Hi Zohaib!
I have been running all scripts including filter_table_by_abundance.py successfully. When running the script align_contigs_to_database.py I get the following output from the script:

It seemingly can't find the tsv-files for concatenation into one file containing all results, but looking at the output it looks like these cat command errors are found in the middle of the script??? and not in the end as expected from the script.
When I investigate deeper I find that when trying to run a command like:
sword -i ./Step5_align_contigs_to_database/TempFiles/Translated_step4_AbundanceFiltered_Trinity.09.fasta -t 12 -o ./Step5_align_contigs_to_database/TempFiles/Translated_step4_AbundanceFiltered_Trinity.09.result.tsv -f bm9 -j /mibi/Jon/CoMW/databases/NCyc_100.faa -c 30000
I get "Illegal instruction" as output. I got the syntax above from the script and even if I shave arguments down to just -i -o -j it gives the same error message. I have checked the -i file and they seem to be in the correct fasta-format. I have also checked lengths of sequences. The longest is just above 2200 bytes, so no problem there (checked because Sword-author on Github recorded an issue with lengths of sequences above 65k).
Can you help with this? Do you have any ideas. I also tried with original Trinity.fasta file.
Kr,
Jon

Hi Zohaib!

I was hoping you could help me with a problem om pallas server regarding installation of CoMW.

When the CoMW.yml file runs I get the following error message: seen in the picture.

Can you help me understand what I need to do to fix this?

I only have terminal access to pallas.

Kind regards,
Jon

Hi Zohaib,
I got the following error while running the annotate step:

Traceback (most recent call last):
  File "scripts/annotate_count_table_v1.py", line 330, in <module>
    annotate_eggNOG(tabfile = inputdir+"/"+inputfile, outfile = outputdir+"/"+outputfile)
  File "scripts/annotate_count_table_v1.py", line 170, in annotate_eggNOG
    x=infile[i][infile[i].index("\t"):infile[i].index("LevelI__")]+"LevelI__"+levelI[list_values[0]]+infile[i][infile[i].index("; LevelII__"):]
IndexError: list index out of range

Here I printed out some values for debugging:

inheritenceII: ['elII__Secondary metabolites biosynthesis, transport and catabolism', 'Chromatin structure and dynamics']
list_values: []
ID: COG0123_1
infile[i]: COG0123	71	80	45	60	69	55	55	52	0	48	51	39	27	71	DB__COG; LevelI__INFORMATION STORAGE AND PROCESSING..METABOLISM; LevelII__Secondary metabolites biosynthesis, transport and catabolism..Chromatin structure and dynamics; LevelIII__Deacetylases, including yeast histone deacetylase and acetoin utilization protein; LevelIV__; LevelV__; LevelVI__

It seems the list_values is empty, any idea?

Thanks,
Shengwei

Hi, I get the following error message from running Mapping orthologs to count table:
Error in library(plyr) : there is no package called ‘plyr’
Execution halted
CoMW environment is activated. The R-script is trying to retrieve library plyr.
Can you help with this?
Kr,
Jon

Hello, I am trying to create the CoMW environment but have ran into an error where Trinity2.6.6 package is not found anymore. I tried changing the script to change the version to a more recent trinity2.15.1 but still have gotten an error and was wondering if there was a way around this. Thank you!

Hi, I get the following error when I retry to create environment (see below) with your revised CoMW.yml file. I also reinstalled anaconda to ensure that it wasn't the installation of Anaconda which was problematic. I have copied the error message here. I hope that you can help with this.
Kr,
Jon

(base) bgp799@pallas:/mibi/Jon/CoMW$ conda env create -f ./CoMW.yml

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/conda_env/cli/main.py", line 80, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/conda_env/cli/main_create.py", line 80, in execute
    directory=os.getcwd())
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/conda_env/specs/__init__.py", line 40, in detect
    if spec.can_handle():
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/conda_env/specs/yaml_file.py", line 18, in can_handle
    self._environment = env.from_file(self.filename)
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/conda_env/env.py", line 151, in from_file
    return from_yaml(yamlstr, filename=filename)
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/conda_env/env.py", line 136, in from_yaml
    data = yaml_load_standard(yamlstr)
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/conda/common/serialize.py", line 76, in yaml_load_standard
    return yaml.load(string, Loader=yaml.Loader, version="1.2")
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/ruamel_yaml/main.py", line 935, in load
    return loader._constructor.get_single_data()
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/ruamel_yaml/constructor.py", line 109, in get_single_data
    node = self.composer.get_single_node()
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/ruamel_yaml/composer.py", line 78, in get_single_node
    document = self.compose_document()
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/ruamel_yaml/composer.py", line 104, in compose_document
    self.parser.get_event()
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/ruamel_yaml/parser.py", line 163, in get_event
    self.current_event = self.state()
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/ruamel_yaml/parser.py", line 239, in parse_document_end
    token = self.scanner.peek_token()
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/ruamel_yaml/scanner.py", line 182, in peek_token
    self.fetch_more_tokens()
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/ruamel_yaml/scanner.py", line 282, in fetch_more_tokens
    return self.fetch_value()
  File "/mibi/Jon/anaconda3/lib/python3.7/site-packages/ruamel_yaml/scanner.py", line 655, in fetch_value
    self.reader.get_mark(),
ruamel_yaml.scanner.ScannerError: mapping values are not allowed here
  in "<unicode string>", line 121, column 73:
     ... r-bar top-0 left-0" style="width: 0%;"></span>
                                         ^ (line: 121)

$ /mibi/Jon/anaconda3/bin/conda-env create -f ./CoMW.yml

environment variables:
CIO_TEST=
CONDA_AUTO_UPDATE_CONDA=false
CONDA_DEFAULT_ENV=base
CONDA_EXE=/mibi/Jon/anaconda3/bin/conda
CONDA_PREFIX=/mibi/Jon/anaconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/mibi/Jon/anaconda3/bin/python
CONDA_ROOT=/mibi/Jon/anaconda3
CONDA_SHLVL=1
LD_LIBRARY_PATH=/root/install/ncbi-blast-2.4.0+-src/c++/local/ncbi-vdb-2.6.1/lib64:
PATH=/mibi/Jon/anaconda3/bin:/mibi/Jon/anaconda3/bin:/mibi/Jon/anaconda3/co
ndabin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/snap/
bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=

 active environment : base
active env location : /mibi/Jon/anaconda3
        shell level : 1
   user config file : /usr/local/home/bgp799/.condarc

populated config files : /usr/local/home/bgp799/.condarc
conda version : 4.8.3
conda-build version : 3.18.11
python version : 3.7.6.final.0
virtual packages : __glibc=2.28
base environment : /mibi/Jon/anaconda3 (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /mibi/Jon/anaconda3/pkgs
/usr/local/home/bgp799/.conda/pkgs
envs directories : /mibi/Jon/anaconda3/envs
/usr/local/home/bgp799/.conda/envs
platform : linux-64
user-agent : conda/4.8.3 requests/2.22.0 CPython/3.7.6 Linux/4.19.0-9-amd64 debian/10 glibc/2.28
UID:GID : 3047:3000
netrc file : None
offline mode : False

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