Databases

[SergeyBaikal]

Dear, developers

During unpacking, the following error occurs.

2022-01-26 05:04:08 (1.72 MB/s) - ‘pdb70_from_mmcif_latest.tar.gz’ saved [23794671727/23794671727]
md5sum
pdb70_a3m.ffdata
tar: pdb70_a3m.ffdata: Cannot write: Invalid argument

I solved this problem by unzipping with another program.

$ python /media/sf_S_DRIVE/Cenote_Taker2/Cenote-Taker2/run_cenote-taker2.py -c testcontigs_RNA_ct2.fasta -r Test_RNA_ct -p True -m 20 -t 4 -db rna_virus /media/sf_S_DRIVE/Cenote_Taker2/Cenote-Taker2 circlator is not found. Exiting. #pip3 install helped me efetch is not found. Exiting. # sudo apt-get install -y efetch helped me bowtie2 is not found. Exiting. # conda helped me tRNAscan-SE is not found. Exiting. # sudo apt install trnascan-se tbl2asn is not found. Exiting.

Many packages were not installed, had to be installed manually.

I installed a new operating system (Debian 11) and found a number of installation errors. How critical are they? 1)

Cloning into 'PHANOTATE'...
make: *** No targets specified and no makefile found.  Stop.

2)

Downloading and Extracting Packages
bedtools-2.30.0      | 17.9 MB   | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
cenote-taker2_env not loaded correctly

3)

-- Installing: /home/sergey/Cenote-Taker2/Cenote-Taker2/hh-suite/build/scripts/splitfasta.pl
updateTaxonomy.sh: 9: [: Linux: unexpected operator
updateTaxonomy.sh: 70: function: not found
Update failed.
updateAccessions.sh: 9: Bad substitution

It will also be a problem for beginners if they have not installed packages pip3 and git since they are not there initially.

If I use 100 contigs and an RNA database, python run_cenote-taker2.py -c 100_RNA.fasta -r results_annotationRNA -m 20 -t 4 -p False -db rna_virus --minimum_length_linear 1000 -am True -hh none

I get the following messages.

/media/sf_S_DRIVE/Cenote_Taker2/Cenote-Taker2/cenote-taker2.1.3.sh: line 2062: bc: command not found
/media/sf_S_DRIVE/Cenote_Taker2/Cenote-Taker2/cenote-taker2.1.3.sh: line 2063: bc: command not found
/media/sf_S_DRIVE/Cenote_Taker2/Cenote-Taker2/cenote-taker2.1.3.sh: line 2064: bc: command not found
/media/sf_S_DRIVE/Cenote_Taker2/Cenote-Taker2/cenote-taker2.1.3.sh: line 2065: bc: command not found

[SergeyBaikal]

This is my log file.

install_ct2.log

[SergeyBaikal]

It seems that the program was set up. Sometimes I get the following output.

removing ancillary files
/home/sergey/Cenote-Taker2/Cenote-Taker2/unlimited_breadsticks_0.1.sh: line 468: /usr/bin/rm: Argument list too long

time update: Finishing  02-24-22---05:47:37
output directory: RNA_viruses
 >>>>>>CENOTE UNLIMITED BREADSTICKS HAS FINISHED SERVING BREADSTICKS<<<<<< 

[mtisza1]

Sergey,

Sorry again for the delay in replying. I'm glad you were able to get Unlimited Breadsticks to run. Your issue with rm and "Argument list too long" is not a fatal issue, but may result in having some intermediate files left over at the end. A user in a previous issue was able to find a solution #21 , though I of course urge caution when editing the script. I will incorporate the fix into the next patch.

Please let me know if you are having other issues.

Best,

Mike

[SergeyBaikal]

Dear, Mike! Thank you very much for your reply! We are looking forward to the new version of the program. The program is now working stably, once again thank you very much!