PGAP error

[0123615177]

Hi

1) I am having trouble with getting PGAP running.

Firstly, I did the installation of docker desktop. https://docs.docker.com/desktop/install/ubuntu/

Docker is located in the following directory; /bin/docker

2) After this, I installed the 3 things needed for PGAP, namely (docker image, the supplementary reference files, CWL code) from: https://github.com/ncbi/pgap/wiki/Installation (using the latest version 2022-12-13)

I got pgap.py with th folowing commands

$ wget https://github.com/ncbi/pgap/raw/prod/scripts/pgap.py $ chmod +x pgap.py $ ./pgap.py --update

All things related to PGAP are in the directory /home/margot:

After the PGAP downloads and installation, the docker contains the following images

So in my wd I also have the files for analysis, namely the genome .fasta file (Thermobofoda.fna), and the two .yaml files: Thermobifida_alba.yaml and Thermobifida_alba_meta.yaml

Here is what the content looks like: Thermobifida_alba.yaml: Thermobifida_alba_meta.yaml:

So after opening docker, I run the following command from my wd: ./pgap.py -r -o Results Thermobifida_alba.yaml

But then I get the following error message: PGAP version 2022-12-13.build6494 is up to date. Output will be placed in: /home/margot/Results WARNING: memory (GiB) is less than the recommended value of 8 WARNING: memory per CPU core (GiB) is less than the recommended value of 2 PGAP failed, docker exited with rc = 125 Unable to find error in log file.

PS. would also like to mention that the 'File sharing' of docker path is set to my wd: /home/margot

I have tried many things, but I do not know how to fix this. Can you please suggest somthing? Thanks so much Margot

[0123615177]

Hi I removed the biosample from the metadata, then in the wd ran:

margot@margot-B365M-DS3H:~$ mkdir -p mytmp margot@margot-B365M-DS3H:~$ export TMPDIR=$(readlink -f mytmp) margot@margot-B365M-DS3H:~$ ./pgap.py -o Results Thermobifida_alba.yaml -n[

It did not work, but here is the error message:

cwltool.log ](url)

[azat-badretdin]

Thanks, Margot. Now it complains about project:

Invalid project 'CP000088.1'

bioproject is also optional. Please remove it as well and try again

[0123615177]

Hi Just for testing, can I remove all optional metadata? That would leave me with only the organism info nl. genus_species in the _meta file.

Thanks

[azat-badretdin]

Just for testing, can I remove all optional metadata?

Sure

[0123615177]

I did this, and it looks like it is running fine! Will confirm.

Thanks

[azat-badretdin]

Excellent! Please let us know how did it go tomorrow.

[0123615177]

Hi

It ran for quite some time...but then unfortunately gave me the following error message:

margot@margot-B365M-DS3H:~$ mkdir -p mytmp margot@margot-B365M-DS3H:~$ export TMPDIR=$(readlink -f mytmp) margot@margot-B365M-DS3H:~$ ./pgap.py -o Results Thermobifida_alba.yaml -n PGAP version 2022-12-13.build6494 is up to date. Output will be placed in: /home/margot/Results.2 WARNING: memory (GiB) is less than the recommended value of 8 WARNING: memory per CPU core (GiB) is less than the recommended value of 2 PGAP failed, docker exited with rc = 1 Unable to find error in log file.

Please see attached the log file with the error: cwltool.zip

Do you know what it was this time?

[azat-badretdin]

It's the error we have already seen:

PermissionError: [Errno 13] Permission denied: '/pgap/output/calls.tab'

Not sure how to handle this.

[azat-badretdin]

Could you please execute

/usr/local/bin/docker run -i --rm --user 1000:1000 \
--volume /home/margot/.pgap/input-2022-12-13.build6494:/pgap/input:ro,z \
--volume /home/margot:/pgap/user_input:z  \
--volume /home/margot/mytmp:/tmp:rw,z \
--volume /home/margot/Results.2:/pgap/output:rw,z \
ncbi/pgap:2022-12-13.build6494 \
touch /pgap/output/myfile

Thanks!

[0123615177]

Hi

I did this:

margot@margot-B365M-DS3H:~$ /usr/local/bin/docker run -i --rm --user 1000:1000 --volume /home/margot/.pgap/input-2022-12-13.build6494:/pgap/input:ro,z --volume /home/margot:/pgap/user_input:z --volume /home/margot/mytmp:/tmp:rw,z --volume /home/margot/Results.2:/pgap/output:rw,z ncbi/pgap:2022-12-13.build6494 touch /pgap/output/myfile docker: Error response from daemon: Bad response from Docker engine. See 'docker run --help'.

