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GabeAl / NINJA-OPS

Ninja Is Not Just Another OTU Picking Solution
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UNSUPPORTED_MAPPING #18

Closed ZeweiSong closed 7 years ago

ZeweiSong commented 7 years ago

Hi, Gabe

I got "UNSUPPORTED_MAPPING" on my taxonomy column when using NINJA in my Ubuntu virtual machine, but the same setting ran fine of MSI (I use the exact same database).

Any idea? Thanks!

Zewei

ZeweiSong commented 7 years ago

Never mind, I think I still used a wrong database! I forgot to change the long label to short name in my FASTA file.

GabeAl commented 7 years ago

Glad it worked!

Also, these tools should work on WSL on Windows now (if you have updated to the Creator's update of Windows 10), so no need for a virtual machine!

Cheers, Gabe

On Wed, Sep 6, 2017 at 10:07 AM, Zewei Song notifications@github.com wrote:

Never mind, I think I still used a wrong database! I forgot to change the long label to short name in my FASTA file.

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ZeweiSong commented 7 years ago

Tried it on Windows today, got this error:

Segmentation fault (core dumped)

Traceback (most recent call last): File "/mnt/e/GoogleDrive/Research/Tools/ninja-ops/bin/ninja.py", line 609, in main(p) File "/mnt/e/GoogleDrive/Research/Tools/ninja-ops/bin/ninja.py", line 587, in main logger.log("NINJA-OPS parse time: " + str(t3.timeit(1)) + "\n") File "/home/zewei/anaconda3/lib/python3.6/timeit.py", line 178, in timeit timing = self.inner(it, self.timer) File "", line 6, in inner File "/mnt/e/GoogleDrive/Research/Tools/ninja-ops/bin/ninja.py", line 585, in logger, legacy_table, run_with_shell=run_with_shell, print_only=args['print_only']) File "/mnt/e/GoogleDrive/Research/Tools/ninja-ops/bin/ninja.py", line 427, in ninja_parse raise ValueError("ERROR: Parsing failed. Exiting.") ValueError: ERROR: Parsing failed. Exiting.

Is it because I am using Python 3.6?

GabeAl commented 7 years ago

Just tried it on 2 windows machines here:

gabe@DCanyon:/mnt/c/Users/Gabe/Desktop/embalmer/reflateN$ ninja.py -i uBiome/bad_noFlash/combined_seqs.fna -o tryme NINJA-OPS v1.5.1 NINJA-OPS database directory is /mnt/c/Users/Gabe/Desktop/embalmer/reflateN/NINJA-OPS-1.5.1/databases/greengenes97 Running NINJA-OPS filter... "/mnt/c/Users/Gabe/Desktop/embalmer/reflateN/NINJA-OPS-1.5.1/bin/ninja_filter_linux" "uBiome/bad_noFlash/combined_seqs.fna" "/mnt/c/Users/Gabe/Desktop/embalmer/reflateN/tryme/ninja" D 1 Not using paired-end reads Performing NINJA replicon-denoising at 1 compacted reads. WARNING: Found 32 sequences with ambiguity (105 ambiguous bases). Number of sequences: 86604 Total reads considered: 86572 Reads sorted. 2 Samples found. Finished. NINJA-OPS filter time: 0.09263800014741719 Running Bowtie2... bowtie2-align-s --no-head -x /mnt/c/Users/Gabe/Desktop/embalmer/reflateN/NINJA-OPS-1.5.1/databases/greengenes97/greengenes97 -S "/mnt/c/Users/Gabe/Desktop/embalmer/reflateN/tryme/alignments.txt" --np 0 --mp "1,1" --rdg "0,1" --rfg "0,1" --score-min "L,0,-0.030000000000000027" --norc -f "/mnt/c/Users/Gabe/Desktop/embalmer/reflateN/tryme/ninja_filt.fa" -p 8 --very-sensitive

