description.tsv

[heziqing]

Hello, I encountered the same error.

  File "/share/home/heziqing/TOGA2/toga2.py", line 2032, in <module>
    toga2()
  File "/share/home/heziqing/miniconda3/envs/toga2/lib/python3.10/site-packages/click/core.py", line 1161, in __call__
    return self.main(*args, **kwargs)
  File "/share/home/heziqing/miniconda3/envs/toga2/lib/python3.10/site-packages/click/core.py", line 1082, in main
    rv = self.invoke(ctx)
  File "/share/home/heziqing/miniconda3/envs/toga2/lib/python3.10/site-packages/click/core.py", line 1697, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/share/home/heziqing/miniconda3/envs/toga2/lib/python3.10/site-packages/click/core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/share/home/heziqing/miniconda3/envs/toga2/lib/python3.10/site-packages/click/core.py", line 788, in invoke
    return __callback(*args, **kwargs)
  File "/share/home/heziqing/TOGA2/toga2.py", line 1213, in run
    TogaMain(**kwargs)
  File "/share/home/heziqing/TOGA2/src/python/modules/toga_main.py", line 651, in __init__
    self.run()
  File "/share/home/heziqing/TOGA2/src/python/modules/toga_main.py", line 826, in run
    self.run_alignment_jobs()
  File "/share/home/heziqing/TOGA2/src/python/modules/toga_main.py", line 2139, in run_alignment_jobs
    job_num: int = int(
ValueError: invalid literal for int() with base 10: ','

Here is the code I run

/share/home/heziqing/TOGA2/toga2.py run \
/dath/heziqing/Hamster_genome/Compartive/Genes/TOGA/test_res/hg38.2bit \
/dath/heziqing/Hamster_genome/Compartive/Genes/TOGA/test_res/mm10.2bit \
/share/home/heziqing/TOGA2/test_input/hg38.mm10.chr11.chain \
/share/home/heziqing/TOGA2/test_input/hg38.genCode27.chr11.bed \
-i /share/home/heziqing/TOGA2/supply/hg38.wgEncodeGencodeCompV34.isoforms.txt \
--u12 /share/home/heziqing/TOGA/supply/hg38.U12sites.tsv \
-b 3,5,7,10,15 -jb 500,20,20,10,5 \
-k --output /dath/heziqing/Hamster_genome/Compartive/Genes/TOGA/test_res/res -name togatest \
-c sge -q all.q -knf \
--nc /share/home/heziqing/TOGA2/he_configs \
--tree_cpus 15 \
--nextflow_exec_script /share/home/heziqing/TOGA2/he_configs/execute_joblist.nf

[ReverendCasy]

@ramoseks @heziqing sorry for the long wait. The issue must be fixed now; please update src/python/modules/toga_main.py and ping me if the solution works.