mtisza1 / cenote_unlimited_breadsticks Goto Github PK

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

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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_GENOME_AA_*AA.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_CIRCULAR_AA_*AA.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

Dear Mike,

Thank you for developing this useful tool! Could you please help me with one question about its application? The GitHub page describing Unlimited Breadsticks says “Unlimited Breadsticks does not do post-hallmark-gene-identification computations to flag plasmid and conjugative element sequences that occasionally slip through”, but Unlimited Breadsticks has an option “--filter_out_plasmids”. Could you please advise, if I specify “--filter_out_plasmids True” when running Unlimited Breadsticks, would it try to remove plasmids from the viral contigs list in the same way as Cenote-Taker2?

Kind regards,
Anastasia