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

[azat-badretdin]

Thank you for your report!

In the *_meta.yaml file, please try indenting line 16 ("-authors:") and replace it with "-author:". Please have a look at https://github.com/ncbi/pgap/wiki/Input-Files, Section Metadata YAML file (submol), Example.

[0123615177]

Hi

I really appreciate your quick response. I changed the *_meta.yaml file to:

Then I ran: /pgap.py -r -o Results Thermobifida_alba.yaml

But I still get the error:

Output will be placed in: /home/margot/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 = 125 Unable to find error in log file.

I am not sure what to do next? i would really appreciate help as I am completely stuck. Thanks Margot

[0123615177]

Apologies, I see the indent is not correct, I will try again

[0123615177]

Hi

I tried again updating the *_meta.yaml file, this time using the https://github.com/ncbi/pgap/wiki/Input-Files as template.

I once again ran /pgap.py -r -o Results Thermobifida_alba.yaml

But unfortunately it generated the same issue:

margot@margot-B365M-DS3H:~$ ./pgap.py -o Results Thermobifida_alba.yaml PGAP version 2022-12-13.build6494 is up to date. Output will be placed in: /home/margot/Results.4 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.

I am not sure what to do next? i would really appreciate help as I am completely stuck. Thanks Margot

[azat-badretdin]

Thank you, Margot! Could you please post cwltool.log file?

[0123615177]

Hi, sure, here it is: (But just to mention, the docker 'file sharing' is set to /home/margot)

Here is the wltool.log file:

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/user_input:z --volume /home/margot/pgap_input_r7q756yy.yaml:/pgap/user_input/pgap_input.yaml:ro,z --volume /tmp:/tmp:rw,z --volume /home/margot/Results.4:/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_duv_169s.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)": 44.0, "virtual memory": "unlimited", "work disk space (GiB)": 1633.6 } --- End Runtime Report ---

docker: Error response from daemon: Mounts denied: The path /tmp is not shared from the host and is not known to Docker. You can configure shared paths from Docker -> Preferences... -> Resources -> File Sharing. See https://docs.docker.com/ for more info. time="2023-03-08T11:10:47+01:00" level=error msg="error waiting for container: "

[0123615177]

Hi

Just with reference to previous mail:

In addition, I have checked that my wd from where I submit the analysis is /home/margot (with pwd): margot@margot-B365M-DS3H:~$ pwd /home/margot

[azat-badretdin]

Thanks, Margot!

Looking into this:

The path /tmp is not shared from the host and is not known to Docker

please try

mkdir -p mytmp
export TMPDIR=$(readlink -f mytmp)

before executing your pgap.py command line.

[azat-badretdin]

Another concern but for now: not for this problem, for the future:

It seems like you are using Kubernetes and I found on the Internet that K8s removed support for Docker.

It seems that you are running docker just find for now, but if this ever becomes a problem in the future you can try to run your command line with --docker singularity option.

[0123615177]

Hi

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

-Then: ./pgap.py -o Results Thermobifida_alba.yaml

-And then I got the error message:

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/user_input:z --volume /home/margot/pgap_input_6mrl5m0w.yaml:/pgap/user_input/pgap_input.yaml:ro,z --volume /home/margot/mytmp:/tmp:rw,z --volume /home/margot/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_8imhjwgv.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)": 44.0, "virtual memory": "unlimited", "work disk space (GiB)": 1633.6 } --- End Runtime Report ---

[2023-03-08 14:03:16] INFO /root/venv/bin/cwltool 3.1.20221201130942 [2023-03-08 14:03:16] INFO Resolved 'pgap/pgap.cwl' to 'file:///pgap/pgap/pgap.cwl' [2023-03-08 14:03:16] ERROR Tool definition failed validation: while scanning for the next token user_input/pgap_input.yaml:2:1: found character '\t' that cannot start any token Traceback (most recent call last): File "/root/venv/lib/python3.9/site-packages/schema_salad/ref_resolver.py", line 1004, in fetch result = cast(Union[CommentedSeq, CommentedMap], next(attachments)) File "/root/venv/lib/python3.9/site-packages/ruamel/yaml/main.py", line 461, in load_all yield constructor.get_data() File "/root/venv/lib/python3.9/site-packages/ruamel/yaml/constructor.py", line 114, in get_data return self.construct_document(self.composer.get_node()) File "/root/venv/lib/python3.9/site-packages/ruamel/yaml/composer.py", line 66, in get_node return self.compose_document() File "/root/venv/lib/python3.9/site-packages/ruamel/yaml/composer.py", line 99, in compose_document node = self.compose_node(None, None) File "/root/venv/lib/python3.9/site-packages/ruamel/yaml/composer.py", line 143, in compose_node node = self.compose_mapping_node(anchor) File "/root/venv/lib/python3.9/site-packages/ruamel/yaml/composer.py", line 223, in compose_mapping_node item_value = self.compose_node(node, item_key) File "/root/venv/lib/python3.9/site-packages/ruamel/yaml/composer.py", line 113, in compose_node if self.parser.check_event(AliasEvent): File "/root/venv/lib/python3.9/site-packages/ruamel/yaml/parser.py", line 146, in check_event self.current_event = self.state() File "/root/venv/lib/python3.9/site-packages/ruamel/yaml/parser.py", line 627, in parse_block_mapping_value if self.scanner.check_token(ValueToken): File "/root/venv/lib/python3.9/site-packages/ruamel/yaml/scanner.py", line 1796, in check_token self._gather_comments() File "/root/venv/lib/python3.9/site-packages/ruamel/yaml/scanner.py", line 1838, in _gather_comments self.fetch_more_tokens() File "/root/venv/lib/python3.9/site-packages/ruamel/yaml/scanner.py", line 323, in fetch_more_tokens raise ScannerError( ruamel.yaml.scanner.ScannerError: while scanning for the next token found character '\t' that cannot start any token in "file:///pgap/user_input/pgap_input.yaml", line 2, column 1

