Error with test 3

[nana-marinbio]

Dear Dr Sahl, I installed LS-BSR and performed tests 1 and 2. But with test 3 I got the following error: LOG: 2017/10/27 13:06:55 - Prodigal done Traceback (most recent call last): File "/Users/AnaPaula/Desktop/LS-BSR/ls_bsr.py", line 596, in options.filter_scaffolds,options.prefix,options.min_pep_length,options.intergenics) File "/Users/AnaPaula/Desktop/LS-BSR/ls_bsr.py", line 268, in main dup_ids = test_duplicate_header_ids("consensus.fasta") File "/Users/AnaPaula/Desktop/LS-BSR/ls_bsr/util.py", line 759, in test_duplicate_header_ids for line in open(fasta_file): IOError: [Errno 2] No such file or directory: 'consensus.fasta' The missing output file is the consensus.fasta, I have the all_gene_seqs.out, for each strain _all.fasta.new, _all.fasta.new_genes.pep and _all.fasta.new_genes.seqs I am OS Sierra 10.12.6 with Prodigal 2.6, blast2.2.28, vsearch 2.5.1. Do you have a clue of what's going wrong? Thanks in advance, Nana

[jasonsahl]

Nana,

Could you please provide your complete command the the complete output log?

thanks, Jason

[nana-marinbio]

Hi Jason,

Here you see:

iMac-de-nana:test_data AnaPaula$ python /Users/AnaPaula/Desktop/LS-BSR/ls_bsr.py -d genomes –c vsearch –x test -p 1

LOG: 2017/10/27 13:06:11 - Testing paths of dependencies

/Applications/ncbi-blast-2.2.28+/bin/blastn

citation: Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, and Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402

/Applications/Prodigal-2.60/prodigal

citation: Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, and Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119

LOG: 2017/10/27 13:06:11 - predicting genes with Prodigal

LOG: 2017/10/27 13:06:55 - Prodigal done

Traceback (most recent call last):

File "/Users/AnaPaula/Desktop/LS-BSR/ls_bsr.py", line 596, in

options.filter_scaffolds,options.prefix,options.min_pep_length,options.intergenics)

File "/Users/AnaPaula/Desktop/LS-BSR/ls_bsr.py", line 268, in main

dup_ids = test_duplicate_header_ids("consensus.fasta")

File "/Users/AnaPaula/Desktop/LS-BSR/ls_bsr/util.py", line 759, in test_duplicate_header_ids

for line in open(fasta_file):

IOError: [Errno 2] No such file or directory: 'consensus.fasta'

later

nana

2017-10-27 13:44 GMT-02:00 Jason Sahl notifications@github.com:

Nana,

Could you please provide your complete command the the complete output log?

thanks, Jason

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/jasonsahl/LS-BSR/issues/21#issuecomment-340008390, or mute the thread https://github.com/notifications/unsubscribe-auth/ATL8fPFdrdQXrWTny6u6di9Rk61E6gPdks5swfpGgaJpZM4QJPGE .

-- Dra. Ana Paula B. Moreira Bióloga ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ Pesquisadora CAPES/PNPD - Depto de Genética, UFRJ Projeto Ilhas Oceânicas Colaboradora Rede Abrolhos e Rede Biotecmar Lattes: http://lattes.cnpq.br/6822555709988709

Tel/Whatsapp: 3938-6567/+55 21 98822-0753

apbmoreira@gmail.com / anapaulabm@biologia.ufrj.br Skype: anapaulabmoreira

[jasonsahl]

Nana,

That helps. Can you confirm that you are using the most up-to-date version of the script? After you update the code with "git pull", please also make sure that vsearch is in your path as "vsearch". After that, please try again and let me know if the problem remains.

regards, Jason

[nana-marinbio]

Jason, I got exactly the same error.

iMac-de-nana:test_data AnaPaula$ python /Users/AnaPaula/Desktop/LS-BSR/ls_bsr.py -d genomes –c vsearch –x test -p 1

LOG: 2017/10/27 15:48:30 - Testing paths of dependencies

/Applications/ncbi-blast-2.2.28+/bin/blastn

citation: Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, and Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402

/Applications/Prodigal-2.60/prodigal

citation: Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, and Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119

