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command not found #34

Closed nana-marinbio closed 2 years ago

nana-marinbio commented 2 years ago

HI BLCA team,

I installed BLCA, ran script 1 and it went fine. But with script 2 I got: $: command not found.

I changed the shebang to #!/usr/bin/env python3, but got the same error, which is weird since step 1 was ok.

Any suggestion is appreciated, tks Ana Paula

YJulyXing commented 2 years ago

Hi, could you send us the exact commands you used that causing the error?

nana-marinbio @.***> 于 2022年4月6日周三 上午5:51写道：

HI BLCA team,

I installed BLCA, ran script 1 and it went fine. But with script 2 I got: $: command not found.

I changed the shebang to #!/usr/bin/env python3, but got the same error, which is weird since step 1 was ok.

Any suggestion is appreciated, tks Ana Paula

— Reply to this email directly, view it on GitHub https://github.com/qunfengdong/BLCA/issues/34, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKABWISN46WTKSQHMZOG6XLVDVNB5ANCNFSM5SVOZGRQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

nana-marinbio commented 2 years ago

Hi @YJulyXing

The command line was ubuntu@ubuntu18:~/BLCA$ <python 2.blca_main.py -i test.fasta> $: command not found

The first command which worked fine was: ubuntu@ubuntu18:~/BLCA$ <python 1.subset_db_acc.py> It worked fine and the final message was:

Loading names.dmp...DONE! Generating a subset of taxonomy file. Taxonomy file generated!

YJulyXing commented 2 years ago

Hi,

That is weird. Could you check if your installations, file directory and everything is correct? Could you send some screenshots of the file directories, and the command line outputs when you run BLCA as well? We need some more information because this issue seems weird. Thank you.

On Wed, Apr 6, 2022 at 9:36 AM nana-marinbio @.***> wrote:

Hi @YJulyXing https://github.com/YJulyXing

The command line was @.***:~/BLCA$ python 2.blca_main.py -i test.fasta $: command not found

The first command which worked fine was: @.***:~/BLCA$ python 1.subset_db_acc.py It worked fine and the final message was:

Loading names.dmp...DONE! Generating a subset of taxonomy file. Taxonomy file generated!

— Reply to this email directly, view it on GitHub https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1090282591, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKABWIW5HEMXTFIBGQVKGQTVDWHPLANCNFSM5SVOZGRQ . You are receiving this because you were mentioned.Message ID: @.***>

-- Yue "July" Xing, Ph.D. Postdoctoral research associate Ph.D. in Genetics and MS in Statistics at Texas A&M University Center for Biomedical Informatics Department of Medicine Stritch School of Medicine Loyola University Chicago

nana-marinbio commented 2 years ago

Hi @YJulyXing,

I was just checking those and found out biopython was under python 2.7, so I re-installed specifying: python3.6 -m pip install biopython

And it worked! Tks anyway

nana-marinbio commented 2 years ago

Hi Dr XIng, I posted an issue , #35 16S database not recognized https://github.com/qunfengdong/BLCA/issues/35#issue-1195688729 Could you please take a look? I followed step 1: $python 1.subset_db_acc.py But the script generates an error message: BLAST Database error: Error: Not a valid version 4 database. (See below the files generated in db directory)

I downloaded manually directly from NCBI and compared both 16S_ribosomal_RNA.tar.gz https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz files with md5sum, and the result was OK, meaning they are identical. I have the latest blast ncbi-blast-2.13.0+, python3.6.9 biopython-1.79 clustalo 1.2.4-1 musclemuscle3.8.31

How can I manage this? Thank you in advance AP

@.**:~/BLCA/db$ ls -lh total 660M -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACC.taxonomy -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACCtaxID* -rw-rw-r-- 1 ubuntu ubuntu 1.2M Mar 29 06:36 16S_ribosomal_RNA.ndb -rw-rw-r-- 1 ubuntu ubuntu 3.4M Mar 29 06:36 16S_ribosomal_RNA.nhr -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.nin -rw-rw-r-- 1 ubuntu ubuntu 175K Mar 29 06:36 16S_ribosomal_RNA.nnd -rw-rw-r-- 1 ubuntu ubuntu 748 Mar 29 06:36 16S_ribosomal_RNA.nni -rw-rw-r-- 1 ubuntu ubuntu 88K Mar 29 06:36 16S_ribosomal_RNA.nog -rw-rw-r-- 1 ubuntu ubuntu 437K Mar 29 06:36 16S_ribosomal_RNA.nos -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.not -rw-rw-r-- 1 ubuntu ubuntu 7.9M Mar 29 06:36 16S_ribosomal_RNA.nsq -rw-rw-r-- 1 ubuntu ubuntu 592K Mar 29 06:36 16S_ribosomal_RNA.ntf -rw-rw-r-- 1 ubuntu ubuntu 154K Mar 29 06:36 16S_ribosomal_RNA.nto -rw-rw-r-- 1 ubuntu ubuntu 37M Mar 29 06:36 16S_ribosomal_RNA.tar.gz -rw-r--r-- 1 ubuntu ubuntu 19M Apr 6 12:29 citations.dmp -rw-r--r-- 1 ubuntu ubuntu 4.2M Apr 6 12:26 delnodes.dmp -rw-r--r-- 1 ubuntu ubuntu 452 Apr 6 12:20 division.dmp -rw-r--r-- 1 ubuntu ubuntu 17K Apr 6 12:29 gc.prt -rw-r--r-- 1 ubuntu ubuntu 4.9K Apr 6 12:20 gencode.dmp -rw-r--r-- 1 ubuntu ubuntu 1.2M Apr 6 12:26 merged.dmp -rw-r--r-- 1 ubuntu ubuntu 208M Apr 6 12:29 names.dmp -rw-r--r-- 1 ubuntu ubuntu 159M Apr 6 12:28 nodes.dmp -rw-rw---- 1 ubuntu ubuntu 2.7K Sep 11 2019 readme.txt -rw-rw-r-- 1 ubuntu ubuntu 149M Mar 29 06:36 taxdb.btd -rw-rw-r-- 1 ubuntu ubuntu 16M Mar 29 06:36 taxdb.bti -rw-rw-r-- 1 ubuntu ubuntu 56M Apr 6 13:25 taxdmp.zip

(((·> ~~ >(((·> ~~ >(((·> Ana Paula B. Moreira, PhD Federal University of Rio de Janeiro- UFRJ Biology Institute Phone: +55 21 988220753 ID Orcid https://orcid.org/0000-0001-9757-1317 ResearchGate https://www.researchgate.net/profile/Ana_Paula_Moreira4 Loop https://loop.frontiersin.org/people/242799/overview Twitter @AnaPaula_BM https://twitter.com/AnaPaula_BM FB @somostodosciencia https://www.facebook.com/somostodosciencia

On Wed, Apr 6, 2022 at 12:40 PM YJulyXing @.***> wrote:

Hi,

That is weird. Could you check if your installations, file directory and everything is correct? Could you send some screenshots of the file directories, and the command line outputs when you run BLCA as well? We need some more information because this issue seems weird. Thank you.

