run_uchime is not working

[tarunaaggarwal]

Hello,

I'm running the eukref_gbretrieve.py script but am getting the following errors. The temp_no_chimeras.fas file that the script is not able to find is located in the same directory as the script and the file is not empty. In the script, the infile was closed after being read so I tried to resolve the issue by commenting out line 235 but no luck...Any suggestions as to how I can resolve this problem? Thank you!

Runing uchime on initial fasta file

Invalid command line
Option --uchime_ref is invalid
For list of command-line options use --help.

Traceback (most recent call last):
  File "eukref_gbretrieve.py", line 344, in <module>
    run_uchime('current_DB.fas', 'temp_initial_db.fas')
  File "eukref_gbretrieve.py", line 233, in run_uchime
    infile = open('temp_no_chimeras.fas')
IOError: [Errno 2] No such file or directory: 'temp_no_chimeras.fas'

[kolecko007]

Hi,

what version of usearch are you using? It seems usearch is commonly changing input options and ouput formats between versions.

I suggest getting usearch 8.0.x..The script should work with that.

cheers Martin

On 27 March 2017 22:00:01 CEST, Taruna notifications@github.com wrote:

Hello,

I'm running the eukref_gbretrieve.py script but am getting the following errors. The temp_no_chimeras.fas file that the script is not able to find is located in the same directory as the script and the file is not empty. In the script, the infile was closed after being read so I tried to resolve the issue by commenting out line 235 but no luck...Any suggestions as to how I can resolve this problem? Thank you!

Runing uchime on initial fasta file

Invalid command line
Option --uchime_ref is invalid
For list of command-line options use --help.

Traceback (most recent call last):
 File "eukref_gbretrieve.py", line 344, in <module>
   run_uchime('current_DB.fas', 'temp_initial_db.fas')
 File "eukref_gbretrieve.py", line 233, in run_uchime
   infile = open('temp_no_chimeras.fas')
IOError: [Errno 2] No such file or directory: 'temp_no_chimeras.fas'

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[tarunaaggarwal]

Thank you. That fixed one problem but now I'm getting a blast error which probably also has to do with the version. Can the script work with other blast version? The oldest one we have on our cluster is 2.2.25.

[kolecko007]

Hi,

can you please send me the error and few last lines of the ouput on the screen it giives you.

thank you, Martin

On 27 March 2017 22:39:05 CEST, Taruna notifications@github.com wrote:

Thank you. That fixed one problem but now I'm getting a blast error which probably also has to do with the version. Can the script work with other blast version? The oldest one we have on our cluster is 2.2.25.

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[tarunaaggarwal]

Sure! My command and the error are below.

Command:

python eukref_gbretrieve.py \
-i polychaeta_sorted_clustered_edited_correctHeaders.fasta \
-dbnt $NCBI_DB/nt \
-dbsi Reference_DB.fas \
-n 100 -p 8 -g Opisthokonta \
-m megablast -idsi 75 -idnt 90 -td tax_d.bin

Error:

Runing uchime on initial fasta file
sh: usearch: command not found
Removing short sequences from initial fasta file
starting cycle 1
running usearch
sh: usearch: command not found
sh: usearch: command not found
running blast
sh: blastn: command not found
Traceback (most recent call last):
  File "eukref_gbretrieve.py", line 370, in <module>
    'temp_DB_clust_500.blastntab')
  File "eukref_gbretrieve.py", line 117, in nt_blast
    infile = open(outf)
IOError: [Errno 2] No such file or directory: 'temp_DB_clust_500.blastntab'