STAR-Fusion line 676 #4
Comments
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Thanks for the detailed info. That's a huge help. I'll look into it
shortly.
~b
…On Wed, Mar 27, 2019 at 2:59 PM vaalers ***@***.***> wrote:
I have tried to run the STAR-Fusion Docker version and came across the
same error repetitively. I figured I might be making a silly mistake and
tried doing this tutorial exactly as it states with the documents it tells
us to use. I have gotten the same error and am no sure how to interpret it
and fix it. My computer has Windows 10 with dual Xenons, +80GB RAM, and 12
TB.
Here is the main error:
* Running CMD: /usr/local/src/STAR-Fusion/util/incorporate_FFPM_into_final_report.pl /data/STAR-Fusion-Tutorial-master/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 0 > /data/STAR-Fusion-Tutorial-master/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM
usage: /usr/local/src/STAR-Fusion/util/incorporate_FFPM_into_final_report.pl finspector.fusion_predictions.final.abridged num_total_rnaseq_frags
Error, cmd: /usr/local/src/STAR-Fusion/util/incorporate_FFPM_into_final_report.pl /data/STAR-Fusion-Tutorial-master/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 0 > /data/STAR-Fusion-Tutorial-master/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM died with ret 65280 No such file or directory at /usr/local/src/STAR-Fusion/PerlLib/Pipeliner.pm line 181.
Pipeliner::run(Pipeliner=HASH(0x2611ce0)) called at /usr/local/src/STAR-Fusion/STAR-Fusion line 676
Like I said not sure whats wrong so Im posting the entire script history.
If you'd like the nontutorial script history I can do that too. Just let
me now.
DockerStarFusionTutorialScriptHistory.txt
<https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/files/3014836/DockerStarFusionTutorialScriptHistory.txt>
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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
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I'm thinking it might have something to do with the Windows vs. Linux and
the target files that are downloaded via git.
Perhaps you could try doing this:
Switch to some new directory on Windows where you want to test this and
it's an empty directory.
Then,
docker run --rm -it -v `pwd`:/data trinityctat/ctatfusion:latest bash
followed by
cd /data
git clone https://github.com/STAR-Fusion/STAR-Fusion-Tutorial.git
cd STAR-Fusion-Tutorial/
and then run through the tutorial steps.
best,
~b
On Wed, Mar 27, 2019 at 4:10 PM Brian Haas ***@***.***> wrote:
Thanks for the detailed info. That's a huge help. I'll look into it
shortly.
~b
On Wed, Mar 27, 2019 at 2:59 PM vaalers ***@***.***> wrote:
>
> I have tried to run the STAR-Fusion Docker version and came across the
same error repetitively. I figured I might be making a silly mistake and
tried doing this tutorial exactly as it states with the documents it tells
us to use. I have gotten the same error and am no sure how to interpret it
and fix it. My computer has Windows 10 with dual Xenons, +80GB RAM, and 12
TB.
>
> Here is the main error:
>
> * Running CMD:
/usr/local/src/STAR-Fusion/util/incorporate_FFPM_into_final_report.pl
/data/STAR-Fusion-Tutorial-master/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered
0 >
/data/STAR-Fusion-Tutorial-master/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM
>
>
> usage:
/usr/local/src/STAR-Fusion/util/incorporate_FFPM_into_final_report.pl
finspector.fusion_predictions.final.abridged num_total_rnaseq_frags
>
> Error, cmd:
/usr/local/src/STAR-Fusion/util/incorporate_FFPM_into_final_report.pl
/data/STAR-Fusion-Tutorial-master/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered
0 >
/data/STAR-Fusion-Tutorial-master/STAR-Fusion_outdir/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM
died with ret 65280 No such file or directory at
/usr/local/src/STAR-Fusion/PerlLib/Pipeliner.pm line 181.
> Pipeliner::run(Pipeliner=HASH(0x2611ce0)) called at
/usr/local/src/STAR-Fusion/STAR-Fusion line 676
>
> Like I said not sure whats wrong so Im posting the entire script history.
> If you'd like the nontutorial script history I can do that too. Just let
me now.
…>
> DockerStarFusionTutorialScriptHistory.txt
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub, or mute the thread.
--
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas
--
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas
|
|
If is run 'pwd' or $pwd it gives me the following error: If I try without the '' then I get an empty folder that I believe is in the docker because I cant find it in the local volume I am sharing. I have given the computer permissions to share the drive with docker containers via the GUI settings pane. If this computer were my own it would be linux os instead of windows but its my works so I have to sadly stick with windows 10. |
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hmm... Try launching the docker like you did earlier, as that seemed to
work fine.
If your current working directory includes spaces in it for some reason,
try simplifying your windows directory name by replacing spaces with
underscores.
You might also look into using cygwin as a linux shell alternative on
windows. I know others that have had good luck with that.
Since you got it working earlier, I have full confidence you'll get it
working again. It's probably something trivial.
good luck!
~b
…On Thu, Mar 28, 2019 at 9:58 AM vaalers ***@***.***> wrote:
If is run 'pwd' or $pwd it gives me the following error:
H:\VictoriaRNAStarFusionFastq>docker run --rm -it -v $pwd:/data trinityctat/ctatfusion:latest bash
docker: Error response from daemon: create $pwd: "$pwd" includes invalid characters for a local volume
name, only "[a-zA-Z0-9][a-zA-Z0-9_.-]" are allowed. If you intended to pass a host directory, use absolute path.
See 'docker run --help'.
If I try without the '' then I get an empty folder that I believe is in
the docker because I cant find it in the local volume I am sharing. I have
given the computer permissions to share the drive with docker containers
via the GUI settings pane.
If this computer were my own it would be linux os instead of windows but
its my works so I have to sadly stick with windows 10.
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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
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I have tried to run the STAR-Fusion Docker version and came across the same error repetitively. I figured I might be making a silly mistake and tried doing this tutorial exactly as it states with the documents it tells us to use. I have gotten the same error and am no sure how to interpret it and fix it. My computer has Windows 10 with dual Xenons, +80GB RAM, and 12 TB.
Here is the main error:
Like I said not sure whats wrong so Im posting the entire script history.
If you'd like the nontutorial script history I can do that too. Just let me now.
DockerStarFusionTutorialScriptHistory.txt
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