Closed SergeyBaikal closed 1 year ago
This is my log file.
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<<<<<<
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
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!
Dear, developers
During unpacking, the following error occurs.
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)
2)
3)
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.