Error while trying to run dfast -- Barrnap and time-piece related

[matrs]

Hello, I used DFAST successfully in mac osx a few weeks ago. Now I'm trying to run it in arch Linux but I'm getting this error:

$DFAST --genome "$PATH1/16572_RC-21.fsa" -o DFAST_16572_RC-21 --cpu 4 --force --debug

2018/10/15 22:33:40 Running on Python 3.6.5 | packaged by conda-forge | (default, Apr  6 2018, 13:39:56) 
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)].
2018/10/15 22:33:40 Loading a config file from /run/media/mibu/BioNano1/dfast_core/dfc/default_config.py
2018/10/15 22:33:40  WARNING Debug mode enabled. Logger level is set to DEBUG and temporary files will be kept. [dfast 121]
2018/10/15 22:33:40     INFO OS type is Linux. [path_util 40]
2018/10/15 22:33:40     INFO Adding /run/media/mibu/BioNano1/dfast_core/bin/Linux to PATH. [path_util 42]
2018/10/15 22:33:40     INFO WORKING Directory is set to an existing directory: 'DFAST_16572_RC-21'. [path_util 19]
2018/10/15 22:33:40     INFO DFAST pipeline started. (version 1.0.8) [pipeline 38]
2018/10/15 22:33:40     INFO Results will be generated into 'DFAST_16572_RC-21'. [pipeline 39]
2018/10/15 22:33:40     INFO Loading a genomic fasta file from prokka_16572_RC-21/16572_RC-21.fsa [genome 36]
2018/10/15 22:33:40     INFO Genome source information: organism=, strain= [genome 60]
2018/10/15 22:33:40     INFO The query genome is treated as a draft genome with 182 sequences. [genome 109]
2018/10/15 22:33:40     INFO Sequences are sorted by length (from longer to shorter). [genome 112]
2018/10/15 22:33:40     INFO Sequences shorter than 200 will be eliminated. [genome 116]
2018/10/15 22:33:40     INFO Sequences will be renamed as sequence001, sequence002... [genome 127]
2018/10/15 22:33:40     INFO Locus_tag settings: locus_tag_prefix=LOCUS and step=10. [locus_tag_generator 18]
2018/10/15 22:33:40     INFO Locus_tags are assigned separately to each feature type. e.g. CDS: LOCUS_000xx, rRNA: LOCUS_r000xx, tRNA: LOCUS_t000xx, tmRNA: LOCUS_tm000xx. [locus_tag_generator 21]
2018/10/15 22:33:40     INFO Remove_Partial_Feature is enabled. [feature_util 25]
2018/10/15 22:33:40     INFO Remove_Overlapping_Feature is enabled. Priority: ['assembly_gap', 'CRISPR', ('tmRNA', 'tRNA', 'rRNA'), 'CDS'] [feature_util 29]
2018/10/15 22:33:40     INFO Initializing structural annotation tools...  [structuralAnnotation 48]
2018/10/15 22:33:40     INFO GAPannotator initialized. (Version 1.0) [gap 45]
2018/10/15 22:33:40     INFO Setting GAPannotator options. {'len_cutoff': 5, 'linkage_evidence': 'paired-ends', 'gap_type': 'within scaffold'} [base_tools 30]
2018/10/15 22:33:40     INFO Checking MetaGeneAnnotator...  [mga 37]
2018/10/15 22:33:40    DEBUG Running command "mga 2>&1" (MGA) [base_tools 67]
2018/10/15 22:33:40     INFO MetaGeneAnnotator initialized. (Version 2008/08/19) [mga 41]
2018/10/15 22:33:40     INFO Setting MetaGeneAnnotator options. {'cmd_options': '-s'} [base_tools 30]
2018/10/15 22:33:40     INFO Checking Aragorn version...  [base_tools 39]
2018/10/15 22:33:40    DEBUG Running command "aragorn -h" (Aragorn) [base_tools 67]
2018/10/15 22:33:40     INFO Aragorn initialized. (Version 1.2.38) [base_tools 49]
2018/10/15 22:33:40     INFO Setting Aragorn options. {'gcode': '-gcbact', 'cmd_options': '-l'} [base_tools 30]
2018/10/15 22:33:40     INFO Checking Barrnap version...  [base_tools 39]
2018/10/15 22:33:40    DEBUG Running command "barrnap --version 2>&1" (Barrnap) [base_tools 67]
2018/10/15 22:33:40    ERROR Barrnap version could not be determined. Aborted... [base_tools 51]
2018/10/15 22:33:40    ERROR This may happen if Time::Piece cannot be found. If you are using CentOS/RedHat, try 'sudo yum install perl-Time-Piece'. [base_tools 53]

It seems to me that all the required software is installed as you can see here (I'm using conda to manage packages):

conda list |grep -E 'barrnap|perl-time-piece'
barrnap                   0.9                           2    bioconda
perl-time-piece           1.27                    pl526_1    bioconda

Also, I can see this in my conda environment /media/mibu/Storage_SSD/Miniconda3/envs/bioc/conda-meta/perl-time-piece-1.27-pl526_1.json

So any help would be really appreciated.

Regards

[nigyta]

Dear matrs,

Thank you for using DFAST.

As I'm not familiar with ArchLinux, I'm not sure if this helps. Hopefully, it works!

I guess you have installed Barrnap (ver 0.9) by yourself. However it is not called from DFAST, because DFAST automatically adds "$DFAST_APP_ROOT/bin/Linux" at the head of "PATH" at execution time, and there is a link to the Barrnap executable in it.

So replace the link ($DFAST_APP_ROOT/bin/Linux/barrnap), and create a new link that points to the one you installed. Then, DFAST will call Barrnap (ver 0.9) instead of the one bundled in the DFAST software package. Alternatively, if barrnap is already in your PATH, just removing the $DFAST_APP_ROOT/bin/Linux/barrnap may work.

If this didn't work, please let me know your perl environment, e.g. path to the perl executable, the PERL5LIB enviromental variable.

Yasuhiro

[matrs]

Hi Yasushiro, thank you for your help.

I solved the issue, it ended up being about a broken barrnap executable. When I decompressed dfast, the barrnap executable was only a few bytes of size and it seems that my disk was the culprit. I decompressed it in other disk and everything worked as expected, so the barrnap executable created in my first disk was broken, that's why it didn't work.

Not related to my previous issue, but i'm gonna mention it because this could be useful for other arch linux users. when i solved the previous issue, dfast failed because blastp was looking for libidn-11 and it couldn't find it. I had to install libidn-133-compat from the aur repository to make it work. Maybe you can mention that in your README although I know It's hard to keep up with all the requirements for all the platforms/ Linux distributions. Arch comes with other version of libidn but luckily there's a compatibility lib in the aur repository.

Thank you again for your prompt answer

Cheers

[nigyta]

libidn-11 requirement is mentioned in README