On Wed, Apr 6, 2022 at 9:36 AM nana-marinbio @.***> wrote:

Hi @YJulyXing https://github.com/YJulyXing

The command line was @.***:~/BLCA$ python 2.blca_main.py -i test.fasta $: command not found

The first command which worked fine was: @.***:~/BLCA$ python 1.subset_db_acc.py It worked fine and the final message was:

Loading names.dmp...DONE! Generating a subset of taxonomy file. Taxonomy file generated!

— Reply to this email directly, view it on GitHub https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1090282591, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AKABWIW5HEMXTFIBGQVKGQTVDWHPLANCNFSM5SVOZGRQ

. You are receiving this because you were mentioned.Message ID: @.***>

-- Yue "July" Xing, Ph.D. Postdoctoral research associate Ph.D. in Genetics and MS in Statistics at Texas A&M University Center for Biomedical Informatics Department of Medicine Stritch School of Medicine Loyola University Chicago

— Reply to this email directly, view it on GitHub https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1090417220, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEZPY7CCIUJWYUPOEWI7UU3VDWV53ANCNFSM5SVOZGRQ . You are receiving this because you authored the thread.Message ID: @.***>

YJulyXing commented 2 years ago

Hi, the database file you downloaded is not a version 4 database. The blast tool you have requires a version 4 database.

nana-marinbio @.***> 于 2022年4月13日周三 上午10:24写道：

Hi Dr XIng, I posted an issue , #35 16S database not recognized https://github.com/qunfengdong/BLCA/issues/35#issue-1195688729 Could you please take a look? I followed step 1: $python 1.subset_db_acc.py But the script generates an error message: BLAST Database error: Error: Not a valid version 4 database. (See below the files generated in db directory)

I downloaded manually directly from NCBI and compared both 16S_ribosomal_RNA.tar.gz https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz files with md5sum, and the result was OK, meaning they are identical. I have the latest blast ncbi-blast-2.13.0+, python3.6.9 biopython-1.79 clustalo 1.2.4-1 musclemuscle3.8.31

How can I manage this? Thank you in advance AP

@.**:~/BLCA/db$ ls -lh total 660M -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACC.taxonomy -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACCtaxID* -rw-rw-r-- 1 ubuntu ubuntu 1.2M Mar 29 06:36 16S_ribosomal_RNA.ndb -rw-rw-r-- 1 ubuntu ubuntu 3.4M Mar 29 06:36 16S_ribosomal_RNA.nhr -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.nin -rw-rw-r-- 1 ubuntu ubuntu 175K Mar 29 06:36 16S_ribosomal_RNA.nnd -rw-rw-r-- 1 ubuntu ubuntu 748 Mar 29 06:36 16S_ribosomal_RNA.nni -rw-rw-r-- 1 ubuntu ubuntu 88K Mar 29 06:36 16S_ribosomal_RNA.nog -rw-rw-r-- 1 ubuntu ubuntu 437K Mar 29 06:36 16S_ribosomal_RNA.nos -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.not -rw-rw-r-- 1 ubuntu ubuntu 7.9M Mar 29 06:36 16S_ribosomal_RNA.nsq -rw-rw-r-- 1 ubuntu ubuntu 592K Mar 29 06:36 16S_ribosomal_RNA.ntf -rw-rw-r-- 1 ubuntu ubuntu 154K Mar 29 06:36 16S_ribosomal_RNA.nto -rw-rw-r-- 1 ubuntu ubuntu 37M Mar 29 06:36 16S_ribosomal_RNA.tar.gz -rw-r--r-- 1 ubuntu ubuntu 19M Apr 6 12:29 citations.dmp -rw-r--r-- 1 ubuntu ubuntu 4.2M Apr 6 12:26 delnodes.dmp -rw-r--r-- 1 ubuntu ubuntu 452 Apr 6 12:20 division.dmp -rw-r--r-- 1 ubuntu ubuntu 17K Apr 6 12:29 gc.prt -rw-r--r-- 1 ubuntu ubuntu 4.9K Apr 6 12:20 gencode.dmp -rw-r--r-- 1 ubuntu ubuntu 1.2M Apr 6 12:26 merged.dmp -rw-r--r-- 1 ubuntu ubuntu 208M Apr 6 12:29 names.dmp -rw-r--r-- 1 ubuntu ubuntu 159M Apr 6 12:28 nodes.dmp -rw-rw---- 1 ubuntu ubuntu 2.7K Sep 11 2019 readme.txt -rw-rw-r-- 1 ubuntu ubuntu 149M Mar 29 06:36 taxdb.btd -rw-rw-r-- 1 ubuntu ubuntu 16M Mar 29 06:36 taxdb.bti -rw-rw-r-- 1 ubuntu ubuntu 56M Apr 6 13:25 taxdmp.zip

(((·> ~~ >(((·> ~~ >(((·> Ana Paula B. Moreira, PhD Federal University of Rio de Janeiro- UFRJ Biology Institute Phone: +55 21 988220753 ID Orcid https://orcid.org/0000-0001-9757-1317 ResearchGate https://www.researchgate.net/profile/Ana_Paula_Moreira4 Loop https://loop.frontiersin.org/people/242799/overview Twitter @AnaPaula_BM https://twitter.com/AnaPaula_BM FB @somostodosciencia https://www.facebook.com/somostodosciencia

On Wed, Apr 6, 2022 at 12:40 PM YJulyXing @.***> wrote:

Hi,

That is weird. Could you check if your installations, file directory and everything is correct? Could you send some screenshots of the file directories, and the command line outputs when you run BLCA as well? We need some more information because this issue seems weird. Thank you.