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 1108, in main job_order_object, input_basedir, jobloader = load_job_order( File "/root/venv/lib/python3.9/site-packages/cwltool/main.py", line 379, in load_job_order job_orderobject, = loader.resolve_ref( File "/root/venv/lib/python3.9/site-packages/schema_salad/ref_resolver.py", line 518, in resolve_ref doc = self.fetch( File "/root/venv/lib/python3.9/site-packages/schema_salad/ref_resolver.py", line 1013, in fetch raise to_validation_exception(e) from e schema_salad.exceptions.ValidationException: while scanning for the next token user_input/pgap_input.yaml:2:1: found character '\t' that cannot start any token

[0123615177]

Thanks for the info on the Kubernetes. In my docker settings it does not seem that they are active:

But I will give the --docker singularity a shot

[0123615177]

I also tried using the --docker singularity approach, but this also did not work: (Maybe I am doing something completely wrong?) Where in the command, should this be used? Or before the command?

margot@margot-B365M-DS3H:~$ ./pgap.py -o Results Thermobifida_alba.yaml --docker singularity PGAP version 2022-12-13.build6494 is up to date. Docker not found.

[azat-badretdin]

Thanks, Margot!

This

found character '\t' that cannot start any token

Quoting from Internet:

A YAML file use spaces as indentation, you can use 2 or 4 spaces for indentation, but no tab. In other words, tab indentation is forbidden: Why does YAML forbid tabs? Tabs have been outlawed since they are treated differently by different editors and tools.

Could you please convert tabs in your YAML files to spaces and run pgap.py again?

Thanks!

[0123615177]

Hi

I changed my yaml files so that they have spaces:

This is my working directory: /home/margot margot@margot-B365M-DS3H:~$ ls

Then I run the command: ./pagp.py -r -o Results Thermobifida_alba.yaml from my wd:

And I get the following error:

But the Thermobifida_alba_meta.yaml file is in the wd directory so can not understand why it is unable to locate the file?

Thanks for the help

[0123615177]

I see that the metafile still has issues with spaces, will fix it! Sorry only seeing it now...and try again

[0123615177]

Hi Here are my .yaml files now. Are they correctly formatted? I can not find any mistake

When I run the command (./pgap.py -r -o Results Thermobifida_alba.yaml from my wd (see below)

I get the following error:

PGAP version 2022-12-13.build6494 is up to date. Output will be placed in: /home/margot/Results.7 Traceback (most recent call last): File "/home/margot/./pgap.py", line 964, in main p = Pipeline(params, args.input, "pgap") File "/home/margot/./pgap.py", line 173, in init self.submol = self.create_submolfile(submol, params.ani_output, params.ani_hr_output, params.args.auto_correct_tax) File "/home/margot/./pgap.py", line 308, in create_submolfile has_authors = self.regexp_file(local_submol, '^authors:') File "/home/margot/./pgap.py", line 291, in regexp_file with open(filename, 'r') as fIn: FileNotFoundError: [Errno 2] No such file or directory: '....Thermobifida_alba_meta.yaml'

I do not understand this because the Thermobifida_alba_meta.yaml file is in the wd? Thanks again Margot

[azat-badretdin]

I do not understand this because the Thermobifida_alba_meta.yaml file is in the wd?

It seems to be the case, Margot.

I am a bit concerned about multiple dots in the standard Python error message here:

FileNotFoundError: [Errno 2] No such file or directory: '....Thermobifida_alba_meta.yaml'

I presume that the dots in the beginnings of YAML lines in the screenshots of the YAML files are visualization of spaces.

is the line

FileNotFoundError: [Errno 2] No such file or directory: '....Thermobifida_alba_meta.yaml'

copied verbatim from the output or you modified it for privacy reasons?

[0123615177]

Hi

It seems as though the yaml files are my issue, especially the meta file. So I went to the https://github.com/ncbi/pgap/wiki/Input-Files website

I copied the meta example, and pasted it into notepad ++. Here I changed the format from Windows to Uniux, and edited my details (not all true, for privacy reasons) Then I pasted the content of the notepad into an online yaml formatter just to make sure. The end result looks like this (which I exported online as a .yaml file) So this is the Thermobifida_alba_meta.yaml file:

Just for interest sake here is also the Thermobifida_alba.yaml file in the wd:

So also here the wd:

Next, from the wd I used the following command: mkdir -p mytmp export TMPDIR=$(readlink -f mytmp) Followed by: ./pgap.py -o Results Thermobifida_alba.yaml This gave me the following error message:

And the error report looks as follows:

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/user_input:z --volume /home/margot/pgap_input_l9axbp6c.yaml:/pgap/user_input/pgap_input.yaml:ro,z --volume /home/margot/mytmp:/tmp:rw,z --volume /home/margot/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_34ipnk74.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)": 44.0, "virtual memory": "unlimited", "work disk space (GiB)": 1632.3 } --- End Runtime Report ---

[2023-03-09 06:48:04] INFO /root/venv/bin/cwltool 3.1.20221201130942 [2023-03-09 06:48:04] 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 [2023-03-09 06:48:16] 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'

any advice would be greatly appreciated Thanks

[0123615177]

Hi From a previous report, I added -n to the execution command:

./pgap.py -o Results Thermobifida_alba.yaml -n It seemed to work when I included the additional parameter '-n' to set report_usage to "False"

it ran for a while and after gave me an error message: PermissionError: [Errno 13] Permission denied: '/pgap/output/Thermobifida_alba.fna'

So is something maybe wrong with the fasta file?

