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marbl / parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
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NameError: name 'nameok' is not defined #51

Closed ramadatta closed 4 years ago

ramadatta commented 6 years ago

Hi,

Some of my datasets run without any problem, but some throw the following error with parsnp v1.2. Kindly request to know to overcome this error. Thanks.

$ parsnp_linux_ignoresize -r ecloacae_ref.fasta -d . -o test_ecloc -x -c

|--Parsnp v1.2--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
***************************
SETTINGS:
|-refgenome:    ecloacae_CP001918.fasta
|-aligner:  libMUSCLE
|-seqdir:   .
|-outdir:   test_ecloc
|-OS:       Linux
|-threads:  32
***************************

<<Parsnp started>>

-->Reading Genome (asm, fasta) files from ...
  |->[OK]
-->Reading Genbank file(s) for reference (.gbk) ..
  |->[WARNING]: no genbank file provided for reference annotations, skipping..
Traceback (most recent call last):
  File "<string>", line 624, in <module>
NameError: name 'nameok' is not defined
marina-manrique commented 6 years ago

I got the same issue and fixed it moving the gb file of the reference genome out of the folder where the genome sequences under analysis were. HTH

ramadatta commented 6 years ago

Hi @marina-manrique. Thanks much for comment. I am not using "gb" files for the job but a bunch of fasta files. The error still persists. May be, it is some kind of version conflict with python. I am using python 2.7.5, not sure if the program requires python3.3. Still figuring the way out.

treangen commented 6 years ago

hi @ramadatta , can you try moving your genomes to a separate dir (instead of current dir -d '.') then run again?

ramadatta commented 6 years ago

hi @ramadatta , can you try moving your genomes to a separate dir (instead of current dir -d '.') then run again?

Hi @treangen , Thank you. Sure. I will try this and come back to you!

bifidoman commented 5 years ago

Hi

is this issue solved? I have teh same problem. However, not with fasta comming from spades but with fasta coming from shovill. The latter have a latter which might be incompatible?:

contig00001 len=1011936 cov=20.2 corr=0 origname=NODE_1_length_1011936_cov_20.218902_pilon sw=shovill-spades/1.0.4 date=20190116

I already deleted al "-" and spaces, which at least solved the "requires 2 or more genomes " error. Howeve,r now I am getting this error

thnaks

marc

innovate-invent commented 5 years ago

https://github.com/marbl/parsnp/blob/63bea137e2726c860133f0b97da688dab3c1b92b/Parsnp.py#L616 I am not sure what this line is accomplishing but if the first file in the genomes dir thats second line does not meet this criteria then nameok is undefined at the next if statement

lch14forever commented 5 years ago

Encountered the same issue. It was caused by having other files than fasta files in the genome dir.

bkille commented 4 years ago

Hello all! Sorry for the late reply. This issue has been fixed. There is now another way to pass in input files w/out having to clean directories. You can now pass -d ./dir/*.fna instead of -d ./dir. This way you will only pass the .fna files to parsnp.

GREATER93 commented 3 years ago

Hello all, I still face the problem of "NameError: name 'nameok' is not defined", even after trying all the above suggested solutions. Any help please? Thank you.

bkille commented 3 years ago

@GREATER93 Happy to help!

Can you please specify how you installed parsnp, and then show the command used as well as the output? Thanks!

GREATER93 commented 3 years ago

Hi Kille, thanks for your response.

I installed parsnp on ubuntu linux, alongside other softwares using this command: conda install -c bioconda -y abyss spades parsnp fasttree raxml-ng phyml mauve modeltest-ng

Then I tried to perform alignment "With reference but without genbank file" using: parsnp -r -d -p

I got this output:

<>

-->Reading Genome (asm, fasta) files from ./genome_gkt.. |->[OK] -->Reading Genbank file(s) for reference (.gbk) .. |->[WARNING]: no genbank file provided for reference annotations, skipping.. Traceback (most recent call last): File "", line 624, in NameError: name 'nameok' is not defined

So I am wondering where the error lies.....

bkille commented 3 years ago

@GREATER93

Please copy the entire command used as well as the entire output, see this reply for an example.

That being said, it looks like you are using Parsnp v1.2. In order to install the latest version, v1.5.6, please refer to the bioconda docs for setting up the channels. Once that is done you can reinstall parsnp.

GREATER93 commented 3 years ago

Welcome to Ubuntu 20.04.2 LTS (GNU/Linux 4.4.0-19041-Microsoft x86_64)

1 update can be applied immediately. To see these additional updates run: apt list --upgradable

The list of available updates is more than a week old. To check for new updates run: sudo apt update

This message is shown once a day. To disable it please create the /home/jszheng/.hushlogin file. (base) jszheng@Greater:~$ ls ./genome_diir '*.fna' KF0124_1_1_flye_chromosome.fasta.sslist KF0125_4_1_flye_chromosome.fasta.sslist (base) jszheng@Greater:~$ ls ./genome_dir {KF0123_26_flye_chromosome.fasta.sslist, (base) jszheng@Greater:~$ parsnp |--Parsnp v1.2--| For detailed documentation please see --> http://harvest.readthedocs.org/en/latest usage: parsnp [options] [-g|-r|-q](see below) -d -p

Parsnp quick start for three example scenarios: 1) With reference & genbank file:

parsnp -g <reference_genbank_file1,reference_genbank_file2,..> -d -p

2) With reference but without genbank file:

parsnp -r -d -p

3) Autorecruit reference to a draft assembly:

parsnp -q -d -p

[Input parameters] <<input/output>> -c = : (c)urated genome directory, use all genomes in dir and ignore MUMi? (default = NO) -d = : (d)irectory containing genomes/contigs/scaffolds -r = : (r)eference genome (set to ! to pick random one from genome dir) -g = : Gen(b)ank file(s) (gbk), comma separated list (default = None) -o = : output directory? default [./P_CURRDATE_CURRTIME] -q = : (optional) specify (assembled) query genome to use, in addition to genomes found in genome dir (default = NONE)

<> -U = : max MUMi distance value for MUMi distribution -M = : calculate MUMi and exit? overrides all other choices! (default: NO) -i = : max MUM(i) distance (default: autocutoff based on distribution of MUMi values)

<> -a = : min (a)NCHOR length (default = 1.1*Log(S)) -C = : maximal cluster D value? (default=100) -z = : min LCB si(z)e? (default = 25)

<> -D = : maximal diagonal difference? Either percentage (e.g. 0.2) or bp (e.g. 100bp) (default = 0.12) -e = greedily extend LCBs? experimental! (default = NO) -n = : alignment program (default: libMUSCLE) -u = : output unaligned regions? .unaligned (default: NO)

<> -x = : enable filtering of SNPs located in PhiPack identified regions of recombination? (default: NO)

<> -h = : (h)elp: print this message and exit -p = : number of threads to use? (default= 1) -P = : max partition size? limits memory usage (default= 15000000) -v = : (v)erbose output? (default = NO) -V = : output (V)ersion and exit

(base) jszheng@Greater:~$ -r ./KF0123_26_flye_chromosome.fasta.sslist -d ./genome_diir -p ./1 -r: command not found (base) jszheng@Greater:~$ parsnp -r ./KF0123_26_flye_chromosome.fasta.sslist -d ./genome_diir -p ./1 |--Parsnp v1.2--| For detailed documentation please see --> http://harvest.readthedocs.org/en/latest

SETTINGS: |-refgenome: ./KF0123_26_flye_chromosome.fasta.sslist |-aligner: libMUSCLE |-seqdir: ./genome_diir |-outdir: /home/jszheng/P_2021_07_20_093412027780 |-OS: Linux |-threads: ./1

<>

-->Reading Genome (asm, fasta) files from ./genome_diir.. |->[OK] -->Reading Genbank file(s) for reference (.gbk) .. |->[WARNING]: no genbank file provided for reference annotations, skipping.. Traceback (most recent call last): File "", line 624, in NameError: name 'nameok' is not defined

GREATER93 commented 3 years ago

Is this okay?

bkille commented 3 years ago

Yup! Thanks, so that confirms that you are still on Parsnp v1.2. Please refer to the bioconda docs linked in the previous message for updating the channels, and then reinstall/update parsnp via conda. Let me know if you have any further questions!