On Wed, Apr 6, 2022 at 9:36 AM nana-marinbio @.***> wrote:

Hi @YJulyXing https://github.com/YJulyXing

The command line was @.***:~/BLCA$ python 2.blca_main.py -i test.fasta $: command not found

The first command which worked fine was: @.***:~/BLCA$ python 1.subset_db_acc.py It worked fine and the final message was:

Loading names.dmp...DONE! Generating a subset of taxonomy file. Taxonomy file generated!

— Reply to this email directly, view it on GitHub <https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1090282591 , or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AKABWIW5HEMXTFIBGQVKGQTVDWHPLANCNFSM5SVOZGRQ

. You are receiving this because you were mentioned.Message ID: @.***>

-- Yue "July" Xing, Ph.D. Postdoctoral research associate Ph.D. in Genetics and MS in Statistics at Texas A&M University Center for Biomedical Informatics Department of Medicine Stritch School of Medicine Loyola University Chicago

— Reply to this email directly, view it on GitHub https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1090417220, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AEZPY7CCIUJWYUPOEWI7UU3VDWV53ANCNFSM5SVOZGRQ

. You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1098115330, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKABWIXQEWES7GIUIOEQJKTVE3KJLANCNFSM5SVOZGRQ . You are receiving this because you were mentioned.Message ID: @.***>

nana-marinbio commented 2 years ago

Which blast tool I need? because the 2.13 is the latest Tks

Em qua., 13 de abr. de 2022 às 11:49, YJulyXing @.***> escreveu:

Hi, the database file you downloaded is not a version 4 database. The blast tool you have requires a version 4 database.

nana-marinbio @.***> 于 2022年4月13日周三 上午10:24写道：

Hi Dr XIng, I posted an issue , #35 16S database not recognized https://github.com/qunfengdong/BLCA/issues/35#issue-1195688729 Could you please take a look? I followed step 1: $python 1.subset_db_acc.py But the script generates an error message: BLAST Database error: Error: Not a valid version 4 database. (See below the files generated in db directory)

I downloaded manually directly from NCBI and compared both 16S_ribosomal_RNA.tar.gz https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz files with md5sum, and the result was OK, meaning they are identical. I have the latest blast ncbi-blast-2.13.0+, python3.6.9 biopython-1.79 clustalo 1.2.4-1 musclemuscle3.8.31

How can I manage this? Thank you in advance AP

@.**:~/BLCA/db$ ls -lh total 660M -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACC.taxonomy -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACCtaxID* -rw-rw-r-- 1 ubuntu ubuntu 1.2M Mar 29 06:36 16S_ribosomal_RNA.ndb -rw-rw-r-- 1 ubuntu ubuntu 3.4M Mar 29 06:36 16S_ribosomal_RNA.nhr -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.nin -rw-rw-r-- 1 ubuntu ubuntu 175K Mar 29 06:36 16S_ribosomal_RNA.nnd -rw-rw-r-- 1 ubuntu ubuntu 748 Mar 29 06:36 16S_ribosomal_RNA.nni -rw-rw-r-- 1 ubuntu ubuntu 88K Mar 29 06:36 16S_ribosomal_RNA.nog -rw-rw-r-- 1 ubuntu ubuntu 437K Mar 29 06:36 16S_ribosomal_RNA.nos -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.not -rw-rw-r-- 1 ubuntu ubuntu 7.9M Mar 29 06:36 16S_ribosomal_RNA.nsq -rw-rw-r-- 1 ubuntu ubuntu 592K Mar 29 06:36 16S_ribosomal_RNA.ntf -rw-rw-r-- 1 ubuntu ubuntu 154K Mar 29 06:36 16S_ribosomal_RNA.nto -rw-rw-r-- 1 ubuntu ubuntu 37M Mar 29 06:36 16S_ribosomal_RNA.tar.gz -rw-r--r-- 1 ubuntu ubuntu 19M Apr 6 12:29 citations.dmp -rw-r--r-- 1 ubuntu ubuntu 4.2M Apr 6 12:26 delnodes.dmp -rw-r--r-- 1 ubuntu ubuntu 452 Apr 6 12:20 division.dmp -rw-r--r-- 1 ubuntu ubuntu 17K Apr 6 12:29 gc.prt -rw-r--r-- 1 ubuntu ubuntu 4.9K Apr 6 12:20 gencode.dmp -rw-r--r-- 1 ubuntu ubuntu 1.2M Apr 6 12:26 merged.dmp -rw-r--r-- 1 ubuntu ubuntu 208M Apr 6 12:29 names.dmp -rw-r--r-- 1 ubuntu ubuntu 159M Apr 6 12:28 nodes.dmp -rw-rw---- 1 ubuntu ubuntu 2.7K Sep 11 2019 readme.txt -rw-rw-r-- 1 ubuntu ubuntu 149M Mar 29 06:36 taxdb.btd -rw-rw-r-- 1 ubuntu ubuntu 16M Mar 29 06:36 taxdb.bti -rw-rw-r-- 1 ubuntu ubuntu 56M Apr 6 13:25 taxdmp.zip

(((·> ~~ >(((·> ~~ >(((·> Ana Paula B. Moreira, PhD Federal University of Rio de Janeiro- UFRJ Biology Institute Phone: +55 21 988220753 ID Orcid https://orcid.org/0000-0001-9757-1317 ResearchGate https://www.researchgate.net/profile/Ana_Paula_Moreira4 Loop https://loop.frontiersin.org/people/242799/overview Twitter @AnaPaula_BM https://twitter.com/AnaPaula_BM FB @somostodosciencia https://www.facebook.com/somostodosciencia

On Wed, Apr 6, 2022 at 12:40 PM YJulyXing @.***> wrote:

Hi,

That is weird. Could you check if your installations, file directory and everything is correct? Could you send some screenshots of the file directories, and the command line outputs when you run BLCA as well? We need some more information because this issue seems weird. Thank you.

On Wed, Apr 6, 2022 at 9:36 AM nana-marinbio @.***> wrote:

Hi @YJulyXing https://github.com/YJulyXing

The command line was @.***:~/BLCA$ python 2.blca_main.py -i test.fasta $: command not found

The first command which worked fine was: @.***:~/BLCA$ python 1.subset_db_acc.py It worked fine and the final message was:

Loading names.dmp...DONE! Generating a subset of taxonomy file. Taxonomy file generated!