Thanks again

[0123615177]

PS. This is what the .fna file looks like:

[azat-badretdin]

PermissionError: [Errno 13] Permission denied: '/pgap/output/Thermobifida_alba.fna'

Could you please post the output of command ls -latrR

[0123615177]

it is extremely long

[0123615177]

Sorry, the output is too long to paste here

[azat-badretdin]

How about ls -latrR output?

[azat-badretdin]

Command:

ls -latrR output

[0123615177]

Hi

it gives the following

margot@margot-B365M-DS3H:~$ ls -latrR output ls: cannot access 'output': No such file or directory

Do you know what we can try next? Thanks

[azat-badretdin]

I presumed that you are still in your home directory, correct?

Could you please post output of

pwd
ls -altrd . ..

[0123615177]

margot@margot-B365M-DS3H:~$ pwd /home/margot margot@margot-B365M-DS3H:~$ ls -altrd . .. drwxr-xr-x 3 root root 4096 dec 1 12:56 .. drwxrwxrwx 28 margot sudo 4096 márc 9 13:19 .

[azat-badretdin]

OK. Thanks. I presume the command line is the same, correct?

In this case please post the output of ls -latrR Results*

Also:

Could you please post again the output of cwltool.log?

Thanks!

[azat-badretdin]

Since in our call to docker we map independently different parts of the same directory tree, I wonder if this could have had an effect in your particular case because of some unusual Docker setup.

let's do also this 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/user_input:z \
--volume /home/margot/pgap_input_l9axbp6c.yaml:/pgap/user_input/pgap_input.yaml:ro,z \
--volume /home/margot/mytmp:/tmp:rw,z \
--volume /home/margot/Results:/pgap/output:rw,z \
ncbi/pgap:2022-12-13.build6494 \
ls -ld /pgap/input /pgap/user_input /pgap/output

Thanks!

[0123615177]

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/pgap_input_l9axbp6c.yaml:/pgap/user_input/pgap_input.yaml:ro,z \ --volume /home/margot/mytmp:/tmp:rw,z \ --volume /home/margot/Results:/pgap/output:rw,z \ ncbi/pgap:2022-12-13.build6494 \ ls -ld /pgap/input /pgap/user_input /pgap/output docker: Error response from daemon: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: error during container init: error mounting "/host_mnt/home/margot/pgap_input_l9axbp6c.yaml" to rootfs at "/pgap/user_input/pgap_input.yaml": mount /host_mnt/home/margot/pgap_input_l9axbp6c.yaml:/pgap/user_input/pgap_input.yaml (via /proc/self/fd/14), flags: 0x5001: not a directory: unknown: Are you trying to mount a directory onto a file (or vice-versa)? Check if the specified host path exists and is the expected type.

[azat-badretdin]

OK. That is because I did not have access to the latest output. Could you please replace /home/margot/pgap_input_l9axbp6c.yaml in your command line with similarly looking file that does exist? Please pick any closest name, it does not matter here.

[0123615177]

margot@margot-B365M-DS3H:~$ /home/margot/Thermobifida_alba.yaml bash: /home/margot/Thermobifida_alba.yaml: Permission denied margot@margot-B365M-DS3H:~$ ls control.tar.xz docker-desktop-4.17.0-amd64 getting-started pgap-2022-12-13.build6494.tar.gz pgap.py Public SomeFile.txt Thermobifida_alba.yaml data.tar.xz docker-desktop-4.17.0-amd64.deb mg37_results pgap_input_l9axbp6c.yaml pgap.py.1 Remove test_genomes debian-binary Documents mytmp pgap_input.yaml pgap.py.2 Results Thermobifida_alba.fna Desktop Downloads pgap-2022-12-13.build6494 pgap-master Pictures snap Thermobifida_alba_meta.yaml

[0123615177]

Hope I understood you correctly

[azat-badretdin]

Thanks, that is actually better than what I asked. I see now that the file about which docker complains here:

error mounting "/host_mnt/home/margot/pgap_input_l9axbp6c.yaml" to rootfs at "/pgap/user_input/pgap_input.yaml": mount /host_mnt/home/margot/pgap_input_l9axbp6c.yaml:/pgap/user_input/pgap_input.yaml (via /proc/self/fd/14), flags: 0x5001: not a directory: unknown: Are you trying to mount a directory onto a file (or vice-versa)? Check if the specified host path exists and is the expected type.

actually exists. It's the docker setup on your computer that disallows mounting files. Let's put aside this new problem for now and focus on why you can't write to docker's output directory:

Could you please run this (I removed the line(s) with offending file mounts)?

/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:/pgap/output:rw,z \
ncbi/pgap:2022-12-13.build6494 \
ls -ld /pgap/input /pgap/user_input /pgap/output

Thanks!

[0123615177]

argot@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:/pgap/output:rw,z \ ncbi/pgap:2022-12-13.build6494 \ ls -ld /pgap/input /pgap/user_input /pgap/output drwxrwxr-x 11 root root 4096 Mar 8 08:17 /pgap/input drwxrwxr-x 2 root root 4096 Mar 9 12:16 /pgap/output drwxrwxrwx 29 root 65534 4096 Mar 9 13:37 /pgap/user_input

[0123615177]

Hi

I hope the above is fine?

