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NCBI Prokaryotic Genome Annotation Pipeline
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PGAP failed, docker exited with rc = 1 #261

Closed mkapadiarch closed 1 year ago

mkapadiarch commented 1 year ago

Case Information: Case #: CAS-1125159-M5L1Y5 Customer Name: Minal Kapadia Customer Email: mkapadia@rchsolutions.com Case Created: 6/9/2023, 10:34:40 AM

Summary: pgap

Details: $ ./scripts/pgap.py -r -o mg37_results.6 -g ASM2732v1.annotation.nucleotide.1.fasta -s 'Mycoplasmoides genitalium' PGAP version 2023-05-17.build6771 is up to date. Output will be placed in: /tmp/tmp.4eVlLgMwWL/mg37_results.6.1 INFO: Using cached SIF image PGAP failed, docker exited with rc = 1 Unable to find error in log file.

azat-badretdin commented 1 year ago

Thank you for your report, user @mkapadiarch !

Could you please post cwltool.log?

mkapadiarch commented 1 year ago

@.***

Original command: ./pgap.py -o results input.yaml -D singularity

Docker command: /usr/bin/singularity exec --bind /hpc/mydata/upt/rb154511/software/pgap/input-2023-05-17.build6771:/pgap/input:ro --bind /hdd_scratch2/rb154511/pgap:/pgap/user_input - -bind /hdd_scratch2/rb154511/pgap/pgap_input_yrcnp8vo.yaml:/pgap/user_input/pgap_input.yaml:ro --bind /tmp:/tmp:rw --bind /hdd_scratch2/rb154511/pgap/results.2:/pgap/output:rw --pwd / pgap docker://ncbi/pgap:2023-05-17.build6771 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: ASM2732v1.annotation.nucleotide.1.fasta submol: class: File location: pgap_submol_vf2dljee.yaml supplemental_data: { class: Directory, location: /pgap/input } --- End YAML Input ---

--- Start Runtime Report --- { "CPU cores": 96, "Docker image": "ncbi/pgap:2023-05-17.build6771", "cpu flags": "fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc art re p_good nopl nonstop_tsc extd_apicid amd_dcm aperfmperf eagerfpu pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapi c cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_l2 cpb hw_pstate sme retpoline_amd ssbd ibpb vmmcall fsgsbase bmi1 a vx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausef ilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca", "cpu model": "AMD EPYC 7451 24-Core Processor", "max user processes": 16384, "memory (GiB)": 503.8, "memory per CPU core (GiB)": 5.2, "open files": 1048576, "tmp disk space (GiB)": 417.1, "virtual memory": "unlimited", "work disk space (GiB)": 1404.3 } --- End Runtime Report ---

INFO: Using cached SIF image [2023-06-13 12:36:51] INFO /root/venv/bin/cwltool 3.1.20230513155734 [2023-06-13 12:36:51] INFO Resolved 'pgap/pgap.cwl' to 'file:///pgap/pgap/pgap.cwl' pgap/pgap.cwl:24:7: Warning: Field 'location' contains undefined reference to 'file:///pgap/pgap/input' [2023-06-13 12:37:12] ERROR Workflow error: Invalid job input record: pgap/pgap.cwl:28:3: Missing required input parameter 'report_usage' Traceback (most recent call last): File "/root/venv/lib/python3.9/site-packages/cwltool/process.py", line 438, in fill_in_defaults raise WorkflowException( cwltool.errors.WorkflowException: Missing required input parameter 'report_usage'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/root/venv/lib/python3.9/site-packages/cwltool/process.py", line 761, in _init_job fill_in_defaults(self.tool["inputs"], job, fs_access) File "/root/venv/lib/python3.9/site-packages/cwltool/process.py", line 438, in fill_in_defaults raise WorkflowException( File "schema_salad/sourceline.py", line 250, in exit cwltool.errors.WorkflowException: pgap/pgap.cwl:28:3: 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 1295, in main (out, status) = real_executor( File "/root/venv/lib/python3.9/site-packages/cwltool/executors.py", line 61, in call return self.execute(process, job_order_object, runtime_context, logger) File "/root/venv/lib/python3.9/site-packages/cwltool/executors.py", line 144, in execute self.run_jobs(process, job_order_object, logger, runtime_context) File "/root/venv/lib/python3.9/site-packages/cwltool/executors.py", line 217, in run_jobs for job in jobiter: File "/root/venv/lib/python3.9/site-packages/cwltool/workflow.py", line 160, in job builder = self._init_job(job_order, runtimeContext) File "/root/venv/lib/python3.9/site-packages/cwltool/process.py", line 822, in _init_job raise WorkflowException("Invalid job input record:\n" + str(err)) from err cwltool.errors.WorkflowException: Invalid job input record: pgap/pgap.cwl:28:3: Missing required input parameter 'report_usage' has context menu

GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information. GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.