— Reply to this email directly, view it on GitHub < https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1090282591 , or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AKABWIW5HEMXTFIBGQVKGQTVDWHPLANCNFSM5SVOZGRQ

. You are receiving this because you were mentioned.Message ID: @.***>

-- Yue "July" Xing, Ph.D. Postdoctoral research associate Ph.D. in Genetics and MS in Statistics at Texas A&M University Center for Biomedical Informatics Department of Medicine Stritch School of Medicine Loyola University Chicago

— Reply to this email directly, view it on GitHub <https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1090417220 , or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AEZPY7CCIUJWYUPOEWI7UU3VDWV53ANCNFSM5SVOZGRQ

. You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1098115330, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AKABWIXQEWES7GIUIOEQJKTVE3KJLANCNFSM5SVOZGRQ

. You are receiving this because you were mentioned.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1098145625, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEZPY7G4FJYUICD4CFWJXV3VE3NFTANCNFSM5SVOZGRQ . You are receiving this because you modified the open/close state.Message ID: @.***>

--

(((·> ~~ >(((·> ~~ >(((·> Ana Paula B. Moreira, PhD Federal University of Rio de Janeiro- UFRJ Biology Institute Phone: +55 21 988220753 ID Orcid https://orcid.org/0000-0001-9757-1317 ResearchGate https://www.researchgate.net/profile/Ana_Paula_Moreira4 Loop https://loop.frontiersin.org/people/242799/overview Twitter @AnaPaula_BM https://twitter.com/AnaPaula_BM FB @somostodosciencia https://www.facebook.com/somostodosciencia

YJulyXing commented 2 years ago

Blast 2.9 is fine. And you could download version 4 database from NCBI. We will work on updating BLCA to make it compatible with the latest blast.

nana-marinbio @.***> 于 2022年4月13日周三 上午10:51写道：

Which blast tool I need? because the 2.13 is the latest Tks

Em qua., 13 de abr. de 2022 às 11:49, YJulyXing @.***> escreveu:

Hi, the database file you downloaded is not a version 4 database. The blast tool you have requires a version 4 database.

nana-marinbio @.***> 于 2022年4月13日周三 上午10:24写道：

Hi Dr XIng, I posted an issue , #35 16S database not recognized https://github.com/qunfengdong/BLCA/issues/35#issue-1195688729 Could you please take a look? I followed step 1: $python 1.subset_db_acc.py But the script generates an error message: BLAST Database error: Error: Not a valid version 4 database. (See below the files generated in db directory)

I downloaded manually directly from NCBI and compared both 16S_ribosomal_RNA.tar.gz https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz files with md5sum, and the result was OK, meaning they are identical. I have the latest blast ncbi-blast-2.13.0+, python3.6.9 biopython-1.79 clustalo 1.2.4-1 musclemuscle3.8.31

How can I manage this? Thank you in advance AP

@.**:~/BLCA/db$ ls -lh total 660M -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACC.taxonomy -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACCtaxID* -rw-rw-r-- 1 ubuntu ubuntu 1.2M Mar 29 06:36 16S_ribosomal_RNA.ndb -rw-rw-r-- 1 ubuntu ubuntu 3.4M Mar 29 06:36 16S_ribosomal_RNA.nhr -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.nin -rw-rw-r-- 1 ubuntu ubuntu 175K Mar 29 06:36 16S_ribosomal_RNA.nnd -rw-rw-r-- 1 ubuntu ubuntu 748 Mar 29 06:36 16S_ribosomal_RNA.nni -rw-rw-r-- 1 ubuntu ubuntu 88K Mar 29 06:36 16S_ribosomal_RNA.nog -rw-rw-r-- 1 ubuntu ubuntu 437K Mar 29 06:36 16S_ribosomal_RNA.nos -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.not -rw-rw-r-- 1 ubuntu ubuntu 7.9M Mar 29 06:36 16S_ribosomal_RNA.nsq -rw-rw-r-- 1 ubuntu ubuntu 592K Mar 29 06:36 16S_ribosomal_RNA.ntf -rw-rw-r-- 1 ubuntu ubuntu 154K Mar 29 06:36 16S_ribosomal_RNA.nto -rw-rw-r-- 1 ubuntu ubuntu 37M Mar 29 06:36 16S_ribosomal_RNA.tar.gz -rw-r--r-- 1 ubuntu ubuntu 19M Apr 6 12:29 citations.dmp -rw-r--r-- 1 ubuntu ubuntu 4.2M Apr 6 12:26 delnodes.dmp -rw-r--r-- 1 ubuntu ubuntu 452 Apr 6 12:20 division.dmp -rw-r--r-- 1 ubuntu ubuntu 17K Apr 6 12:29 gc.prt -rw-r--r-- 1 ubuntu ubuntu 4.9K Apr 6 12:20 gencode.dmp -rw-r--r-- 1 ubuntu ubuntu 1.2M Apr 6 12:26 merged.dmp -rw-r--r-- 1 ubuntu ubuntu 208M Apr 6 12:29 names.dmp -rw-r--r-- 1 ubuntu ubuntu 159M Apr 6 12:28 nodes.dmp -rw-rw---- 1 ubuntu ubuntu 2.7K Sep 11 2019 readme.txt -rw-rw-r-- 1 ubuntu ubuntu 149M Mar 29 06:36 taxdb.btd -rw-rw-r-- 1 ubuntu ubuntu 16M Mar 29 06:36 taxdb.bti -rw-rw-r-- 1 ubuntu ubuntu 56M Apr 6 13:25 taxdmp.zip

(((·> ~~ >(((·> ~~ >(((·> Ana Paula B. Moreira, PhD Federal University of Rio de Janeiro- UFRJ Biology Institute Phone: +55 21 988220753 ID Orcid https://orcid.org/0000-0001-9757-1317 ResearchGate https://www.researchgate.net/profile/Ana_Paula_Moreira4 Loop https://loop.frontiersin.org/people/242799/overview Twitter @AnaPaula_BM https://twitter.com/AnaPaula_BM FB @somostodosciencia https://www.facebook.com/somostodosciencia

On Wed, Apr 6, 2022 at 12:40 PM YJulyXing @.***> wrote:

Hi,

That is weird. Could you check if your installations, file directory and everything is correct? Could you send some screenshots of the file directories, and the command line outputs when you run BLCA as well? We need some more information because this issue seems weird. Thank you.

On Wed, Apr 6, 2022 at 9:36 AM nana-marinbio @.***> wrote:

Hi @YJulyXing https://github.com/YJulyXing

The command line was @.***:~/BLCA$ python 2.blca_main.py -i test.fasta $: command not found

The first command which worked fine was: @.***:~/BLCA$ python 1.subset_db_acc.py It worked fine and the final message was:

Loading names.dmp...DONE! Generating a subset of taxonomy file. Taxonomy file generated!

