MaxBin / Tickets / #2 Error running FragGeneScan

ZOU - 2019-04-07

I have the same problem as well. Would you mind telling me how do you solve this problem?

Thanks in advance.

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Bikeparty - 2019-05-21

Hi,
Did anyone got this back and running? I'm using FragGeneScan1.31 with Maxbin and also got the "Output recorded" - Thanks

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ZOU - 2019-05-27

Hi,

Sorry for the late reply. Are you running a Mac？I emailed the author and she told me that FragGeneScan could not be used on mac os system. And she recommended me to find a linux machine to run this software.
I hope this would make sense.

Kind regards,
Yuting

发自我的华为手机

-------- 原始邮件 --------
主题：[maxbin:tickets] #2 Error running FragGeneScan
发件人：Maude David <bikeparty2@users.sourceforge.net>
收件人："[maxbin:tickets] " <2@tickets.maxbin.p.re.sourceforge.net>
抄送：

Hi,
Did anyone got this back and running? I'm using FragGeneScan1.31 with Maxbin and also got the "Output recorded" - Thanks

[tickets:#2] Error running FragGeneScan

Status: open
Milestone: 2.0
Created: Thu Sep 06, 2018 04:39 AM UTC by s4251484
Last Updated: Sun Apr 07, 2019 12:51 PM UTC
Owner: Yu-Wei Wu

Hi there, i encounter error with fgs when i'm running MaxBin2. I installed the auxillary programs spearately in my Mac OS 10.12.

I tried running run_FragGeneScan.pl (version 1.31) by itself and it works fine (see below).

MEs-MacBook-Pro:example me$ /Users/me/Library/FragGeneScan/run_FragGeneScan.pl -genome=NC_000913.fna -out=NC_000913-fgs -complete=1 -train=complete
/Users/me/Library/FragGeneScan/FragGeneScan -s NC_000913.fna -o NC_000913-fgs -w 1 -t complete -p 1
Using 1 threads.
no. of seqs: 1
prepare gff file..
Time elapsed: 0 hours 0 minutes and 0 seconds.

but error occurs when it is running within MaxBin2 (see below)

MEs-MacBook-Pro:~ me$ /Users/me/Library/MaxBin/run_MaxBin.pl -contig /Users/me/Desktop/S44c_k33/S44contigs.fasta -reads /Users/me/Desktop/S44c_k33/S44c_R1.fq -reads2 /Users/me/Desktop/S44c_k33/S44c_R2.fq -out s44
MaxBin 2.2.4
Input contig: /Users/me/Desktop/S44c_k33/S44contigs.fasta
Located reads file [/Users/me/Desktop/S44c_k33/S44c_R1.fq]
Located reads file [/Users/me/Desktop/S44c_k33/S44c_R2.fq]
out header: s44
Running Bowtie2 on reads file [/Users/me/Desktop/S44c_k33/S44c_R1.fq]...this may take a while...
Reading SAM file to estimate abundance values...
Running Bowtie2 on reads file [/Users/me/Desktop/S44c_k33/S44c_R2.fq]...this may take a while...
Reading SAM file to estimate abundance values...
Searching against 107 marker genes to find starting seed contigs for [/Users/me/Desktop/S44c_k33/S44contigs.fasta]...
Running FragGeneScan....
Error running FragGeneScan. Output recorded in s44.contig.tmp.frag.out and s44.contig.tmp.frag.err.
=== Please make sure that you are running FragGeneScan 1.18 or above. ===
=== There are known bugs in v1.17 and before that will crash FragGeneScan program. ===

s44.contig.tmp.frag.out file says:
prepare gff file..
Time elapsed: 0 hours 0 minutes and 0 seconds.

while s44.contig.tmp.frag.err is empty.

Please help.

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</bikeparty2@users.sourceforge.net>
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- Bikeparty - 2019-05-28
  
  Thanks for your reply. The problem came from the access permission which
  needed to be re-set.
  Thanks again.
  
