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dr-joe-wirth / phantasm

PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes
MIT License
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Stuck in the step of "Finding missing relationships and updating the Taxonomy object" #8

Closed yisuo1994 closed 1 year ago

yisuo1994 commented 1 year ago

INFO:main:/home/ycc/phantasm/phantasm.py refinePhylogeny --locus_tag JPOANJ_02130 L7829.gbff exxxx@axxxxxx.org INFO:main:v1.0.4 INFO:main:num cpus: 16 INFO:main:max leaves: 30 INFO:main:reduce num core: True INFO:main:bootstrap tree: True INFO:main:num bootstraps: 100

INFO:main:start refinePhylogeny

INFO:PHANTASM.findMissingNeighbors.phyloMarkerBlastRunner:Using the phylogenetic marker(s) to search for closely-related genomes ... INFO:PHANTASM.findMissingNeighbors.blastPhyloMarkerSeqRecords: Searching 122304_L7829-JPOANJ_02130 against NCBI's nr database ... INFO:PHANTASM.findMissingNeighbors.blastPhyloMarkerSeqRecords: Done. INFO:PHANTASM.findMissingNeighbors.phyloMarkerBlastRunner:Done.

INFO:PHANTASM.findMissingNeighbors.xenogiInterfacer_2:Finding missing relatives and updating the Taxonomy object ... CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.elink:failed to retreive the result from NCBI after 5 tries CRITICAL:PHANTASM.utilities.__elink:failed to retreive the result from NCBI after 5 tries

dr-joe-wirth commented 1 year ago

Would you be willing to share some files with me? Specifically, the .tax file in the initialAnalysis folder and initialAnalysis/phylogeneticMarker.blastp.

I might need others, but I should be able to investigate this issue with those two files.

yisuo1994 commented 1 year ago

initialAnalysis.zip

dr-joe-wirth commented 1 year ago

Thanks for sharing this with me. This is actually normal behavior, although the log messages for the elink error are definitely a little too loud. The CRITICAL error you are seeing is actually being handled under the hood. The elink command is used to link two unique IDs between two different NCBI databases. In this case it is linking the protein database (blastp hits) with the assembly database (wgs). However, not every blastp hit has a corresponding assembly, which results in an error. The calling function relies on this error to know which proteins to skip. In the next release, I will make try to make the log messages associated with elink a little less boisterous.

Thanks again for bringing this to my attention.

yisuo1994 commented 1 year ago

Thank you for your prompt reply. After multiple CRITICAL errors occur, the resources occupied by the program are released, the terminal is stuck, and CTRL+c cannot kill the thread.

Should I keep waiting for it to end?

dr-joe-wirth commented 1 year ago

I would just let it keep running. When I ran that step on my machine, it took several minutes but eventually it finished. I am honestly unsure why it can't be killed with ^ + C. I think it has something to do with the Bio.Entrez package wanting to finish its http request. Identifying assemblies is also a long process that requires interfacing with NCBI databases several times.

yisuo1994 commented 1 year ago

Okay. Thank you.

dr-joe-wirth commented 1 year ago

A fix to this issue will be added to the next release. Marking this issue as closed.