Open a-lud opened 2 years ago
I'm having the same issue. I get the same error and I'm not sure what I'm supposed to do since I'm working on a big cluster, I don't have any symlinks but I guess the cluster works with them.
Hi,
Recent versions of Trinity have an option: --no_symlink
Try using that and let's see if that resolves the symlink related issue.
best,
~b
On Sun, Jan 8, 2023 at 10:22 PM JuanCamargoTavares @.***> wrote:
I'm having the same issue. I get the same error and I'm not sure what I'm supposed to do since I'm working on a big cluster, I don't have any symlinks but I guess the cluster works with them.
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Thanks for your help. Unfortunately I still get a similar error:
Monday, January 9, 2023: 12:49:15 CMD: touch /localscratch/artefac.2359679.0/trinity_reference_AA9/AA9.sort.bam.norm_200.bam.ok
Monday, January 9, 2023: 12:49:15 CMD: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/trinity/2.14.0/trinityrnaseq-v2.14.0/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /localscratch/artefac.2359679.0/trinity_reference_AA9/AA9.sort.bam.norm_200.bam -I 15000 --sort_buffer 180G --CPU 18
CMD: cp /localscratch/artefac.2359679.0/trinity_reference_AA9/AA9.sort.bam.norm_200.bam AA9.sort.bam.norm_200.bam
cp: '/localscratch/artefac.2359679.0/trinity_reference_AA9/AA9.sort.bam.norm_200.bam' and 'AA9.sort.bam.norm_200.bam' are the same file
Error, command cp /localscratch/artefac.2359679.0/trinity_reference_AA9/AA9.sort.bam.norm_200.bam AA9.sort.bam.norm_200.bam died with ret 256 at /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/trinity/2.14.0/trinityrnaseq-v2.14.0/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl line 221.
main::process_cmd("cp /localscratch/artefac.2359679.0/trinity_reference_AA9/AA9."...) called at /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/trinity/2.14.0/trinityrnaseq-v2.14.0/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl line 123
Error, cmd: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/trinity/2.14.0/trinityrnaseq-v2.14.0/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /localscratch/artefac.2359679.0/trinity_reference_AA9/AA9.sort.bam.norm_200.bam -I 15000 --sort_buffer 180G --CPU 18 died with ret 256 at /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/trinity/2.14.0/trinityrnaseq-v2.14.0/Trinity line 2879.
main::process_cmd("/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Cor"...) called at /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/trinity/2.14.0/trinityrnaseq-v2.14.0/Trinity line 3541
main::run_genome_guided_Trinity("/home/artefac/scratch/cip_transcriptomes/scripts/../data/refe"..., undef) called at /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/trinity/2.14.0/trinityrnaseq-v2.14.0/Trinity line 1427
I have no idea what the issue could be.
I think I see what the issue is.
Can you share your Trinity command?
thx,
~b
On Mon, Jan 9, 2023 at 4:31 PM JuanCamargoTavares @.***> wrote:
Thanks for your help. Unfortunately I still get a similar error:
Monday, January 9, 2023: 12:49:15 CMD: touch /localscratch/artefac.2359679.0/trinity_reference_AA9/AA9.sort.bam.norm_200.bam.ok Monday, January 9, 2023: 12:49:15 CMD: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/trinity/2.14.0/trinityrnaseq-v2.14.0/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /localscratch/artefac.2359679.0/trinity_reference_AA9/AA9.sort.bam.norm_200.bam -I 15000 --sort_buffer 180G --CPU 18 CMD: cp /localscratch/artefac.2359679.0/trinity_reference_AA9/AA9.sort.bam.norm_200.bam AA9.sort.bam.norm_200.bam cp: '/localscratch/artefac.2359679.0/trinity_reference_AA9/AA9.sort.bam.norm_200.bam' and 'AA9.sort.bam.norm_200.bam' are the same file Error, command cp /localscratch/artefac.2359679.0/trinity_reference_AA9/AA9.sort.bam.norm_200.bam AA9.sort.bam.norm_200.bam died with ret 256 at /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/trinity/2.14.0/trinityrnaseq-v2.14.0/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl line 221. main::process_cmd("cp /localscratch/artefac.2359679.0/trinity_reference_AA9/AA9."...) called at /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/trinity/2.14.0/trinityrnaseq-v2.14.0/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl line 123 Error, cmd: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/trinity/2.14.0/trinityrnaseq-v2.14.0/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl --coord_sorted_SAM /localscratch/artefac.2359679.0/trinity_reference_AA9/AA9.sort.bam.norm_200.bam -I 15000 --sort_buffer 180G --CPU 18 died with ret 256 at /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/trinity/2.14.0/trinityrnaseq-v2.14.0/Trinity line 2879. main::process_cmd("/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Cor"...) called at /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/trinity/2.14.0/trinityrnaseq-v2.14.0/Trinity line 3541 main::run_genome_guided_Trinity("/home/artefac/scratch/cip_transcriptomes/scripts/../data/refe"..., undef) called at /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/trinity/2.14.0/trinityrnaseq-v2.14.0/Trinity line 1427
I have no idea what the issue could be.
