Singularity error: cannot locate file #1415
Comments
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Hi,
Try explicitly binding the directory like so:
singularity exec -B /scratch/aubfjb001/DeNovo/Trinity
followed by the rest.
I haven't used -W before
You could include
singularity exec -e -H /tmp -B `pwd`
where pwd is surrounded by backticks
and see if that helps
…On Wed, May 15, 2024 at 3:07 PM FaithBoyer ***@***.***> wrote:
I am attempting to run Trinity 2.14.0 through Singularity. This is my code:
#!/bin/bash
export TRINITY_HOME=/scratch/aubfjb001/DeNovo/Trinity
FQ1="/scratch/aubfjb001/DeNovo/Trinity/C12_0_1_fwd_paired.fastq"
FQ2="/scratch/aubfjb001/DeNovo/Trinity/C12_0_1_rvs_paired.fastq"
singularity exec -W /scratch/aubfjb001/DeNovo/Trinity trinityrnaseq.v2.14.0.simg Trinity \
--seqType fq \
--left "$FQ1" \
--right "$FQ2" \
--max_memory 1G --CPU 4 \
I am confident about the locations of my files and directories, but I am
getting this error:
Error, cannot locate file:
/scratch/aubfjb001/DeNovo/TrinityDocker/C12_0_1_fwd_paired.fastq at
/usr/local/bin/Trinity line 2848.
main::create_full_path(ARRAY(0x55d0091fa3d8), 1) called at
/usr/local/bin/Trinity line 1319
I *think* the problem is that trinity is looking in /usr/local/bin, as
that is where singularity default unpacks, but I need it to look in my
current working directory.
Any insights on how to fix this issue are much appreciated.
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Brian J. Haas
The Broad Institute
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Thank you for your feedback. I tried both of these options, but am getting the same error. Could it be anything else? I am running the job on an HPC, so it may not be a problem with Trinity, but rather my permissions on my side. |
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The best way to troubleshoot this it to try an interactive session on the
HPC, run the singularity image in an interactive way (singularity 'shell'
with the same parameters except for the trinity command), and see if you
can view the
file /scratch/aubfjb001/DeNovo/TrinityDocker/C12_0_1_fwd_paired.fastq
using 'less'
If it can't access it, then there's an issue with singularity
interaction with the file system, probably due to symbolic links - in which
case you'd need to figure out the real path to the file (using 'realpath' )
On Thu, May 16, 2024 at 10:21 AM FaithBoyer ***@***.***>
wrote:
… Hi, Try explicitly binding the directory like so: singularity exec -B
/scratch/aubfjb001/DeNovo/Trinity followed by the rest. I haven't used -W
before You could include singularity exec -e -H /tmp -B pwd where pwd is
surrounded by backticks and see if that helps
… <#m_8004242355516848330_>
On Wed, May 15, 2024 at 3:07 PM FaithBoyer *@*.*> wrote: I am attempting
to run Trinity 2.14.0 through Singularity. This is my code: #!/bin/bash
export TRINITY_HOME=/scratch/aubfjb001/DeNovo/Trinity
FQ1="/scratch/aubfjb001/DeNovo/Trinity/C12_0_1_fwd_paired.fastq"
FQ2="/scratch/aubfjb001/DeNovo/Trinity/C12_0_1_rvs_paired.fastq"
singularity exec -W /scratch/aubfjb001/DeNovo/Trinity
trinityrnaseq.v2.14.0.simg Trinity \ --seqType fq \ --left "$FQ1" \ --right
"$FQ2" \ --max_memory 1G --CPU 4 \ I am confident about the locations of my
files and directories, but I am getting this error: Error, cannot locate
file: /scratch/aubfjb001/DeNovo/TrinityDocker/C12_0_1_fwd_paired.fastq at
/usr/local/bin/Trinity line 2848.
main::create_full_path(ARRAY(0x55d0091fa3d8), 1) called at
/usr/local/bin/Trinity line 1319 I think the problem is that trinity is
looking in /usr/local/bin, as that is where singularity default unpacks,
but I need it to look in my current working directory. Any insights on how
to fix this issue are much appreciated. — Reply to this email directly,
view it on GitHub <#1415
<#1415>>, or
unsubscribe
https://github.com/notifications/unsubscribe-auth/ABZRKX7WDY3NSD7TMRDHCBTZCOW5ZAVCNFSM6AAAAABHYX3QHOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI4TQNRUGM4TQMQ
<https://github.com/notifications/unsubscribe-auth/ABZRKX7WDY3NSD7TMRDHCBTZCOW5ZAVCNFSM6AAAAABHYX3QHOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI4TQNRUGM4TQMQ>
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-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas
http://broad.mit.edu/~bhaas
Thank you for your feedback. I tried both of these options, but am getting
the same error. Could it be anything else? I am running the job on an HPC,
so it may not be a problem with Trinity, but rather my permissions on my
side.
—
Reply to this email directly, view it on GitHub
<#1415 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ABZRKX6IARRKPRXD3JMZJKDZCS6E7AVCNFSM6AAAAABHYX3QHOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJVGM4DGMZWGY>
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You are receiving this because you commented.Message ID:
***@***.***>
--
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
|
|
This issue has been resolved through the HPC side of things. Thank you for your help! |
I am attempting to run Trinity 2.14.0 through Singularity. This is my code:
I am confident about the locations of my files and directories, but I am getting this error:
Error, cannot locate file: /scratch/aubfjb001/DeNovo/TrinityDocker/C12_0_1_fwd_paired.fastq at /usr/local/bin/Trinity line 2848.
main::create_full_path(ARRAY(0x55d0091fa3d8), 1) called at /usr/local/bin/Trinity line 1319
I think the problem is that trinity is looking in /usr/local/bin, as that is where singularity default unpacks, but I need it to look in my current working directory.
Any insights on how to fix this issue are much appreciated.
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