mkapadiarch commented 1 year ago

Original command: ./pgap.py -o results input.yaml -D singularity

Docker command: /usr/bin/singularity exec --bind /hpc/mydata/upt/rb154511/software/pgap/input-2023-05-17.build6771:/pgap/input:ro --bind /hdd_scratch2/rb154511/pgap:/pgap/user_input - -bind /hdd_scratch2/rb154511/pgap/pgap_input_yrcnp8vo.yaml:/pgap/user_input/pgap_input.yaml:ro --bind /tmp:/tmp:rw --bind /hdd_scratch2/rb154511/pgap/results.2:/pgap/output:rw --pwd / pgap docker://ncbi/pgap:2023-05-17.build6771 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: ASM2732v1.annotation.nucleotide.1.fasta submol: class: File location: pgap_submol_vf2dljee.yaml supplemental_data: { class: Directory, location: /pgap/input } --- End YAML Input ---

--- Start Runtime Report --- { "CPU cores": 96, "Docker image": "ncbi/pgap:2023-05-17.build6771", "cpu flags": "fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc art re p_good nopl nonstop_tsc extd_apicid amd_dcm aperfmperf eagerfpu pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapi c cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_l2 cpb hw_pstate sme retpoline_amd ssbd ibpb vmmcall fsgsbase bmi1 a vx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausef ilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca", "cpu model": "AMD EPYC 7451 24-Core Processor", "max user processes": 16384, "memory (GiB)": 503.8, "memory per CPU core (GiB)": 5.2, "open files": 1048576, "tmp disk space (GiB)": 417.1, "virtual memory": "unlimited", "work disk space (GiB)": 1404.3 } --- End Runtime Report ---

INFO: Using cached SIF image [2023-06-13 12:36:51] INFO /root/venv/bin/cwltool 3.1.20230513155734 [2023-06-13 12:36:51] INFO Resolved 'pgap/pgap.cwl' to 'file:///pgap/pgap/pgap.cwl' pgap/pgap.cwl:24:7: Warning: Field 'location' contains undefined reference to 'file:///pgap/pgap/input' [2023-06-13 12:37:12] ERROR Workflow error: Invalid job input record: pgap/pgap.cwl:28:3: Missing required input parameter 'report_usage' Traceback (most recent call last): File "/root/venv/lib/python3.9/site-packages/cwltool/process.py", line 438, in fill_in_defaults raise WorkflowException( cwltool.errors.WorkflowException: Missing required input parameter 'report_usage'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/root/venv/lib/python3.9/site-packages/cwltool/process.py", line 761, in _init_job fill_in_defaults(self.tool["inputs"], job, fs_access) File "/root/venv/lib/python3.9/site-packages/cwltool/process.py", line 438, in fill_in_defaults raise WorkflowException( File "schema_salad/sourceline.py", line 250, in exit cwltool.errors.WorkflowException: pgap/pgap.cwl:28:3: 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 1295, in main (out, status) = real_executor( File "/root/venv/lib/python3.9/site-packages/cwltool/executors.py", line 61, in call return self.execute(process, job_order_object, runtime_context, logger) File "/root/venv/lib/python3.9/site-packages/cwltool/executors.py", line 144, in execute self.run_jobs(process, job_order_object, logger, runtime_context) File "/root/venv/lib/python3.9/site-packages/cwltool/executors.py", line 217, in run_jobs for job in jobiter: File "/root/venv/lib/python3.9/site-packages/cwltool/workflow.py", line 160, in job builder = self._init_job(job_order, runtimeContext) File "/root/venv/lib/python3.9/site-packages/cwltool/process.py", line 822, in _init_job raise WorkflowException("Invalid job input record:\n" + str(err)) from err cwltool.errors.WorkflowException: Invalid job input record: pgap/pgap.cwl:28:3: Missing required input parameter 'report_usage' has context menu GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information. GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.

azat-badretdin commented 1 year ago

It says: "Missing required input parameter 'report_usage'"

Could you please try to add one of these two parameters: 

  -r, --report-usage-true
                        Report anonymized usage metadata to NCBI.
  -n, --report-usage-false
                        Do not report anonymized usage metadata to NCBI.

Thanks

mkapadiarch commented 1 year ago

Could you please show the full syntax where to add this parameter?

From: Azat Badretdin @.> Sent: Wednesday, June 14, 2023 9:52 AM To: ncbi/pgap @.> Cc: Kapadia, Minal @.>; Mention @.> Subject: Re: [ncbi/pgap] PGAP failed, docker exited with rc = 1 (Issue #261)

Caution: This email originated from outside of RCH Solutions. Please be mindful of the message, and do not click on links unless you recognize the sender and have confidence that the content is safe. If you have concerns about this email, send it as an attachment to @.**@.>.

It says: "Missing required input parameter 'report_usage'"

Could you please try to add one of these two parameters:

-r, --report-usage-true

                    Report anonymized usage metadata to NCBI.

-n, --report-usage-false

                    Do not report anonymized usage metadata to NCBI.

Thanks

— Reply to this email directly, view it on GitHubhttps://github.com/ncbi/pgap/issues/261#issuecomment-1591251488, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BARVJMRJXK4W5CXIPCCQX4TXLG6YHANCNFSM6AAAAAAZFRZTNQ. You are receiving this because you were mentioned.Message ID: @.**@.>>

azat-badretdin commented 1 year ago

Sure:

./pgap.py -o results input.yaml -D singularity -n

or

./pgap.py -o results input.yaml -D singularity -r