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lfaino / LoReAn

Long Reads Annotation pipeline
MIT License
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prepareEvmInputs.py, NameError #17

Open zcrself opened 5 years ago

zcrself commented 5 years ago

prepareEvmInputs.py, line 110, in move_single_file raise NameError('') NameError

I do not know what is the reason? How to solve it?

I am very nervous getting the final result I want to get the result as quickly as possible. Could anyone give me some suggestions?

amazon_ec2_evm_error (1)

OS: ubuntu 16.04 LTS CPUs: 36 cpus Memory: 72G Disk: 2T Platform: amazon aws Command_line: lorean -rp repeats.fix.bed -sr SR_1.fastq,SR_2.fastq -lr Long.fasta -pr all_pep.fasta -sp rice P_heterocycla_v1_Scaffolds_Poaceae_masked.fa -t 36 --keep_tmp 1>1.out 2>2.out &

lfaino commented 5 years ago

Hi @zcrself , sorry if I answer so late. are you using only long reads without short reads?

Cheers Luigi

zcrself commented 5 years ago

Using short reads and long reads

On Mon, May 13, 2019 at 4:51 PM Luigi Faino notifications@github.com wrote:

Hi @zcrself https://github.com/zcrself , sorry if I answer so late. are you using only long reads without short reads?

Cheers Luigi

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lfaino commented 5 years ago

can you send me the command that you used?

lfaino commented 5 years ago

and the content of evm_input and evm_output folder, please

zcrself commented 5 years ago

Only evm_input folder, I have tared it. http://119.78.67.235/doc/maozhu/evm.tar.bz2 No evm_output folder

On Mon, May 13, 2019 at 5:05 PM Luigi Faino notifications@github.com wrote:

and the content of evm_input and evm_output folder, please

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lfaino commented 5 years ago

a screen shot of the content is enough

zcrself commented 5 years ago

My command line: lorean -rp repeats.fix.bed -sr SR_1.fastq,SR_2.fastq -lr Long.fasta -pr all_pep.fasta -sp rice P_heterocycla_v1_Scaffolds_Poaceae_masked.fa -t 36 --keep_tmp 1>1.out 2>2.out &

On Mon, May 13, 2019 at 5:09 PM Smith Waterman zcrself@gmail.com wrote:

Only evm_input folder, I have tared it. http://119.78.67.235/doc/maozhu/evm.tar.bz2 No evm_output folder

On Mon, May 13, 2019 at 5:05 PM Luigi Faino notifications@github.com wrote:

and the content of evm_input and evm_output folder, please

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lfaino/LoReAn/issues/17#issuecomment-491740037, or mute the thread https://github.com/notifications/unsubscribe-auth/ADSIDODORIBRJTVKHFESZDTPVEVOBANCNFSM4HLPXBAQ .

zcrself commented 5 years ago

evm_input

zcrself commented 5 years ago

Could I run evm software alone using these four gff3 files?

lfaino commented 5 years ago

No. looks like that PASA did not work correctly. are you using docker or singularity to run lorean?

zcrself commented 5 years ago

singularity

zcrself commented 5 years ago

Could I resume my lorean job?

lfaino commented 5 years ago

you need to remove the PASA directory, the evm directories and the gmap directory before. it should work

zcrself commented 5 years ago

thanks for your reply

On Mon, May 13, 2019 at 5:29 PM Luigi Faino notifications@github.com wrote:

you need to remove the PASA directory, the evm directories and the gmap directory before. it should work

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lfaino commented 5 years ago

I would suggest to download the latest image (just to be sure)

zcrself commented 5 years ago

Because my server is very slowly!

On Mon, May 13, 2019 at 5:44 PM Smith Waterman zcrself@gmail.com wrote:

I give my data, Could you help me test it ?

On Mon, May 13, 2019 at 5:44 PM Smith Waterman zcrself@gmail.com wrote:

thanks for your reply

On Mon, May 13, 2019 at 5:29 PM Luigi Faino notifications@github.com wrote:

you need to remove the PASA directory, the evm directories and the gmap directory before. it should work

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lfaino/LoReAn/issues/17#issuecomment-491748453, or mute the thread https://github.com/notifications/unsubscribe-auth/ADSIDOEBJPDAGNCR4MJ6XNTPVEYI7ANCNFSM4HLPXBAQ .

lfaino commented 5 years ago

yes you can send to me. I can test it

zcrself commented 5 years ago

Wonderful, very appreciated! After tidying up, I will my test data to you! Thank you once again!

On Mon, May 13, 2019 at 5:45 PM Luigi Faino notifications@github.com wrote:

I would suggest to download the latest image (just to be sure)

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zcrself commented 5 years ago

There are six files in my command line.

  1. http://119.78.67.235/doc/bamboo/SR_1.fastq.bz2
  2. http://119.78.67.235/doc/bamboo/SR_2.fastq.bz2

  3. http://119.78.67.235/doc/bamboo/P_heterocycla_v1_Scaffolds_Poaceae_masked.fasta.bz2

  4. http://119.78.67.235/doc/bamboo/all_pep.fasta.bz2
  5. http://119.78.67.235/doc/bamboo/repeats.fix.bed.bz2
  6. http://119.78.67.235/doc/bamboo/Long.fasta.bz2

My command line is:

lorean -rp repeats.fix.bed -sr SR_1.fastq,SR_2.fastq -lr Long.fasta -pr all_pep.fasta -sp rice P_heterocycla_v1_Scaffolds_Poaceae_masked.fa -t 36 --keep_tmp 1>1.out 2>2.out &

Thanks for your wonderful work!

On Mon, May 13, 2019 at 5:58 PM Luigi Faino notifications@github.com wrote:

yes you can send to me. I can test it

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