Error with the latest version of UCSC commands

[ASUQ]

While running Braker3 for the gene prediction, the job failed at MakeHub.

The below is from makehub.log in the braker output directory.

Warning: did not set args.traingenes because none of the expected training gene structure files exists in <braker3_output_directory>/
Warning: did not set args.aug_ab_initio because the file augustus.ab_initio.gtf does not exist in <braker3_output_directory>/
Warning: did not set args.aug_ab_initio_utr because the file augustus.ab_initio_utr.gtf does not exist in <braker3_output_directory>/
Warning: did not set args.aug_hints_utr because the file augustus.hints_utr.gtf does not exist in <braker3_output_directory>/
Was unable to locate bedToBigBed on your system, will try to download it from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed...
Was unable to locate genePredCheck on your system, will try to download it from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredCheck...
Was unable to locate faToTwoBit on your system, will try to download it from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit...
Was unable to locate gtfToGenePred on your system, will try to download it from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred...
Was unable to locate hgGcPercent on your system, will try to download it from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/hgGcPercent...
Was unable to locate ixIxx on your system, will try to download it from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ixIxx...
Was unable to locate twoBitInfo on your system, will try to download it from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/twoBitInfo...
Was unable to locate wigToBigWig on your system, will try to download it from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig...
Was unable to locate genePredToBed on your system, will try to download it from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToBed...
Was unable to locate genePredToBigGenePred on your system, will try to download it from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToBigGenePred...
Was unable to locate file bigGenePred.as in /opt/MakeHub and ./tmp-hub_<short_label>/, will try to download it from http://genome.ucsc.edu/goldenPath/help/examples/...
Trying to download http://genome.ucsc.edu/goldenPath/help/examples/bigGenePred.as and store into ./tmp-hub_<short_label>//bigGenePred.as
Stored file at ./tmp-hub_<short_label>//bigGenePred.as.
Was unable to locate file cytoBand.as in /opt/MakeHub and ./tmp-hub_<short_label>/, will try to download it from http://genome.ucsc.edu/goldenPath/help/examples/...
Trying to download http://genome.ucsc.edu/goldenPath/help/examples/cytoBand.as and store into ./tmp-hub_<short_label>//cytoBand.as
Stored file at ./tmp-hub_<short_label>//cytoBand.as.
Generating genome 2bit file ./hub_<short_label>/hub_<short_label>/hub_<short_label>.2bit...
Error in file /opt/MakeHub/make_hub.py at line 544: Return code of subprocess was 127['<braker3_output_directory>/faToTwoBit', '<braker3_output_directory>/genome.fa', './hub_<short_label>/hub_<short_label>/hub_<short_label>.2bit']

The job also failed when running twoBitInfo by adding the output from faToTwoBit ran independently.

This error was circumvented by replacing the UCSC commands with the older version (linux.x86_64.v385/).

The error might be due to the latest version of UCSC commands, updated last month (Nov 2024).

Environment

CentOS Linux release 8.5.2111
Linux version 4.18.0
Singularity 4.1.4
braker3.sif (singularity build braker3.sif docker://teambraker/braker3:latest (v3.0.7.4))
(image was built on March 2024 with singularity v3.5.2)