[0123615177]

Is docker the issue here?

[azat-badretdin]

Yes, it looks like that

[0123615177]

Do you have any suggestions how we can test docker?

[azat-badretdin]

When I have a technical issue which is out of the scope of the domain of my expertise I often try to find a local expert in this area.

I already asked couple of systems experts from our group if they have any ideas.

I would suggest to be proactive on your side as well.

[azat-badretdin]

Maybe you can describe the process of using pgap.py on your computer. As far as I understand it's a Windows 11 box. How do you get to UNIX shell? Are you using WSL 2?

[0123615177]

Hi

I set up this PC given to me at work by myself. I deleted the prior OS, and installed ubuntu 22.04 jammy Jelly fish. I have managed to run several softwares like this, eg. fastqc etc.

To access the terminal, I click on the terminal icon. With regards to the wsl:

margot@margot-B365M-DS3H:~$ wsl -l -v Command 'wsl' not found, but can be installed with: sudo apt install wsl

I am still learning.....

[0123615177]

When I have a technical issue which is out of the scope of the domain of my expertise I often try to find a local expert in this area.

I already asked couple of systems experts from our group if they have any ideas.

I would suggest to be proactive on your side as well.

Ok, i will try/ am trying. I do the same through mails with bioinformaticians I do know. Unfortunately I have had no luck so far, and no one in my research group knows bioinformatic/pc related issues.

[azat-badretdin]

and installed ubuntu 22.04 jammy Jelly fish

Thanks, this is very useful. I am surprised we are not detecting that.

[0123615177]

I did, however install wsl now:

sudo apt install wsl and it seems I have wsl 2 now Wsman Shell commandLine, version 0.2.1

[azat-badretdin]

I did, however install wsl now:

Sure, you can try that as well. Just for the record: I did not mean to recommend using it, it's just what I have at home for my Windows 11 box.

[0123615177]

Hi Do you think I should uninstall docker and pgap and try again from the start?

[azat-badretdin]

This is one of the generic approaches to this sort of thing, yes. But more specific approaches have more chances for success.

[0123615177]

Hi How do you think we should proceed? Thanks

[azat-badretdin]

Unfortunately, I do not know at this point. Consultations with our experts also did not lead to any advice.

[ericjove]

Hello, sorry for the delayed communication. I'd like to report that from a fresh AWS(Amazon Web Service) Ubuntu 22.04.1 VM, I was successfully able to run the instructions from PGAP’s quick start instruction i.e., https://github.com/ncbi/pgap/wiki/Quick-Start page.

To ensure that we're on the same page, can you confirm the following specific versions I have listed below match what you have? I included the commands I used to obtain this information.

i.e.,

OS Information: To check the OS information, use the:

lsb_release -a

My output: No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 22.04.1 Release: 22.04

To check the kernel version, use the following command: uname -r

My output: 5.15.0-1031-aws

To check the Docker version, use: docker --version

My output: Docker version 23.0.1, build a5ee5b1

Also, to get PGAP to work, I had to manually install Docker on the fresh instance of Ubuntu. I did this by using the commands below. I bring this up because the only roadblock that I hit was that when Docker was installing, its install script prompted me to check if it could upgrade the OS’s kernel.

The first time I installed Docker I said no to this kernel upgrade request, and consequently I was not able to run PGAP (and encounter the same errors that you are reporting).

Then I uninstalled and reinstalled Docker, I allowed Docker to upgrade the OS’s Kernal.

After this, I was able to successfully run PGAP’s quick start instructions listed above.

If your Docker version or Kernel version is different then what I have listed above, can you uninstall Docker and follow the commands I have listed below?

Install Instructions for Docker on Ubuntu 22.04:

Update the package index and install necessary packages:

sudo apt-get update sudo apt-get install apt-transport-https ca-certificates curl software-properties-common

Add Docker's official GPG key:

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg

Add the Docker repository: For Ubuntu 22.04, use the following command to set up the stable repository:

echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null

Update the package index and install Docker:

sudo apt-get update sudo apt-get install docker-ce docker-ce-cli containerd.io

Verify that Docker is installed and running:

sudo systemctl status docker

You should see output indicating that the Docker service is active and running. If it is not active, you can start the Docker service with the following command:

sudo systemctl start docker

Now you have Docker installed on your Ubuntu 22.04 system. You can check the Docker version again using docker --version to verify the installation.

