user008855
commented
10 months ago Hi, I am also dealing with same error. Any suggestion how can I resolve this?
Closed zcalamari closed 7 months ago
user008855
commented
10 months ago Hi, I am also dealing with same error. Any suggestion how can I resolve this?
brianjohnhaas
commented
10 months ago Hi,
Sorry about that. Can you try rerunning that command, and instead of this:
-B /home/zcalamari/nas5/ctat_deer/:/ctat_deer:ro
use
-B /home/zcalamari/nas5/ctat_deer/:/ctat_deer
(dropping the :ro suffix)? That suffix makes it read-only, which is generally a good thing to do, but not here where we need to build that part of the genome lib.
The upcoming genome libs will include this mm2 index so it won't be an issue and the prep step won't be needed going forward (coming out in the next week, hopefully). In the meantime, dropping the :ro should 'fix' this.
best,
Brian
On Thu, Oct 26, 2023 at 2:14 AM user008855 @.***> wrote:
Hi, I am also dealing with same error. Any suggestion how can I resolve this?
— Reply to this email directly, view it on GitHub https://github.com/trinityrnaseq/TrinityFusion/issues/4#issuecomment-1780476734, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX3BFOPCXT3C3HCTHITYBH5VRAVCNFSM6AAAAAA5S3F76SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBQGQ3TMNZTGQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
zcalamari
commented
10 months ago That seems to have worked! Thanks for the help.
brianjohnhaas
commented
10 months ago Glad it worked!
On Thu, Oct 26, 2023 at 3:30 PM zcalamari @.***> wrote:
That seems to have worked! Thanks for the help.
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Hello,
I am trying to prepare a CTAT genome library for TrinityFusion, but I keep getting an error. I have attempted with both the singularity image and a regular installation. When I run the command:
singularity exec -e -B /home/zcalamari/nas5/ctat_deer/:/ctat_deer:ro trinityfusion.v0.4.0.simg /usr/local/src/TrinityFusion/CTAT-LR-fusion/ctat-LR-fusion --prep_reference_only -T O2FC_1P.fq.gz --genome_lib_dir /ctat_deer
I receive the error:
Error, cannot write to /ctat_deer/mm2_prep_chkpts/pipeliner.16351.cmds at /usr/local/src/TrinityFusion/CTAT-LR-fusion/PerlLib/Pipeliner.pm line 85. Pipeliner::new("Pipeliner", "-verbose", 2, "-checkpoint_dir", "/ctat_deer/mm2_prep_chkpts") called at /usr/local/src/TrinityFusion/CTAT-LR-fusion/ctat-LR-fusion line 573 main::prep_minimap2_reference("/ctat_deer/ref_genome.fa", "/ctat_deer", "/ctat_deer/ref_genome.fa.mm2", "/ctat_deer/ref_annot.gtf.mm2.splice.bed", "/ctat_deer/ref_annot.gtf") called at /usr/local/src/TrinityFusion/CTAT-LR-fusion/ctat-LR-fusion line 259
If I try to run the preparation step directly from the full TrinityFusion installation with the command "./TrinityFusion-v0.4.0/CTAT-LR-fusion/ctat-LR-fusion --prep_reference_only -T ./O2FC_1P.fq.gz --genome_lib_dir ctat_deer", I get a different error:
"TrinityFusion-v0.4.0/CTAT-LR-fusion/ctat-minimap2/" does not have a file or directory called ctat-minimap2, which should explain the second error, but I do not know how to fix the issue.
I have successfully run STAR-Fusion with this genome library, and would like to complement those analyses with TrinityFusion. Any advice for fixing this would be appreciated!