Thanks

[azat-badretdin]

Yes, thanks! I am going to see if perms match to what I have on our test server.

[0123615177]

Thanks

[azat-badretdin]

But before doing that I still need the output from

ls -latrR Results*

[0123615177]

margot@margot-B365M-DS3H:~$ ls -latrR Results* Results: total 7264 drwxrwxr-x 2 margot margot 4096 márc 9 13:16 . -rw-rw-r-- 1 margot margot 7427096 márc 9 13:19 cwltool.log drwxrwxrwx 29 margot sudo 4096 márc 9 14:37 ..

Do you need anything else?

[azat-badretdin]

Thanks! Permissions seem fine.

Could you please post the output of

id -a

[0123615177]

margot@margot-B365M-DS3H:~$ id -a uid=1000(margot) gid=1000(margot) groups=1000(margot),4(adm),24(cdrom),27(sudo),30(dip),46(plugdev),122(lpadmin),134(lxd),135(sambashare)

[azat-badretdin]

That's enigmatic

I have the same perms and ownership on our local server as well, posting here for the record:

drwxrwxr-x  11 5371 562  4096 Jan 17 21:11 /pgap/input
drwxrwxr-x   2 5371 562  4096 Mar  9 14:15 /pgap/output
drwxr-xr-x 161 5371 536 94208 Mar  9 14:15 /pgap/user_input

Except in our case mapped directory user_input is even more restrictive than yours.

Hmmm...

You posted a small snippet from your last attempt to run pgap.py

PermissionError: [Errno 13] Permission denied: '/pgap/output/Thermobifida_alba.fna'

Could you please post more lines preceding that, including most importantly Python stack output?

Thanks!

[0123615177]

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 = 1 Printing log starting from failed job:

