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covid19_cme_analysis's Issues

returned non-zero exit status 255 for 5_epa_outgroup_rooting.py and IndexError: list index out of range for 6_root_digger_rooting.py

Hi @idaios

I prepare my dataset from scratch having high quality 10 sars-cov2 genome with 2 outgruop so total sequences in my data are 12 for which I again ran all script, this time I am stuck at 5th script

When first time ran 5th script the ERROR was :

ERROR: Must run iqtree_tests stage of pipeline first
Traceback (most recent call last):
  File "/home/vinita/covid19_cme_analysis/./pipeline/5_epa_outgroup_rooting.py", line 23, in <module>
    raise e
  File "/home/vinita/covid19_cme_analysis/./pipeline/5_epa_outgroup_rooting.py", line 20, in <module>
    util.expect_file_exists( paths.raxml_credible_ml_trees )
  File "/home/vinita/covid19_cme_analysis/scripts/util.py", line 99, in expect_file_exists
    raise RuntimeError( "File doesn't exist: " + file_path )
RuntimeError: File doesn't exist: /home/vinita/covid19_cme_analysis/work_dir/2021-11-17_05/smsao/results/trees/credible_ml_trees.newick

Then I ran 7th script first which is 7_iqtree_tests.py and again ran 5th script which is giving following error

./pipeline/5_epa_outgroup_rooting.py work_dir/2021-11-17_05/smsao

0  /  13
No protocol specified
No protocol specified
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/vinita/covid19_cme_analysis/./pipeline/5_epa_outgroup_rooting.py", line 71, in <module>
    cur_modelfile = raxml_launcher.evaluate(tree_file, ref_msa, cur_outdir)
  File "/home/vinita/covid19_cme_analysis/scripts/raxml_launcher.py", line 75, in evaluate
    sub.check_call(cmd, cwd=out_dir, stdout=sub.DEVNULL)
  File "/home/vinita/miniconda3/lib/python3.9/subprocess.py", line 373, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/home/vinita/covid19_cme_analysis/software/raxml-ng/bin/raxml-ng-mpi', '--evaluate', '--msa', '/home/vinita/covid19_cme_analysis/work_dir/2021-11-17_05/smsao/data/covid_edited.fasta', '--model', 'GTR+FO+G4', '--tree', '/home/vinita/covid19_cme_analysis/work_dir/2021-11-17_05/smsao/runs/epa_runs/0/tree.newick', '--prefix', 'eval', '--threads', '4', '--blopt', 'nr_safe', '--redo', '--blmin', '0.000000001']' returned non-zero exit status 255.

Further I tried 6th script

./pipeline/6_root_digger_rooting.py work_dir/2021-11-17_05/fmsan/

Traceback (most recent call last):
  File "/home/vinita/covid19_cme_analysis/./pipeline/6_root_digger_rooting.py", line 84, in <module>
    writer = csv.DictWriter(csv_file, fieldnames=results[0].keys())
IndexError: list index out of range
(name_of_my_env) ./pipeline/6_root_digger_rooting.py work_dir/2021-11-17_05/smsao/
Traceback (most recent call last):
  File "/home/vinita/covid19_cme_analysis/./pipeline/6_root_digger_rooting.py", line 84, in <module>
    writer = csv.DictWriter(csv_file, fieldnames=results[0].keys())
IndexError: list index out of range

But somehow 8_tree_thinning.py, 9_mptp_on_all_trees.py, compare_llhs, and extract_thinned_dataset.py worked on 4 dataset which are FMSAO, SMSAO, FMSAN & SMSAN

For wuhan_placement.py also get some erro

./pipeline/wuhan_placement.py work_dir/2021-11-17_05/smsao/

ERROR: Must run placement stage of pipeline first
Traceback (most recent call last):
  File "/home/vinita/covid19_cme_analysis/./pipeline/wuhan_placement.py", line 18, in <module>
    raise e
  File "/home/vinita/covid19_cme_analysis/./pipeline/wuhan_placement.py", line 15, in <module>
    util.expect_dir_exists( paths.epa_rooting_dir )
  File "/home/vinita/covid19_cme_analysis/scripts/util.py", line 95, in expect_dir_exists
    raise RuntimeError( "Directory doesn't exist: " + dir_path )
RuntimeError: Directory doesn't exist: /home/vinita/covid19_cme_analysis/work_dir/2021-11-17_05/smsao/results/epa_rooting

KIndly help me to understand these issue wether they are interlinked with my data or something which is not present in my data thats why root_digger_lwr.csv is empty in smsao/results/rootdigger_rooting

It would be very great if you could look at these errors and suggest me how I should solve these.