Please let me know if you need any clarification or if you run into anything else. Sincerely, Eric Jovenitti

[0123615177]

Hi

Thank you for looking into this. I have:

(gapseq-dev) margot@margot-B365M-DS3H:~/PGAP$ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 22.04.2 LTS Release: 22.04 Codename: jammy

(gapseq-dev) margot@margot-B365M-DS3H:~/PGAP$ uname -r 5.19.0-35-generic

(gapseq-dev) margot@margot-B365M-DS3H:~/PGAP$ docker --version Docker version 23.0.1, build a5ee5b1

My docker version and kernel version seems to be the same as yours

[0123615177]

Hi

I will send more info tomorrow. Thanks again for the help.

[0123615177]

Hi

So I have the two input files, as well as the genome.fna file. Please see these below. We minimized the info in the .yaml meta file, because there were a lot of errors with.

This is the directory that I am working from /home/margot/PGAP

This is the content of my directory:

argot@margot-B365M-DS3H:~/PGAP$ ls control.tar.xz M_results M_results.2 pgap-2022-12-13.build6494 pgap_input_l9axbp6c.yaml pgap-master pgap.py.1 Thermobifida_alba.fna Thermobifida_alba.yaml mg37_results M_results.1 mytmp pgap-2022-12-13.build6494.tar.gz pgap_input.yaml pgap.py pgap.py.2 Thermobifida_alba_meta.yaml margot@margot-B365M-DS3H:~/PGAP$

I run the following command: mkdir -p mytmp export TMPDIR=$(readlink -f mytmp)

./pgap.py -o Results Thermobifida_alba.yaml

Then i get: PGAP version 2022-12-13.build6494 is up to date. Output will be placed in: /home/margot/PGAP/Results WARNING: memory (GiB) is less than the recommended value of 8 WARNING: memory per CPU core (GiB) is less than the recommended value of 2 PGAP failed, docker exited with rc = 1 Unable to find error in log file. /home/margot/PGAP/Results/cwltool.log

Is there anything you could suggest? i think docker is the issue... I have to mention to you, that in order to activate docker, I click on the docker app in my desktop and then it boots up. Then i run the commands as specified above.

Any help appreciated Thanks

[0123615177]

Sorry, here is the error report:

Original command: ./pgap.py -o Results Thermobifida_alba.yaml

Docker command: /usr/local/bin/docker run -i --rm --user 1000:1000 --volume /home/margot/.pgap/input-2022-12-13.build6494:/pgap/input:ro,z --volume /home/margot/PGAP:/pgap/user_input:z --volume /home/margot/PGAP/pgap_input_11apbnx3.yaml:/pgap/user_input/pgap_input.yaml:ro,z --volume /home/margot/PGAP/mytmp:/tmp:rw,z --volume /home/margot/PGAP/Results:/pgap/output:rw,z ncbi/pgap:2022-12-13.build6494 cwltool --timestamps --debug --disable-color --preserve-entire-environment --outdir /pgap/output pgap/pgap.cwl /pgap/user_input/pgap_input.yaml

--- Start YAML Input --- fasta: class: File location: Thermobifida_alba.fna submol: class: File location: pgap_submol__7wvf9or.yaml supplemental_data: { class: Directory, location: /pgap/input } --- End YAML Input ---

--- Start Runtime Report --- { "CPU cores": 4, "Docker image": "ncbi/pgap:2022-12-13.build6494", "cpu flags": "fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon rep_good nopl xtopology cpuid tsc_known_freq pni pclmulqdq vmx ssse3 fma cx16 pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch cpuid_fault invpcid_single ssbd ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid mpx rdseed adx smap clflushopt xsaveopt xsavec xgetbv1 xsaves arat umip md_clear arch_capabilities", "cpu model": "Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz", "max user processes": "unlimited", "memory (GiB)": 7.6, "memory per CPU core (GiB)": 1.9, "open files": 1048576, "tmp disk space (GiB)": 41.6, "virtual memory": "unlimited", "work disk space (GiB)": 1620.0 } --- End Runtime Report ---

