prepareEvmInputs.py, NameError

[zcrself]

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?

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]

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

Cheers
Luigi

[zcrself]

Using short reads and long reads

…

On Mon, May 13, 2019 at 4:51 PM Luigi Faino ***@***.***> wrote: Hi @zcrself <https://github.com/zcrself> , sorry if I answer so late. are you using only long reads without short reads? Cheers Luigi — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#17 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADSIDOHPHQNV57AV5FS2ATDPVET27ANCNFSM4HLPXBAQ> .

[lfaino]

can you send me the command that you used?

[lfaino]

and the content of evm_input and evm_output folder, please

[zcrself]

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 ***@***.***> 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 <#17 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADSIDODORIBRJTVKHFESZDTPVEVOBANCNFSM4HLPXBAQ> .

[lfaino]

a screen shot of the content is enough

[zcrself]

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 ***@***.***> 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 ***@***.***> 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 > <#17 (comment)>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/ADSIDODORIBRJTVKHFESZDTPVEVOBANCNFSM4HLPXBAQ> > . >

[zcrself]

[zcrself]

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

[lfaino]

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

[zcrself]

singularity

[zcrself]

Could I resume my lorean job?

[lfaino]

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

[zcrself]

thanks for your reply

…

On Mon, May 13, 2019 at 5:29 PM Luigi Faino ***@***.***> 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 <#17 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADSIDOEBJPDAGNCR4MJ6XNTPVEYI7ANCNFSM4HLPXBAQ> .

[lfaino]

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

[zcrself]

Because my server is very slowly!

…

On Mon, May 13, 2019 at 5:44 PM Smith Waterman ***@***.***> wrote: I give my data, Could you help me test it ? On Mon, May 13, 2019 at 5:44 PM Smith Waterman ***@***.***> wrote: > thanks for your reply > > On Mon, May 13, 2019 at 5:29 PM Luigi Faino ***@***.***> > 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 >> <#17 (comment)>, or mute >> the thread >> <https://github.com/notifications/unsubscribe-auth/ADSIDOEBJPDAGNCR4MJ6XNTPVEYI7ANCNFSM4HLPXBAQ> >> . >> >

[lfaino]

yes you can send to me. I can test it

[zcrself]

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 ***@***.***> wrote: I would suggest to download the latest image (just to be sure) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#17 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADSIDOBLGDRM5GEMG6TIIF3PVE2DNANCNFSM4HLPXBAQ> .

[zcrself]

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 ***@***.***> wrote: yes you can send to me. I can test it — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#17 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADSIDOANE7LAMVP662UYNN3PVE3SRANCNFSM4HLPXBAQ> .