Closed byeollee closed 3 years ago
OK, its holiday times here, but I will try to have a look at this in the weekend.
LS
From: byeollee notifications@github.com Sent: torsdag 2. juli 2020 06:31 To: larssnip/micropan micropan@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [larssnip/micropan] hi. i can't solve this problems (Column 'V2' not found in ',data' (#6)
When I try to get distances by bDIst()
dst.tbl <- bDist(file.path("blast1", list.files("blast1", pattern = "txt$")))
I get a error message :
bDist: ...reading 2 self alignments... error: Column V2 not found in .data Run rlang::last_error() to see where the error occurred.
and also i am showing the file list blast1 : /home/star/blast1/GID1_vs_GID1.txt /home/star/blast1/GID10_vs_GID1.txt /home/star/blast1/GID11_vs_GID1.txt /home/star/blast1/GID12_vs_GID1.txt /home/star/blast1/GID13_vs_GID1.txt /home/star/blast1/GID14_vs_GID1.txt /home/star/blast1/GID15_vs_GID1.txt /home/star/blast1/GID16_vs_GID1.txt /home/star/blast1/GID17_vs_GID1.txt /home/star/blast1/GID100_vs_GID1.txt /home/star/blast1/GID101_vs_GID1.txt /home/star/blast1/GID102_vs_GID1.txt /home/star/blast1/GID103_vs_GID1.txt /home/star/blast1/GID104_vs_GID1.txt /home/star/blast1/GID105_vs_GID1.txt /home/star/blast1/GID106_vs_GID1.txt /home/star/blast1/GID107_vs_GID1.txt /home/star/blast1/GID108_vs_GID1.txt /home/star/blast1/GID109_vs_GID1.txt /home/star/blast1/GID110_vs_GID1.txt /home/star/blast1/GID111_vs_GID1.txt /home/star/blast1/GID112_vs_GID1.txt /home/star/blast1/GID113_vs_GID1.txt /home/star/blast1/GID114_vs_GID1.txt /home/star/blast1/GID115_vs_GID1.txt /home/star/blast1/GID116_vs_GID1.txt /home/star/blast1/GID117_vs_GID1.txt /home/star/blast1/GID118_vs_GID1.txt ... etc
Total 84 txt file, I want to analysis these all.
Please help
Thank you
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Could you please email me the file GID1_vs_GID1.txt?
The error message also indicates there is something else wrong here. It says it finds 2 self-alignment files. There should be many more, right? All genomes should have a self-alignment BLAST-file. The listing above contains 28 different genomes (GID1, GID10, GID11...etc). All of them should have a self-alignment file (GID10_vs_GID10.txt, GID11_vs_GID11.txt...etc). How many genomes are in this study?
Wow.. Thank you for your kindness
I hope that you spent your holiday well :)
When I try to get only two genome file, My problems is not coming
Could you tell me that how many genome we can analysis??
I try to get blast results from 289 genome file again.
Thank you so much
Hi,
The number of genomes is only limited by your time and your computer memory.
Try to start with a few genomes. Run the blastpAllAll, and the rest of the procedure, to verify it works. Then add a few more genomes, and re-run. Use the same folders, both for the genomes and the blast results.
With N genomes there should always be N self-alignments files, i.e. blast results files where a genome is compared against itself.
LS
From: byeollee notifications@github.com Sent: onsdag 8. juli 2020 02:44 To: larssnip/micropan micropan@noreply.github.com Cc: Lars-Gustav Snipen lars.snipen@nmbu.no; Comment comment@noreply.github.com Subject: Re: [larssnip/micropan] hi. i can't solve this problems (Column 'V2' not found in ',data' (#6)
Wow.. Thank you for your kindness
I hope that you spent your holiday well :)
When I try to get only two genome file, My problems is not coming
Could you tell me that how many genome we can analysis??
Thank you so much
— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/larssnip/micropan/issues/6#issuecomment-655213490, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADJZZFW67D3NOJEDKKD72QLR2O6OBANCNFSM4OOP7L5Q.
When I try to get distances by bDIst()
dst.tbl <- bDist(file.path("blast1", list.files("blast1", pattern = "txt$")))
I get a error message :
bDist: ...reading 2 self alignments... error: Column
V2
not found in.data
Runrlang::last_error()
to see where the error occurred.and also i am showing the file list blast1 : /home/star/blast1/GID1_vs_GID1.txt /home/star/blast1/GID10_vs_GID1.txt /home/star/blast1/GID11_vs_GID1.txt /home/star/blast1/GID12_vs_GID1.txt /home/star/blast1/GID13_vs_GID1.txt /home/star/blast1/GID14_vs_GID1.txt /home/star/blast1/GID15_vs_GID1.txt /home/star/blast1/GID16_vs_GID1.txt /home/star/blast1/GID17_vs_GID1.txt /home/star/blast1/GID100_vs_GID1.txt /home/star/blast1/GID101_vs_GID1.txt /home/star/blast1/GID102_vs_GID1.txt /home/star/blast1/GID103_vs_GID1.txt /home/star/blast1/GID104_vs_GID1.txt /home/star/blast1/GID105_vs_GID1.txt /home/star/blast1/GID106_vs_GID1.txt /home/star/blast1/GID107_vs_GID1.txt /home/star/blast1/GID108_vs_GID1.txt /home/star/blast1/GID109_vs_GID1.txt /home/star/blast1/GID110_vs_GID1.txt /home/star/blast1/GID111_vs_GID1.txt /home/star/blast1/GID112_vs_GID1.txt /home/star/blast1/GID113_vs_GID1.txt /home/star/blast1/GID114_vs_GID1.txt /home/star/blast1/GID115_vs_GID1.txt /home/star/blast1/GID116_vs_GID1.txt /home/star/blast1/GID117_vs_GID1.txt /home/star/blast1/GID118_vs_GID1.txt ... etc
Total 84 txt file, I want to analysis these all.
Please help
Thank you