GREATER93 commented 3 years ago

Okay. Let me try that. I will tell you my experience. Thanks.

GREATER93 commented 3 years ago

@bkille I have tried to update the channels and update parsnp, but I seem not to break through yet.

First, I set up the channels: conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge

Second, I installed parsnp: conda install parsnp

Then, I updated parsnp: conda update parsnp

I noticed that the version still reads v1.2. I ran my analysis again and got the same error prompt.

(base) jszheng@Greater:~$ conda config --add channels defaults Warning: 'defaults' already in 'channels' list, moving to the top (base) jszheng@Greater:~$ conda config --add channels bioconda Warning: 'bioconda' already in 'channels' list, moving to the top (base) jszheng@Greater:~$ conda config --add channels conda-forge Warning: 'conda-forge' already in 'channels' list, moving to the top (base) jszheng@Greater:~$ conda install bwa Collecting package metadata (current_repodata.json): done Solving environment: done

All requested packages already installed.

(base) jszheng@Greater:~$ conda install parsnp Collecting package metadata (current_repodata.json): done Solving environment: done

All requested packages already installed.

(base) jszheng@Greater:~$ conda update parsnp Collecting package metadata (current_repodata.json): done Solving environment: done

All requested packages already installed.

(base) jszheng@Greater:~$ parsnp -r ./KF0123_26_flye_chromosome.fasta -d ./genome_diir .p ./1 |--Parsnp v1.2--| For detailed documentation please see --> http://harvest.readthedocs.org/en/latest

SETTINGS: |-refgenome: ./KF0123_26_flye_chromosome.fasta |-aligner: libMUSCLE |-seqdir: ./genome_diir |-outdir: /home/jszheng/P_2021_07_20_142009039288 |-OS: Linux |-threads: 32

<>

-->Reading Genome (asm, fasta) files from ./genome_diir.. |->[OK] -->Reading Genbank file(s) for reference (.gbk) .. |->[WARNING]: no genbank file provided for reference annotations, skipping.. Traceback (most recent call last): File "", line 624, in NameError: name 'nameok' is not defined

bkille commented 3 years ago

@GREATER93 then my next guess is that your environment is not compatible w parsnp. What happens if you install parsnp in a fresh python 3.7 environment?

GREATER93 commented 3 years ago

Oh! Let me check that.

GREATER93 commented 3 years ago

@bkille Hello, I installed python 3.7 and proceeded to set up channels in order to install parsnp, but I got this:

it (AMD64)] on win32 Type "help", "copyright", "credits" or "license" for more information.

conda config --add channels defaults File "", line 1 conda config --add channels defaults ^ SyntaxError: invalid syntax

What to do? I am very sorry for my many questions; I am just a beginner in programming, I hope you understand.

bkille commented 3 years ago

It looks like you're entering those commands in via the python interpreter. You need to be running the conda commands via bash like you have been previously.

Don't worry, we were all beginners at some point (:

GREATER93 commented 3 years ago

Thanks for your understanding!

You mean something like this: Python 3.7.0a2 (v3.7.0a2:f7ac4fe, Oct 17 2017, 17:06:29) [MSC v.1900 64 bit (AMD64)] on win32 Type "help", "copyright", "credits" or "license" for more information.

bash Miniconda3-py39_4.9.2-Linux-x86_64.sh File "", line 1 bash Miniconda3-py39_4.9.2-Linux-x86_64.sh ^ SyntaxError: invalid syntax wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.9.2-Linux-x86_64.sh File "", line 1 wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.9.2-Linux-x86_64.sh ^ SyntaxError: invalid syntax

bkille commented 3 years ago

It looks like you are still in the python interpreter. Ctrl+D should close the interpreter and return you to bash.

That being said, you don't need to reinstall conda to get a new python 3.7 environment. See the conda docs:

conda create -n parsnp-test python=3.7 parsnp

Will create a new environment with parsnp already installed. You can then activate the environment with 

conda activate test-parsnp
GREATER93 commented 3 years ago

Oh, Okay.

Sorry to ask, this should still be in python 3.7, or I can continue to use ubuntu?

GREATER93 commented 3 years ago

I think I got it now. Let me finish and get back to you.

GREATER93 commented 3 years ago

@bkille Now, I successfully updated parsnp. Thanks for your guidance.

However, I proceeded to run my analysis but got some error again. Do you know what it means?

(parsnp-test) jszheng@Greater:~$ parsnp -r ./KF0123_26_flye_chromosome.fasta.sslist -d ./genome_diir -p 1
|--Parsnp 1.5.6--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
Traceback (most recent call last):
  File "/home/jszheng/yes/envs/parsnp-test/bin/parsnp", line 650, in <module>
    rfd = rf.read()
  File "/home/jszheng/yes/envs/parsnp-test/lib/python3.7/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xdf in position 9: invalid continuation byte
(parsnp-test) jszheng@Greater:~$
bkille commented 3 years ago

Yes, so the cause of this is the same as the reason the old version didn't work. You have some file(s) in the genome_diir that isn't a valid input file. For example it is often a "hidden file".

To circumvent this, you can use a regular expression. For example, if all of the desired files in the genome_diir end in ".fasta", you can run 

parsnp -r ./KF0123_26_flye_chromosome.fasta.sslist -d ./genome_diir/*.fasta -p 1

You can replace the ".fasta" with whatever the file extension is of your input files.

GREATER93 commented 3 years ago

Oh, I see. Let me check.

GREATER93 commented 3 years ago

The files end with ".fasta.sslist", so I ran for both ".fasta" and ".sslist". But got error.

(parsnp-test) jszheng@Greater:~$ parsnp -r ./KF0123_26_flye_chromosome.fasta.sslist -d ./genome_diir/.fasta -p 1 |--Parsnp 1.5.6--| For detailed documentation please see --> http://harvest.readthedocs.org/en/latest 09:50:34 - ERROR - ./genome_diir/.fasta is not a valid file 09:50:34 - CRITICAL - Less than 2 input sequences provided...

(parsnp-test) jszheng@Greater:~$ parsnp -r ./KF0123_26_flye_chromosome.fasta.sslist -d ./genome_diir/*.sslist -p 1 |--Parsnp 1.5.6--| For detailed documentation please see --> http://harvest.readthedocs.org/en/latest Traceback (most recent call last): File "/home/jszheng/yes/envs/parsnp-test/bin/parsnp", line 650, in rfd = rf.read() File "/home/jszheng/yes/envs/parsnp-test/lib/python3.7/codecs.py", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xdf in position 9: invalid continuation byte

bkille commented 3 years ago

My guess is you have a .sslist file that isn't properly formatted. How many files should there be? If its a reasonably small number, you can try:

head genome_diir/*.sslist

to view the first few lines of all of the fasta files to verify they are formatted correctly.

