Closed dlhuseby29 closed 1 year ago
azat-badretdin
commented
1 year ago Thank you for your report!
For starters, could you please post some of these error messages that bother you?
Also: most likely, you are fine since you got your annotation.
dlhuseby29
commented
1 year ago Hello,
Thank you for your reply.
The output is extensive. The screen looks like it puts out a similar set of information as the cwltool.log, which is this case is 25 mb of text.
We may have complicated matters further; in trying to fix this we noticed that there were some python errors popping up, so we updated python. Now we get essentially the same errors, but now we do not get a .gbk file as an output, only a .gff file.
Searching for the first occurrence of a permanentfail and tracking backward a bit reveals the following large section of text where the problems seem to be originating from:
Error: (CFileException::eFileIO) Error opening checkm dombtblout: /tmp/izql0mp0/checkm.242201698190784wDcQrZ/fasta_by_scaffold/checkm.out; Stack trace:; /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/checkm_wnode :0 offset=0x0 addr=0x4134fd; /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/checkm_wnode :0 offset=0x0 addr=0x4114ce; /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/checkm_wnode :0 offset=0x0 addr=0x412406; /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/lib/libgpxlib.so /export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/gpexec/queue/lib/wn_worker_thread.cpp:274 ncbi::CWorkerThread::x_DoJob(ncbi::CRef<ncbi::objects::CGPX_Job, ncbi::CObjectCounterLocker>, ncbi::CDiagContext&) offset=0x0 addr=0x7f1e64ab96c8; /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/lib/libgpxlib.so /export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/gpexec/queue/lib/wn_worker_thread.cpp:477 ncbi::CParallelWorkerThread::Main() offset=0x0 addr=0x7f1e64abb068; /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/ncbithr.cpp:578 ncbi::CThread::Wrapper(void) offset=0x0 addr=0x7f1e4ba6174f; /usr/lib64/libpthread-2.17.so :0 offset=0x0 addr=0x7f1e5613dea4; /usr/lib64/libc-2.17.so :0 offset=0x0 addr=0x7f1e4a471b0c; :0 offset=0x0 addr=0xffffffffffffffff;
Error: Error calling ProcessCheckMResults block: (CFileException::eFileIO) Error opening checkm dombtblout: /tmp/izql0mp0/checkm.242201698190784wDcQrZ/fasta_by_scaffold/checkm.out
Error: (CFileException::eFileIO) Error opening checkm dombtblout: /tmp/izql0mp0/checkm.242201698190784wDcQrZ/fasta_by_scaffold/checkm.out; Stack trace:; /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/checkm_wnode :0 offset=0x0 addr=0x4134fd; /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/checkm_wnode :0 offset=0x0 addr=0x4114ce; /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/checkm_wnode :0 offset=0x0 addr=0x412406; /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/lib/libgpxlib.so /export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/gpexec/queue/lib/wn_worker_thread.cpp:274 ncbi::CWorkerThread::x_DoJob(ncbi::CRef<ncbi::objects::CGPX_Job, ncbi::CObjectCounterLocker>, ncbi::CDiagContext&) offset=0x0 addr=0x7f1e64ab96c8; /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/lib/libgpxlib.so /export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/gpexec/queue/lib/wn_worker_thread.cpp:477 ncbi::CParallelWorkerThread::Main() offset=0x0 addr=0x7f1e64abb068; /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/ncbithr.cpp:578 ncbi::CThread::Wrapper(void) offset=0x0 addr=0x7f1e4ba6174f; /usr/lib64/libpthread-2.17.so :0 offset=0x0 addr=0x7f1e5613dea4; /usr/lib64/libc-2.17.so :0 offset=0x0 addr=0x7f1e4a471b0c; :0 offset=0x0 addr=0xffffffffffffffff;
Error: Error in the body of Process: (CFileException::eFileIO) Error opening checkm dombtblout: /tmp/izql0mp0/checkm.242201698190784wDcQrZ/fasta_by_scaffold/checkm.out
Error: (CFileException::eFileIO) Error opening checkm dombtblout: /tmp/izql0mp0/checkm.242201698190784wDcQrZ/fasta_by_scaffold/checkm.out; Stack trace:; /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/checkm_wnode :0 offset=0x0 addr=0x4134fd; /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/checkm_wnode :0 offset=0x0 addr=0x4114ce; /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/checkm_wnode :0 offset=0x0 addr=0x412406; /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/lib/libgpxlib.so /export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/gpexec/queue/lib/wn_worker_thread.cpp:274 ncbi::CWorkerThread::x_DoJob(ncbi::CRef<ncbi::objects::CGPX_Job, ncbi::CObjectCounterLocker>, ncbi::CDiagContext&) offset=0x0 addr=0x7f1e64ab96c8; /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/lib/libgpxlib.so /export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/gpexec/queue/lib/wn_worker_thread.cpp:477 ncbi::CParallelWorkerThread::Main() offset=0x0 addr=0x7f1e64abb068; /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/ncbithr.cpp:578 ncbi::CThread::Wrapper(void) offset=0x0 addr=0x7f1e4ba6174f; /usr/lib64/libpthread-2.17.so :0 offset=0x0 addr=0x7f1e5613dea4; /usr/lib64/libc-2.17.so :0 offset=0x0 addr=0x7f1e4a471b0c; :0 offset=0x0 addr=0xffffffffffffffff;
