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Error: "could not convert string to float" #216
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Dear @xiaofei, As for the main error, I think I changed the format of the list. May I ask you which version have you installed? It should be 1.2, correct? |
Yes, it is v1.2.4. |
Dear @Xiaofei-git , I am about to release a new release candidate this afternoon. That version has the bug fixed (together with many other enhancements). Best |
Let me know when you finish the release. Thank you so much! BEST, Xiaofei |
Dear @Xiaofei-git , the new release can be found here: https://github.com/EI-CoreBioinformatics/mikado/releases/tag/2.0rc5 Best |
If I'd like to install by "pip3 install mikado", how could I install the new release one? Thanks a lot! |
Dear @Xiaofei-git, I added to the release page two binary packages (the ones that finish with .whl), one for python 3.6 and another for python 3.7. Either should function by doing a
If you have a different version of python or you are not on a Linux system, then please download the source package (either the tar.gz or the .zip file), unpack them, then
You might need to install wheel, if it complains, with pip.
I hope this helps. Best |
I used "pip install --user Mikado-2.0rc5-cp36-cp36m-linux_x86_64.whl" to install it, it gave me error but showed me "successfully installed" in the end as below, could I ignor the error and move forward to use it? Thanks a lot! ERROR: pygenometracks 2.1 requires hicexplorer>=2.1.1, which is not installed. |
Dear @Xiaofei-git , |
I am moving forward on the sample_data. Then, I still move forward with the generated "mikado.blast.xml.gz" for "mikado serialise". Unfortunately, another error as below, I did't get any help by googling, do you have any ideas? Also, am I right for the value of "--blast_targets" option? So, I asked 3 questions above, hope I didn't mess it up. Thanks a lot! $ makeblastdb -in uniprot_sprot_plants.fasta -dbtype prot -parse_seqids > blast_prepare.log $ mikado serialise --json-conf configuration.yaml --xml mikado.blast.xml.gz --orfs mikado.bed --blast_targets uniprot_sprot_plants.fasta The above exception was the direct cause of the following exception: Traceback (most recent call last): |
Dear @Xiaofei-git , regarding the first error (in Regarding the second issue: unfortunately I think this has to do with the specifics of your system rather than with Mikado. The problem is that the SQLite database used by Mikado crashes. My suspicion is that you are working on a NFS filesystem, which will cause SQLite to fail (I am having a similar issue on some of my machines as well). I would check with your sysadmin. I hope this helps. |
Dear @lucventurini, |
Dear @Xiaofei-git, thank you for updating us. Glad it worked out in the end. |
However, when I run the code "$ mikado serialise --json-conf configuration.yaml --xml mikado.blast.xml.gz --orfs mikado.bed --blast_targets uniprot_sprot_plants.fasta", I got the error below, which complained that the provided ORFs do not match the transcripts provided and already present in the database. Actually, if I don't provide "--orfs mikado.bed", it will go through successfully, just skip it for loading ORFs, "2019-10-10 14:27:41,768 - serialiser - serialise.py:155 - INFO - load_orfs - MainProcess - No ORF data provided, skipping". Why does it complain the provided ORFs do not match the transcripts provided when I used "--orfs mikado.bed"? Another question is how should I set the value for '--blast_targets'? If I work on Sorghum, it should be fine to use "--blast_targets uniprot_sprot_plants.fasta", right? Thanks a lot! $ more serialise.log |
Yes. Transdecoder or prodigal (or any other orf caller) must be run on the output of |
I am sorry I feel confused. I don't think I asked the error before about "The provided ORFs do not match th |
That's our fault in not making the documentation clear enough. You are not the first person to make this mistake. As I mentioned, you are not the first one to make this mistake, so it is clearly on us to clarify the procedure. |
Thank you so much! Now, it is clear to me and I run through mikado successfully. Here is the code I used for "serialise" step as below. FYI, #114 helped me too, because I had to delete the mikado.db file before re-running Mikado serialise, otherwise it will report that $ mikado serialise --json-conf configuration.yaml --xml mikado.blast.xml.gz --orfs mikado_prepared.fasta.transdecoder.bed --blast_targets uniprot_sprot_plants.fasta -–transcripts mikado_prepared.fasta BTW, I think it might be better to update the document for serialise here https://mikado.readthedocs.io/en/latest/Tutorial/index.html#creating-the-configuration-file-for-mikado too, because I run through the manual to get familiar with Mikado. Thank you so much for your help to walk through the errors I met! |
No problem @Xiaofei-git , very glad I was able to assist you through this! Please let us know if you encounter any other issue.
Yes, I can understand that. I probably should delete the database when
Working on that, thank you! |
… to use the output FASTA file for `mikado serialise`, and `mikado serialise` will tell users to use the `mikado_prepared.fasta` file if it crashes during ORF loading.
I "pip3 install mikado" installed the mikado on our hpc cluster and used the "sample_data" to test it from command line. I got same error as "#164". Could you direct me what is the issue?
There is warning message at the beginning "calling yaml.load() without Loader=... is deprecated", might it be a problem for the error? Also, I need to copy "plants.yaml" manually to my working directory. It might be a problem, right? Could you help me figure it out?
Thanks a lot!
Xiaofei
$ mikado configure --list list.txt --reference chr5.fas --mode permissive --scoring plants.yaml -t 8 \
..../.local/lib/python3.6/site-packages/Mikado/configuration/configurator.py:529: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
scoring = yaml.load(scoring_file)
2019-09-23 14:30:27,523 - main - init.py:124 - ERROR - main - MainProcess - Mikado crashed, cause:
2019-09-23 14:30:27,523 - main - init.py:125 - ERROR - main - MainProcess - Malformed inputs file. Error:
could not convert string to float:
Traceback (most recent call last):
File ".../.local/lib/python3.6/site-packages/Mikado/subprograms/configure.py", line 217, in create_config
score = float(_fields[3])
ValueError: could not convert string to float:
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File ".../.local/lib/python3.6/site-packages/Mikado/init.py", line 110, in main
args.func(args)
File ".../.local/lib/python3.6/site-packages/Mikado/subprograms/configure.py", line 222, in create_config
raise ValueError("Malformed inputs file. Error:\n{}".format(exc))
ValueError: Malformed inputs file. Error:
could not convert string to float:
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