Thank you very much
Vinita

subprocess.CalledProcessError:

Hi

I clone this repo in my Ubuntu system and run the setup.sh and everything ran perfectcly. I ran first script ./pipeline/0_get_data.py path to my fasta file and it created a folder with current date in work_dir, But when I tried to run the ./pipeline/1_preprocess_data.py work_dir/2021-10-13_00/fmsan it gives following error :

/home/vinita/covid19_cme_analysis-master/scripts/preanalysis1.sh /home/vinita/covid19_cme_analysis-master/work_dir/2021-10-13_00/covid_raw_unaligned.fasta fmsan /home/vinita/covid19_cme_analysis-master/scripts /home/vinita/covid19_cme_analysis-master/software/mafft/mafft.bat /home/vinita/covid19_cme_analysis-master/config/outgroups.txt /home/vinita/covid19_cme_analysis-master/work_dir/2021-10-13_00 48
Totally 0 sequences pass the filter of less than 10 Ns
/home/vinita/covid19_cme_analysis-master/scripts/preanalysis1.sh: line 92: /home/vinita/covid19_cme_analysis-master/scripts/../software/genesis/bin/apps/remove_sequences: No such file or directory
Traceback (most recent call last):
  File "/home/vinita/covid19_cme_analysis-master/./pipeline/1_preprocess_data.py", line 14, in <module>
    preprocessing.trim_separate_align(paths.raw_sequences,
  File "scripts/preprocessing.py", line 24, in trim_separate_align
    subprocess.check_call(cmd, cwd=runsdir)
  File "/home/vinita/.local/lib/python3.9/subprocess.py", line 373, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/home/vinita/covid19_cme_analysis-master/scripts/preanalysis1.sh', '/home/vinita/covid19_cme_analysis-master/work_dir/2021-10-13_00/covid_raw_unaligned.fasta', 'fmsan', '/home/vinita/covid19_cme_analysis-master/scripts', '/home/vinita/covid19_cme_analysis-master/software/mafft/mafft.bat', '/home/vinita/covid19_cme_analysis-master/config/outgroups.txt', '/home/vinita/covid19_cme_analysis-master/work_dir/2021-10-13_00', '48']' returned non-zero exit status 127

I have checked this genesis older for bin/apps/remove_sequences but this remove_sequences are present in build folder
I tried to install this repo in Mac as well as in Linux mint but the setup.sh is giving error and not able to installed on these two OS

Kindly have a look and suggest me how to run these script to get better results for my Sars-Cov2 data

TypeError: object of type '_io.TextIOWrapper' has no len() for `9_mptp_on_all_trees.py`

Hi @Pbdas

I ran ./pipeline/9_mptp_on_all_trees.py work_dir/2021-11-19_00/fmsan/ and I got following error on my terminal

WARNING: delimit was not compiled with libgsl. Likelihood ratio test disabled.
WARNING: A speciation edge is smaller than the specified minimum branch length.
mptp 0.2.4_linux_x86_64, 1008GB RAM, 96 cores
https://github.com/Pas-Kapli/mptp
WARNING: delimit was not compiled with libgsl. Likelihood ratio test disabled.
WARNING: A speciation edge is smaller than the specified minimum branch length.
WARNING: delimit was not compiled with libgsl. Likelihood ratio test disabled.
Traceback (most recent call last):
File "/home/vinita/covid19_cme_analysis/./pipeline/9_mptp_on_all_trees.py", line 191, in
run_mptp_all_rootings_on_trees_one_histogram(paths.raxml_credible_ml_trees, paths.mptp_output, paths.mptp_output_summary_all_rootings_one_histogram)
File "/home/vinita/covid19_cme_analysis/./pipeline/9_mptp_on_all_trees.py", line 181, in run_mptp_all_rootings_on_trees_one_histogram
species = get_all_rootings_counts_one_histogram(results_all_rootings_ml + "/output.txt", species)
File "/home/vinita/covid19_cme_analysis/./pipeline/9_mptp_on_all_trees.py", line 105, in get_all_rootings_counts_one_histogram
for i in range(4, len(lines)):
TypeError: object of type '_io.TextIOWrapper' has no len()

I also found so many tempOutFooBar_.svg something around 3000 in number , Please have a look at this error .

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