Error: error processing job: (CFileException::eFileIO) Error opening checkm dombtblout: /tmp/izql0mp0/checkm.242201698190784wDcQrZ/fasta_by_scaffold/checkm.out
terminate called after throwing an instance of 'ncbi::CException'
what(): NCBI C++ Exception:
Error: LIB(CException::eUnknown) "/export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/gpexec/queue/lib/wn_app.cpp", line 411: ncbi::CGPX_WorkerApp::Run() --- 1 jobs failed
Stack trace:
/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/lib/libgpxlib.so /export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/gpexec/queue/lib/wn_app.cpp:409 ncbi::CGPX_WorkerApp::Run() offset=0x0 addr=0x7f1e64acbc09
/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/checkm_wnode :0 offset=0x0 addr=0x41a540
/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=0x7f1e4b969472
/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
Stack trace (most recent call last):
Aborted (Signal sent by tkill() 2422 501) [2023-03-14 08:53:48] INFO [job checkm_wnode] Max memory used: 31MiB [2023-03-14 08:53:48] WARNING [job checkm_wnode] was terminated by signal: SIGABRT [2023-03-14 08:53:48] WARNING [job checkm_wnode] completed permanentFail [2023-03-14 08:53:48] DEBUG [job checkm_wnode] outputs { "outdir": { "location": "file:///tmp/qk6mf4gi/output", "basename": "output", "nameroot": "output", "nameext": "", "class": "Directory" } } [2023-03-14 08:53:48] DEBUG [step checkm_wnode] produced output { "file:///pgap/pgap/task_types/tt_checkm_wnode.cwl#checkm_wnode/outdir": { "location": "file:///tmp/qk6mf4gi/output", "basename": "output", "nameroot": "output", "nameext": "", "class": "Directory" } } [2023-03-14 08:53:48] WARNING [step checkm_wnode] completed permanentFail [2023-03-14 08:53:48] DEBUG [job checkm_wnode] Removing input staging directory /tmp/p1rybzqw [2023-03-14 08:53:48] DEBUG [job checkm_wnode] Removing temporary directory /tmp/izql0mp0 [2023-03-14 08:53:48] INFO [workflow run_checkm] completed permanentFail [2023-03-14 08:53:48] DEBUG [workflow run_checkm] outputs { "checkm_raw": null, "checkm_results": null } [2023-03-14 08:53:48] DEBUG [step run_checkm] produced output { "file:///pgap/pgap/checkm/wf_checkm.cwl#run_checkm/checkm_raw": null, "file:///pgap/pgap/checkm/wf_checkm.cwl#run_checkm/checkm_results": null } [2023-03-14 08:53:48] WARNING [step run_checkm] completed permanentFail [2023-03-14 08:53:48] INFO [workflow checkm] completed permanentFail [2023-03-14 08:53:48] DEBUG [workflow checkm] outputs { "checkm_raw": null, "checkm_results": null } [2023-03-14 08:53:48] DEBUG [step checkm] produced output { "file:///pgap/pgap/wf_common.cwl#checkm/checkm_raw": null, "file:///pgap/pgap/wf_common.cwl#checkm/checkm_results": null } [2023-03-14 08:53:48] WARNING [step checkm] completed permanentFail [2023-03-14 08:53:48] INFO [workflow standard_pgap] completed permanentFail [2023-03-14 08:53:48] 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": { "location": "file:///tmp/k4xon_hf/annot.gff", "basename": "annot.gff", "nameroot": "annot", "nameext": ".gff", "class": "File", "checksum": "sha1$f4ec46edc1105e02cae1ef65f912d335eac9aa8e", "size": 298069, "http://commonwl.org/cwltool#generation": 0 }, "gff_enhanced": null, "initial_asndisc_error_diag": { "location": "file:///tmp/a1y2c7sf/initial_asndisc_diag.xml", "basename": "initial_asndisc_diag.xml", "nameroot": "initial_asndisc_diag", "nameext": ".xml", "class": "File", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "size": 0, "http://commonwl.org/cwltool#generation": 0 }, "initial_asnval_error_diag": { "location": "file:///tmp/mrllf3lb/initial_asnval_diag.xml", "basename": "initial_asnval_diag.xml", "nameroot": "initial_asnval_diag", "nameext": ".xml", "class": "File", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "size": 0, "http://commonwl.org/cwltool#generation": 