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Nanosim hangs in the middle #184
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Can you please report the exact command? |
simulator.py metagenome -gl metagenome_list.tsv -a abundance.tsv -dl dna_type.tsv -c /home/devuser/omega_id/nanosim/NanoSim/pre-trained_models/metagenome_ERR3152364_Even/training -o bacteria --fastq -b guppy -t 10 --abun_var -0.5 0.5 --chimeric --max_len 1700 |
and yes we used it from master branch |
As a test, you could try taking out these options: |
I ran the code removing |
Hi @aastha-batta Do you get any sort of error messages in those cases or is the script stuck with no output? I suspect this might be also related to issue #185 We will look into it. Thanks for reporting this. |
Would you also kindly provide more information on this @aastha-batta ? What do you mean by making "any small change"? |
Hello @SaberHQ OK, so basically i tried changing the number of entries in the genome list and the subsequent lists to see if the script simulator.py is able to generate the results every time i run it successfully. It was not happening. I am yet to try this with a self trained model. I was not able to point out the exact reason for it to get stuck, especially when we are using the --max_reads flag. |
Also, @SaberHQ I was using the conda channel - bioconda nanosim package and since it has not been updated for the most recent commit in |
I have been trying to undestand the Let's say that I have genomes with max length of 1000 and I specify if not s or length > max(seq_len[s].values()):
s = random.choice(list(seq_len.keys())) will change the species (variable Other case is the one I reported in #185, when Now let's say that I have genomes with max length of 1000 and I specify for each_ref in ref_length_list:
middle, middle_ref, error_dict, error_count = \
error_list(each_ref, match_markov_model, match_ht_list, error_par, trans_error_pr, fastq)
total += middle
seg_length_list.append(middle_ref)
seg_error_dict_list.append(error_dict)
seg_error_count_list.append(error_count) In my tests if I specify |
This worked because the ~100 nt buffer accounted for the insertion error bases (and possibly head/tail regions) I think @danpal96 is right about the buggy parts of the code. |
Hi @danpal96, @ahfitzpa , @aastha-batta , and @rameezmj I have created pull request #189. Can you please check whether my changes would resolve the hanging issues on your end? |
@kmnip I made some small tests and it didnt get stuck, I will do more tests when I have more time. Sorry for the late response for some reason github is not notifying of the mentions |
@danpal96 No worries, we appreciate your help! |
Hi @kmnip Yes, we will look into the changes. I am sorry I was unable to reply to this. Will let you know asap. |
OK, So, We are using a pretrained model for metagenome simulations, We have a standard read count and 2 samples are getting generated, however when we are changing the no. of species that should be included in the sample the process hangs in the middle and does not finish. the read count is 100 and 1000 so it's not very large for NanoSim to run simulations, I am not understanding why is this happening.
Not only this if we are making any small change the process gets stuck and until we restart the terminal it does not run successfully.
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