Invalid command code K

[susheelbhanu]

Hi,

I'm getting the following error, trying to run the test file included with the package.

awk: division by zero
input record number 192, file
source line number 1
sed: 1: "krona/F3D0.tmp": invalid command code k
sed: 1: "1iAccum%": command i expects \ followed by text
sed: 1: "krona/F3D0.tsv": invalid command code k
awk: division by zero
input record number 186, file
source line number 1
sed: 1: "krona/F3D9.tmp": invalid command code k
sed: 1: "1iAccum%": command i expects \ followed by text
sed: 1: "krona/F3D9.tsv": invalid command code k
awk: division by zero
input record number 161, file
source line number 1
sed: 1: "krona/MOCK.tmp": invalid command code k
sed: 1: "1iAccum%": command i expects \ followed by text
sed: 1: "krona/MOCK.tsv": invalid command code k
sed: 1: "krona/F3D0.tmp": invalid command code k
sed: 1: "krona/F3D9.tmp": invalid command code k
sed: 1: "krona/MOCK.tmp": invalid command code k
./OTUsamples2krona.v0.2.3.sh: line 100: rename: command not found
sed: 1: "krona/F3D0.tmp.tax": invalid command code k
Writing krona/F3D0.tmp.tax.html...
sed: 1: "krona/F3D9.tmp.tax": invalid command code k
Writing krona/F3D9.tmp.tax.html...
sed: 1: "krona/MOCK.tmp.tax": invalid command code k
Writing krona/MOCK.tmp.tax.html...
./OTUsamples2krona.v0.2.3.sh: line 111: rename: command not found
\e[33m3 Krona charts have been created in krona/\e[0m
Adios

Any help is appreciated. Thank you!!

[GenomicaMicrob]

Hi, sorry to hear this, it is a bit difficult to trace the error without more info, it seems that somehow the script was not able to read or process the samples-tax.tsv file. It does not have many dependencies other than the Kronatools and some programs that come bundled by default with any linux/Ubuntu distribution (sed, awk, cut, paste, etc.). Can you check that the example file is correct by opening it with head, for example and see that it has the following structure: F3D0 F3D9 MOCK domain;phylum;class;order;family;genus;species 2 0 0 Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Unclassified_g;Unclassified_s 0 0 621 Bacteria;Firmicutes;Bacilli;Bacillales;Staphylococcaceae;Unclassified_g;Unclassified_s 0 3 0 Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Coriobacteriaceae;Unclassified_g;Unclassified_s I assume you run ./OTUsamples2krona.v0.2.3.sh samples-tax.tsv Bruno Gomez-Gil CIAD, Mazatlán Unit AP 711 Mazatlán, Sinaloa México 82000 +(52) 669 9898700 ext 245 https://www.researchgate.net/profile/Bruno_Gomez-Gil El 2 de jul de 2019 6:10 -0600, Susheel Bhanu Busi <notifications@github.com>, escribió:

…

Hi, I'm getting the following error, trying to run the test file included with the package. awk: division by zero input record number 192, file source line number 1 sed: 1: "krona/F3D0.tmp": invalid command code k sed: 1: "1iAccum%": command i expects \ followed by text sed: 1: "krona/F3D0.tsv": invalid command code k awk: division by zero input record number 186, file source line number 1 sed: 1: "krona/F3D9.tmp": invalid command code k sed: 1: "1iAccum%": command i expects \ followed by text sed: 1: "krona/F3D9.tsv": invalid command code k awk: division by zero input record number 161, file source line number 1 sed: 1: "krona/MOCK.tmp": invalid command code k sed: 1: "1iAccum%": command i expects \ followed by text sed: 1: "krona/MOCK.tsv": invalid command code k sed: 1: "krona/F3D0.tmp": invalid command code k sed: 1: "krona/F3D9.tmp": invalid command code k sed: 1: "krona/MOCK.tmp": invalid command code k ./OTUsamples2krona.v0.2.3.sh: line 100: rename: command not found sed: 1: "krona/F3D0.tmp.tax": invalid command code k Writing krona/F3D0.tmp.tax.html... sed: 1: "krona/F3D9.tmp.tax": invalid command code k Writing krona/F3D9.tmp.tax.html... sed: 1: "krona/MOCK.tmp.tax": invalid command code k Writing krona/MOCK.tmp.tax.html... ./OTUsamples2krona.v0.2.3.sh: line 111: rename: command not found \e[33m3 Krona charts have been created in krona/\e[0m Adios Any help is appreciated. Thank you!! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[susheelbhanu]

Hi Bruno,

Thanks for the reply. Here's the 'head' of the file

F3D0 F3D9 MOCK domain;phylum;class;order;family;genus;species
2 0 0 Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Unclassified_g;Unclassified_s
0 0 621 Bacteria;Firmicutes;Bacilli;Bacillales;Staphylococcaceae;Unclassified_g;Unclassified_s
0 3 0 Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Coriobacteriaceae;Unclassified_g;Unclassified_s
2 0 0 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;S24-7_f;Unclassified_g;Unclassified_s
2 0 0 Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Unclassified_g;Unclassified_s
2 0 0 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Unclassified_g;Unclassified_s
0 2 0 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Bacteroidaceae;Unclassified_g;Unclassified_s
0 2 0 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Rikenellaceae;Unclassified_g;Unclassified_s
12 0 0 Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Unclassified_g;Unclassified_s

And yes, I was running ./OTUsamples2krona.v0.2.3.sh samples-tax.tsv.

[liubingdong]

Hi,

I'm getting the following error, trying to run the test file included with the package.

awk: division by zero
input record number 192, file
source line number 1
sed: 1: "krona/F3D0.tmp": invalid command code k
sed: 1: "1iAccum%": command i expects \ followed by text
sed: 1: "krona/F3D0.tsv": invalid command code k
awk: division by zero
input record number 186, file
source line number 1
sed: 1: "krona/F3D9.tmp": invalid command code k
sed: 1: "1iAccum%": command i expects \ followed by text
sed: 1: "krona/F3D9.tsv": invalid command code k
awk: division by zero
input record number 161, file
source line number 1
sed: 1: "krona/MOCK.tmp": invalid command code k
sed: 1: "1iAccum%": command i expects \ followed by text
sed: 1: "krona/MOCK.tsv": invalid command code k
sed: 1: "krona/F3D0.tmp": invalid command code k
sed: 1: "krona/F3D9.tmp": invalid command code k
sed: 1: "krona/MOCK.tmp": invalid command code k
./OTUsamples2krona.v0.2.3.sh: line 100: rename: command not found
sed: 1: "krona/F3D0.tmp.tax": invalid command code k
Writing krona/F3D0.tmp.tax.html...
sed: 1: "krona/F3D9.tmp.tax": invalid command code k
Writing krona/F3D9.tmp.tax.html...
sed: 1: "krona/MOCK.tmp.tax": invalid command code k
Writing krona/MOCK.tmp.tax.html...
./OTUsamples2krona.v0.2.3.sh: line 111: rename: command not found
\e[33m3 Krona charts have been created in krona/\e[0m
Adios

Any help is appreciated. Thank you!!

Hi, I encountered the same problem, and solved it. Just install KronaTools using conda install krona before you run the code ./OTUsamples2krona.v0.2.3.sh samples-tax.tsv. I hope it could help u.