ERROR running test genome after successful installation

Describe the bug This is what comes out of pgap after running test genome annotation MG37: PGAP failed, docker exited with rc = 1 Printing log starting from failed job:

[2022-07-20 09:55:10] DEBUG [step Cache_WGS_contig_FASTA] job input { "file:///pgap/pgap/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/input": { "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" } } [2022-07-20 09:55:10] DEBUG [step Cache_WGS_contig_FASTA] evaluated job input to { "file:///pgap/pgap/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/input": { "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" } } [2022-07-20 09:55:10] INFO [step Cache_WGS_contig_FASTA] start [2022-07-20 09:55:10] DEBUG [job Cache_WGS_contig_FASTA] initializing from file:///pgap/pgap/progs/prime_cache.cwl as part of step Cache_WGS_contig_FASTA [2022-07-20 09:55:10] DEBUG [job Cache_WGS_contig_FASTA] { "input": { "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" }, "biosource": null, "cache_dir": "sequence_cache", "ifmt": "fasta", "inst_mol": null, "molinfo": null, "seq_ids_name": "oseq-ids.seqids", "submit_block_template": null, "taxid": null, "taxon_db": null } [2022-07-20 09:55:10] DEBUG [job Cache_WGS_contig_FASTA] path mappings is { "file:///pgap/user_input/ASM2732v1.annotation.nucleotide.1.fasta": [ "/pgap/user_input/ASM2732v1.annotation.nucleotide.1.fasta", "/tmp/s_g_87kr/stgaa13e357-3584-40f4-ba5e-71e0b2f68215/ASM2732v1.annotation.nucleotide.1.fasta", "File", true ] } [2022-07-20 09:55:10] DEBUG [job Cache_WGS_contig_FASTA] command line bindings is [ { "position": [ -1000000, 0 ], "datum": "prime_cache" }, { "prefix": "-cache", "position": [ 0, "cache_dir" ], "datum": "sequence_cache" }, { "prefix": "-ifmt", "position": [ 0, "ifmt" ], "datum": "fasta" }, { "prefix": "-i", "position": [ 0, "input" ], "datum": { "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", "path": "/tmp/s_g_87kr/stgaa13e357-3584-40f4-ba5e-71e0b2f68215/ASM2732v1.annotation.nucleotide.1.fasta", "dirname": "/tmp/s_g_87kr/stgaa13e357-3584-40f4-ba5e-71e0b2f68215" } }, { "prefix": "-oseq-ids", "position": [ 0, "seq_ids_name" ], "datum": "oseq-ids.seqids" } ] [2022-07-20 09:55:10] DEBUG [job Cache_WGS_contig_FASTA] initial work dir {} [2022-07-20 09:55:10] INFO [job Cache_WGS_contig_FASTA] /tmp/gmpglypi$ prime_cache \ -cache \ sequence_cache \ -ifmt \ fasta \ -i \ /tmp/s_g_87kr/stgaa13e357-3584-40f4-ba5e-71e0b2f68215/ASM2732v1.annotation.nucleotide.1.fasta \ -oseq-ids \ oseq-ids.seqids [2022-07-20 09:55:10] DEBUG Could not collect memory usage, job ended before monitoring began. [2022-07-20 09:55:10] WARNING [job Cache_WGS_contig_FASTA] was terminated by signal: SIGILL [2022-07-20 09:55:10] ERROR [job Cache_WGS_contig_FASTA] Job error: ("Error collecting output for parameter 'asn_cache': pgap/progs/prime_cache.cwl:58:9: Did not find output file with glob pattern: '['sequence_cache']'.", {}) [2022-07-20 09:55:10] WARNING [job Cache_WGS_contig_FASTA] completed permanentFail [2022-07-20 09:55:10] DEBUG [job Cache_WGS_contig_FASTA] outputs {} [2022-07-20 09:55:10] ERROR [step Cache_WGS_contig_FASTA] Output is missing expected field file:///pgap/pgap/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/asn_cache [2022-07-20 09:55:10] ERROR [step Cache_WGS_contig_FASTA] Output is missing expected field file:///pgap/pgap/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/oseq_ids [2022-07-20 09:55:10] DEBUG [step Cache_WGS_contig_FASTA] produced output {} [2022-07-20 09:55:10] WARNING [step Cache_WGS_contig_FASTA] completed permanentFail [2022-07-20 09:55:10] DEBUG [job Cache_WGS_contig_FASTA] Removing input staging directory /tmp/s_g_87kr [2022-07-20 09:55:10] DEBUG [job Cache_WGS_contig_FASTA] Removing temporary directory /tmp/qwzlmner [2022-07-20 09:55:10] INFO [workflow default_plane] completed permanentFail [2022-07-20 09:55:10] DEBUG [workflow default_plane] outputs { "adaptor_blastdb_dir": null, "contig_ids_out": null, "feats": null, "hits": null, "out_cache_dir": null } [2022-07-20 09:55:10] DEBUG [step default_plane] produced output { "file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/adaptor_blastdb_dir": null, "file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/contig_ids_out": null, "file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/feats": null, "file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/hits": null, "file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/out_cache_dir": null } [2022-07-20 09:55:10] WARNING [step default_plane] completed permanentFail [2022-07-20 09:55:10] INFO [workflow vecscreen] completed permanentFail [2022-07-20 09:55:10] DEBUG [workflow vecscreen] outputs { "adaptor_blastdb_dir": null, "blast_align": null, "calls": null, "contamination_feats": null, "filtered_align": null, "foreign_feats": null, "hits": null, "out_cache_dir": null, "success": null } [2022-07-20 09:55:10] DEBUG [step vecscreen] produced output { "file:///pgap/pgap/pgap.cwl#vecscreen/success": null, "file:///pgap/pgap/pgap.cwl#vecscreen/calls": null } [2022-07-20 09:55:10] WARNING [step vecscreen] completed permanentFail [2022-07-20 09:55:10] INFO [workflow ] completed permanentFail [2022-07-20 09:55:10] DEBUG [workflow ] outputs { "calls": null, "final_asndisc_error_diag": null, "final_asnval_error_diag": null, "gbk": null, "gff": null, "initial_asndisc_error_diag": null, "initial_asnval_error_diag": null, "input_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" }, "input_submol": { "class": "File", "location": "file:///pgap/user_input/pgap_submol_x67l08a9.yaml", "size": 1667, "basename": "pgap_submol_x67l08a9.yaml", "nameroot": "pgap_submol_x67l08a9", "nameext": ".yaml" }, "nucleotide_fasta": null, "protein_fasta": null, "sqn": null } [2022-07-20 09:55:10] DEBUG Copying /pgap/user_input/ASM2732v1.annotation.nucleotide.1.fasta to /pgap/output/ASM2732v1.annotation.nucleotide.1.fasta [2022-07-20 09:55:10] DEBUG Copying /pgap/user_input/pgap_submol_x67l08a9.yaml to /pgap/output/pgap_submol_x67l08a9.yaml [2022-07-20 09:55:10] DEBUG Removing intermediate output directory /tmp/kbourmw4 [2022-07-20 09:55:10] DEBUG Removing intermediate output directory /tmp/gmpglypi [2022-07-20 09:55:10] DEBUG Removing intermediate output directory /tmp/wm1h8lhd [2022-07-20 09:55:10] DEBUG Removing intermediate output directory /tmp/1noz6t7w [2022-07-20 09:55:10] DEBUG Removing intermediate output directory /tmp/z8dyo9q6 [2022-07-20 09:55:10] WARNING Final process status is permanentFail { "calls": null, "final_asndisc_error_diag": null, "final_asnval_error_diag": null, "gbk": null, "gff": null, "initial_asndisc_error_diag": null, "initial_asnval_error_diag": null, "input_fasta": { "class": "File", "location": "file:///pgap/output/ASM2732v1.annotation.nucleotide.1.fasta", "size": 588482, "basename": "ASM2732v1.annotation.nucleotide.1.fasta", "checksum": "sha1$f6129783cc8562db7bca3c87310d57d8dd07ce2c", "path": "/pgap/output/ASM2732v1.annotation.nucleotide.1.fasta" }, "input_submol": { "class": "File", "location": "file:///pgap/output/pgap_submol_x67l08a9.yaml", "size": 1667, "basename": "pgap_submol_x67l08a9.yaml", "checksum": "sha1$c76170f856551e6f31a13cd29e4ab394c153385f", "path": "/pgap/output/pgap_submol_x67l08a9.yaml" }, "nucleotide_fasta": null, "protein_fasta": null, "sqn": null } I attach log files. I would be very grateful for any hint what is going wrong with that.

To Reproduce If you are having trouble with your genome, please ensure that you can run the pipeline with one of our test genomes first. If your installation works fine with the sample input, please tell us if you are willing and able to share your genome with us, if asked.

Expected behavior A clear and concise description of what you expected to happen.

Software versions (please complete the following information): "CPU cores": 48, "Docker image": "ncbi/pgap:2022-04-14.build6021", "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 3dnowext 3dnow constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid amd_dcm pni monitor cx16 popcnt lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt nodeid_msr hw_pstate vmmcall npt lbrv svm_lock nrip_save pausefilter", "cpu model": "AMD Opteron(tm) Processor 6172", "max user processes": "unlimited", "memory (GiB)": 94.3, "memory per CPU core (GiB)": 2.0, "open files": 1048576, "tmp disk space (GiB)": 412.3, "virtual memory": "unlimited", "work disk space (GiB)": 412.3

Log Files cwltool.log

Additional context Add any other context about the problem here.

ncbi / pgap

ERROR running test genome after successful installation #215