[2023-03-09 12:19:55] DEBUG [step Prepare_Unannotated_Sequences] job input { "file:///pgap/pgap/wf_common.cwl#Prepare_Unannotated_Sequences/asncache": { "location": "file:///var/tmp/m20ldqp/sequence_cache", "basename": "sequence_cache", "nameroot": "sequence_cache", "nameext": "", "class": "Directory" }, "file:///pgap/pgap/wf_common.cwl#Prepare_Unannotated_Sequences/gc_assembly": { "location": "file:///var/tmp/95cc89ve/gencoll.asn", "basename": "gencoll.asn", "nameroot": "gencoll", "nameext": ".asn", "class": "File", "checksum": "sha1$c27c977492e559e79f7301b8f1cbeff59f5ecafd", "size": 1096, "http://commonwl.org/cwltool#generation": 0 }, "file:///pgap/pgap/wf_common.cwl#Prepare_Unannotated_Sequences/ids": { "location": "file:///var/tmp/hvn_upg3/all.gi", "basename": "all.gi", "nameroot": "all", "nameext": ".gi", "class": "File", "checksum": "sha1$b0ce5ad49acec6f8b218c7acb7c91566a815c85f", "size": 31, "http://commonwl.org/cwltool#generation": 0 }, "file:///pgap/pgap/wf_common.cwl#Prepare_Unannotated_Sequences/no_internet": null, "file:///pgap/pgap/wf_common.cwl#Prepare_Unannotated_Sequences/submit_block": { "location": "file:///var/tmp/oj5ii22k/submit_block_template.asn", "basename": "submit_block_template.asn", "nameroot": "submit_block_template", "nameext": ".asn", "class": "File", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "size": 0, "http://commonwl.org/cwltool#generation": 0 }, "file:///pgap/pgap/wf_common.cwl#Prepare_Unannotated_Sequences/taxon_db": { "class": "File", "location": "file:///pgap/input/uniColl_path/taxonomy.sqlite3", "basename": "taxonomy.sqlite3", "size": 1083080704, "nameroot": "taxonomy", "nameext": ".sqlite3" } } [2023-03-09 12:19:55] DEBUG [step Prepare_Unannotated_Sequences] evaluated job input to { "file:///pgap/pgap/wf_common.cwl#Prepare_Unannotated_Sequences/asncache": { "location": "file:///var/tmp/m20ldqp/sequence_cache", "basename": "sequence_cache", "nameroot": "sequence_cache", "nameext": "", "class": "Directory" }, "file:///pgap/pgap/wf_common.cwl#Prepare_Unannotated_Sequences/gc_assembly": { "location": "file:///var/tmp/95cc89ve/gencoll.asn", "basename": "gencoll.asn", "nameroot": "gencoll", "nameext": ".asn", "class": "File", "checksum": "sha1$c27c977492e559e79f7301b8f1cbeff59f5ecafd", "size": 1096, "http://commonwl.org/cwltool#generation": 0 }, "file:///pgap/pgap/wf_common.cwl#Prepare_Unannotated_Sequences/ids": { "location": "file:///var/tmp/hvn_upg3/all.gi", "basename": "all.gi", "nameroot": "all", "nameext": ".gi", "class": "File", "checksum": "sha1$b0ce5ad49acec6f8b218c7acb7c91566a815c85f", "size": 31, "http://commonwl.org/cwltool#generation": 0 }, "file:///pgap/pgap/wf_common.cwl#Prepare_Unannotated_Sequences/no_internet": null, "file:///pgap/pgap/wf_common.cwl#Prepare_Unannotated_Sequences/submit_block": { "location": "file:///var/tmp/oj5ii22k/submit_block_template.asn", "basename": "submit_block_template.asn", "nameroot": "submit_block_template", "nameext": ".asn", "class": "File", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "size": 0, "http://commonwl.org/cwltool#generation": 0 }, "file:///pgap/pgap/wf_common.cwl#Prepare_Unannotated_Sequences/taxon_db": { "class": "File", "location": "file:///pgap/input/uniColl_path/taxonomy.sqlite3", "basename": "taxonomy.sqlite3", "size": 1083080704, "nameroot": "taxonomy", "nameext": ".sqlite3" } } [2023-03-09 12:19:55] INFO [step Prepare_Unannotated_Sequences] start [2023-03-09 12:19:55] DEBUG [job Prepare_Unannotated_Sequences] initializing from file:///pgap/pgap/bacterial_prepare_unannotated.cwl as part of step Prepare_Unannotated_Sequences [2023-03-09 12:19:55] DEBUG [job Prepare_Unannotated_Sequences] { "asncache": { "location": "file:///var/tmp/m20ldqp/sequence_cache", "basename": "sequence_cache", "nameroot": "sequencecache", "nameext": "", "class": "Directory", "listing": [ { "class": "File", "location": "file:///var/tmp/m20ldqp/sequence_cache/seq_id_cache.idx", "basename": "seq_idcache.idx", "size": 131072 }, { "class": "File", "location": "file:///var/tmp/m20ldqp/sequence_cache/seq_id_chunk", "basename": "seq_idchunk", "size": 22 }, { "class": "File", "location": "file:///var/tmp/m20ldqp/sequencecache/chunk.00001", "basename": "chunk.00001", "size": 1132421 }, { "class": "File", "location": "file:///var/tmp/m20ldqp/sequence_cache/asn_cache.idx", "basename": "asn_cache.idx", "size": 131072 } ] }, "gc_assembly": { "location": "file:///var/tmp/95cc89ve/gencoll.asn", "basename": "gencoll.asn", "nameroot": "gencoll", "nameext": ".asn", "class": "File", "checksum": "sha1$c27c977492e559e79f7301b8f1cbeff59f5ecafd", "size": 1096, "http://commonwl.org/cwltool#generation": 0 }, "ids": { "location": "file:///var/tmp/hvn_upg3/all.gi", "basename": "all.gi", "nameroot": "all", "nameext": ".gi", "class": "File", "checksum": "sha1$b0ce5ad49acec6f8b218c7acb7c91566a815c85f", "size": 31, "http://commonwl.org/cwltool#generation": 0 }, "no_internet": null, "submit_block": { "location": "file:///var/tmp/oj5ii22k/submit_block_template.asn", "basename": "submit_block_template.asn", "nameroot": "submit_block_template", "nameext": ".asn", "class": "File", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "size": 0, "http://commonwl.org/cwltool#generation": 0 }, "taxon_db": { "class": "File", "location": "file:///pgap/input/uniColl_path/taxonomy.sqlite3", "basename": "taxonomy.sqlite3", "size": 1083080704, "nameroot": "taxonomy", "nameext": ".sqlite3" }, "master_desc_name": "master-desc.asn", "plasmids_name": "plasmids.seqids", "sequences_name": "sequences.asn" } [2023-03-09 12:19:55] DEBUG [job Prepare_UnannotatedSequences] path mappings is { "file:///var/tmp/m20ldqp/sequencecache": [ "/var/tmp/m20ldqp/sequence_cache", "/var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db/sequencecache", "Directory", true ], "file:///var/tmp/m20ldqp/sequence_cache/seq_idcache.idx": [ "/var/tmp/m20ldqp/sequence_cache/seq_id_cache.idx", "/var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db/sequence_cache/seq_idcache.idx", "File", false ], "file:///var/tmp/m20ldqp/sequence_cache/seq_idchunk": [ "/var/tmp/m20ldqp/sequence_cache/seq_id_chunk", "/var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db/sequence_cache/seq_idchunk", "File", false ], "file:///var/tmp/m20ldqp/sequencecache/chunk.00001": [ "/var/tmp/m20ldqp/sequence_cache/chunk.00001", "/var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db/sequencecache/chunk.00001", "File", false ], "file:///var/tmp/m20ldqp/sequence_cache/asncache.idx": [ "/var/tmp/m20ldqp/sequence_cache/asn_cache.idx", "/var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db/sequence_cache/asn_cache.idx", "File", false ], "file:///var/tmp/95cc89ve/gencoll.asn": [ "/var/tmp/95cc89ve/gencoll.asn", "/var/tmp/4lieh6ld/stge7df6e39-3c5e-4c26-99a8-f034870a526c/gencoll.asn", "File", true ], "file:///var/tmp/hvn_upg3/all.gi": [ "/var/tmp/hvn_upg3/all.gi", "/var/tmp/4lieh6ld/stg256663c7-2304-498c-bba7-0ba3b3411923/all.gi", "File", true ], "file:///var/tmp/oj5ii22k/submit_block_template.asn": [ "/var/tmp/oj5ii22k/submit_block_template.asn", "/var/tmp/4lieh6ld/stg0e6bcb82-8138-4fad-82a5-3de6eef706a2/submit_block_template.asn", "File", true ], "file:///pgap/input/uniColl_path/taxonomy.sqlite3": [ "/pgap/input/uniColl_path/taxonomy.sqlite3", "/var/tmp/4lieh6ld/stg2b246d37-9849-4682-a0b9-a3801cb07174/taxonomy.sqlite3", "File", true ] } [2023-03-09 12:19:55] DEBUG [job Prepare_Unannotated_Sequences] command line bindings is [ { "position": [ -1000000, 0 ], "datum": "bacterial_prepare_unannotated" }, { "position": [ 0, 0 ], "datum": "-submission-mode-genbank" }, { "position": [ 0, 1 ], "datum": "-nogenbank" }, { "prefix": "-asn-cache", "position": [ 0, "asncache" ], "datum": { "location": "file:///var/tmp/m20ldqp/sequence_cache", "basename": "sequence_cache", "nameroot": "sequencecache", "nameext": "", "class": "Directory", "listing": [ { "class": "File", "location": "file:///var/tmp/m20ldqp/sequence_cache/seq_id_cache.idx", "basename": "seq_id_cache.idx", "size": 131072, "path": "/var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db/sequence_cache/seq_id_cache.idx", "dirname": "/var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db/sequence_cache", "nameroot": "seq_idcache", "nameext": ".idx" }, { "class": "File", "location": "file:///var/tmp/m20ldqp/sequence_cache/seq_id_chunk", "basename": "seq_id_chunk", "size": 22, "path": "/var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db/sequence_cache/seq_id_chunk", "dirname": "/var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db/sequence_cache", "nameroot": "seq_idchunk", "nameext": "" }, { "class": "File", "location": "file:///var/tmp/m20ldqp/sequence_cache/chunk.00001", "basename": "chunk.00001", "size": 1132421, "path": "/var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db/sequence_cache/chunk.00001", "dirname": "/var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db/sequencecache", "nameroot": "chunk", "nameext": ".00001" }, { "class": "File", "location": "file:///var/tmp/m20ldqp/sequence_cache/asn_cache.idx", "basename": "asn_cache.idx", "size": 131072, "path": "/var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db/sequence_cache/asn_cache.idx", "dirname": "/var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db/sequence_cache", "nameroot": "asn_cache", "nameext": ".idx" } ], "path": "/var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db/sequence_cache", "dirname": "/var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db" } }, { "prefix": "-gc-assembly", "position": [ 0, "gc_assembly" ], "datum": { "location": "file:///var/tmp/95cc89ve/gencoll.asn", "basename": "gencoll.asn", "nameroot": "gencoll", "nameext": ".asn", "class": "File", "checksum": "sha1$c27c977492e559e79f7301b8f1cbeff59f5ecafd", "size": 1096, "http://commonwl.org/cwltool#generation": 0, "path": "/var/tmp/4lieh6ld/stge7df6e39-3c5e-4c26-99a8-f034870a526c/gencoll.asn", "dirname": "/var/tmp/4lieh6ld/stge7df6e39-3c5e-4c26-99a8-f034870a526c" } }, { "prefix": "-ids", "position": [ 0, "ids" ], "datum": { "location": "file:///var/tmp/hvn_upg3/all.gi", "basename": "all.gi", "nameroot": "all", "nameext": ".gi", "class": "File", "checksum": "sha1$b0ce5ad49acec6f8b218c7acb7c91566a815c85f", "size": 31, "http://commonwl.org/cwltool#generation": 0, "path": "/var/tmp/4lieh6ld/stg256663c7-2304-498c-bba7-0ba3b3411923/all.gi", "dirname": "/var/tmp/4lieh6ld/stg256663c7-2304-498c-bba7-0ba3b3411923" } }, { "prefix": "-master-desc", "position": [ 0, "master_desc_name" ], "datum": "master-desc.asn" }, { "prefix": "-plasmids", "position": [ 0, "plasmids_name" ], "datum": "plasmids.seqids" }, { "prefix": "-o", "position": [ 0, "sequences_name" ], "datum": "sequences.asn" }, { "prefix": "-submit-block", "position": [ 0, "submit_block" ], "datum": { "location": "file:///var/tmp/oj5ii22k/submit_block_template.asn", "basename": "submit_block_template.asn", "nameroot": "submit_block_template", "nameext": ".asn", "class": "File", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "size": 0, "http://commonwl.org/cwltool#generation": 0, "path": "/var/tmp/4lieh6ld/stg0e6bcb82-8138-4fad-82a5-3de6eef706a2/submit_block_template.asn", "dirname": "/var/tmp/4lieh6ld/stg0e6bcb82-8138-4fad-82a5-3de6eef706a2" } }, { "prefix": "-taxon-db", "position": [ 0, "taxon_db" ], "datum": { "class": "File", "location": "file:///pgap/input/uniColl_path/taxonomy.sqlite3", "basename": "taxonomy.sqlite3", "size": 1083080704, "nameroot": "taxonomy", "nameext": ".sqlite3", "path": "/var/tmp/4lieh6ld/stg2b246d37-9849-4682-a0b9-a3801cb07174/taxonomy.sqlite3", "dirname": "/var/tmp/4lieh6ld/stg2b246d37-9849-4682-a0b9-a3801cb07174" } } ] [2023-03-09 12:19:55] DEBUG [job Prepare_Unannotated_Sequences] initial work dir {} [2023-03-09 12:19:55] INFO [job Prepare_Unannotated_Sequences] /var/tmp/cw7qngpm$ bacterial_prepare_unannotated \ -submission-mode-genbank \ -nogenbank \ -asn-cache \ /var/tmp/4lieh6ld/stg887901cc-2fe6-4df7-bf34-6a5fd2fbc2db/sequence_cache \ -gc-assembly \ /var/tmp/4lieh6ld/stge7df6e39-3c5e-4c26-99a8-f034870a526c/gencoll.asn \ -ids \ /var/tmp/4lieh6ld/stg256663c7-2304-498c-bba7-0ba3b3411923/all.gi \ -master-desc \ master-desc.asn \ -plasmids \ plasmids.seqids \ -o \ sequences.asn \ -submit-block \ /var/tmp/4lieh6ld/stg0e6bcb82-8138-4fad-82a5-3de6eef706a2/submit_block_template.asn \ -taxon-db \ /var/tmp/4lieh6ld/stg2b246d37-9849-4682-a0b9-a3801cb07174/taxonomy.sqlite3 Reading assembly found 1 ids Reading the submit block information Processing sequences... processing lcl|Thermobifida terminate called after throwing an instance of 'ncbi::CException' what(): NCBI C++ Exception: Error: ASN_PROC(CException::eUnknown) "/export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/asn_proc/markup_tool.cpp", line 193: ncbi::objects::CMarkupTool::x_FixDBLink() --- Invalid sample 'PRNA94' Stack trace: /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/lib/libbacterial_pipeline_proc.so /export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/asn_proc/markup_tool.cpp:193 ncbi::objects::CMarkupTool::x_FixDBLink(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator >&) offset=0x0 addr=0x7f2af564ceb1 /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/lib/libbacterial_pipeline_proc.so /export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/asn_proc/markup_tool.cpp:134 ncbi::objects::CMarkupTool::FixDBLink(ncbi::objects::CSeqdesc&) offset=0x0 addr=0x7f2af564d1c8 /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/bacterial_prepare_unannotated :0 offset=0x0 addr=0x418ff6 /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/bacterial_prepare_unannotated :0 offset=0x0 addr=0x41cc43 /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/bacterial_prepare_unannotated :0 offset=0x0 addr=0x41f75f /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/lib/libxncbi.so /export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/corelib/ncbiapp.cpp:702 ncbi::CNcbiApplicationAPI::x_TryMain(ncbi::EAppDiagStream, char const, int, bool) offset=0x0 addr=0x7f2ad960a472 /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/lib/libxncbi.so /export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/corelib/ncbiapp.cpp:1014 ncbi::CNcbiApplicationAPI::AppMain(int, char const const, char const const, ncbi::EAppDiagStream, char const, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) offset=0x0 addr=0x7f2ad960da3c /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/bacterial_prepare_unannotated :0 offset=0x0 addr=0x4121cc /usr/lib64/libc-2.17.so :0 offset=0x0 addr=0x7f2ad8036554 /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/bacterial_prepare_unannotated :0 offset=0x0 addr=0x412223 :0 offset=0x0 addr=0xffffffffffffffff

