mtisza1
commented
2 years ago Hi Sergey,
Thank you for opening this issue.
First, let me apologize for the delay in replying. I've been extremely busy lately, and I've had to decide to not reply to Cenote-Taker 2 issues temporarily. I will be "back" to quick responses and updates(!) at the end of February.
Here's a quick response which I hope fixes the issue. I noticed you're having a variety of issues with the Cenote-Taker 2 install, and I will address those in your other comment. Those problems could cause additional problems in Unlimited Breadsticks.
I'm fairly confident that this whole issue will be fixed if you can install bc on your operating system. I wrongly assumed that all operating systems had this by default. Try the most appropriate command:
apt-get install bc
or
sudo apt-get install bc
Please let me know if you have additional issues,
Mike
SergeyBaikal
Dear, developers
Hmm... I have the problem there are no such directories and command not found, I can't figure it out. I am using this script in a package with a full cenote-taker2 installation.
python unlimited_breadsticks.py -c contigs.fasta -r viruses_RNA_results -m 20 -t 4 -p False -db rna_virus --minimum_length_linear 3000 --lin_minimum_hallmark_genes 2 --circ_minimum_hallmark_genes 1
@@@@@@@@@@@@@@@@@@@@@@@@@ time update: locating inputs: 01-27-22---06:50:07 /media/sf_S_DRIVE/Cenote_Taker2/Cenote-Taker2/contigs.fasta File with .fasta extension detected, attempting to keep contigs over 1000 nt and find circular sequences with apc.pl viruses_RNA_results1050.fasta is circular/has DTRs viruses_RNA_results108.fasta is circular/has DTRs viruses_RNA_results11878.fasta is circular/has DTRs viruses_RNA_results12114.fasta is circular/has DTRs viruses_RNA_results1229.fasta is circular/has DTRs viruses_RNA_results1340.fasta is circular/has DTRs viruses_RNA_results1398.fasta is circular/has DTRs viruses_RNA_results1438.fasta is circular/has DTRs viruses_RNA_results1451.fasta is circular/has DTRs viruses_RNA_results14681.fasta is circular/has DTRs viruses_RNA_results1472.fasta is circular/has DTRs viruses_RNA_results15476.fasta is circular/has DTRs viruses_RNA_results15601.fasta is circular/has DTRs viruses_RNA_results1592.fasta is circular/has DTRs viruses_RNA_results16857.fasta is circular/has DTRs
Circular fasta file(s) detected
Putting non-circular contigs in a separate directory Looking for non-circular contigs that have at least 1 virus-specific or plasmid-specific domain time update: running prodigal on linear contigs 01-27-22---07:37:13 time update: splitting running hmmscan for linear contigs against virus hallmark gene database: rna_virus 01-27-22---07:46:38 /media/sf_S_DRIVE/Cenote_Taker2/Cenote-Taker2/unlimited_breadsticks_0.1.sh: line 241: bc: command not found /media/sf_S_DRIVE/Cenote_Taker2/Cenote-Taker2/unlimited_breadsticks_0.1.sh: line 242: bc: command not found /media/sf_S_DRIVE/Cenote_Taker2/Cenote-Taker2/unlimited_breadsticks_0.1.sh: line 243: [: =: unary operator expected awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted in %' cat: 'SPLIT_LARGE_GENOMEAAAA.hmmscan.out': No such file or directory time update: Calling ORFs for circular/DTR sequences with prodigal 01-27-22---07:47:06 /media/sf_S_DRIVE/Cenote_Taker2/Cenote-Taker2/unlimited_breadsticks_0.1.sh: line 328: bc: command not found /media/sf_S_DRIVE/Cenote_Taker2/Cenote-Taker2/unlimited_breadsticks_0.1.sh: line 329: bc: command not found /media/sf_S_DRIVE/Cenote_Taker2/Cenote-Taker2/unlimited_breadsticks_0.1.sh: line 330: [: =: unary operator expected awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted in %' time update: running hmmscan on circular/DTR contigs on virus hallmark gene database: rna_virus 01-27-22---07:47:16 cat: 'SPLIT_CIRCULARAAAA.hmmscan.out': No such file or directory removing ancillary files
time update: Finishing 01-27-22---07:47:23 output directory: viruses_RNA_results CENOTE UNLIMITED BREADSTICKS HAS FINISHED SERVING BREADSTICKS