0 }, "nucleotide_fasta": null, "proc_annot_stats": { "location": "file:///tmp/o5efg8rq/var_proc_annot_stats.xml", "basename": "var_proc_annot_stats.xml", "nameroot": "var_proc_annot_stats", "nameext": ".xml", "class": "File", "checksum": "sha1$003481cdfe43aed0344f280719a7300decb3e3dc", "size": 25542, "http://commonwl.org/cwltool#generation": 0 }, "protein_fasta": null, "sqn": null } [2023-03-14 08:53:48] DEBUG [step standard_pgap] produced output { "file:///pgap/pgap/pgap.cwl#standard_pgap/gbent": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/gbk": null, "file:///pgap/pgap/pgap.cwl#standard_pgap/gff": { "location": "file:///tmp/k4xon_hf/annot.gff", "basename": "annot.gff", "nameroot": "annot", "nameext": ".gff", "class": "File", "checksum": "sha1$f4ec46edc1105e02cae1ef65f912d335eac9aa8e", "size": 298069, "http://commonwl.org/cwltool#generation": 0 }, "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": { "location": "file:///tmp/a1y2c7sf/initial_asndisc_diag.xml", "basename": "initial_asndisc_diag.xml", "nameroot": "initial_asndisc_diag", "nameext": ".xml", "class": "File", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "size": 0, "http://commonwl.org/cwltool#generation": 0 }, "file:///pgap/pgap/pgap.cwl#standard_pgap/initial_asnval_error_diag": { "location": "file:///tmp/mrllf3lb/initial_asnval_diag.xml", "basename": "initial_asnval_diag.xml", "nameroot": "initial_asnval_diag", "nameext": ".xml", "class": "File", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "size": 0, "http://commonwl.org/cwltool#generation": 0 }, "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 } [2023-03-14 08:53:48] WARNING [step standard_pgap] completed permanentFail [2023-03-14 08:53:48] INFO [workflow ] completed permanentFail [2023-03-14 08:53:48] DEBUG [workflow ] outputs {
azat-badretdin
commented
1 year ago Thank you. This is informative.
The Python conflict happens inside docker image when we are trying to run third party CheckM with the python that we have inside.
Not sure how this could have happened
Could you please post the beginning of your cwltool.log output, the part that contains calling command lines and system information? Thanks
dlhuseby29
commented
1 year ago That's great that we're getting somewhere.
Here is the beginning of the cwltool.log:
Original command: ./pgap.py -r -o mg37_results /Users/diarmaid3/.pgap/test_genomes/MG37/input.yaml
Docker command: /usr/local/bin/docker run -i --rm --user 501:20 --volume /Users/diarmaid3/.pgap/input-2022-12-13.build6494:/pgap/input:ro,z --volume /Users/diarmaid3/.pgap/test_genomes/MG37:/pgap/user_input:z --volume /Users/diarmaid3/.pgap/test_genomes/MG37/pgap_input_5sw59dcb.yaml:/pgap/user_input/pgap_input.yaml:ro,z --volume /var/folders/bt/2j865c0d6zjghn_t1kc01_280000gn/T/:/tmp:rw,z --volume /Users/diarmaid3/Desktop/Annotation_Queue/mg37_results.12:/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: ASM2732v1.annotation.nucleotide.1.fasta submol: class: File location: pgap_submol_29p_il51.yaml supplemental_data: { class: Directory, location: /pgap/input } report_usage: true --- End YAML Input ---
--- Start Runtime Report --- { "CPU cores": 12, "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 ht pbe syscall nx pdpe1gb lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid pni pclmulqdq dtes64 ds_cpl ssse3 cx16 xtpr pcid dca sse4_1 sse4_2 popcnt aes hypervisor lahf_lm arat", "cpu model": "Intel(R) Xeon(R) CPU E5645 @ 2.40GHz", "max user processes": "unlimited", "memory (GiB)": 47.1, "memory per CPU core (GiB)": 3.9, "open files": 1048576, "tmp disk space (GiB)": 195.4, "virtual memory": "unlimited", "work disk space (GiB)": 306.6 } --- End Runtime Report ---
[2023-03-14 07:47:12] INFO /root/venv/bin/cwltool 3.1.20221201130942
[2023-03-14 07:47:12] 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
[2023-03-14 07:47:51] DEBUG [workflow ] initialized from file:///pgap/pgap/pgap.cwl
[2023-03-14 07:47:51] INFO [workflow ] start
[2023-03-14 07:47:51] DEBUG [workflow ] inputs {
"fasta": {
"class": "File",
"location": "file:///pgap/user_input/ASM2732v1.annotation.nucleotide.1.fasta",
"size": 588482,
"basename": "ASM2732v1.annotation.nucleotide.1.fasta",
"nameroot": "ASM2732v1.annotation.nucleotide.1",
"nameext": ".fasta"
},
azat-badretdin
commented
1 year ago Thanks, that is helpful
Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
Are you running this under Ubuntu or some other Linux distro for PCs or MSL 2 under Windows?