— Reply to this email directly, view it on GitHub < https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1090282591 , or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AKABWIW5HEMXTFIBGQVKGQTVDWHPLANCNFSM5SVOZGRQ

. You are receiving this because you were mentioned.Message ID: @.***>

-- Yue "July" Xing, Ph.D. Postdoctoral research associate Ph.D. in Genetics and MS in Statistics at Texas A&M University Center for Biomedical Informatics Department of Medicine Stritch School of Medicine Loyola University Chicago

— Reply to this email directly, view it on GitHub < https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1090417220 , or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AEZPY7CCIUJWYUPOEWI7UU3VDWV53ANCNFSM5SVOZGRQ

. You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub <https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1098115330 , or unsubscribe <

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. You are receiving this because you were mentioned.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1098145625, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AEZPY7G4FJYUICD4CFWJXV3VE3NFTANCNFSM5SVOZGRQ

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nana-marinbio commented 2 years ago

Many tks

Em qua., 13 de abr. de 2022 às 12:21, YJulyXing @.***> escreveu:

Blast 2.9 is fine. And you could download version 4 database from NCBI. We will work on updating BLCA to make it compatible with the latest blast.

nana-marinbio @.***> 于 2022年4月13日周三 上午10:51写道：

Which blast tool I need? because the 2.13 is the latest Tks

Em qua., 13 de abr. de 2022 às 11:49, YJulyXing @.***> escreveu:

Hi, the database file you downloaded is not a version 4 database. The blast tool you have requires a version 4 database.

nana-marinbio @.***> 于 2022年4月13日周三 上午10:24写道：

Hi Dr XIng, I posted an issue , #35 16S database not recognized https://github.com/qunfengdong/BLCA/issues/35#issue-1195688729 Could you please take a look? I followed step 1: $python 1.subset_db_acc.py But the script generates an error message: BLAST Database error: Error: Not a valid version 4 database. (See below the files generated in db directory)

I downloaded manually directly from NCBI and compared both 16S_ribosomal_RNA.tar.gz https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz files with md5sum, and the result was OK, meaning they are identical. I have the latest blast ncbi-blast-2.13.0+, python3.6.9 biopython-1.79 clustalo 1.2.4-1 musclemuscle3.8.31

How can I manage this? Thank you in advance AP

@.**:~/BLCA/db$ ls -lh total 660M -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACC.taxonomy -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACCtaxID* -rw-rw-r-- 1 ubuntu ubuntu 1.2M Mar 29 06:36 16S_ribosomal_RNA.ndb -rw-rw-r-- 1 ubuntu ubuntu 3.4M Mar 29 06:36 16S_ribosomal_RNA.nhr -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.nin -rw-rw-r-- 1 ubuntu ubuntu 175K Mar 29 06:36 16S_ribosomal_RNA.nnd -rw-rw-r-- 1 ubuntu ubuntu 748 Mar 29 06:36 16S_ribosomal_RNA.nni -rw-rw-r-- 1 ubuntu ubuntu 88K Mar 29 06:36 16S_ribosomal_RNA.nog -rw-rw-r-- 1 ubuntu ubuntu 437K Mar 29 06:36 16S_ribosomal_RNA.nos -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.not -rw-rw-r-- 1 ubuntu ubuntu 7.9M Mar 29 06:36 16S_ribosomal_RNA.nsq -rw-rw-r-- 1 ubuntu ubuntu 592K Mar 29 06:36 16S_ribosomal_RNA.ntf -rw-rw-r-- 1 ubuntu ubuntu 154K Mar 29 06:36 16S_ribosomal_RNA.nto -rw-rw-r-- 1 ubuntu ubuntu 37M Mar 29 06:36 16S_ribosomal_RNA.tar.gz -rw-r--r-- 1 ubuntu ubuntu 19M Apr 6 12:29 citations.dmp -rw-r--r-- 1 ubuntu ubuntu 4.2M Apr 6 12:26 delnodes.dmp -rw-r--r-- 1 ubuntu ubuntu 452 Apr 6 12:20 division.dmp -rw-r--r-- 1 ubuntu ubuntu 17K Apr 6 12:29 gc.prt -rw-r--r-- 1 ubuntu ubuntu 4.9K Apr 6 12:20 gencode.dmp -rw-r--r-- 1 ubuntu ubuntu 1.2M Apr 6 12:26 merged.dmp -rw-r--r-- 1 ubuntu ubuntu 208M Apr 6 12:29 names.dmp -rw-r--r-- 1 ubuntu ubuntu 159M Apr 6 12:28 nodes.dmp -rw-rw---- 1 ubuntu ubuntu 2.7K Sep 11 2019 readme.txt -rw-rw-r-- 1 ubuntu ubuntu 149M Mar 29 06:36 taxdb.btd -rw-rw-r-- 1 ubuntu ubuntu 16M Mar 29 06:36 taxdb.bti -rw-rw-r-- 1 ubuntu ubuntu 56M Apr 6 13:25 taxdmp.zip

(((·> ~~ >(((·> ~~ >(((·> Ana Paula B. Moreira, PhD Federal University of Rio de Janeiro- UFRJ Biology Institute Phone: +55 21 988220753 ID Orcid https://orcid.org/0000-0001-9757-1317 ResearchGate < https://www.researchgate.net/profile/Ana_Paula_Moreira4> Loop https://loop.frontiersin.org/people/242799/overview Twitter @AnaPaula_BM https://twitter.com/AnaPaula_BM FB @somostodosciencia https://www.facebook.com/somostodosciencia

On Wed, Apr 6, 2022 at 12:40 PM YJulyXing @.***> wrote:

Hi,

That is weird. Could you check if your installations, file directory and everything is correct? Could you send some screenshots of the file directories, and the command line outputs when you run BLCA as well? We need some more information because this issue seems weird. Thank you.

On Wed, Apr 6, 2022 at 9:36 AM nana-marinbio @.***> wrote:

Hi @YJulyXing https://github.com/YJulyXing

The command line was @.***:~/BLCA$ python 2.blca_main.py -i test.fasta $: command not found

The first command which worked fine was: @.***:~/BLCA$ python 1.subset_db_acc.py It worked fine and the final message was:

Loading names.dmp...DONE! Generating a subset of taxonomy file. Taxonomy file generated!

