Comments (11)
leepc12
commented on July 21, 2024
Please check permission for directories and files on your pipeline output
directory (`/media/nico/data/home2/projects/macrophages`).
Jin
…On Thu, Dec 7, 2017 at 3:14 AM, michdass ***@***.***> wrote:
Hey,
I installed everything according to your instructions without noticing any
errors, but I cannot get chipseq.py to work. If I use fastq or bam as
input, I get an error of the following form
fork/exec /media/nico/data/home2/projects/macrophages/chip_
ana2/8-ENCODE-pipeline/chipseq.bds.20171207_115700_844/
task.postalign_bam.dedup_bam_1_rep1.line_155.id_10.sh: permission denied
If I use peaks as input, the error has the following form:
Error (/home/nico/TF_chipseq_pipeline/modules/input_peak.bds, line 31,
pos 33): File not found!
The files pass the initial check, though.
I don't know what to do next.
Here is the stderr output when running with a fastq and with a peak input.
log-17_12_07-11:56:57.txt
<https://github.com/kundajelab/chipseq_pipeline/files/1538790/log-17_12_07-11.56.57.txt>
log-17_12_07-11:54:38.txt
<https://github.com/kundajelab/chipseq_pipeline/files/1538791/log-17_12_07-11.54.38.txt>
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michdass
commented on July 21, 2024
the directory is drwxrwxr-x
and the files are -rw-rw-r--
the bam files are even -rwxrwxrwx
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leepc12
commented on July 21, 2024
What about pipeline's repo directory (chipseq_pipeline/)?
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michdass
commented on July 21, 2024
TF_chipseq_pipeline/ has drwxrwxr-x as well. I'm assuming the Aquas-Pipeline directory does not have to be put into a specific place? It's right now in my home directory.
Gesendet: Samstag, 09. Dezember 2017 um 19:21 Uhr
Von: "Jin Lee" <[email protected]>
An: kundajelab/chipseq_pipeline <[email protected]>
Cc: michdass <[email protected]>, Author <[email protected]>
Betreff: Re: [kundajelab/chipseq_pipeline] permission denied / file not found (#23)
What about pipeline's repo directory (chipseq_pipeline/)?
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leepc12
commented on July 21, 2024
I am sorry for long delay.
Permissions on the pipeline source directory looks okay, but I suspect that
you still have a permission issue on your output directories. Our pipeline
makes many temporary files and directories under your working directory
(it's not -out_dir but where you run the pipeline command line). Does your
cluster limit file/dir permission on your working directories?
Please run the following command lines and post outputs here.
$ touch /media/nico/data/home2/projects/macrophages/chip_
ana2/8-ENCODE-pipeline/file_permission_test
$ mkdir /media/nico/data/home2/projects/macrophages/chip_
ana2/8-ENCODE-pipeline/dir_permission_test
$ touch /media/nico/data/home2/projects/macrophages/chip_
ana2/8-ENCODE-pipeline/dir_permission_test/file_permission_test
Thanks,
Jin
…On Mon, Dec 11, 2017 at 1:06 AM, michdass ***@***.***> wrote:
TF_chipseq_pipeline/ has drwxrwxr-x as well. I'm assuming the
Aquas-Pipeline directory does not have to be put into a specific place?
It's right now in my home directory.
Gesendet: Samstag, 09. Dezember 2017 um 19:21 Uhr
Von: "Jin Lee" ***@***.***>
An: kundajelab/chipseq_pipeline ***@***.***>
Cc: michdass ***@***.***>, Author ***@***.***>
Betreff: Re: [kundajelab/chipseq_pipeline] permission denied / file not
found (#23)
What about pipeline's repo directory (chipseq_pipeline/)?
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michdass
commented on July 21, 2024
Hey Jin,
currently I am trying to set up the pipeline on my local machine, not on a cluster. So there shouldn't be any permission restrictions in the output or working directories. Those commands are executed without any errors.
Thanks,
Nico
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leepc12
commented on July 21, 2024
Can you try installing pipeline on your /home/$USERID/chipseq_pipelines?
How is your output directory mounted to the system?
$ df -h /media/nico/data/home2/projects/macrophages/chip_ana2
Jin
…On Thu, Jan 11, 2018 at 5:42 AM, michdass ***@***.***> wrote:
Hey Jin,
currently I am trying to set up the pipeline on my local machine, not on a
cluster. So there shouldn't be any permission restrictions in the output or
working directories. Those commands are executed without any errors.
Thanks,
Nico
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michdass
commented on July 21, 2024
The pipeline was installed in my home directory before, I re-downloaded it and reinstalled the dependencies and the genome data, but I still get the same errors.
df output:
Filesystem Size Used Avail Use% Mounted on
/dev/sdb1 1.8T 1.5T 242G 87% /media/nico/data
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leepc12
commented on July 21, 2024
Did you have enough disk space on /tmp, $TMP and $TMPDIR? What is your $TMP
and $TMPDIR?
echo $TMP
echo $TMPDIR
df -h $TMP
df -h $TMPDIR
df -h /tmp
Jin
…On Fri, Jan 12, 2018 at 3:11 AM, michdass ***@***.***> wrote:
The pipeline was installed in my home directory before, I re-downloaded it
and reinstalled the dependencies and the genome data, but I still get the
same errors.
df output:
Filesystem Size Used Avail Use% Mounted on
/dev/sdb1 1.8T 1.5T 242G 87% /media/nico/data
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michdass
commented on July 21, 2024
Currently I indeed do not have a lot of space on my main drive.
df -h /tmp
Filesystem Size Used Avail Use% Mounted on
/dev/sda2 86G 76G 5.1G 94% /
$TMP and $TMPDIR are not defined.
I cannot make more than 15 GB available on the main drive currently, but I could define a temporary directory on another drive if that doesn't suffice.
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leepc12
commented on July 21, 2024
You will need at least 30GB in your /tmp for the pipeline. Subtasks in the
pipeline sometimes make very large temporary BAM files.
Jin
…On Wed, Jan 24, 2018 at 1:34 AM, michdass ***@***.***> wrote:
Currently I indeed do not have a lot of space on my main drive.
df -h /tmp
Filesystem Size Used Avail Use% Mounted on
/dev/sda2 86G 76G 5.1G 94% /
$TMP and $TMPDIR are not defined.
I cannot make more than 15 GB available on the main drive currently, but I
could define a temporary directory on another drive if that doesn't suffice.
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