  On Mon, May 27, 2019 at 3:30 AM ZOU yutingzou@users.sourceforge.net wrote:
  
  Hi,
  
  Sorry for the late reply. Are you running a Mac？I emailed the author and
  she told me that FragGeneScan could not be used on mac os system. And she
  recommended me to find a linux machine to run this software.
  I hope this would make sense.
  
  Kind regards,
  Yuting
  
  发自我的华为手机
  
  -------- 原始邮件 --------
  主题：[maxbin:tickets] #2 Error running FragGeneScan
  发件人：Maude David bikeparty2@users.sourceforge.net
  收件人："[maxbin:tickets] " 2@tickets.maxbin.p.re.sourceforge.net
  抄送：
  
  Hi,
  Did anyone got this back and running? I'm using FragGeneScan1.31 with
  Maxbin and also got the "Output recorded" - Thanks
  
  [tickets:#2] https://sourceforge.net/p/maxbin/tickets/2/ Error running
  FragGeneScan*
  
  Status: open
  Milestone: 2.0
  Created: Thu Sep 06, 2018 04:39 AM UTC by s4251484
  Last Updated: Sun Apr 07, 2019 12:51 PM UTC
  Owner: Yu-Wei Wu
  
  Hi there, i encounter error with fgs when i'm running MaxBin2. I installed
  the auxillary programs spearately in my Mac OS 10.12.
  
  I tried running run_FragGeneScan.pl (version 1.31) by itself and it works
  fine (see below).
  
  MEs-MacBook-Pro:example me$
  /Users/me/Library/FragGeneScan/run_FragGeneScan.pl -genome=NC_000913.fna
  -out=NC_000913-fgs -complete=1 -train=complete
  /Users/me/Library/FragGeneScan/FragGeneScan -s NC_000913.fna -o
  NC_000913-fgs -w 1 -t complete -p 1
  Using 1 threads.
  no. of seqs: 1
  prepare gff file..
  Time elapsed: 0 hours 0 minutes and 0 seconds.
  
  but error occurs when it is running within MaxBin2 (see below)
  
  MEs-MacBook-Pro:~ me$ /Users/me/Library/MaxBin/run_MaxBin.pl -contig
  /Users/me/Desktop/S44c_k33/S44contigs.fasta -reads
  /Users/me/Desktop/S44c_k33/S44c_R1.fq -reads2
  /Users/me/Desktop/S44c_k33/S44c_R2.fq -out s44
  MaxBin 2.2.4
  Input contig: /Users/me/Desktop/S44c_k33/S44contigs.fasta
  Located reads file [/Users/me/Desktop/S44c_k33/S44c_R1.fq]
  Located reads file [/Users/me/Desktop/S44c_k33/S44c_R2.fq]
  out header: s44
  Running Bowtie2 on reads file
  [/Users/me/Desktop/S44c_k33/S44c_R1.fq]...this may take a while...
  Reading SAM file to estimate abundance values...
  Running Bowtie2 on reads file
  [/Users/me/Desktop/S44c_k33/S44c_R2.fq]...this may take a while...
  Reading SAM file to estimate abundance values...
  Searching against 107 marker genes to find starting seed contigs for
  [/Users/me/Desktop/S44c_k33/S44contigs.fasta]...
  Running FragGeneScan....
  Error running FragGeneScan. Output recorded in s44.contig.tmp.frag.out and
  s44.contig.tmp.frag.err.
  === Please make sure that you are running FragGeneScan 1.18 or above. ===
  === There are known bugs in v1.17 and before that will crash FragGeneScan
  program. ===
  
  s44.contig.tmp.frag.out file says:
  prepare gff file..
  Time elapsed: 0 hours 0 minutes and 0 seconds.
  
  while s44.contig.tmp.frag.err is empty.
  
  Please help.
  