GREATER93 commented 3 years ago

I have just two files in genome_diir and both end in .fasta.sslist

I tried your suggestion....I got this:

(parsnp-test) jszheng@Greater:~$ head genome_diir/.sslist ==> genome_diir/KF0124_1_1_flyechromosome.fasta.sslist <==  #;CD-!$l%!4h%I0?Dh5#$  [J$N+}8 h _)M%7/0m{P],0 (s?4 $1<zE C7& aA1'D7T2(>"#7r4r']2 'D,o1<5 H0;:&#x` s19l/j& 9+]A, 1 3~'eE<<!;x'ƿ FpY)!#,<6[e" 3o#q9F8$O3m)D~/( ;,s{;v.`21g,U"˓1vS%ab; Jv05,CW4foK9+ޚG#%/A) &/s#S1/e/)2 1'.o(r$35G.<(+y+h G]h]+3( H!8<!1 '\V%h<f=Z0;D+6+؛/t[R"T%&2M<~^T%QU &6B$4(%9(T$e'1Y04tT5Ż<Q/d)_,:!O3D'k- Elb#Q8t'g3.|# ,2;:T4< $5C8$5hn)޵6TcA$8E#'^1M7>

==> genome_diir/KF0125_4_1_flyechromosome.fasta.sslist <==  #;CD-!$l%!4h%I0?Dh5#$  [J$N+}8 h _)M%7/0m{P],0 (s?4 $1<zE C7& aA1'D7T2(>"#7r4r']2 'D,o1<5 H0;:&#x` s19l/j& 9+]A, 1 3~'eE<<!;x'ƿ FpY)!#,<6[e" 3o#q9F8$O3m)D~/( ;,s{;v.`21g,U"˓1vS%ab; Jv05,CW4foK9+ޚG#%/A) &/s#S1/e/)2 1'.o(r$35G.<(+y+h G]h]+3( H!8<!1 '\V%h<f=Z0;D+6+؛/t[R"T%&2M<~^T%QU &6B$4(%9(T$e'1Y04tT5Ż<Q/d)_,:!O3D'k- Elb#*Q8t'g3.|# ,2;:T4< $5C8$5hn)޵6TcA$8E#'^1M7>

GREATER93 commented 3 years ago

@bkille Hi, are you still there?

bkille commented 3 years ago

@GREATER93 As suspected, those files are not text files. You will need to have valid fasta input files for parsnp to work. For example, here is an example fasta file.

GREATER93 commented 3 years ago

Alright, got it. Thanks very much for your assistance.

GREATER93 commented 3 years ago

@bkille Now I put fasta files and checked. I got this:

