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GabeAl / NINJA-OPS

Ninja Is Not Just Another OTU Picking Solution
ISC License
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NINJA Segmentation error #16

Open swati0689 opened 7 years ago

swati0689 commented 7 years ago

I am trying to run NINJA on linux

I get the following error on using the command

python /home/genetics/Desktop/Ruchi_SRF/NINJA-OPS-master/bin/ninja.py -i /home/genetics/Desktop/Ruchi_SRF/Cases_Controls/combined/combined_seqs.fna -o ninja

Running NINJA-OPS filter... "/mnt/e/Data/SNA_16S/ninja-ops/bin/ninja_filter_linux" "merge.pear.maxee1.fasta" "/mnt/e/Data/SNA_16S/ninja_otu/ninja" D 1 LOG

Segmentation fault (core dumped)

Traceback (most recent call last): File "ninja-ops/bin/ninja.py", line 609, in main(p) File "ninja-ops/bin/ninja.py", line 566, in main logger.log("NINJA-OPS filter time: " + str(t1.timeit(1))) File "/usr/lib/python2.7/timeit.py", line 195, in timeit timing = self.inner(it, self.timer) File "/usr/lib/python2.7/timeit.py", line 100, in inner _func() File "ninja-ops/bin/ninja.py", line 564, in run_with_shell=run_with_shell, print_only=args['print_only']) File "ninja-ops/bin/ninja.py", line 289, in ninja_filter raise ValueError("ERROR: Filtering failed. One possible explanation is a problem with input FASTA formatting. Please rerun with '--check_fasta'. Exiting.") ValueError: ERROR: Filtering failed. One possible explanation is a problem with input FASTA formatting. Please rerun with '--check_fasta'. Exiting. Any idea how to resolve the same

GabeAl commented 7 years ago

Hi, thanks for reporting!

A couple of quick questions for you, if that's okay:

  1. What version of NINJA are you using? Currently only v1.5.1 and later are supported, so it's good to use the freshest one.
  2. What is the file size of the fasta file you're using? Are the sequences linear or do the sequences contain line breaks?
  3. How much memory (ram) is available on your linux system?

The reason for these questions is that the most common causes of segmentation problems is either using an old version of NINJA, having formatting incompatibility in your fasta file, or having insufficient RAM to run the program on large data.

Thanks! Gabe

On Jun 1, 2017 9:42 PM, "swati0689" notifications@github.com wrote:

I am trying to run NINJA on linux

I get the following error on using the command

python /home/genetics/Desktop/Ruchi_SRF/NINJA-OPS-master/bin/ninja.py -i /home/genetics/Desktop/Ruchi_SRF/Cases_Controls/combined/combined_seqs.fna -o ninja

Running NINJA-OPS filter... "/mnt/e/Data/SNA_16S/ninja-ops/bin/ninja_filter_linux" "merge.pear.maxee1.fasta" "/mnt/e/Data/SNA_16S/ninja_otu/ninja" D 1 LOG

Segmentation fault (core dumped)

Traceback (most recent call last): File "ninja-ops/bin/ninja.py", line 609, in main(p) File "ninja-ops/bin/ninja.py", line 566, in main logger.log("NINJA-OPS filter time: " + str(t1.timeit(1))) File "/usr/lib/python2.7/timeit.py", line 195, in timeit timing = self.inner(it, self.timer) File "/usr/lib/python2.7/timeit.py", line 100, in inner _func() File "ninja-ops/bin/ninja.py", line 564, in run_with_shell=run_with_shell, print_only=args['print_only']) File "ninja-ops/bin/ninja.py", line 289, in ninja_filter raise ValueError("ERROR: Filtering failed. One possible explanation is a problem with input FASTA formatting. Please rerun with '--check_fasta'. Exiting.") ValueError: ERROR: Filtering failed. One possible explanation is a problem with input FASTA formatting. Please rerun with '--check_fasta'. Exiting. Any idea how to resolve the same

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