FileNotFoundError: [Errno 2] No such file or directory: './Wdir/rafah_out/Full_CDS_Prediction.faa'

[刘梓峰]

$ iphop predict -f ../test_input_phages.fna -o ./ -d /hl/zhoumengqing/anaconda3/envs/ViWrap/ViWrap_db/iPHoP_db/iPHoP_db/ -t 104 
### Welcome to iPHoP ###
Looks like everything is now set up, we will first clean up the input file, and then we will start the host prediction steps themselves
[1/1/Run] Running blastn against genomes...
[1/3/Run] Get relevant blast matches...
[2/1/Run] Running blastn against CRISPR...
[2/2/Run] Get relevant crispr matches...
[3/1/Run] Running WIsH...
[3/2/Run] Get relevant WIsH hits...
[4/1/Run] Running VHM s2 similarities...
[4/2/Run] Get relevant VHM hits...
[5/1/Run] Running PHP...
[5/2/Run] Get relevant PHP hits...
[6/1/Run] Running RaFAH...
[6/2/Run] Get relevant RaFAH scores...
RaFAH results were empty this may be ok, but is still unusual, so you may want to check the rafah log (Wdir/rafah.log)
[6.5/1/Run] Running Diamond comparison to RaFAH references...
[6.5/2/Run] Get AAI distance to RaFAH refs...
Traceback (most recent call last):
  File "/hl/zhoumengqing/anaconda3/envs/ViWrap/ViWrap-iPHoP/bin/iphop", line 10, in <module>
    sys.exit(cli())
  File "/hl/zhoumengqing/anaconda3/envs/ViWrap/ViWrap-iPHoP/lib/python3.8/site-packages/iphop/iphop.py", line 122, in cli
    args["func"](args)
  File "/hl/zhoumengqing/anaconda3/envs/ViWrap/ViWrap-iPHoP/lib/python3.8/site-packages/iphop/modules/master_predict.py", line 87, in main
    aai_to_ref.run_and_parse_aai(args)
  File "/hl/zhoumengqing/anaconda3/envs/ViWrap/ViWrap-iPHoP/lib/python3.8/site-packages/iphop/modules/aai_to_ref.py", line 30, in run_and_parse_aai
    get_aai_results(faa_file,db_info,args["aai_out"],args["aai_parsed"])
  File "/hl/zhoumengqing/anaconda3/envs/ViWrap/ViWrap-iPHoP/lib/python3.8/site-packages/iphop/modules/aai_to_ref.py", line 56, in get_aai_results
    for index, r in enumerate(SeqIO.parse(faa, 'fasta')):
  File "/hl/zhoumengqing/anaconda3/envs/ViWrap/ViWrap-iPHoP/lib/python3.8/site-packages/Bio/SeqIO/__init__.py", line 605, in parse
    return iterator_generator(handle)
  File "/hl/zhoumengqing/anaconda3/envs/ViWrap/ViWrap-iPHoP/lib/python3.8/site-packages/Bio/SeqIO/FastaIO.py", line 183, in __init__
    super().__init__(source, mode="t", fmt="Fasta")
  File "/hl/zhoumengqing/anaconda3/envs/ViWrap/ViWrap-iPHoP/lib/python3.8/site-packages/Bio/SeqIO/Interfaces.py", line 48, in __init__
    self.stream = open(source, "r" + mode)
FileNotFoundError: [Errno 2] No such file or directory: './Wdir/rafah_out/Full_CDS_Prediction.faa'

‌

[Simon Roux]

Hi,

This looks like an issue with RaFAH. Can you check what information is in the log of RaFAH (Wdir/RaFAH.log) ?

[刘梓峰]

I seem to have solved the problem, thank you

[die hu]

Hi, Simon,

I have the same issue, and the rafah.log shows that “Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /gpfs1/schlecker/home/hudi/.conda/envs/iphop/lib/perl5/site_perl/5.22.2/x86_64-linux-thread-multi /gpfs1/schlecker/home/hudi/.conda/envs/iphop/lib/perl5/site_perl/5.22.2 /gpfs1/schlecker/home/hudi/.conda/envs/iphop/lib/perl5/5.22.2/x86_64-linux-thread-multi /gpfs1/schlecker/home/hudi/.conda/envs/iphop/lib/perl5/5.22.2 .) at /home/hudi/.conda/envs/iphop/lib/python3.8/site-packages/iphop/utils/RaFAH_v0.3.pl line 5.
BEGIN failed--compilation aborted at /home/hudi/.conda/envs/iphop/lib/python3.8/site-packages/iphop/utils/RaFAH_v0.3.pl line 5.”
Do you have any idea?

[Simon Roux]

Hi,

This seems like an issue with BioPerl. The first thing to verify is typically to check that BioPerl is correctly installed in your conda environment, and then making sure that it is in the place Perl expects it to be (i.e. one of these folders: /gpfs1/schlecker/home/hudi/.conda/envs/iphop/lib/perl5/site_perl/5.22.2/x86_64-linux-thread-multi /gpfs1/schlecker/home/hudi/.conda/envs/iphop/lib/perl5/site_perl/5.22.2 /gpfs1/schlecker/home/hudi/.conda/envs/iphop/lib/perl5/5.22.2/x86_64-linux-thread-multi /gpfs1/schlecker/home/hudi/.conda/envs/iphop/lib/perl5/5.22.2).
The way that issue was resolved may help as well: https://bitbucket.org/srouxjgi/iphop/issues/42/error-running-rafah

[die hu]

Hi Simon,

Thanks for your information.

I followed the process https://bitbucket.org/srouxjgi/iphop/issues/42/error-running-rafah, the Perl is exact here.

But when I checked the /home/hudi/.conda/envs/iphop/etc/conda/activate.d/, there are activate-r-base.sh libglib_activate.sh libxml2_activate.sh openjdk_activate.sh, without iphop_activate.sh.

I found it in the Stable versions of iPHoP (iphop_env which was installed before), then I copied it to /home/hudi/.conda/envs/iphop/etc/conda/activate.d/ and “chmod g+w /home/hudi/.conda/envs/iphop/etc/conda/activate.d/iphop_activate.sh”.

In this file, it shows:

“export OLD_PERL5LIB=$PERL5LIB
export PERL5LIB=${CONDA_PREFIX}/lib/perl5/site_perl/5.22.0:${CONDA_PREFIX}/lib/perl5/site_perl/:${PERL5LIB}”

There is not give me any output When I run: perl -e "use Bio::SeqIO;" , after I run “export PERL5LIB=/home/hudi/.conda/envs/iphop/lib/perl5/site_perl/5.22.0:/home/hudi/.conda/envs/iphop/lib/perl5/site_perl/:${PERL5LIB}” and “echo $PERL5LIB”.

‌

So I submitted the job again, and hopefully, it goes well.

Kind regards,

Die

‌