brianjohnhaas
commented
1 year ago Hi,
I haven't encountered this before. Try killing it and rerunning it. It has checkpoints built in so it should pick up where it left off.
If it gets hung up again, I'd be happy to look at it directly. You'd just need to tar.gz up the current working directory and share it with me privately.
best,
~brian
On Sun, Jan 15, 2023 at 4:32 AM sxz-ivan @.***> wrote:
Hi,
I have been trying to run STAR-Fusion on pair-end rRNA-depleted RNA-seq data on a machine with 3T memory for 3 days, and I haven't been able to finish the first run. This doesn't appear normal according to the Genome Biology paper, where STAR-Fusion took several hours to finish.
My bash command: ~/bin/star-fusion/STAR-Fusion-v1.11.1/STAR-Fusion --left_fq ~/data/DH_tumour11_Clean_Data_unaligned.1.fq.gz --right_fq ~/data/DH_tumour11_Clean_Data_unaligned.2.fq.gz --genome_lib_dir ~/data/myrefs/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/GRCh38_gencode_v37_CTAT_lib_Mar012021.source/ctat_genome_lib_build_dir --CPU 8 --output_dir ~/test --outTmpDir ~/test/temp1 --tmpdir /test/temp2 1>>/test/master.log 2>&1 &
[image: 屏幕截图 2023-01-15 172422] https://user-images.githubusercontent.com/36357132/212533134-80f91725-275b-4c63-bc77-559a8213cd5a.png
The pipeline seem to have stuck in perl. Please find the log in my attachment.
What adjustment can I make to improve the run time?
Thanks a lot!
master.log https://github.com/STAR-Fusion/STAR-Fusion/files/10419844/master.log
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Hi,
I have been trying to run STAR-Fusion on pair-end rRNA-depleted RNA-seq data on a machine with 3T memory for 3 days, and I haven't been able to finish the first run. This doesn't appear normal according to the Genome Biology paper, where STAR-Fusion took several hours to finish.
My bash command: /home/me/bin/star-fusion/STAR-Fusion-v1.11.1/STAR-Fusion --left_fq /home/me/data/DH_tumour11_Clean_Data_unaligned.1.fq.gz --right_fq /home/me/data/DH_tumour11_Clean_Data_unaligned.2.fq.gz --genome_lib_dir /home/me/data/myrefs/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/GRCh38_gencode_v37_CTAT_lib_Mar012021.source/ctat_genome_lib_build_dir --CPU 8 --output_dir /home/me/test --outTmpDir /home/me/test/temp1 --tmpdir /home/me/test/temp2 1>>/home/me/test/master.log 2>&1 &
The pipeline seem to have stuck in perl. Please find the log in my attachment.
What adjustment can I make to improve the run time?
Thanks a lot!
master.log