Stack trace (most recent call last):

16 Object "", at 0xffffffffffffffff, in

15 Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/bacterial_prepare_unannotated", at 0x412223, in _start

14 Object "/usr/lib64/libc-2.17.so", at 0x7f2ad8036554, in __libc_start_main

13 Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/bacterial_prepare_unannotated", at 0x4121cc, in main

12 Source "/export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/corelib/ncbiapp.cpp", line 1014, in AppMain [0x7f2ad960da3c]

11 Source "/export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/corelib/ncbiapp.cpp", line 702, in x_TryMain [0x7f2ad960a472]

10 Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/bacterial_prepare_unannotated", at 0x41f75f, in CBacterialPrepareUnannotatedApp::Run()

9 Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/bacterial_prepare_unannotated", at 0x41cc43, in CBacterialPrepareUnannotatedApp::ProcessSequences(std::map<ncbi::objects::CSeq_id_Handle, ncbi::objects::CSeq_entry_Handle, ncbi::objects::CSeq_id_Handle::PLessOrdered, std::allocator<std::pair<ncbi::objects::CSeq_id_Handle const, ncbi::objects::CSeq_entry_Handle> > > const&, std::cxx11::list<ncbi::CRef<ncbi::objects::CSeqdesc, ncbi::CObjectCounterLocker>, std::allocator<ncbi::CRef<ncbi::objects::CSeqdesc, ncbi::CObjectCounterLocker> > >&, std::cxx11::list<ncbi::CRef<ncbi::objects::CSeqdesc, ncbi::CObjectCounterLocker>, std::allocator<ncbi::CRef<ncbi::objects::CSeqdesc, ncbi::CObjectCounterLocker> > >&, std::set<ncbi::objects::CSeq_id_Handle, ncbi::objects::CSeq_id_Handle::PLessOrdered, std::allocator >&)

8 Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/bacterial_prepare_unannotated", at 0x418ff6, in

7 Source "/export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/asn_proc/markup_tool.cpp", line 134, in FixDBLink [0x7f2af564d1c8]

6 Source "/export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/asn_proc/markup_tool.cpp", line 193, in x_FixDBLink [0x7f2af564cf05]

5 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_throw.cc", line 93, in __cxa_throw [0x7f2ad8bb8222]

4 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_terminate.cc", line 57, in terminate [0x7f2ad8bb7fe0]

3 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_terminate.cc", line 47, in __cxa_begin_catch [0x7f2ad8bb7f95]

2 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/vterminate.cc", line 95, in __verbose_terminate_handler [0x7f2ad8bba1a4]