— Reply to this email directly, view it on GitHub < https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1090282591 , or unsubscribe <

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YJulyXing commented 2 years ago

Hi, I looked at your issue again. Since you are using the latest version of BLAST, it should work with the default database link. Could you double check if your BLAST module actually used by BLCA is version 2.13?

On Wed, Apr 13, 2022 at 11:44 AM nana-marinbio @.***> wrote:

Many tks

Em qua., 13 de abr. de 2022 às 12:21, YJulyXing @.***> escreveu:

Blast 2.9 is fine. And you could download version 4 database from NCBI. We will work on updating BLCA to make it compatible with the latest blast.

nana-marinbio @.***> 于 2022年4月13日周三 上午10:51写道：

Which blast tool I need? because the 2.13 is the latest Tks

Em qua., 13 de abr. de 2022 às 11:49, YJulyXing @.***> escreveu:

Hi, the database file you downloaded is not a version 4 database. The blast tool you have requires a version 4 database.

nana-marinbio @.***> 于 2022年4月13日周三 上午10:24写道：

Hi Dr XIng, I posted an issue , #35 16S database not recognized https://github.com/qunfengdong/BLCA/issues/35#issue-1195688729 Could you please take a look? I followed step 1: $python 1.subset_db_acc.py But the script generates an error message: BLAST Database error: Error: Not a valid version 4 database. (See below the files generated in db directory)

I downloaded manually directly from NCBI and compared both 16S_ribosomal_RNA.tar.gz https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz files with md5sum, and the result was OK, meaning they are identical. I have the latest blast ncbi-blast-2.13.0+, python3.6.9 biopython-1.79 clustalo 1.2.4-1 musclemuscle3.8.31

How can I manage this? Thank you in advance AP

@.**:~/BLCA/db$ ls -lh total 660M -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACC.taxonomy -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACCtaxID* -rw-rw-r-- 1 ubuntu ubuntu 1.2M Mar 29 06:36 16S_ribosomal_RNA.ndb -rw-rw-r-- 1 ubuntu ubuntu 3.4M Mar 29 06:36 16S_ribosomal_RNA.nhr -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.nin -rw-rw-r-- 1 ubuntu ubuntu 175K Mar 29 06:36 16S_ribosomal_RNA.nnd -rw-rw-r-- 1 ubuntu ubuntu 748 Mar 29 06:36 16S_ribosomal_RNA.nni -rw-rw-r-- 1 ubuntu ubuntu 88K Mar 29 06:36 16S_ribosomal_RNA.nog -rw-rw-r-- 1 ubuntu ubuntu 437K Mar 29 06:36 16S_ribosomal_RNA.nos -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.not -rw-rw-r-- 1 ubuntu ubuntu 7.9M Mar 29 06:36 16S_ribosomal_RNA.nsq -rw-rw-r-- 1 ubuntu ubuntu 592K Mar 29 06:36 16S_ribosomal_RNA.ntf -rw-rw-r-- 1 ubuntu ubuntu 154K Mar 29 06:36 16S_ribosomal_RNA.nto -rw-rw-r-- 1 ubuntu ubuntu 37M Mar 29 06:36 16S_ribosomal_RNA.tar.gz -rw-r--r-- 1 ubuntu ubuntu 19M Apr 6 12:29 citations.dmp -rw-r--r-- 1 ubuntu ubuntu 4.2M Apr 6 12:26 delnodes.dmp -rw-r--r-- 1 ubuntu ubuntu 452 Apr 6 12:20 division.dmp -rw-r--r-- 1 ubuntu ubuntu 17K Apr 6 12:29 gc.prt -rw-r--r-- 1 ubuntu ubuntu 4.9K Apr 6 12:20 gencode.dmp -rw-r--r-- 1 ubuntu ubuntu 1.2M Apr 6 12:26 merged.dmp -rw-r--r-- 1 ubuntu ubuntu 208M Apr 6 12:29 names.dmp -rw-r--r-- 1 ubuntu ubuntu 159M Apr 6 12:28 nodes.dmp -rw-rw---- 1 ubuntu ubuntu 2.7K Sep 11 2019 readme.txt -rw-rw-r-- 1 ubuntu ubuntu 149M Mar 29 06:36 taxdb.btd -rw-rw-r-- 1 ubuntu ubuntu 16M Mar 29 06:36 taxdb.bti -rw-rw-r-- 1 ubuntu ubuntu 56M Apr 6 13:25 taxdmp.zip

(((·> ~~ >(((·> ~~ >(((·> Ana Paula B. Moreira, PhD Federal University of Rio de Janeiro- UFRJ Biology Institute Phone: +55 21 988220753 ID Orcid https://orcid.org/0000-0001-9757-1317 ResearchGate < https://www.researchgate.net/profile/Ana_Paula_Moreira4> Loop https://loop.frontiersin.org/people/242799/overview Twitter @AnaPaula_BM https://twitter.com/AnaPaula_BM FB @somostodosciencia https://www.facebook.com/somostodosciencia

On Wed, Apr 6, 2022 at 12:40 PM YJulyXing @.***> wrote:

Hi,

That is weird. Could you check if your installations, file directory and everything is correct? Could you send some screenshots of the file directories, and the command line outputs when you run BLCA as well? We need some more information because this issue seems weird. Thank you.

On Wed, Apr 6, 2022 at 9:36 AM nana-marinbio @.***> wrote:

Hi @YJulyXing https://github.com/YJulyXing

The command line was @.***:~/BLCA$ python 2.blca_main.py -i test.fasta $: command not found

The first command which worked fine was: @.***:~/BLCA$ python 1.subset_db_acc.py It worked fine and the final message was:

Loading names.dmp...DONE! Generating a subset of taxonomy file. Taxonomy file generated!

— Reply to this email directly, view it on GitHub <

https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1090282591

,

or unsubscribe <

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— Reply to this email directly, view it on GitHub < https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1090417220 , or unsubscribe <

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nana-marinbio commented 2 years ago

@.***:~/BLCA$ echo $PATH /home/ubuntu/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/ubuntu/muscle:/home/ubuntu/ncbi-blast+/ncbi-blast-2.13.0+

(((·> ~~ >(((·> ~~ >(((·> Ana Paula B. Moreira, PhD Federal University of Rio de Janeiro- UFRJ Biology Institute Phone: +55 21 988220753 ID Orcid https://orcid.org/0000-0001-9757-1317 ResearchGate https://www.researchgate.net/profile/Ana_Paula_Moreira4 Loop https://loop.frontiersin.org/people/242799/overview Twitter @AnaPaula_BM https://twitter.com/AnaPaula_BM FB @somostodosciencia https://www.facebook.com/somostodosciencia

On Wed, Apr 13, 2022 at 2:59 PM YJulyXing @.***> wrote:

Hi, I looked at your issue again. Since you are using the latest version of BLAST, it should work with the default database link. Could you double check if your BLAST module actually used by BLCA is version 2.13?