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
This was my Trinity command:
$Trinity --no_symlink \
--genome_guided_bam ${REF_DIR}${NAME}.sort.bam \
--genome_guided_max_intron 15000 \
--max_memory ${MEM} --CPU ${THREADS} \
--output ${TEMP_DIR}
I'm working on a compute canada cluster as you can see in my last comment.
Juan
Thanks. Can you try replacing:
${REF_DIR}${NAME}.sort.bam
with just ${NAME}.sort.bam and let's see if that works...?
On Tue, Jan 10, 2023 at 10:02 AM JuanCamargoTavares < @.***> wrote:
This was my Trinity command:
$Trinity --no_symlink \ --genome_guided_bam ${REF_DIR}${NAME}.sort.bam \ --genome_guided_max_intron 15000 \ --max_memory ${MEM} --CPU ${THREADS} \ --output ${TEMP_DIR}
I'm working on a compute canada cluster as you can see in my last comment.
Juan
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
It fails because it cannot find the bam file: Failed to open file "AA9.sort.bam" : No such file or directory
Juan
OK. The only solution I can come up with here is if I modify one of the Trinity scripts. If I do that, would you be able to patch your software installation with it?
On Tue, Jan 10, 2023 at 10:42 AM JuanCamargoTavares < @.***> wrote:
It fails because it cannot find the bam file: Failed to open file "AA9.sort.bam" : No such file or directory
Juan
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Yes I can make a custom installation in my personal storage in the cluster. Here is my email: juan.camargotavares@mail.mcgill.ca
The updated script is here: https://github.com/trinityrnaseq/trinityrnaseq/blob/devel/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl
You can just drop in a replacement for that script and try running Trinity again.
If you need to have it run from your personal storage area, then try recursively copying your current Trinity software distribution from wherever it's currently installed to your local area, and drop this replacement script in there. Just be sure it's executable: chmod 775 prep_rnaseq_alignments_for_genome_assisted_assembly.pl
Please let me know how it goes.
best,
~b
On Tue, Jan 10, 2023 at 10:51 AM JuanCamargoTavares < @.***> wrote:
Yes I can make a custom installation in my personal storage in the cluster. Here is my email: @.***
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
It's working now, thanks!
cheers, Juan
Great! Thanks!
~b
On Tue, Jan 10, 2023 at 12:02 PM JuanCamargoTavares < @.***> wrote:
It's working now, thanks!
cheers, Juan
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Hi,
I've discovered an edge case issue where
prep_rnaseq_alignments_for_genome_assisted_assembly.pl
fails by trying to create a symlink toprefix.bam.norm_200.bam
in a directory where it already exists.As you'll see, this is very much an issue caused by my bad habits, so I'm not really sure if it needs to be fixed. Just figured I'd put this here in case anyone else encounters the same problem!
Compute: Linux HPC Version: Trinity v2.14.0 Singularity image
How I broke it
I have a symlink in my
$HOME
directory to a data directory for convenience (saves me little bit of typing).Absolute path:
/g/data/xl04/al4518
Shortcut path:/home/566/al4518/al
Where
al -> /g/data/xl04/al4518
, which enables me tocd al
when I log in to our cluster to get to my data files rather than having to docd /g/data/xl04/al4518
constantly.In my genome guided trinity command I used the shortcut path. Consequently, this broke
prep_rnaseq_alignments_for_genome_assisted_assembly.pl
at the following lines (line 121).I'm guessing
cwd()
returns the absolute path (?) which differs to the path that I provided, meaning it tries to link the file to the output directory, but as it already exists there it causes the following error:Again, this is a consequence of my laziness, so figured I'd put this here to remind people to use absolute paths!
Cheers Al