PGAP failed, docker exited with rc = 1 #261
Comments
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Thank you for your report, user @mkapadiarch ! Could you please post |
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***@***.***
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'
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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 - --- Start YAML Input --- --- Start Runtime Report --- INFO: Using cached SIF image During handling of the above exception, another exception occurred: Traceback (most recent call last): The above exception was the direct cause of the following exception: Traceback (most recent call last): |
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It says: "Missing required input parameter 'report_usage'" Could you please try to add one of these two parameters: Thanks |
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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
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Sure: or |
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.
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