dlhuseby29
commented
1 year ago This is running on a Mac Pro:
Model Name: Mac Pro Model Identifier: MacPro5,1 Processor Name: 6-Core Intel Xeon Processor Speed: 2.4 GHz Number of Processors: 2 Total Number of Cores: 12 L2 Cache (per Core): 256 KB L3 Cache (per Processor): 12 MB Memory: 64 GB
Though we have tried it also on another newer Mac Pro, for what it is worth:
Model Name: Mac Pro Model Identifier: MacPro6,1 Processor Name: 12-Core Intel Xeon E5 Processor Speed: 2.7 GHz Number of Processors: 1 Total Number of Cores: 12 L2 Cache (per Core): 256 KB L3 Cache: 30 MB Hyper-Threading Technology: Enabled Memory: 64 GB
dlhuseby29
commented
1 year ago Ran it again and this time we got the .gbk file in addition to the .gff and other files.
Seems strange that there should apparently be some randomness in the results files that we get out each time.
Here were the output files for 3 consecutive runs of the test genome. Only difference in the input was that the first one was run with the --debug flag.
azat-badretdin
commented
1 year ago Could be memory related. Would you like to try it with --cpus 1 switch?
dlhuseby29
commented
1 year ago With the --cpus 1 flag, it fails in exactly the same way.
One idea we had was to roll back to the previous version that worked for us. Not an entirely satisfying solution, but maybe one that could allow us to annotate again.
Or, as you said, could it be that everything is 'working' in the sense that we are generating annotations? Is there any reason why these annotations would be suspicious --or importantly, un-submit-able to NCBI?
azat-badretdin
commented
1 year ago If the annotation is produced: it is fine.
dlhuseby29
commented
1 year ago So I guess we will handle this by ignoring the errors if the .gbk file is generated?
We did run it last night again on one our actual genomes that we wish to annotate and it didn't manage to generate the .gbk file. In this case I guess we run it again a few times and see if it can complete it.
I have been worried that the problem is this specific system because it cannot be upgraded past OS 10.13 because of the age of the computer. We have run it a few times on a similar, but newer system currently running OS 12.6.3 and a newer version of Docker. We checked the logs and this computer generates an error log that seems extremely similar to the one on the older system. This makes me suspect that this could be a general Mac problem. I saw in the notes that you cannot be certain that this will work on Mac systems at all, so maybe this is a situation where we have encountered an incompatibility.
azat-badretdin
commented
1 year ago Thank you for this information!
These seem all valid concerns to me.
dlhuseby29
commented
1 year ago I can add to this that after running the pipeline a few dozen times we have a success rate of generating the .gbk file at the end of the process of about 50%.
azat-badretdin
commented
1 year ago Thank you for reporting these stats!
at the end of the process of about 50%.
Sorry to hear about that.
george-coulouris
commented
1 year ago @dlhuseby29, thanks for reporting. I believe I was able to reproduce this issue, we'll take a look.
george-coulouris
commented
4 months ago I can no longer reproduce this issue.
Since updating to the latest version of pgap, we have been unable to complete an annotation run without errors. The process appears to finish, as judged by generating a .gbk file, but it does spit out a number of error messages. Looking at the log file, we can find the first permanentFail message seems to be associated with checkm. Checkm, as far as we can tell, is working as judged by running it by itself on its own test data. Checkm was not a part of the version of pgap that we previously had working correctly (Build 5508).
Since we have had this problem, we've tried to re-run the test genome many times and no matter how we have tried to change various parameters, always seems to generate these errors.
Running on: Mac Pro with OS 10.13.6 pgap.py build 6494 Docker version 20.10.8 (We generate the same error on a newer Mac Pro running OS 12.6.3, pgap.py build 6494, Docker version 20.10.23)
Debug Logs.zip cwltool.log.zip
Any suggestions would be appreciated!