[2023-03-31 08:02:19] INFO /root/venv/bin/cwltool 3.1.20221201130942 [2023-03-31 08:02:19] INFO Resolved 'pgap/pgap.cwl' to 'file:///pgap/pgap/pgap.cwl' pgap/pgap.cwl:22:7: Warning: Field location contains undefined reference to file:///pgap/pgap/input [2023-03-31 08:02:30] ERROR Workflow error: Invalid job input record: pgap/pgap.cwl:29:3: Missing required input parameter 'report_usage' Traceback (most recent call last): File "/root/venv/lib/python3.9/site-packages/cwltool/process.py", line 436, in fill_in_defaults raise WorkflowException( cwltool.errors.WorkflowException: Missing required input parameter 'report_usage'

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/root/venv/lib/python3.9/site-packages/cwltool/process.py", line 774, in _init_job fill_in_defaults(self.tool["inputs"], job, fs_access) File "/root/venv/lib/python3.9/site-packages/cwltool/process.py", line 436, in fill_in_defaults raise WorkflowException( File "/root/venv/lib/python3.9/site-packages/schema_salad/sourceline.py", line 255, in exit raise self.makeError(str(exc_value)) from exc_value cwltool.errors.WorkflowException: pgap/pgap.cwl:29:3: Missing required input parameter 'report_usage'

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/root/venv/lib/python3.9/site-packages/cwltool/main.py", line 1361, in main (out, status) = real_executor( File "/root/venv/lib/python3.9/site-packages/cwltool/executors.py", line 60, in call return self.execute(process, job_order_object, runtime_context, logger) File "/root/venv/lib/python3.9/site-packages/cwltool/executors.py", line 143, in execute self.run_jobs(process, job_order_object, logger, runtime_context) File "/root/venv/lib/python3.9/site-packages/cwltool/executors.py", line 228, in run_jobs for job in jobiter: File "/root/venv/lib/python3.9/site-packages/cwltool/workflow.py", line 164, in job builder = self._init_job(job_order, runtimeContext) File "/root/venv/lib/python3.9/site-packages/cwltool/process.py", line 833, in _init_job raise WorkflowException("Invalid job input record:\n" + str(err)) from err cwltool.errors.WorkflowException: Invalid job input record: pgap/pgap.cwl:29:3: Missing required input parameter 'report_usage'

[azat-badretdin]

Thank you for your report!

Original command: ./pgap.py -o Results Thermobifida_alba.yaml

Missing required input parameter 'report_usage'

Please add pgap.py -r or pgap.py -n parameter to your command line.

[0123615177]

(base) margot@margot-B365M-DS3H:~/PGAP$ ./pgap.py -r -o Results Thermobifida_alba.yaml PGAP version 2022-12-13.build6494 is up to date. Output will be placed in: /home/margot/PGAP/Results.1 WARNING: memory (GiB) is less than the recommended value of 8 WARNING: memory per CPU core (GiB) is less than the recommended value of 2 PGAP failed, docker exited with rc = 1 Unable to find error in log file.

It failed again, but here is the error file:

[0123615177]

It ran for quite a while, but the error file is too big to upload. (27MB)

[0123615177]

Here is the first bit:

Original command: ./pgap.py -r -o Results Thermobifida_alba.yaml

Docker command: /usr/local/bin/docker run -i --rm --user 1000:1000 --volume /home/margot/.pgap/input-2022-12-13.build6494:/pgap/input:ro,z --volume /home/margot/PGAP:/pgap/user_input:z --volume /home/margot/PGAP/pgap_input_fzqp2yri.yaml:/pgap/user_input/pgap_input.yaml:ro,z --volume /home/margot/PGAP/mytmp:/tmp:rw,z --volume /home/margot/PGAP/Results.1:/pgap/output:rw,z ncbi/pgap:2022-12-13.build6494 cwltool --timestamps --debug --disable-color --preserve-entire-environment --outdir /pgap/output pgap/pgap.cwl /pgap/user_input/pgap_input.yaml

--- Start YAML Input --- fasta: class: File location: Thermobifida_alba.fna submol: class: File location: pgap_submol_supj4gx6.yaml supplemental_data: { class: Directory, location: /pgap/input } report_usage: true --- End YAML Input ---

--- Start Runtime Report --- { "CPU cores": 4, "Docker image": "ncbi/pgap:2022-12-13.build6494", "cpu flags": "fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon rep_good nopl xtopology cpuid tsc_known_freq pni pclmulqdq vmx ssse3 fma cx16 pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch cpuid_fault invpcid_single ssbd ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid mpx rdseed adx smap clflushopt xsaveopt xsavec xgetbv1 xsaves arat umip md_clear arch_capabilities", "cpu model": "Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz", "max user processes": "unlimited", "memory (GiB)": 7.6, "memory per CPU core (GiB)": 1.9, "open files": 1048576, "tmp disk space (GiB)": 38.8, "virtual memory": "unlimited", "work disk space (GiB)": 1617.4 } --- End Runtime Report ---