LOG: 2017/10/27 15:48:30 - predicting genes with Prodigal

LOG: 2017/10/27 15:49:16 - Prodigal done

Traceback (most recent call last):

File "/Users/AnaPaula/Desktop/LS-BSR/ls_bsr.py", line 596, in

options.filter_scaffolds,options.prefix,options.min_pep_length,options.intergenics)

File "/Users/AnaPaula/Desktop/LS-BSR/ls_bsr.py", line 268, in main

dup_ids = test_duplicate_header_ids("consensus.fasta")

File "/Users/AnaPaula/Desktop/LS-BSR/ls_bsr/util.py", line 759, in test_duplicate_header_ids

for line in open(fasta_file):

IOError: [Errno 2] No such file or directory: 'consensus.fasta'

I used git pull, and vsearch is in my path. Also in manpath there is a link to man/vsearch. It's the 2.5.1 in the paths, but when I ask for version I get

iMac-de-nana:test_data AnaPaula$ vsearch -v

vsearch v2.0.4_osx_x86_64, 16.0GB RAM, 4 cores

https://github.com/torognes/vsearch

Do you think this is the problem?

thanks

2017-10-27 14:11 GMT-02:00 Jason Sahl notifications@github.com:

Nana,

That helps. Can you confirm that you are using the most up-to-date version of the script? After you update the code with "git pull", please also make sure that vsearch is in your path as "vsearch". After that, please try again and let me know if the problem remains.

regards, Jason

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/jasonsahl/LS-BSR/issues/21#issuecomment-340015930, or mute the thread https://github.com/notifications/unsubscribe-auth/ATL8fLUWNLVwQIn8p8LvGQ_hrDW_e8arks5swgDKgaJpZM4QJPGE .

-- Dra. Ana Paula B. Moreira Bióloga ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ Pesquisadora CAPES/PNPD - Depto de Genética, UFRJ Projeto Ilhas Oceânicas Colaboradora Rede Abrolhos e Rede Biotecmar Lattes: http://lattes.cnpq.br/6822555709988709

Tel/Whatsapp: 3938-6567/+55 21 98822-0753

apbmoreira@gmail.com / anapaulabm@biologia.ufrj.br Skype: anapaulabmoreira

[jasonsahl]

Nana, One reason that I'm confused is that the script should look for vsearch and report back the PATH to where it was found. Here is my output by running the script the same way:

mggen65:run jasonsahl$ python ../ls_bsr.py -d genomes/ -c vsearch -x test -p 1 LOG: 2017/10/27 11:38:14 - Testing paths of dependencies /usr/local/ncbi/blast/bin/blastn citation: Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, and Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402 /opt/local/bin/prodigal citation: Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, and Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119 /opt/local/bin/vsearch citation: Rognes, T., Flouri, T., Nichols, B., Qunice, C., Mahe, Frederic. 2016. VSEARCH: a versatile open source tool for metagenomics. PeerJ Preprints. DOI: https://doi.org/10.7287/peerj.preprints.2409v1 LOG: 2017/10/27 11:38:14 - predicting genes with Prodigal LOG: 2017/10/27 11:39:01 - Prodigal done LOG: 2017/10/27 11:39:01 - clustering with VSEARCH at an ID of 0.9, using 1 processors

If you don't have vsearch in your PATH, you should get the following error: LOG: 2017/10/27 11:42:21 - Testing paths of dependencies /usr/local/ncbi/blast/bin/blastn citation: Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, and Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402 /opt/local/bin/prodigal citation: Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, and Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119 vsearch is not in your path, but needs to be!

Could you do a: >ls test And report back what the file contents are?

thanks, Jason

[nana-marinbio]

weird i don't get any info on vsearch, if it's clustering or if it's not in path.

Also I can't get test directory, only date/time, even including –x test.