On Wed, Apr 13, 2022 at 11:44 AM nana-marinbio @.***> wrote:

Many tks

Em qua., 13 de abr. de 2022 às 12:21, YJulyXing @.***> escreveu:

Blast 2.9 is fine. And you could download version 4 database from NCBI. We will work on updating BLCA to make it compatible with the latest blast.

nana-marinbio @.***> 于 2022年4月13日周三 上午10:51写道：

Which blast tool I need? because the 2.13 is the latest Tks

Em qua., 13 de abr. de 2022 às 11:49, YJulyXing @.***> escreveu:

Hi, the database file you downloaded is not a version 4 database. The blast tool you have requires a version 4 database.

nana-marinbio @.***> 于 2022年4月13日周三 上午10:24写道：

Hi Dr XIng, I posted an issue , #35 16S database not recognized https://github.com/qunfengdong/BLCA/issues/35#issue-1195688729 Could you please take a look? I followed step 1: $python 1.subset_db_acc.py But the script generates an error message: BLAST Database error: Error: Not a valid version 4 database. (See below the files generated in db directory)

I downloaded manually directly from NCBI and compared both 16S_ribosomal_RNA.tar.gz https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz files with md5sum, and the result was OK, meaning they are identical. I have the latest blast ncbi-blast-2.13.0+, python3.6.9 biopython-1.79 clustalo 1.2.4-1 musclemuscle3.8.31

How can I manage this? Thank you in advance AP

@.**:~/BLCA/db$ ls -lh total 660M -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACC.taxonomy -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACCtaxID* -rw-rw-r-- 1 ubuntu ubuntu 1.2M Mar 29 06:36 16S_ribosomal_RNA.ndb -rw-rw-r-- 1 ubuntu ubuntu 3.4M Mar 29 06:36 16S_ribosomal_RNA.nhr -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.nin -rw-rw-r-- 1 ubuntu ubuntu 175K Mar 29 06:36 16S_ribosomal_RNA.nnd -rw-rw-r-- 1 ubuntu ubuntu 748 Mar 29 06:36 16S_ribosomal_RNA.nni -rw-rw-r-- 1 ubuntu ubuntu 88K Mar 29 06:36 16S_ribosomal_RNA.nog -rw-rw-r-- 1 ubuntu ubuntu 437K Mar 29 06:36 16S_ribosomal_RNA.nos -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.not -rw-rw-r-- 1 ubuntu ubuntu 7.9M Mar 29 06:36 16S_ribosomal_RNA.nsq -rw-rw-r-- 1 ubuntu ubuntu 592K Mar 29 06:36 16S_ribosomal_RNA.ntf -rw-rw-r-- 1 ubuntu ubuntu 154K Mar 29 06:36 16S_ribosomal_RNA.nto -rw-rw-r-- 1 ubuntu ubuntu 37M Mar 29 06:36 16S_ribosomal_RNA.tar.gz -rw-r--r-- 1 ubuntu ubuntu 19M Apr 6 12:29 citations.dmp -rw-r--r-- 1 ubuntu ubuntu 4.2M Apr 6 12:26 delnodes.dmp -rw-r--r-- 1 ubuntu ubuntu 452 Apr 6 12:20 division.dmp -rw-r--r-- 1 ubuntu ubuntu 17K Apr 6 12:29 gc.prt -rw-r--r-- 1 ubuntu ubuntu 4.9K Apr 6 12:20 gencode.dmp -rw-r--r-- 1 ubuntu ubuntu 1.2M Apr 6 12:26 merged.dmp -rw-r--r-- 1 ubuntu ubuntu 208M Apr 6 12:29 names.dmp -rw-r--r-- 1 ubuntu ubuntu 159M Apr 6 12:28 nodes.dmp -rw-rw---- 1 ubuntu ubuntu 2.7K Sep 11 2019 readme.txt -rw-rw-r-- 1 ubuntu ubuntu 149M Mar 29 06:36 taxdb.btd -rw-rw-r-- 1 ubuntu ubuntu 16M Mar 29 06:36 taxdb.bti -rw-rw-r-- 1 ubuntu ubuntu 56M Apr 6 13:25 taxdmp.zip

(((·> ~~ >(((·> ~~ >(((·> Ana Paula B. Moreira, PhD Federal University of Rio de Janeiro- UFRJ Biology Institute Phone: +55 21 988220753 ID Orcid https://orcid.org/0000-0001-9757-1317 ResearchGate < https://www.researchgate.net/profile/Ana_Paula_Moreira4> Loop https://loop.frontiersin.org/people/242799/overview Twitter @AnaPaula_BM https://twitter.com/AnaPaula_BM FB @somostodosciencia < https://www.facebook.com/somostodosciencia>

On Wed, Apr 6, 2022 at 12:40 PM YJulyXing @.***> wrote:

Hi,

That is weird. Could you check if your installations, file directory and everything is correct? Could you send some screenshots of the file directories, and the command line outputs when you run BLCA as well? We need some more information because this issue seems weird. Thank you.

On Wed, Apr 6, 2022 at 9:36 AM nana-marinbio @.***> wrote:

Hi @YJulyXing https://github.com/YJulyXing

The command line was @.***:~/BLCA$ python 2.blca_main.py -i test.fasta $: command not found

The first command which worked fine was: @.***:~/BLCA$ python 1.subset_db_acc.py It worked fine and the final message was:

Loading names.dmp...DONE! Generating a subset of taxonomy file. Taxonomy file generated!