[2023-03-31 09:01:01] INFO /root/venv/bin/cwltool 3.1.20221201130942 [2023-03-31 09:01:01] INFO Resolved 'pgap/pgap.cwl' to 'file:///pgap/pgap/pgap.cwl' pgap/pgap.cwl:22:7: Warning: Field location contains undefined reference to file:///pgap/pgap/input [2023-03-31 09:01:12] DEBUG [workflow ] initialized from file:///pgap/pgap/pgap.cwl [2023-03-31 09:01:12] INFO [workflow ] start [2023-03-31 09:01:12] DEBUG [workflow ] inputs { "fasta": { "class": "File", "location": "file:///pgap/user_input/Thermobifida_alba.fna", "size": 4973382, "basename": "Thermobifida_alba.fna", "nameroot": "Thermobifida_alba", "nameext": ".fna"

[azat-badretdin]

Thank you.

Could you please upload `cwltool.permanentFail.10000.txt produced by

grep -B10000 permanentFail cwltool.log | head -10000 > cwltool.permanentFail.10000.txt

?

Thanks!

[0123615177]

Hi

i navigated to the directory where he cwltool.log file is located and executed above commands... But is is taking forever to run...can i reduce the head to 5000?

grep -B5000 permanentFail cwltool.log | head -5000 > cwltool.permanentFail.10000.txt?

Thanks

[azat-badretdin]

That won't reduce the time

Could you please let it run? How long did it run when you decided to interrupt?

[0123615177]

Hi It was about 10min. will run it again. Will send when done. Thanks

[azat-badretdin]

Also:

memory per CPU core (GiB)": 1.9,

is not enough. See https://github.com/ncbi/pgap/wiki/Quick-Start /Requirements:

2GB-4GB of memory available per CPU

[azat-badretdin]

It was about 10min

I am not sure why your machine is so slow. The processor is relatively new (2019), must be really tiny memory. Modern Desktops tend to have at least 32Gb.

[0123615177]

Hi

I got caught up in other matters and analyses, but am running late. I will be away until April 12 2023, and can then continue with this matter.

By the way, I have managed to install and use other software (eg. CRISPRdisco) using docker... Just for interest sake.

Thanks

[azat-badretdin]

I will be away until April 12 2023

Thank you for providing the date, we will keep it open.

I have managed to install and use other software (eg. CRISPRdisco) using docker

CRISPRdisco - 1, PGAP - 0 :-(

[0123615177]

Good day, I am back but have no time, will continue tomorrow. Thank you!

Margot

[0123615177]

Good day

I tried the analyses again and it seems to be running fine. Will let you know if success.

Thanks

[0123615177]

Hi

The run was interrupted. Am running it again. Apologies. Will post the outcome.

[0123615177]

Hi

After executing for almost two hours, the run failed. The cwltool.txt file was too big to upload, so I ran your command from last time: grep -B10000 permanentFail cwltool.log | head -10000 > cwltool.permanentFail.10000.txt

This immediately generated a cwltool.permanentFail.10000.txt file which is empty unforunately...

[azat-badretdin]

Thanks. Could you please post the head of it with the system information and docker calls and the tail of it (1000 lines)?

[0123615177]

Hi

Here is the head:

Original command: ./pgap.py -r -o Results Thermobifida_alba.yaml

Docker command: /usr/local/bin/docker run -i --rm --user 1000:1000 --volume /home/margot/.pgap/input-2022-12-13.build6494:/pgap/input:ro,z --volume /home/margot/PGAP:/pgap/user_input:z --volume /home/margot/PGAP/pgap_input_4ileqlbv.yaml:/pgap/user_input/pgap_input.yaml:ro,z --volume /home/margot/PGAP/mytmp:/tmp:rw,z --volume /home/margot/PGAP/Results.1:/pgap/output:rw,z ncbi/pgap:2022-12-13.build6494 cwltool --timestamps --debug --disable-color --preserve-entire-environment --outdir /pgap/output pgap/pgap.cwl /pgap/user_input/pgap_input.yaml

--- Start YAML Input --- fasta: class: File location: Thermobifida_alba.fna submol: class: File location: pgap_submol_xh9w1vsz.yaml supplemental_data: { class: Directory, location: /pgap/input } report_usage: true --- End YAML Input ---