(parsnp-test) jszheng@Greater:~$ head genome_diirt/*.fq
==> genome_diirt/KF0124_1_1.fq <==
@00279652-9b8d-4492-9cf4-faa9fc632a92 ch=112 start_time=2021-05-12T21:25:49
GCTGGAATTTACGTCTGCTCATCCAGGCTATGGATATCAATTGTTATATTGGCTATGGTGATGGTGTATCCATTATGTTAAGCAATTTGTCGCGCTTGATGGCAAACTTTTGTGGTATGAATTATCGATATGATTGCATTGATGTCGCAATACTCAAGTAAAACTTGGCACAAAATGTGCATAACTGCTCTTTGGGGAAATCACCGTTGTGATTTACTCATGTGGCTGAAGCAAATCACAATCTGAATGAATTACCTTTGCCGTCCAGTTCTCGCCCAGTCCGTCAGGGTGATTAAAAGTCACTAAATAAAAAATCGAGCTTATTGCAGTTAGCGCCAATAATCATCTGTAGGTTGGCATTTCCTGTATTTAAAACCGCTCCGTAACGTATCTGACCATTGACTAAATTTGTGAAAAATGGATCATCTTCATAATTGCTTACCCATAGGATACAAAACTATCTTTGCCTTATAATACCAATGCATTAACGGCAAACCAACAGAGACATTAGAGGCAATGTAAGAATCAAATGGAAAATTAAACAACGAACATCATCAGATGGCATCCGCATAATAAGCTCTAATCCCATAAGGTTACATATTTATACTTTCACAAATTTGAAGTAAATAAAGGTTATCTGTGGTGCACAAATAAATTTATATTTAAGCAAACATTATAAAGCTGCATATCTCCTACTTTGATTTGCCCACCACTAAAAATATACATAATTCATCATTTGTTCTTGGGTATCTGAACTGATATCTTCTAAAGCTTCAGTTTTACAAATAAATCATCCTACTCAAACATAGTATTAAGTGGCTAAAATGCTAGCTCTTGTTGCAAAATAAGTGCATTTTGCAATTAAAATAACCTTGTGTATTTGCTAATTGCTGCTGTGCAAGGCAATAATACATCTCCCGTTATATCGCAAAAGTATGCAGTTGACGGAACACAGAAATGACACTCTAAATGAGTAGTTCCATTGTCCTATTAAAACACAATACCCTGTTCCAATCTAGCCCAACAATAGTCAACTTTCGTTCTCTTTACATTCAACAATAACAGCACTTGAACCACAAAAAAACATCATATTTTTCATGCCACTTTTCTCGCACTCCTAATGGGCGATAATCGAGATAGTCCCATAGATAAATAAAATACAGTAATTCTTCTTTGAACAATTTGCCGCATCACAAAACAAAACCCGCTGATTATCGAAACCTCCGCCCAATCGTGACTGGGCGTGTGGAGAATTTCGGCAGATAACATAACGTTGGAGTGATTGTAACGCACGGCACAAACGATTAAAACATGTGCAGCATTAAACGCCATGACCTTGCTGAAACGTGCGTAGCGTTGTATGAACGATGTACTATCCGGTTGATATGGCATCTTTGCAAAATATTTCACTGAGCAAAGCAGCTGTTGTCGATCTTTGACAGTTAAATTCTGGCAAAATGCACAACCACAGTTTAAGCATCATATTTAGTGGCCTCTTGTACTTTGGAGAAATAGATTTATTGGTATAGATATCTACTCCTCCATTTCTGTATTTAGGAAGGGGCCCAAGCCCTTGTTAAAAACAGTAAGGTGCTGATACTCATAACGCTGGTAGCCGTTATCGAATATTAAAATATCTCTTTGAGCGTCTTGTCGCAGGCAGCTGATTGCCCAATTCATAGCGGATGTTGATGCAGCGATGTTTGAGCATCATTGCTATGTTTTTAGCAGTTTCAATTAAGTCATAATGCGTTGATGATTAGCATCAATTTCATAATTATGCCTCGAACATATATTCCAACTGCTGGGTAAATTATAATAAGCTTCCCCAATTTGGATGATTTTAATAATTGCATGTTGAGTTGTAATTTATTCCTATATGAGTCCATTCAGCTGTTGAAGTAATTGTTCTAACTCCTGCAGACTGTAGAGGTCTTGCTGAAAACGTAGTCGTATATCAAATAATTCTATCTTTTGTCTAAATGCAGAAATAACGCTATATCTTCATGTTCAGTATCAGTATTTATGATTACCAAGCACTTTCTAACTAAAGCCTGATTTTAATGAATCAGGATGACTATTGGGACTCGCTTAATCCCATGATTTAATTCTGCATAAGCATTTTGAAGATAATATTCCTGGTAACTCTTGGAGATATTATATCTTTGAGAAATAGCAACTGATTCAGTAATGAATATGTTTGTTGATCAGCATAGCAATTCATTAATTCTGCTTGATCATCCCTCACAATGCTGCTGCAATTGGGCTTCATTTAGCATCATCTGTAAATGGCAAATTCATACAGCAATTGAATTCGCATGCACCTAACGACCCAGCCAACGATGTGGTGCGCACTCGAATTGAGTAAGACCAAAATTTCCTCTTTAACCAACCATTAAGAATGTAGCGTTTCAACAACCCATGTATCTTTAATACCTCCTCCTTGTGAGAAGTCATAAACTAAAGAACCTGCCTGCAATGGCCGTGTTAAACCTCCGGGCACAATTTTCGTTTAATAAGAAAACTGAGTACAAAACGGGCGTAGGTCATGTCGATCATCAAGACGAGTGGGTGATTGCCGTGACAAGTCGGTGCAACAATAAAACCAAATGTTGGCTGAAATATATTCATGCGGTGTAGCAAGCAAGTTTTGTCTAAATTCATCAATTTCCCCTGAACTTGCTTTCATACCAATTAACATGCCCATATCCACCATTACTTGAGCTTCTTTAATGACCATGAGCCTAAAGTACATAGTCCGATGTTCTTCTCACTCCACTTAGTAGGTACCATTCTTCAGATTGGTGTTTCACACAAATAATATTGGATCGTCTGATCAACATATGGATAAATCGATTTATCATCAGCTACTCCGCAGCTCATATAATTGAAGATGACTACGTTTTTCTGTAAATAAGCAGAACATTAAACCTGCCACACTAAAAGCACTATCAGGTCTAAATGCAAGTGGATCTAAAAAAATCATCATCTAATATGCGATAAATCACATCAACCTTTTGACATACGAATCGTTTTTACAAATACTTGATCATTTTCACAAATAAATCTCGATTGGTGACCAGTGGCACACTCCATTTCGCGTGCTAAAAAAGCGTGTTCTATAATAAGCACTGTTAAAACGTCCTGGCGTTAAAAACAATAAAAGCGCTGATCAATCTCAGAAATTATTTCTTTTAAACTGGGTAGTGTTCAAACCTTGCAGATTGTTGACTAGAGCTCAAGCATGACTGTGTTTACTAAACTGTACTGCATTTCAATCATATGAGACGCCAGATGGTGTCTTAAAATTATCTTCGATCGAATACTTCTACTTGTCACGAATAATATCTATTCCGCTAATTTGAGAATAAATTTTGCCTTTTGAGCGTGTGTTTTAAAGCATACTGGGCTGAAAAGCCTCATGACAAAATAATCTGACTTTCCGGAATTAATTGCTCTTTAAAAGCCTGTTCACATGATAGATGTCATCAAAAAATAATTAAGCTTTAACTCGCTGTTCAAGAAGCTTATTTTTTTCCCACTGTTTTCAATAACCATTGGAATGAGATATCAAAAGGTATCGTTCTCTCCACTCCTCATTATCACCGTATACGTTAAATGTAATGCCGTGATAGAGAAAATGTTGCTTAGCCTCCGCATTTAATTGTTTCAACTCAGTACAAAAAATTACTCAGCCATGTTCAGTTTTAGAATAGCATGCTACGTTACATCATCCAACATCTCATTAAAAAACTGCAATTTTTAGTTGTTCGATAGTTCATTTAGAAAGATTTTCTAAACGAAGTTTGGTTCAGTAATGCGTTGGTCGCTGTTCCTGTACCGAGACATCCAT
+
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@00711f37-3081-43c4-b32f-2ef1c0c37fbc ch=3 start_time=2021-05-12T23:56:48
ATCATTCCTGTCTCTTATTACTTTAAATGCTCAAGTTAAACTTCGCTATCGTTTTTAAGTAAAAAAAACTCTAACTCATCATTTCAGCAGCTTTTATTTGTCGTTAGATACCCCAGTATTAAAGGTTTGTTCTGATAAGCGGGCTATGTTATTGTAATTAAAGCTATCAATGAAAACTAATACTTAACAAAGCATAGTGTGTTTGCTTGGCTTTTATTCGCCATTCACAGCGACTCCAATAAACTAATGAACTTATTCACTTATCCATATGTTAGGAATAACATGACTGTAGATGTCACTGAAACCATTTCTCAAACTGTTCACCCTGCGTTTCAGTGCAACGTCGCCGCATGTTGAAGCATTGAGATATTTTAGTGTCTGAATATAAACAAACACATTTTCACAGGTTGCTGGTGCATTATCACTTGGCAACTGATTATGATGAAAATGTATTTCTTGTTGCTTGCAGAACACAACCATCCTATCACTAAGGAACTGCATAACTTTTAGAGCATACTTAACTTTATGTGGCTCTGAAAGTTTCCTGTTCGTGATCCATTCTTCTTAATGATACGCCGTTAATTAAATACACTTTATGAACAGTTTAAGCAGCCAAATTGGGACTGCATATCCATTTGCAACTCAAAATAAGAAGATTTCCAAAACTTATTATCTGTTTTCTGCCTGCTGCTTTCTCGGCAAAGTATTTGAATGCCTCTGGATTTTGACTCAGGAATTAGTATTGAACTTGAAAATGGTCAGCCTGTATAAGGCGTAGTCTTCATGAAATAGAAAAGGTGCATGAGTGCACCTTCAGATCAGCTTTATGACCAGTTGTATCATGACATCATCTATTCCCTGAAACCACTTATCACTAAAACTCATGATCATGCCAAAAGACATTCCTGACTTATACAGGCTGAGATAAGTTAGTTGAATTTTAACAAAACCCATTATCATCCCAGTCATTAGTTATGTATGACTTTGGTAGCAAAAGACTATGAATTACAAAAACAAATTTGAAAACTCATCACCAAAAGTTCACTGCTGGTACAACTTTATATAACTTCGAATCAGAAATAAGTATGATACTGTTGAAGTTACTGAACTTATGCTGTTAATGGCAAGATGAGTTAAAAGACAATATTACCATGTATTGTCGTGGTTATTACCTCAGGCATGACATTAAACTTCGTCTGGATTATCCAAAGACGTTTACTCGAAAACTCAGCTTCACGCTTCGTCATTATTTAGAAACTTGTGATTGCTCAGTCTATGGTCCTTTAATGGGGTAGACGATATGACTTTGAAATGACGTTCTATTTGGTGTTCAGTTTCAAATCCAGATGCAGAGAGCTTTAGAGAGGCGTTTTACAACGTTTGCGTGAAGTAGCTGCAAAACCAAGTGACTCATCGTGCTTTTAATGCAATTTTGCATCAAATTACGAAAGTTACCACCAACGTGAAATTAATGGTGATGGTACACCATATGGCTTAATACCTAATTTTAAATGGGTTAAGTGGTTGCGATTCACATAACAATTACAATTCAAATTTGGGATGTTGATAGTGCCATTGCTCAGGTCAGAAAGAACTCCAAGACCCAATGTGGTTATCTATACCTGATTCAAACCCATTTATTGGGCTAATCCGCACCGACGTGCAATGACTTTTAGTACCGGATGCAGGCAAAGTCAGCGAAAAGAGCAAGAAGCTGAAAAAGCGCGTTTAGCTGCAATTGGTGAAAAATAACTGAAGAAGATAAAGCAGAGATCATCGCACCAGACAAAGCATTTAAGAACGTCAAGATACCACCAGATAATCTTGAACTGTTGCCAAAAAGTAGGTCTAGAAGACGTAACAGCACTGACTTGCATATTGTACAGGTCAATTGCGTGAAATTATTTGTAATCGAAATCATACGCCGTTGAATTTGTATCATGCAGAATAAATGGTATTTACTATCAACAAGTCCTCATTCCGATTCCTGATGATGTGGTTAAATCACCAGACACTTCATTTGCTCTCTATTTAATGGGTGAAGTTGGTGCAGGTGAGTATGACTACCTTGAACTCCAGAACTTACAAACAGCTGTAAGTGGTGGTTGGAATGGGTGCTTCGTTACGCAGTAAGGTTAATGATAAAAACACAAATTAGTGCTTGGTTAACTTTAACAACTAAATCTTTACTCAGAAGTTCAATTAAATTCATTTATTAAAATTAGCATTTGAACTTTACGTTTTGATGAAAAAGAGCGAATCATTGAGTTATTGGGCAAACGTAACAGACGCTGGCAGTCTCGTTTATCTGGTGCTGGTCAATAGTTATGCAGATTGGGAGCATATTGCTTCTGCGTAATATGAGTGCGTTACTCAACGCGATCAAACACTGGCTTAGGTGCGTTGAACTGGTTAGGCGAGCTTGTTACTAAAATTACCCAAGATGATGCTGCTTATGATGCGCTTATTGCTGAATTGAAGCATATTTGCAAGCAAAATTATTGCAAGCACCTAAACCAGTTTCCGGGCTCGTATGTGGAGCATCAGTCAGAGCGTTTAGTTGAAGAAATTCAAAATGTTTGGGATATAAATTAAACGTTGATACAGCAGCAAAACTGAGTTAACAAGTTGAGCAAGAAAATGATAATGAAACATGAAGCTTGGTTAATTCAACCAATGTTCACAGTTCTGGTTTCCTCTGCATATCAACTGTGGAAGTATCTCTAATCAGATGCGGCACCTCATCGCTTGGCAGCTTACCTTGCGTAATGGTTTCTTGCACAGTGCTATCCGTGAAAAGGTGGTTATGTATCTGTGGGGGCATTTATGACGAAATGCATGTTCATTCCGTTGTACCGTGACCCACGCTAGCTGAGACTTTAAGATTTTGAAATAAGCGTGCAATGGTTGTTAAACAGAGCACAACCATATCAGCTTGAAGAAGCAATTCTTGGTCTGGTGGCATTATGGACAACCTGGTCACACCAACACTTGAAGCAATAACAGCGTGTTATGCATTGTTGCATGCAGAACTCCGACTTTCCGTCGTACATTACGTGAAGATTATTGCATGTAGTTTAGGAGAAGATTTACAACGTGTTGCGCGTCATATTTAATTGAACAAGCTATGTAAAAGCTTGTCGTTGATATTTTGCAAAACGTGATGAATTGCAACAACTGGGCCATTTAAATCTATTTAATTAAAATAAAATTGGAGATGAACATGGCGTTCATAAATTTGAACACACATCTTCACAGCTAAGTATGGAACCCTGCTTACCGGTATGTGCGTCGATGCTATGCCCGACTACCTTAGCCCCTGTACAAACCTGCAGAGTGTAGATGCATGTGTTGCCTTGCAATGCTGATCACTAGCTTGTTATGATGCTGTGTTTAAACCATCGGCCTTACCATTAGTTTCATATAGCAGTAGTACCAGAGCTGTTAAAAAATTGATAAACCTGTTGTTCAACCTGAAACATTTAAAGAAAAGGTTGTAAATAAGGTAAGTAGATATCAGTAATGTGGTAAGCAGACCACACTTGAATCCGTCTTTACTAGATCAACGTGGGGAGTTGTCTGAAAAAAGTAAACTGGGTGTTTGGAATATTCGTGCTTATCAACCTGTTTACTTGCAAGCCAGTTCTGGACGAGCGATAAAAATGAGTTTCAAAGCAGCAGTCCAGGCAAAACAACCGGTGAAGAGCCCAAAACCTTAATCAACTGAAAGTAAATTTCAGATTTCTTTGAAACGAATTGGGAAAATATTTTGGTAACAGATGGTACTGTGGGTAGGTTATAAAATCTTCACGTTGGCATATATTTAAAATAAGAGTCTCGTCCATTCCGTGAATAGAACTATGAGCCAGGAACAAAGTTTAATGTTAGAACTATGAGTTGCTTGGCTTAATGGTCGTTTGGTGGGGGCCTTTAAATCACCAGTCAAATGGACGTTCTCATCCTTTATCTCGTAGTTCGAAGCGGTGTCATCTTTAATGTGGGTTTAGAAGCGGTAACTGTACTTTAATGCTTCGTCCATGGATACGCCTTGAAGAAGACAGCAAGATGGCGCGCAATCCAGATATGGAAGATTGGCATCGGTCGTTCTTGGTAATTTAACTGCTTTTATAAAAGTGGAAGCAAAATGACTTCTCATTAAGTAAACGTCACTCTTTAAAAGGTGGTGATGATTCTCATGGTGCTGTTCAGTTTGACTGGGCTTTCCCGATGCTGGCAGCTTGGTACAGCCTTCCATTATTTAATGGTTCTGGTGAAAGCTTAATTACTATAACATAGTCCAACTTATTAGACCTTGGGTGTTTCACTCATGAACTGGTACTAAAGTTGACCTATAAAATGCCTTTTTACATAAGGCCTTTTTTATTAACAGATTTGAATGTTGGCTTGAGGATGTTTGAGGGGCCTTTTAGGAGTAGCAATTAAATAGGCATTGTTAAGGGCCAGCTCCTGAAACATAAATGCGAATTAAAAATAAATAAAACATTGTGTAAATCTGGCGTGATACTAGGAAAAGGCCTACCGTACCAGGCTGCTGAAACGACTTCTCAAGCATAAGTTCATAAAGTCTGCTTTAGGTTCTAAAGTAAAGAATAAGAACCCGATAAATATGAGAATACTGGTAATTGCTTTAACAAAGGCTTTAGATCGCTTTCGTGAGGAATAGCAGTAATTGAAAACCCTCCTTCCTCCTTACGTCTTAAAAGGAAAGTACACTTAAAACTAAATATGATAAGGTGCCGACTTTTATAAGCCAAGGCAGTACTGAGTGAAACTCAATAAATGAACATGAGTAACATGATAATTAAAGAAGCTGTTGGTCATATTGCTCCAGTATCAATAGTATTGAACCCTGAAGAACGTGGAACAGTCAGTGAAACCATGCATTTAAAGCTTGATCACCTCGCCATTGAGCAGACCTAAGGTATGAGGATTTTGTGATTTCCAAAACAAATTAATACAAACGCAATACAAATTAATAATCGCAATAGTTGTTTAGATGAGGTTTGCCTTTGATCATTTTTCCATTTTATTTGTTTGATATCCATGAGGACTAAAAAACCCAGTCCACTAATGTATAGAGCAAACTAATCATGTAATACATATAAGTAGGTTGACTTTGGAAGTTAACTAAACTGTTGCTAAATAGTGAAAAACTAATTGTTAAATGATGAGATATATAGAAAACTGCATAATATAGTCCTCCATGATAAAACATGCTTGTAAATGCGGTAGTTAAGATCACTGTTCCAAATCAGTTCTCAAAAAGAAGTGTGTAAGTAACAACACCTTTAACAAAGTAACCTAGTGAAAGATAGTCTGCCAAGCTATCTGCCCATCATTTGCTGTTTAAGGCCAACTTTAGAGATAATTAATGCTGCCAAAATGGCAAAAAGTCATAAAGCCTAATAGCTGACTGAATCAATAATAAAATAATGACCTGTCGGAAAAGTGTAAAGATTCATGAATATTGTACAGCGGATAGACCTGTAATAGTGACTGCCGAGTACGTAAAATAGAGCATCATCCAACTACATGTCCGTTATTGGCAATAGGAAGTTTAAGCAACCGATGTGCCAAGACAAACAAAGCCCCAGAAAACAGTGCTGCCTACAGGAGAAGGTGGGCTTAAATTTAGTGTTTTATGCGGTTTAGGCTTAGAGACATATTTCTGGTTCGTTTTTCTTATGAAACAATTTGAGAGTTTTTTTAGCTGCTGTAAATGACCTTCTAAAATAAGAATATCATGCGTTTGTAAATTAAAGTCTCTTCGGTTTCAAATAAATCTGCTGTTGTCTTTTACAAGAAGCGTTTTTATTGCCAACACTTGCTGCGCATAATTCCGTACAAATTAATGCCGTTTTACTTCTCTGGAATATCAATTTTACATACTAGTGCTCATCATCTAAAGACATATAGCTCCTCCATTTATCACTTTGATTGCTTGAGCACCTAGTTACTAGATGTCTTCTTCAGGATGAATGGATTTATTGATATTTAGATGAGATAAGATTGTATGATGTGCTTTGGTTTAGTTTACCCAAATTTTATCAATGCCCCAATTTTTAAATTCAACATAAAATACTGGCTTCAATATCTTCACCAATTGCTACAACCACTGCATCTAATTTTTGAATGTTTAATTCATCCAATACATGTTCATCTGTAGCATCAGCAATGACAGCATGAGTTGAAACATCGGCAAGTTCTCAACATTCTTTTTGACTGTATCAATACCCAAACACATCATGGTTAATCTCGTAAGTTCCTGAGCAACATTCCCCAAAACTTCCCAAAGCCATGACCCATGTGCCATAGTTGTCCTTTTATATTAGTTTAGGCTTTATTTTTAATGATATTTTCTTTGAGAATAAGAGAAGCAATGTAAAATATAAAAATAATAAATGCATGATAAAAATACTATATTGCCGGCTTTCCAAATGAAGGTTACTTCAAGAAACGTTATAGCCCAATTGTCAGTAATTTCTGCAATGGATAACATTTGCTCAGAGTTTCAATTAAACCATCTGGGTTTGTTTAGCATCTGTTGCTTGTACCATAAGCCTAAATAGTACCGATATTCAGCAGCGCCGTGGTGAACGATAATGGAACAGCACGTAAATATTGTGGGTTGATAAACGAGTTAAGAAAGGTGAGTAAAGCAACTCGTCAGGAACTCAACGGAAAATCTTTCGTCATCCAGATTGGGCATGACCACCAATCAAGTAACGAATATGCAAATTTTGGCAACTTCATCATCCCACGATAAATCATCACCAGCATAATTTTGCTGTTTAAGTTGTCACATTCAGGCCGTTCAGTGTCACCACCTTTTATAGCTAAATACCCAGCAAACTTGTGCTTCTTTCTGTGTTATTTAAGCCGTAATTTAAACTCGGTAATGTTACGGCCCTGTAGAGCACGGCAGAATAAGAATGCGCCTTTTTCTTCAGAGGATGACTGCATAAATGGCTTCACGTTGTTCACCAATTCCGTTACTCTGCAATGTAACGTAGAGCGTAGTGGAGTTCATGTTGGCGCGACGCAAACAATCGATACCATGTTTTTACCGCCGCGATTTTATGCTCGGCAACATATTTTGATATAATAGGGGCCATCGCACCTGACGGTTCAGCGATGATGCGGTTTCATCAAAAGTATTCATTGCAGCACAGATCTCATCTGTATTTACAGTAACAATATCTGGTTCAACAAATTGGTCCAGAATTATCTGATTTGCGTAGACGAACGATATCGATTAAGGCACCAATTTGAGCAACTGCTGCGCATCGGGCAATAATACTACGTGGGGTGACGACTACGCGTTCAGATTGCTTCGCACCGCTGCTTTCACGCAGGTATGACTCTTCATATTCAACACATCACTCTTTGCCATGCGGTGCAACATCACCGCCATTAATATTGAACACCAGCAATTAAGCCACCACCACCGACCAGCAGCAGACATATTCCATCACGCATTGGCGTAAAATTCATTCGCAATTGTGCCTTGGCCGAAATAACCAACTCGTCGTCATAAGGTGGAATAAAAACTAATCCTTCAACTTCGGCACCTTTTTATGCAGCGTCTTGTTGCGACTATCAAAACTATCGCCATGTAATACAACTTGGAGCAACGCTTCACTGCCTGAACTTTAATGTCAGGGTTATATCTATTGGCATATAACAATAATTGCAGGAATACCGCGCGTTGACCAGACAACGATAATCGTGCACATGGTTGCCGGCAGATGCGCAATCGACGCGTTCAGTTGTTCTTTCGGTGATTGGCACAGCCGATGTTATAGGCACGCGTAATTTTAAAAGAAAAACTGGTTGATAATCTTCACGCTTAAAACGAATTGTGTTTGATTTTCATAATTCTCGTGGAGCTGATTGGAGGAGGTGTTCATATTGCAACATCATAAACCGTTGCTTGTAAATTTGTCCGTCACGAGACAGCATGTTCATCTTCCCTATAACAGTTTAAAATAGGAAATTATTGTAGCAAACCCTTGTCCATTTGCGCGTTTTATTGGCGAAATAAATGTCAAAAAATAGTTGAGTGATGTAAATGAGCCTATATGCAACCAAGATGAAAAAGAAACAGCTGCTGCGAAAGCTGCTTTAAGACCTTACCCAAAAGGGTGAAAAGTTTGGGGTTAGGGAACTGGAAGTGACTGAATTTCCTGATTGAGTTATTGTAGCATACAATTAGAAACACAACAGTAGCAAGTTCTCAAAGCAACAGCAGATCGTCTTAAAAAATTAGGCATAGAAGTGGTTGGCTACTGAACCATGTGGGAGCCTTGATGCTGCTGTTGATGGTGCAGATGAGATTGATCGTCGTAATGCAACCATGCGGCGCAGCATTAACTCGTGAAAAATTGTAACTCAATTGCTAAAAAGTTTGTATGTATCGTTGATGATTCAGATGTGTGGCTGACTTGGTCGTGATTTTACATTTACGAAGTGATATTCAATGGCGCGTTCTGCTGTAGCGCGTAAAATTGGTAAATTAGGGTGATCCGGTTTATCGTGAAGGTGTGGTAACAGAACGGAAACGTTATTTAGATGTATTTAAATTTGAACATCTCTTGATTAGCAATTGATTTGGAAAAGACAATTAATAATATTCCCGGGCGTTGTACTCGGTATTTTGCGGTCGATCGAGCAACCATTGCAAATTGTTGCAACAATGGCATCTTATTGAAGAGCTTCTATGCCCAGTAATGTCTGTGGAAAATGCCAAGAAAATTAAATTGTTCGTCACGTAAGGGCAAGAAAATTGCGCTTACGTGTAGAGCCTGCGTTACACTTCTGTGCGTTATTTTGTAGTAAAGGAGCAATTCAATGAGTTTAGCTCAGTCCAATGGTTAATCGAGACGTGGAATAAACAGCTACACGTTCAATCTACCTCATTTGAAATTCCTTCAGAAATTTCTTTTTTAATAGAACAGCCTTTTCAAATTGTGTGTGCAGAAGCAAACATCGCATTTTTTCAATTTTAAAGTGGGAAGATATAGTTATTTATTTATTAAAGATCATCAACCAGTAAATATTTACAAACTATGTTATTGCTTATGCAAAACGAGTTGCCAGCACTTTTGTCAGAACTTAGCCAAAAAACTCGACTGAGTTATGCAAGAGTGTACAATTCGGCGTCCCAGGGCTTTGGGGAAGTGCATTAGTCAACATAATATTATGCTGCATTAAGTTTCTGCTGCTGCTCAATTACCCGTTATTATGTTTGCATTCATGAACTAGCACACCAAGCTTCAACATAGTCCTGCATTTGGGCCGAAGTTGCAAGTTCAACCCTACTATGCATAACATCACAGACAATTAAAAGGTAAATCCATTGCTGCATGTGGTATGTTACAACTTAGCTAAATATACACTCTAATTGTGTGGTGTACATAACTTTGCGGCTATATCAAGGCCTTATATTGCACCACATTGTTCTATTTTTAATATGTATACTGTAAATTATTGCTGTGTTGAATTGTTAGGTTCTAGCTGAACTTGGATTGCTAAGTAAATATACTATTTGCAGCGTCATGTTTGCAGTAAATTTATCTGCCTATCTGCACTTAGAACAGATAAAAGCTTTGAGAGCCTTTAATTAATTCAATTTGACCATTAGCACGGAAGTTAAGTTGGCAGCCTGTTGTACTGTCTTCATAGTACCAACTAAAGCACGTTTGATGTATGTGTTGGGTCCGGAAAATATTGATACTAGTTAATACCTTGTTTACGGATAAGCCGAACCATTGCAGGTCGTTGTAATACACTAAAGCCAACAGCACGTCGGTAATCTCCCGCACCCATCACGGAAAATTCTTACCCAGCAGGTATAATCCCAAAGATATTGTTTCTTGTCAAAGTAGATCAAAACTTGGGTTGGGGAGATGGATTGGATCTTGCAATCTTAGTTACAGTGGCTGCTCTTAGATTAGTGGCAAAATAATCACGTGTTACCTTTTGATTAGCTGCGATATCTAAGTGTTTTTGCTGGATCAATATTATCAAGGCTGAGGTGAAGATATAACAAGATAAATTTGTCCCCAAACCAGTTTTTGCCGTCCAAATATCCATCTTTAAATCTGTAGCGAGACTTGGTGAGATCTTGAAAGTGAATTCGTATTATGGATGCTTGACCAATATTGAGATAACCAAAGCTTAGATAACTCCACATAAGTACTTGGCTTTGTGGTTGAGTATTTCAAACACATTTAAAATTGTAAGCGTACTTGCCGGACTTAAACTTGGAATATTGGTATCTTTAAACATTAAGAAGAGATCTGTAGACATCTTGAGAGGCTAAGTCAACATGTAATTGTTCAATACCGGGTGGGATAATTGTCTCATTAGGCAACTGAACCCTCAGGGAAGATCACAGCACGTTAAAAATTGCTTCTGAACTTGGGCTGATCAATTGTGTTTTTATTGCTTATCTAAGTGGGGTAAACAGCGTGAGCCACCACACCCATATACTTTTGATATGTAAGACATTTGGTTGGATCAAATACTTGAGATGAGCCTTGGGTCCTTCGGTTGCATCACACAAATAAGCAAATGAATACTTGTCTTGGAAGTTTACAATCGTAACTCGTTAAACTGGCAACTTGGGTATCAATCAAAATACTTGTCATTGTATGCTCATACCTTGAGTTGAACATTGCGCATTTCAAAAGGGTTTTAAGCGTAATATCCCGTCATGACTTCAGGAGTGGGTTCCAATACGGTTCGAGTTCGATGAACCTCTATCCTGCTACCACCACCACCCTAGCCAGGCTCACTTAAATTAAATTGGTGAGGCCGAAGAACAGTGACACTTTTAAGTG
+
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@0091875b-c15b-4f76-b5ac-a6cdd52dcbe1 ch=147 start_time=2021-05-12T23:55:48
TGCTCAAGTCGGTCCTTATTATAGATTCAGGATCAAGCGGTTCTTAACGTATTAGATCAGCTTTAATGATATACAAGGTGCTTTGTTAAAAAGATGAAGATTGACTGATCTTACGGCATAAAATATGCTACAAACAGCCGTCAGCGCTTAAGCCAAAATGATGAATGACCAAAAATCGCTCATTATTTTACAGCAATTCGTTGATGCTCAGTGTATTAAATCGATGTAGTATGTTAAGACACAGAGTCATGATCTGGATAATGATGCCTAACGAACTTGCATCATTACCCAAATTTGAGTCAAAGATGCTTTAGTATGAAATTGGCATAATATCCTTTCCTGACTTATGCCAATTGCAATTCGACTTAAAACAGTTTACAATTTGTTATTTGCACTATCTACCCGAAAAACTTTATATGCTTATACCGCTTCAGCCTGTTCCTTACAGTATCAGAAGCTGAGCAACGTAATGCACAACTTCTTATCTGGCGCAGCGCAATAAAATCAGCACAAAATCTGGGCGATTATGGGCGTAATTTTTAGCCCTTGCGATTTTAGGTCTTATCTTTATCAAAGAACTATACAGTGATTTGCTGGGTTTAGTGTCTGGTTAGTACTTTATTACAATACGCAAATATGGTTTTGGAATGGTACGTTAAGCGTAAAGATGAATGATTTTCCTGTGCAGGAAATCAAAGGTATTCGCTTGATAGGTGTAAAACCCTCACGGTATCGTAATGCGCCAGCAAATCATTACAGAAAGTTGTTGGAATATCTCAAATGGAAATATCTATGAATGGTACAACACGCTTATTAAGTAGATGCCCCTCTCC