For the last trial I got:

$ ls 20171027154830

E2348_69_all.fasta.new H10407_all.fasta.new_genes.pep O157_H7_sakai_all.fasta.new_genes.seqs all_gene_seqs.out

E2348_69_all.fasta.new_genes.pep H10407_all.fasta.new_genes.seqs SSON_046_all.fasta.new

E2348_69_all.fasta.new_genes.seqs O157_H7_sakai_all.fasta.new SSON_046_all.fasta.new_genes.pep

H10407_all.fasta.new O157_H7_sakai_all.fasta.new_genes.pep SSON_046_all.fasta.new_genes.seqs

2017-10-27 16:45 GMT-02:00 Jason Sahl notifications@github.com:

Nana, One reason that I'm confused is that the script should look for vsearch and report back the PATH to where it was found. Here is my output by running the script the same way:

mggen65:run jasonsahl$ python ../ls_bsr.py -d genomes/ -c vsearch -x test -p 1 LOG: 2017/10/27 11:38:14 - Testing paths of dependencies /usr/local/ncbi/blast/bin/blastn citation: Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, and Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402 /opt/local/bin/prodigal citation: Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, and Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119 /opt/local/bin/vsearch citation: Rognes, T., Flouri, T., Nichols, B., Qunice, C., Mahe, Frederic. 2016. VSEARCH: a versatile open source tool for metagenomics. PeerJ Preprints. DOI: https://doi.org/10.7287/peerj.preprints.2409v1 https://doi.org/10.7287/peerj.preprints.2409v1 LOG: 2017/10/27 11:38:14 - predicting genes with Prodigal LOG: 2017/10/27 11:39:01 - Prodigal done LOG: 2017/10/27 11:39:01 - clustering with VSEARCH at an ID of 0.9, using 1 processors

If you don't have vsearch in your PATH, you should get the following error: LOG: 2017/10/27 11:42:21 - Testing paths of dependencies /usr/local/ncbi/blast/bin/blastn citation: Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, and Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402 /opt/local/bin/prodigal citation: Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, and Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119 vsearch is not in your path, but needs to be!

Could you do a:

ls test And report back what the file contents are?

thanks, Jason

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/jasonsahl/LS-BSR/issues/21#issuecomment-340053743, or mute the thread https://github.com/notifications/unsubscribe-auth/ATL8fMYLzNuJdWgNW-j7AMfQMG2vZWvhks5swiTDgaJpZM4QJPGE .

-- Dra. Ana Paula B. Moreira Bióloga ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ Pesquisadora CAPES/PNPD - Depto de Genética, UFRJ Projeto Ilhas Oceânicas Colaboradora Rede Abrolhos e Rede Biotecmar Lattes: http://lattes.cnpq.br/6822555709988709

Tel/Whatsapp: 3938-6567/+55 21 98822-0753

apbmoreira@gmail.com / anapaulabm@biologia.ufrj.br Skype: anapaulabmoreira

[jasonsahl]

Ah, I think I figured it out. Please don't copy/paste from the manual, but type in the command manually. So please type in your command from scratch and try again. What happens is that the dashes in the manual get turned into something different in a terminal. I can try to figure out a way for LS-BSR to check for this and report an error. If I paste your command, I get the same error, but if I type it in manually, it works as expected.

[nana-marinbio]

Hi Jason, all done!

I had to leave desk and could only test now, but I am so happy you figured ou what was going on and that it was a simple solution! Many thanks!

Warm regards from Rio

2017-10-27 17:04 GMT-02:00 Jason Sahl notifications@github.com:

Ah, I think I figured it out. Please don't copy/paste from the manual, but type in the command manually. So please type in your command from scratch and try again. What happens is that the dashes in the manual get turned into something different in a terminal. I can try to figure out a way for LS-BSR to check for this and report an error. If I paste your command, I get the same error, but if I type it in manually, it works as expected.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/jasonsahl/LS-BSR/issues/21#issuecomment-340058753, or mute the thread https://github.com/notifications/unsubscribe-auth/ATL8fEo2gVp_5vUz_JTTNljmHcLLhE9Pks5swikygaJpZM4QJPGE .

-- Dra. Ana Paula B. Moreira Bióloga ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ Pesquisadora CAPES/PNPD - Depto de Genética, UFRJ Projeto Ilhas Oceânicas Colaboradora Rede Abrolhos e Rede Biotecmar Lattes: http://lattes.cnpq.br/6822555709988709

Tel/Whatsapp: 3938-6567/+55 21 98822-0753

apbmoreira@gmail.com / anapaulabm@biologia.ufrj.br Skype: anapaulabmoreira

[jasonsahl]

Great, thanks Nana, please let me know if you run into any other problems