--- Start Runtime Report --- { "CPU cores": 4, "Docker image": "ncbi/pgap:2022-12-13.build6494", "cpu flags": "fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon rep_good nopl xtopology cpuid tsc_known_freq pni pclmulqdq vmx ssse3 fma cx16 pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch cpuid_fault invpcid_single ssbd ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid mpx rdseed adx smap clflushopt xsaveopt xsavec xgetbv1 xsaves arat umip md_clear arch_capabilities", "cpu model": "Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz", "max user processes": "unlimited", "memory (GiB)": 7.6, "memory per CPU core (GiB)": 1.9, "open files": 1048576, "tmp disk space (GiB)": 38.8, "virtual memory": "unlimited", "work disk space (GiB)": 1610.4 } --- End Runtime Report ---

[2023-04-17 06:46:23] INFO /root/venv/bin/cwltool 3.1.20221201130942 [2023-04-17 06:46:23] INFO Resolved 'pgap/pgap.cwl' to 'file:///pgap/pgap/pgap.cwl' pgap/pgap.cwl:22:7: Warning: Field location contains undefined reference to file:///pgap/pgap/input [2023-04-17 06:46:34] DEBUG [workflow ] initialized from file:///pgap/pgap/pgap.cwl [2023-04-17 06:46:34] INFO [workflow ] start [2023-04-17 06:46:34] DEBUG [workflow ] inputs { "fasta": { "class": "File", "location": "file:///pgap/user_input/Thermobifida_alba.fna", "size": 4973382, "basename": "Thermobifida_alba.fna", "nameroot": "Thermobifida_alba", "nameext": ".fna"

LAST lines:-it is very hard to get the end because the screen turns black when I get there, but this is what I managed to get:

[2023-04-17 08:24:07] DEBUG [job Validate_Annotation_collect_annot_stats] Removing input staging directory /var/tmp/xfrj9agc [2023-04-17 08:24:07] DEBUG [job Validate_Annotation_collect_annot_stats] Removing temporary directory /var/tmp/3x7fwrar [2023-04-17 08:24:07] DEBUG Moving /var/tmp/ripic4o2/calls.tab to /pgap/output/calls.tab [2023-04-17 08:24:08] ERROR Unhandled error: [Errno 13] Permission denied: '/pgap/output/calls.tab' Traceback (most recent call last): File "/opt/python-3.9/lib/python3.9/shutil.py", line 825, in move os.rename(src, real_dst) OSError: [Errno 18] Invalid cross-device link: '/var/tmp/ripic4o2/calls.tab' -> '/pgap/output/calls.tab'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/root/venv/lib/python3.9/site-packages/cwltool/main.py", line 1361, in main (out, status) = real_executor( File "/root/venv/lib/python3.9/site-packages/cwltool/executors.py", line 60, in call return self.execute(process, job_order_object, runtime_context, logger) File "/root/venv/lib/python3.9/site-packages/cwltool/executors.py", line 150, in execute self.final_output[0] = relocateOutputs( File "/root/venv/lib/python3.9/site-packages/cwltool/process.py", line 384, in relocateOutputs stage_files(pm, stage_func=_relocate, symlink=False, fix_conflicts=True) File "/root/venv/lib/python3.9/site-packages/cwltool/process.py", line 280, in stage_files stage_func(entry.resolved, entry.target) File "/root/venv/lib/python3.9/site-packages/cwltool/process.py", line 357, in _relocate shutil.move(src, dst) File "/opt/python-3.9/lib/python3.9/shutil.py", line 845, in move copy_function(src, real_dst) File "/opt/python-3.9/lib/python3.9/shutil.py", line 444, in copy2 copyfile(src, dst, follow_symlinks=follow_symlinks) File "/opt/python-3.9/lib/python3.9/shutil.py", line 266, in copyfile with open(dst, 'wb') as fdst: PermissionError: [Errno 13] Permission denied: '/pgap/output/calls.tab'

[azat-badretdin]

Key error as you posted before:

Permission denied: '/pgap/output/calls.tab'

It maps to directory /home/margot/PGAP/Results.1

I believe that there is some local idiosyncratic way docker operates on your system that disallows mapping.

Is there anything in that directory?

[0123615177]

hi

In my PGAP folder, from where I run the analyses there is no 'output' directory:

[azat-badretdin]

I meant here: /home/margot/PGAP/Results.1