==> genome_diirt/KF0125_4_1.fq <==
@0010fd31-d7bb-4022-8716-6bc5fe9512f4 ch=34 start_time=2021-05-12T20:19:47
AGGCTCATTCAGGTCCTGCTGGCCTGTAAGGTCAATTAAAAGTCTCTACGAATAATGGTACGATTACTCAGAACAGACATTGTAAAGTAACAGGTAGCAACATTACTGTCGAAAGCTGATACTACGAGTATTGTATTGTTGATGCTACAACTCTCATGTTAGAGGTGATCTGAACAGCAGTGGATTAACAGCTGTAGATGCAAATGGTGCAAACTTTTAGCAAACCAATAATTACACTTAAGTTAGAAATTCAGTTTAAATGGTGTCAAAATTTACTCCTAATGCACACAATCCTGATTTGAAATGGTCAGATCAAGCTATACTTTATCTCTTTAGTGAAAATCAGGAACCCATCATAAGTAGGTCAGGTATCCTTAAAAATTGTTAGAAACAATTGATCTAAATTATATCTAAATGATGTATTGGTGATATTGGATTAATGCAGTCTAGCACTGCGTAAGAGGGATAAAGCGGGAAGATTCAGTGATGGAGTCATAATAAAAAGCTTTCATTAAAGTGACTGATGTGGATGGTAAACCGATACGCAATCAAAATGTAGTCATGGGCGTTATGCTCTTGCGTATTAAAGGTCGATATGGGTTTGTTGATACCTTCTAATCCAACTGATGGTAAACAGATGAATATCTTCCTGTTTATGGACAATATGTACATGACCAGTCCAGCTGGGAATGCTCTTCCTCCATGATG
+
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
@002965d4-94e5-4a74-b59f-9f7b778620b5 ch=214 start_time=2021-05-12T20:22:55
ATTATCATTCGTCTGTCTTATGTAACTGGTTAGGTACATTGTTCCAGTCGGAATGGCGCTTATGGAGCTTGAGCGTGAAGGAGCAGGTATTGAAGGTATAACCGGTGCTTCATATCAAGTCTGGCTTTTACTTCAACAGCTGTTAAGGTTGAGTGGTACATCACAGTTCTAAGGGTGGAATTTTACCAACTCACGGTGAATGAGCACGTTATGTTGCCAGGTGGAAGTGCAAACGTCTGATGGGAGAACAAGGGCCAGAAGCAATCAATCCTGCCTCGCGATTCATCCTGCAGACTCGGTGTTTTCCCATGTTGGGGCGCTTTAGCTTCAATACGACATGCAAATCACCGTTCATTACAATCACCGTAACCAACGATGGAAGCTCTTCTACGAGCGCATCTGGCGGTGATGCTCCAAGAATATAAGCATCAGAACAGGTCAGAACATTGTCATGAGCACCTGCCAAACAGCAAACCGGGGAGGAAGATTATAAGAAATAATATAATTACCTTTAATATTAGTAATAGACTTACTTGGCCAATTAGGTGGGCTATTGCATTTCATTCTGATTGGAATTTATTTGGAAGCCAATTTGGGCGCTGAGAAAGTCGAAAAGCTTCCGTCTCTACGGTCAATTTTAATGATGGCTACGAAGTTCAATTCTATTAACCCAGTGCGGGTATGGAACTTAAGCCTGACCAATAAACCTGCAACGGCAAAATGAAATGCCGAGTTCTTAGCAAAAGCCAATGGCACAACCGTTTGATTGGATTGACCAGCAAAAAGGGCAATTTCGTCTGCCGCGAATGGAAGATGAAATCAATCAAATTTGGTGTTTTTTCCAATTACGCAGTGATATTGAAGAGGTTTATGAATATGGCGAGAAAATCGCGTAGCTGAAATTCAATCGTTGTCAACAACAGCAGAAGTTGAACTGTTGTTATTGATACAACTAATTTGGACAATGTTATTCGTTTTGTTCTGGCGTAAATGCGTTTCTACAACCCGATCTACTGGCAGGAAAGCTCTACCCTTTGCTATTGAAGCAGTGACTTTGATGTAAGCAGTCAGGGCATTGCCACGCCTAATAATTCTGGCAAACGTTAAGTGGCTTATTTTCGTCACTTGCGGGACACAAAACTCCTAAACCTTATTGGATGCAAGGTTATCAGTTAAATAGTCATTTGGCAGTCTCCTGACGCGAGTGTGCAACTTTCCGCAATGGAAATCCCGAAGGCCTACCAGCCAACATTTAAGATGCAGATTTCTTTTATTGATCGAAGGTTAATGAAAGCCGCGTTTCAATTGAATGGAATTGGCATCAGCCGGTGATTTCCAAGGCGTTCAACACTTTTCGTCAGTGACAAGAATGATGTCATCATATTACATAAGTGTCACATATGCGGTGTGT
+
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
@00fa0b2d-843c-40f2-bd26-cbdb334cf804 ch=347 start_time=2021-05-13T00:23:00
GATTCGGTCCTGCTCTTCTCATGAATGCCCCAAAATTATTTACACATCTCGTTATCAAGTCGTTCATTTAATTATACCAGATTTTATAAATTATTTAGAAAGAGATAATTACCTTTTTCATAAACCGCTCCCAGCGGATTAATCGTCTTTTGAAATTTCCCAAATTTCAAATACTGTCCATAGAGCCGTAAGTAAGCTGTCACCAAAAAACTTATACGTTTTCAGGCCATGTATTTAGCTTGTATTGCACTAGTTTCTACTTTAAACCCATACAAAATTAAGTCTATTGTGATATAACTGCTTGAAAAAGAAAATGGAACAAAATACTTAAAGTATATTATGGAAATTTATTTCTCAAATTTACAGATATTAAGCATTTCTAAAGTAATTAATAATTCTACAAAACTTTCAAATTACAAATAGATAAAAATAAAAAATCATACAATATGGTCTAAAATAGCAGAAAAAAGGTCATATTCTTGAGGATTTTAGTCCATCACAAAAAAACAATACTTCTTTAGCTTTAATTCTATGATAAAGCACTAAATTTAATAATCATAATCATTTCATTCATAATTTTATAAATCTTTTATCTCATCACAAATTATCAAAGAACAATTACATTTAGATTTAATTTTATCTAAAAGCTTCTCTTATTTTTGGACAATCCTCATGAACAGGGAAATTTCAAGCCAGCCTTGCCCTTTTACATAATAAGGAGGATCTAATCCATAAAAATGAATTATCAGGTAAAAATTCATCACTTTCTGGATCAGCATCAAAGCATCTTCATTATAAACGTGAATTCGGGACGCATTTTGCTCCAACTTTTTCAATACGTTAGTGAATTTGCTTTATTAAATCTAGCATCAAGGGTTGTAATTACCATCTTGCTTTCTTCCTCCATTAAACACCTTTAAGATACCTGACCTATTTGTCCTATTCAGAAAAAAATGCTGCAAAGCTTTAAGTAAATGATCCTTACAAACCAATCATTCAATATATTTCTGTTTATGCCATTCATCAATAGTTATTGGTGAATCAAATGAATTAATTTCAAAAAATCATCAGTATGTTCAGTTATAGATTTCCGAAAAATATACATATCAATATCATTGATATGTGATATCTGAAAACGAATCCACTAAAGTAAATCAGTGCAATAACTAACTACACTGCAGACAGCTCCAAGATAATGACCACCTTTTAATCCATTAAAGTTAAAATAGATTTCACAACAGAGCAAAATTTTCCCTTTCCTCCTGGGTATCTTAAAGGCGTAAAAAAGGTATCAAATCATTACTTAACAGCTAGATCTTTATGCAATTTCTATCATCTATACACCTTTAAACACTTAGATATTTACTTAATTTTTAAGAAGTCTTTTATACTATCTTTCAGTAGGATGATTGGTACTTATCGGTATAAAGAGTTTCTTAATAAATCTTTCCTGAAAAGTATTATATTTCTCTAGATTATAATCTGAAGGATTATCTCATCTGTTCATTTGATTAGGATTGAATAAAGAATTTCATTTTATAGAAATTTTTAAATTTTTCTCTCGCTTTCCCTCCTGACTCACACTGGAGCTCTTTCTCTAAAATGATAGTTCAAAGTCATAATTTCCGTAGAAGTTTGGTCAGATTAAAAAATTCACCAAATTGCAATAACTTCTTAAAAATACTGGTTTAGAAAAGCTAATTTTATTATTTTTCCAATACATATCATCGGCAGTAATCTATAAGAAAATCAAATAAGAGTTGATCTGAATTAACTGATCACAAGTGCGTGTTAGTTTTGCTCATTCCGTCGGTATTATCGAATTCGTCCTAGCACAAAATCAAAATGCACCAGTTG
GREATER93 commented 3 years ago