  Sent from sourceforge.net because you indicated interest in
  https://sourceforge.net/p/maxbin/tickets/2/
  
  To unsubscribe from further messages, please visit
  https://sourceforge.net/auth/subscriptions/
  
  [tickets:#2] https://sourceforge.net/p/maxbin/tickets/2/ Error running
  FragGeneScan*
  
  Status: open
  Milestone: 2.0
  Created: Thu Sep 06, 2018 04:39 AM UTC by s4251484
  Last Updated: Tue May 21, 2019 10:28 PM UTC
  Owner: Yu-Wei Wu
  
  Hi there, i encounter error with fgs when i'm running MaxBin2. I installed
  the auxillary programs spearately in my Mac OS 10.12.
  
  I tried running run_FragGeneScan.pl (version 1.31) by itself and it works
  fine (see below).
  
  MEs-MacBook-Pro:example me$
  /Users/me/Library/FragGeneScan/run_FragGeneScan.pl -genome=NC_000913.fna
  -out=NC_000913-fgs -complete=1 -train=complete
  /Users/me/Library/FragGeneScan/FragGeneScan -s NC_000913.fna -o
  NC_000913-fgs -w 1 -t complete -p 1
  Using 1 threads.
  no. of seqs: 1
  prepare gff file..
  Time elapsed: 0 hours 0 minutes and 0 seconds.
  
  but error occurs when it is running within MaxBin2 (see below)
  
  MEs-MacBook-Pro:~ me$ /Users/me/Library/MaxBin/run_MaxBin.pl -contig
  /Users/me/Desktop/S44c_k33/S44contigs.fasta -reads
  /Users/me/Desktop/S44c_k33/S44c_R1.fq -reads2
  /Users/me/Desktop/S44c_k33/S44c_R2.fq -out s44
  MaxBin 2.2.4
  Input contig: /Users/me/Desktop/S44c_k33/S44contigs.fasta
  Located reads file [/Users/me/Desktop/S44c_k33/S44c_R1.fq]
  Located reads file [/Users/me/Desktop/S44c_k33/S44c_R2.fq]
  out header: s44
  Running Bowtie2 on reads file [/Users/me/Desktop/S44c_k33/S44c_R1.fq]...this
  may take a while...
  Reading SAM file to estimate abundance values...
  Running Bowtie2 on reads file [/Users/me/Desktop/S44c_k33/S44c_R2.fq]...this
  may take a while...
  Reading SAM file to estimate abundance values...
  Searching against 107 marker genes to find starting seed contigs for
  [/Users/me/Desktop/S44c_k33/S44contigs.fasta]...
  Running FragGeneScan....
  Error running FragGeneScan. Output recorded in s44.contig.tmp.frag.out and
  s44.contig.tmp.frag.err.
  === Please make sure that you are running FragGeneScan 1.18 or above. ===
  === There are known bugs in v1.17 and before that will crash FragGeneScan
  program. ===
  
  s44.contig.tmp.frag.out file says:
  prepare gff file..
  Time elapsed: 0 hours 0 minutes and 0 seconds.
  
  while s44.contig.tmp.frag.err is empty.
  
  Please help.
  
  Sent from sourceforge.net because you indicated interest in
  https://sourceforge.net/p/maxbin/tickets/2/
  
  To unsubscribe from further messages, please visit
  https://sourceforge.net/auth/subscriptions/
  
  /bikeparty2@users.sourceforge.net
  
  Related
  
  Tickets: #2
  
  alternate
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
  - liaochen - 2021-05-21
    
    Hello, I have the same problem on Mac system. When I run fraggenescan against the test example, the output file .out is empty. So I started to run the command FragGeneScan directly without running the wrapper run_FrageGeneScan.pl, it generates the error code "bus error: 10". Could you elaborate a bit more about how to "reset the permission"?
    
