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NBChub / bgcflow

Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)
https://github.com/NBChub/bgcflow/wiki
MIT License
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GECCO Error #359

Open andrekind17 opened 1 month ago

andrekind17 commented 1 month ago

Hi Matin, when I run GECCO on the Lactobacillus_delbrueckii example dataset with bgcflow run, I get this error:

/usr/bin/bash: line 2: 657128 Illegal instruction (core dumped) gecco run --genome data/interim/processed-genbank/GCA_000014405.1.gbk --output-dir data/interim/gecco/0.9.10/GCA_000014405.1 --antismash-sideload --jobs 2 --force-tsv 2>> logs/gecco/run/0.9.10_GCA_000014405.1.log

[Wed Sep 25 13:46:48 2024] Error in rule gecco: jobid: 98 input: data/interim/processed-genbank/GCA_000014405.1.gbk output: data/interim/gecco/0.9.10/GCA_000014405.1/GCA_000014405.1.clusters.tsv log: logs/gecco/run/0.9.10_GCA_000014405.1.log (check log file(s) for error details) conda-env: /mnt/data/studenti/agentile/bgcflow/.snakemake/conda/fc38642a72f0d9780c1726281ad2a8f0_ shell:

gecco run --genome data/interim/processed-genbank/GCA_000014405.1.gbk --output-dir data/interim/gecco/0.9.10/GCA_000014405.1 --antismash-sideload --jobs 2 --force-tsv 2>> logs/gecco/run/0.9.10_GCA_000014405.1.log

(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-09-25T134640.083718.snakemake.log WorkflowError: At least one job did not complete successfully. Stopping panoptes server: PID 655760

This is the log file: 2024-09-25T134640.083718.snakemake.log

If I run GECCO with snakemake -s /home/agentile/data/bgcflow/workflow/rules/gecco.smk, I get this specific error:

WorkflowError in file /home/agentile/data/bgcflow/workflow/rules/gecco.smk, line 22: Rule antismash_db_setup is not defined in this workflow. Available rules: gecco

Seems like it's finding problems in the snakefile.

matinnuhamunada commented 1 month ago

Hi @andrekind17, can you also send me this file for debugging? logs/gecco/run/0.9.10_GCA_000014405.1.log

From the error message: /usr/bin/bash: line 2: 657128 Illegal instruction (core dumped), it seems that the issue came from the machine? Where are you running this?

andrekind17 commented 1 month ago

Here it is, it's always empty (I run it multiple times):

0.9.10_GCA_000014405.1.log

All the other rules work on the example dataset, and I'm now trying on my data.

I'm running BGCFlow on a Linux server. These are the specifications:

uname -a Linux elio 5.15.0-122-generic #132-Ubuntu SMP Thu Aug 29 13:45:52 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 22.04.5 LTS Release: 22.04 Codename: jammy

lshw -short -C memory H/W path Device Class Description /0/0 memory 144GiB System memory

lscpu Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Address sizes: 46 bits physical, 48 bits virtual Byte Order: Little Endian CPU(s): 24 On-line CPU(s) list: 0-23 Vendor ID: GenuineIntel Model name: Intel(R) Xeon(R) CPU E5-2630L v2 @ 2.40GHz CPU family: 6 Model: 62 Thread(s) per core: 2 Core(s) per socket: 6 Socket(s): 2 Stepping: 4 CPU max MHz: 2800.0000 CPU min MHz: 1200.0000 BogoMIPS: 4799.81 Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon p ebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monito r ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_d eadline_timer aes xsave avx f16c rdrand lahf_lm cpuid_fault pti ssbd ibrs ibpb stibp tpr _shadow vnmi flexpriority ept vpid fsgsbase smep erms xsaveopt dtherm ida arat pln pts m d_clear flush_l1d Virtualization features: Virtualization: VT-x Caches (sum of all): L1d: 384 KiB (12 instances) L1i: 384 KiB (12 instances) L2: 3 MiB (12 instances) L3: 30 MiB (2 instances) NUMA: NUMA node(s): 2 NUMA node0 CPU(s): 0,2,4,6,8,10,12,14,16,18,20,22 NUMA node1 CPU(s): 1,3,5,7,9,11,13,15,17,19,21,23 Vulnerabilities: Gather data sampling: Not affected Itlb multihit: KVM: Mitigation: VMX disabled L1tf: Mitigation; PTE Inversion; VMX conditional cache flushes, SMT vulnerable Mds: Mitigation; Clear CPU buffers; SMT vulnerable Meltdown: Mitigation; PTI Mmio stale data: Unknown: No mitigations Reg file data sampling: Not affected Retbleed: Not affected Spec rstack overflow: Not affected Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl and seccomp Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization Spectre v2: Mitigation; Retpolines; IBPB conditional; IBRS_FW; STIBP conditional; RSB filling; PBRSB -eIBRS Not affected; BHI Not affected Srbds: Not affected Tsx async abort: Not affected