1 Object "/usr/lib64/libc-2.17.so", at 0x7f2ad804ba77, in abort

0 Object "/usr/lib64/libc-2.17.so", at 0x7f2ad804a387, in raise

Aborted (Signal sent by tkill() 262 1000) [2023-03-09 12:19:56] INFO [job Prepare_Unannotated_Sequences] Max memory used: 83MiB [2023-03-09 12:19:56] WARNING [job Prepare_Unannotated_Sequences] was terminated by signal: SIGABRT [2023-03-09 12:19:56] ERROR [job Prepare_Unannotated_Sequences] Job error: ("Error collecting output for parameter 'master_desc': pgap/bacterial_prepare_unannotated.cwl:53:7: Did not find output file with glob pattern: '['master-desc.asn']'.", {}) [2023-03-09 12:19:56] WARNING [job Prepare_Unannotated_Sequences] completed permanentFail [2023-03-09 12:19:56] DEBUG [job Prepare_Unannotated_Sequences] outputs {} [2023-03-09 12:19:56] ERROR [step Prepare_Unannotated_Sequences] Output is missing expected field file:///pgap/pgap/wf_common.cwl#Prepare_Unannotated_Sequences/master_desc [2023-03-09 12:19:56] ERROR [step Prepare_Unannotated_Sequences] Output is missing expected field file:///pgap/pgap/wf_common.cwl#Prepare_Unannotated_Sequences/sequences [2023-03-09 12:19:56] ERROR [step Prepare_Unannotated_Sequences] Output is missing expected field file:///pgap/pgap/wf_common.cwl#Prepare_Unannotated_Sequences/plasmids [2023-03-09 12:19:56] DEBUG [step Prepare_Unannotated_Sequences] produced output {} [2023-03-09 12:19:56] WARNING [step Prepare_Unannotated_Sequences] completed permanentFail [2023-03-09 12:19:56] DEBUG [job Prepare_Unannotated_Sequences] Removing input staging directory /var/tmp/4lieh6ld [2023-03-09 12:19:56] DEBUG [job Prepare_UnannotatedSequences] Removing temporary directory /var/tmp/sksw1ph [2023-03-09 12:19:56] INFO [workflow standard_pgap] completed permanentFail [2023-03-09 12:19:56] DEBUG [workflow standard_pgap] outputs { "cds_nucleotide_fasta": null, "cds_protein_fasta": null, "checkm_raw": null, "checkm_results": null, "final_asndisc_error_diag": null, "final_asnval_error_diag": null, "gbent": null, "gbk": null, "gff": null, "gff_enhanced": null, "initial_asndisc_error_diag": null, "initial_asnval_error_diag": null, "nucleotide_fasta": null, "proc_annot_stats": null, "protein_fasta": null, "sqn": null } [2023-03-09 12:19:56] DEBUG [step standard_pgap] produced output { "file:///pgap/pgap/pgap.cwl#standard_pgap/gbent": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/gbk": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/gff": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/gff_enhanced": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/nucleotide_fasta": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/protein_fasta": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/cds_nucleotide_fasta": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/cds_protein_fasta": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/sqn": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/initial_asndisc_error_diag": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/initial_asnval_error_diag": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/final_asndisc_error_diag": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/final_asnval_error_diag": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/checkm_raw": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/checkm_results": null } [2023-03-09 12:19:56] WARNING [step standard_pgap] completed permanentFail [2023-03-09 12:19:56] INFO [workflow ] completed permanentFail [2023-03-09 12:19:56] DEBUG [workflow ] outputs { "calls": { "location": "file:///var/tmp/l24ckttb/calls.tab", "basename": "calls.tab", "nameroot": "calls", "nameext": ".tab", "class": "File", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "size": 0, "http://commonwl.org/cwltool#generation": 0 }, "cds_nucleotide_fasta": null, "cds_protein_fasta": null, "checkm_raw": null, "final_asndisc_error_diag": null, "final_asnval_error_diag": null, "gbk": null, "gff": null, "gff_enhanced": null, "initial_asndisc_error_diag": null, "initial_asnval_error_diag": null, "input_fasta": { "class": "File", "location": "file:///pgap/user_input/Thermobifida_alba.fna", "size": 4973318, "basename": "Thermobifida_alba.fna", "nameroot": "Thermobifida_alba", "nameext": ".fna" }, "input_submol": { "class": "File", "location": "file:///pgap/user_input/pgap_submol_xpb21cs6.yaml", "size": 733, "basename": "pgap_submol_xpb21cs6.yaml", "nameroot": "pgap_submol_xpb21cs6", "nameext": ".yaml" }, "nucleotide_fasta": null, "protein_fasta": null, "sqn": null } [2023-03-09 12:19:56] DEBUG Moving /var/tmp/l24ckttb/calls.tab to /pgap/output/calls.tab [2023-03-09 12:19:56] 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/l24ckttb/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'

[0123615177]

Since the last failure of the run, I made a small edit to my .fna file but changed it back and everytime I run the analyses its now: PermissionError: [Errno 13] Permission denied: '/pgap/output/calls.tab'

So the 'call.tab' instead of the .fna name: Thermobifida_alba.yaml

[0123615177]

I mean Thermobifida_alba.fna...sorry!

[0123615177]

But from now on I will not try anything unless specified here

[azat-badretdin]

Thank you! This helps actually (in the future, it is probably better to supply large files as attachments to a ticket)

I see now that the first error is:

Error: ASN_PROC(CException::eUnknown) "/export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/asn_proc/markup_tool.cpp", line 193: ncbi::objects::CMarkupTool::x_FixDBLink() --- Invalid sample 'PRNA94'

That does not look like biosample. Please have in mind that this parameter is optional, see https://github.com/ncbi/pgap/wiki/Input-Files for reference.

I would suggest to remove the biosample line from your metadata YAML and run again.

[azat-badretdin]

General note: The most important part of cwltool.log is the first permanentFail message and the errors that precede that. So whenever your execution ends in some visible errors in the end of the output it is advisable to always find the first occurrence of permanentFail in cwltool.log and go from there....