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Yu-Wei Wu - 2019-05-29

Hi. I just noticed that there are tickets on Souceforge. Sorry for being late. Yes as Zou thankfully pointed out that the auxiliary software FragGeneScan cannot make it to Mac so that I recommend using a Linux system--I have tested it on a variety of Linux systems so that it should work well on most Linux machine. Thank you.

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ZOU - 2019-05-29

Hi,
Many thanks for your email!
It works fine on Linux machine.

Kind regards,
Yuting
发自我的华为手机

-------- 原始邮件 --------
主题：[maxbin:tickets] #2 Error running FragGeneScan
发件人：Yu-Wei Wu <yuwwu@users.sourceforge.net>
收件人："[maxbin:tickets] " <2@tickets.maxbin.p.re.sourceforge.net>
抄送：

Hi. I just noticed that there are tickets on Souceforge. Sorry for being late. Yes as Zou thankfully pointed out that the auxiliary software FragGeneScan cannot make it to Mac so that I recommend using a Linux system--I have tested it on a variety of Linux systems so that it should work well on most Linux machine. Thank you.

[tickets:#2] Error running FragGeneScan

Status: open
Milestone: 2.0
Created: Thu Sep 06, 2018 04:39 AM UTC by s4251484
Last Updated: Tue May 21, 2019 10:28 PM UTC
Owner: Yu-Wei Wu

Hi there, i encounter error with fgs when i'm running MaxBin2. I installed the auxillary programs spearately in my Mac OS 10.12.

I tried running run_FragGeneScan.pl (version 1.31) by itself and it works fine (see below).

MEs-MacBook-Pro:example me$ /Users/me/Library/FragGeneScan/run_FragGeneScan.pl -genome=NC_000913.fna -out=NC_000913-fgs -complete=1 -train=complete
/Users/me/Library/FragGeneScan/FragGeneScan -s NC_000913.fna -o NC_000913-fgs -w 1 -t complete -p 1
Using 1 threads.
no. of seqs: 1
prepare gff file..
Time elapsed: 0 hours 0 minutes and 0 seconds.

but error occurs when it is running within MaxBin2 (see below)

MEs-MacBook-Pro:~ me$ /Users/me/Library/MaxBin/run_MaxBin.pl -contig /Users/me/Desktop/S44c_k33/S44contigs.fasta -reads /Users/me/Desktop/S44c_k33/S44c_R1.fq -reads2 /Users/me/Desktop/S44c_k33/S44c_R2.fq -out s44
MaxBin 2.2.4
Input contig: /Users/me/Desktop/S44c_k33/S44contigs.fasta
Located reads file [/Users/me/Desktop/S44c_k33/S44c_R1.fq]
Located reads file [/Users/me/Desktop/S44c_k33/S44c_R2.fq]
out header: s44
Running Bowtie2 on reads file [/Users/me/Desktop/S44c_k33/S44c_R1.fq]...this may take a while...
Reading SAM file to estimate abundance values...
Running Bowtie2 on reads file [/Users/me/Desktop/S44c_k33/S44c_R2.fq]...this may take a while...
Reading SAM file to estimate abundance values...
Searching against 107 marker genes to find starting seed contigs for [/Users/me/Desktop/S44c_k33/S44contigs.fasta]...
Running FragGeneScan....
Error running FragGeneScan. Output recorded in s44.contig.tmp.frag.out and s44.contig.tmp.frag.err.
=== Please make sure that you are running FragGeneScan 1.18 or above. ===
=== There are known bugs in v1.17 and before that will crash FragGeneScan program. ===

s44.contig.tmp.frag.out file says:
prepare gff file..
Time elapsed: 0 hours 0 minutes and 0 seconds.

while s44.contig.tmp.frag.err is empty.

Please help.

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/maxbin/tickets/2/

To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

</div></blockquote></div>

</yuwwu@users.sourceforge.net>
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Error running FragGeneScan

An automatic tool for binning metagenomics sequences

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