How to generate .tbl when running the docker image?

[nathaliagg]

I'm running Mfannot via docker image, and it is running ok as far as I can tell. I was wondering how to generate the .tbl file, which is provided when running a job in the web server.

Thank you!

[natacha-beck]

Hello,

If you run MFannot with the --sqn option, MFannot will generate the .sqn file. And if you add the -d option, MFannot will keep all the intermediate file included the .tbl file.

[nathaliagg]

Adding the -d option didn't work for me. This was an example of my run:

docker run -v $(pwd):/working-dir  -w /working-dir 071cbd1a9412 mfannot --sqn -d -g 4 -l logfile filename.fasta

The outputs were the log, .new, and .sqn files. The .tbl file was not created.

[natacha-beck]

Can you cut and paste the trace of the run of Mfannot, the last 5-10 lines.

You need to go inside the temporary workdirectory to find the .tbl file.

[nathaliagg]

[nathalia] $  docker run -ti -v $(pwd):/working-dir  -w /working-dir --mount type=tmpfs,destination=/working-dir/tmp 071cbd1a9412 mfannot --sqn -d -g 4 -l logfile_ks28.txt ks28_mt_scaffolded.fasta

(...)

15) Intron ORF annotation...

----------------------------------
       This is it, Folks !     
----------------------------------
Added : 57
Writing new masterfile in /working-dir/ks28_mt_scaffolded.fasta.new
/usr/local/bin/mf2sqn -a Generic -m /working-dir/ks28_mt_scaffolded.fasta.new -t/usr/local/bin/mf2sqn -a Generic -m /working-dir/ks28_mt_scaffolded.fasta.new -tclose Logfile : logfile_ks28.txt
Temporary work directory /tmp/mfannot.1 NOT cleaned up ...

I tried using --tmpfs, and then --mount configuration as shown above. Using either option to mount, the /tmp/mfannot.1 didn't exist:

[nathalia] $  docker run --rm -it --entrypoint=/bin/bash 071cbd1a9412
root@9619df62882b:/# cd tmp/
root@d446f68c14c7:/tmp# ls -Ra
.:
.  ..  PCyaqO4osP  upvWGcLlr5.tmp.bioperl

./PCyaqO4osP:
.  ..

The /tmp was created in the working-dir, but it was empty:

[nathalia] $  pwd
/Users/grachetng/MFannot 
[nathalia] $  cd tmp/
[nathalia] $  ls -la
total 0
drwxr-xr-x   2 grachetng  staff    64 Aug  4 09:40 .
drwxr-xr-x  43 grachetng  staff  1376 Aug  4 09:44 ..

I am not used to running containers, so this issue might be my lack of knowledge.

[natacha-beck]

You will be able to redirect the temporary workdirectory by using the option --T like that:

docker run -ti -v $(pwd):/working-dir -w /working-dir nbeck/mfannot:latest mfannot --sqn -d -g 4 --T /working-dir/tmp fasta_file

then when you go in /working-dir/tmp you will find a file named fasta.new.tbl.

Let me know if it is ok now ?

[nathaliagg]

The temporary directory is created using the --T option, however it still does not work. Now, the code breaks at:

  --- SCRIPT /working-dir/tmphcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1 END ---
  DEBUG: Executing external script block 'B-0' for 'rrn5'.
  --- COMMAND : cd '/working-dir/tmphcw2/Contig/err_out';/bin/bash '/working-dir/tmphcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1' >'/working-dir/tmphcw2/Contig/err_out/out.rrn5.B-0.MfGC.1' 2>'/working-dir/tmphcw2/Contig/err_out/err.rrn5.B-0.MfGC.1'
  --- SCRIPT /working-dir/tmphcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1 START ---

    RNAfinder -m rrn5 -g 4 -d /working-dir/tmphcw2/Contig/contig3 -M /working-dir/tmphcw2/Contig/contig3-rrn5.xml

  --- SCRIPT /working-dir/tmphcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1 END ---
  DEBUG: Executing external script block 'B-0' for 'rrn5'.
  --- COMMAND : cd '/working-dir/tmphcw2/Contig/err_out';/bin/bash '/working-dir/tmphcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1' >'/working-dir/tmphcw2/Contig/err_out/out.rrn5.B-0.MfGC.1' 2>'/working-dir/tmphcw2/Contig/err_out/err.rrn5.B-0.MfGC.1'
  --- SCRIPT /working-dir/tmphcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1 START ---

    RNAfinder -m rrn5 -g 4 -d /working-dir/tmphcw2/Contig/contig1 -M /working-dir/tmphcw2/Contig/contig1-rrn5.xml

  --- SCRIPT /working-dir/tmphcw2/Contig/err_out/bashcom.rrn5.B-0.MfGC.1 END ---
11) Adjust intron boundaries...
12) Identify start codons; identify gene fusions...
13) Find extra genes with HMM
Cannot open /working-dir/tmphcw2/contig/contig1/contig1.faa in GetORFForLowConservedGenes

In addition, working-dir/tmphcw2/contig/ does not exist, but working-dir/tmphcw2/Contig/ exists. But working-dir/tmphcw2/Contig/contig1/ does not exist because contig1 is a fasta file.

[natacha-beck]

Can you please send me the full log trace and the input file I will take a look. I re-run an example on my side and I did not have any issue. I really want to help you and understand what happened.

[nathaliagg]

Sure. I really appreciate your help!

This was the code I ran:

[nathalia] $  docker run -ti -v $(pwd):/working-dir -w /working-dir nbeck/mfannot:latest mfannot --sqn -d -g 4 --T /working-dir/tmp_hcw2 -l logfile_hcw2.txt hcw2_mt_scaffolded.fasta > logfile_stdout_hcw2.txt

This is the data file: hcw2_mt_scaffolded.fasta.txt

These are the log files: logfile_hcw2.txt
logfile_stdout_hcw2.txt

[natacha-beck]

I run the same command line as you. And did not get any issue. I will think of your issue.

In the mean time, here is the *.tbl file

hcw2_mt_scaffolded.fasta.txt.new.tbl.txt

I just rename it with the txt extension to attach the file on github.