— Reply to this email directly, view it on GitHub <

https://github.com/qunfengdong/BLCA/issues/34#issuecomment-1090282591

,

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— Reply to this email directly, view it on GitHub <

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nana-marinbio commented 1 year ago

@.***:~/BLCA$ echo $PATH /home/ubuntu/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/ubuntu/muscle:/home/ubuntu/ncbi-blast+/ncbi-blast-2.13.0+

I also checked the ncbi_package_info inside ncbi-blast-2.13.0+

Below you see just the head of the file, all packages are listed as version Package: blast 2.13.0

PACKAGE_NAME: blast PACKAGE_VERSION: 2.13.0 PACKAGE_SIGNATURE: GCC_730-ReleaseMT64--x86_64-unknown-linux3.10.0-gnu2.17-coremake22 PACKAGE_CONFIG: Linux64-Centos : gcc : ./c++/compilers/unix/GCC.sh --with-static --without-dll --with-bin-release --with-strip --without-debug --without-pcre --with-mt --with-openmp --with-flat-makefile --with-experimental=Int8GI --without-gnutls --without-gcrypt --with-vdb=/panfs/traces01.be-md.ncbi.nlm.nih.gov/trace_software/vdb --with-static-vdb --with-build-root-sfx=--Linux64-Centos-gcc --with-flat-makefile --with-ncbi-public --without-ccache --without-caution --without-runpath --without-makefile-auto-update --with-projects=scripts/projects/blast/project.lst --with-internal

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On Wed, Apr 13, 2022 at 2:59 PM YJulyXing @.***> wrote:

Hi, I looked at your issue again. Since you are using the latest version of BLAST, it should work with the default database link. Could you double check if your BLAST module actually used by BLCA is version 2.13?

On Wed, Apr 13, 2022 at 11:44 AM nana-marinbio @.***> wrote:

Many tks

Em qua., 13 de abr. de 2022 às 12:21, YJulyXing @.***> escreveu:

Blast 2.9 is fine. And you could download version 4 database from NCBI. We will work on updating BLCA to make it compatible with the latest blast.

nana-marinbio @.***> 于 2022年4月13日周三 上午10:51写道：

Which blast tool I need? because the 2.13 is the latest Tks

Em qua., 13 de abr. de 2022 às 11:49, YJulyXing @.***> escreveu:

Hi, the database file you downloaded is not a version 4 database. The blast tool you have requires a version 4 database.

nana-marinbio @.***> 于 2022年4月13日周三 上午10:24写道：

Hi Dr XIng, I posted an issue , #35 16S database not recognized https://github.com/qunfengdong/BLCA/issues/35#issue-1195688729 Could you please take a look? I followed step 1: $python 1.subset_db_acc.py But the script generates an error message: BLAST Database error: Error: Not a valid version 4 database. (See below the files generated in db directory)

I downloaded manually directly from NCBI and compared both 16S_ribosomal_RNA.tar.gz https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz files with md5sum, and the result was OK, meaning they are identical. I have the latest blast ncbi-blast-2.13.0+, python3.6.9 biopython-1.79 clustalo 1.2.4-1 musclemuscle3.8.31

How can I manage this? Thank you in advance AP

@.**:~/BLCA/db$ ls -lh total 660M -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACC.taxonomy -rw-rw-r-- 1 ubuntu ubuntu 0 Apr 6 13:25 16S_ribosomal_RNA.ACCtaxID* -rw-rw-r-- 1 ubuntu ubuntu 1.2M Mar 29 06:36 16S_ribosomal_RNA.ndb -rw-rw-r-- 1 ubuntu ubuntu 3.4M Mar 29 06:36 16S_ribosomal_RNA.nhr -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.nin -rw-rw-r-- 1 ubuntu ubuntu 175K Mar 29 06:36 16S_ribosomal_RNA.nnd -rw-rw-r-- 1 ubuntu ubuntu 748 Mar 29 06:36 16S_ribosomal_RNA.nni -rw-rw-r-- 1 ubuntu ubuntu 88K Mar 29 06:36 16S_ribosomal_RNA.nog -rw-rw-r-- 1 ubuntu ubuntu 437K Mar 29 06:36 16S_ribosomal_RNA.nos -rw-rw-r-- 1 ubuntu ubuntu 262K Mar 29 06:36 16S_ribosomal_RNA.not -rw-rw-r-- 1 ubuntu ubuntu 7.9M Mar 29 06:36 16S_ribosomal_RNA.nsq -rw-rw-r-- 1 ubuntu ubuntu 592K Mar 29 06:36 16S_ribosomal_RNA.ntf -rw-rw-r-- 1 ubuntu ubuntu 154K Mar 29 06:36 16S_ribosomal_RNA.nto -rw-rw-r-- 1 ubuntu ubuntu 37M Mar 29 06:36 16S_ribosomal_RNA.tar.gz -rw-r--r-- 1 ubuntu ubuntu 19M Apr 6 12:29 citations.dmp -rw-r--r-- 1 ubuntu ubuntu 4.2M Apr 6 12:26 delnodes.dmp -rw-r--r-- 1 ubuntu ubuntu 452 Apr 6 12:20 division.dmp -rw-r--r-- 1 ubuntu ubuntu 17K Apr 6 12:29 gc.prt -rw-r--r-- 1 ubuntu ubuntu 4.9K Apr 6 12:20 gencode.dmp -rw-r--r-- 1 ubuntu ubuntu 1.2M Apr 6 12:26 merged.dmp -rw-r--r-- 1 ubuntu ubuntu 208M Apr 6 12:29 names.dmp -rw-r--r-- 1 ubuntu ubuntu 159M Apr 6 12:28 nodes.dmp -rw-rw---- 1 ubuntu ubuntu 2.7K Sep 11 2019 readme.txt -rw-rw-r-- 1 ubuntu ubuntu 149M Mar 29 06:36 taxdb.btd -rw-rw-r-- 1 ubuntu ubuntu 16M Mar 29 06:36 taxdb.bti -rw-rw-r-- 1 ubuntu ubuntu 56M Apr 6 13:25 taxdmp.zip

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On Wed, Apr 6, 2022 at 12:40 PM YJulyXing @.***> wrote:

Hi,

That is weird. Could you check if your installations, file directory and everything is correct? Could you send some screenshots of the file directories, and the command line outputs when you run BLCA as well? We need some more information because this issue seems weird. Thank you.

On Wed, Apr 6, 2022 at 9:36 AM nana-marinbio @.***> wrote:

Hi @YJulyXing https://github.com/YJulyXing

The command line was @.***:~/BLCA$ python 2.blca_main.py -i test.fasta $: command not found

The first command which worked fine was: @.***:~/BLCA$ python 1.subset_db_acc.py It worked fine and the final message was:

Loading names.dmp...DONE! Generating a subset of taxonomy file. Taxonomy file generated!

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