Closed nana-marinbio closed 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: $: command not found.
I changed the shebang to #!/usr/bin/env python3, but got the same error, which is weird since step 1 was ok.
Any suggestion is appreciated, tks Ana Paula
— Reply to this email directly, view it on GitHub https://github.com/qunfengdong/BLCA/issues/34, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKABWISN46WTKSQHMZOG6XLVDVNB5ANCNFSM5SVOZGRQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Hi @YJulyXing
The command line was ubuntu@ubuntu18:~/BLCA$ <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!
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
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
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: @.***>
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
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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 <
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(((·> ~~ >(((·> ~~ >(((·> 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
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 <
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(((·> ~~ >(((·> ~~ >(((·> 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
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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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(((·> ~~ >(((·> ~~ >(((·> 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
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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-- 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 <
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-- 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
@.***:~/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
,
or unsubscribe <
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-- 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 <
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(((·> ~~ >(((·> ~~ >(((·> 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
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-- 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
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@.***:~/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
(((·> ~~ >(((·> ~~ >(((·> 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!
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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