STAR-Fusion line 676

Question

STAR-Fusion line 676

Opened this issue 6 years ago · 4 comments

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

Answer 1 · 2019-03-27T20:11:11.000Z

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> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHMVX4rZwrBpeiE9KBBmUmu__HS6XnkLks5va7-hgaJpZM4cOjcC> .

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

Answer 2 · 2019-03-27T20:57:18.000Z

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

Answer 3 · 2019-03-28T13:58:13.000Z

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.

Answer 4 · 2019-03-28T14:35:28.000Z

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. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#4 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHMVX6Gjfj-OW7_Mid9kie7lPO0h7d7nks5vbMp1gaJpZM4cOjcC> .

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>