Bowtie time: 2.9872389999218285 Running NINJA-OPS compact... "/mnt/c/Users/Gabe/Desktop/embalmer/reflateN/NINJA-OPS-1.5.1/bin/ninja_compact_linux" "/mnt/c/Users/Gabe/Desktop/embalmer/reflateN/tryme/alignments_uncompacted.txt" "/mnt/c/Users/Gabe/Desktop/embalmer/reflateN/NINJA-OPS-1.5.1/databases/greengenes97/greengenes97.tcf" "/mnt/c/Users/Gabe/Desktop/embalmer/reflateN/tryme/alignments.txt" Done. NINJA-OPS compact time: 0.3699719998985529 Running NINJA-OPS parse... "/mnt/c/Users/Gabe/Desktop/embalmer/reflateN/NINJA-OPS-1.5.1/bin/ninja_parse_filtered_linux" "/mnt/c/Users/Gabe/Desktop/embalmer/reflateN/tryme/ninja" "/mnt/c/Users/Gabe/Desktop/embalmer/reflateN/tryme/alignments.txt" "/mnt/c/Users/Gabe/Desktop/embalmer/reflateN/NINJA-OPS-1.5.1/databases/greengenes97/greengenes97.db" "/mnt/c/Users/Gabe/Desktop/embalmer/reflateN/NINJA-OPS-1.5.1/databases/greengenes97/greengenes97.taxonomy" Opened /mnt/c/Users/Gabe/Desktop/embalmer/reflateN/tryme/ninja_otutable.biom for OTU Table writing Total OTUs available to pick from: 99322 Number of unique samples: 2, max reads: 29884 Total chimeric alignments: 0 Total reads expanded: 38688 Run complete. NINJA-OPS parse time: 0.08933900017291307 gabe@DCanyon:/mnt/c/Users/Gabe/Desktop/embalmer/reflateN$

Here's how I did a clean setup: wget https://github.com/GabeAl/NINJA-OPS/archive/v1.5.1.zip unzip v1.5.1.zip cd NINJA-OPS-1.5.1/bin wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.3/bowtie2-2.3.3-linux-x86_64.zip/download -O bt2.zip unzip bt2.zip mv bowtie2-2.3.3/bowtie2-align-s . PATH=$PATH:$(pwd)

To test:

cd /somewhere/else/with/data ninja.py -i combined_seqs.fna -o tryme

You can clean up the unnecessary intermediates (the zip files, the bowtie2 directory that got extracted, etc) and add the ninja-ops bin directory to your PATH in your ~/.bashrc to have it always runnable.

If this doesn't work, to debug your setup, I'll need to know the following:

  1. What input file are you using?
  2. Is NINJA-OPS in your PATH? (do echo $PATH and make sure you see the NINJA-OPS bin in there)
  3. What version of NINJA-OPS is this? (Only v1.5.1 is supported! Check with ninja.py --version)
  4. What version of Windows 10 are you using? (Check in cmd -- not the BASH shell, but a new cmd prompt in Windows -- with ver . Only Microsoft Windows [Version 10.0.15063] and later are supported)

Let me know! Gabe

On Thu, Sep 7, 2017 at 2:31 PM, Zewei Song notifications@github.com wrote:

Tried it on Windows today, got this error:

Segmentation fault (core dumped)

Traceback (most recent call last): File "/mnt/e/GoogleDrive/Research/Tools/ninja-ops/bin/ninja.py", line 609, in main(p) File "/mnt/e/GoogleDrive/Research/Tools/ninja-ops/bin/ninja.py", line 587, in main logger.log("NINJA-OPS parse time: " + str(t3.timeit(1)) + "\n") File "/home/zewei/anaconda3/lib/python3.6/timeit.py", line 178, in timeit timing = self.inner(it, self.timer) File "", line 6, in inner File "/mnt/e/GoogleDrive/Research/Tools/ninja-ops/bin/ninja.py", line 585, in logger, legacy_table, run_with_shell=run_with_shell, print_only=args['print_only']) File "/mnt/e/GoogleDrive/Research/Tools/ninja-ops/bin/ninja.py", line 427, in ninja_parse raise ValueError("ERROR: Parsing failed. Exiting.") ValueError: ERROR: Parsing failed. Exiting.

Is it because I am using Python 3.6?

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