But why is it not all sequences, there are still some wrong texts; is something wrong?

GREATER93 commented 3 years ago

@bkille Good day. Thanks for always. I was thinking if it is possible to convert .fq files to .fa files in Ubuntu; if yes, can you help me with the command lines. Thanks

bkille commented 3 years ago

https://github.com/lh3/seqtk

GREATER93 commented 3 years ago

@bkille Thanks so much

GREATER93 commented 3 years ago

@bkille I got this. What could be run?

(base) jszheng@Greater:~/seqtk$ seqtk seq -a KF0124_1_1.fastq > KF0124_1_1.fasta [E::stk_seq] failed to open the input file/stream.

bkille commented 3 years ago

@GREATER93 This is out of the scope of a GitHub issue for parsnp. I'd suggest asking this on the bioinformatics StackExchange site.

GREATER93 commented 3 years ago

Okay @bkille . Thanks very much.

GREATER93 commented 3 years ago

Hello @bkille , I crave your indulgence to disturb you again. Thanks in advance. I have proceeded with the analysis, now with fasta files but got a new error (TOO FEW SPECIES). What to do, pls?

14:31:16 - INFO - <> 14:31:16 - INFO - No genbank file provided for reference annotations, skipping.. 14:31:16 - INFO - Recruiting genomes... 14:31:27 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 14:31:57 - INFO - Reconstructing core genome phylogeny... 14:31:57 - CRITICAL - The following command failed:

$ raxmlHPC-PTHREADS -m GTRCAT -p 12345 -T 1 -s /home/jszheng/P_2021_07_29_143116530188/parsnp.snps.mblocks -w /tmp/tmpe8eph5ac -n OUTPUT Please veryify input data and restart Parsnp. If the problem persists please contact the Parsnp development team.

  STDOUT:

WARNING: The number of threads is currently set to 1 You can specify the number of threads to run via -T numberOfThreads NumberOfThreads must be set to an integer value greater than 1

RAxML, will now set the number of threads automatically to 2 !

Warning, you specified a working directory via "-w" Keep in mind that RAxML only accepts absolute path names, not relative ones!

RAxML can't, parse the alignment file as phylip file it will now try to parse it as FASTA file

TOO FEW SPECIES

GREATER93 commented 3 years ago

Hello @bkille I still look forward to your response, please. I have tried to check the thread https://www.gitmemory.com/issue/marbl/parsnp/88/743690240 that addressed similar query but I could not get through. Kindly help!