cactus-update-prepare add branch output adds erroneous text and causes pipeline to fail when run

[foreignsand]

When I run the following command:

cactus-update-prepare add branch --parentGenome fullTreeAnc212 --childGenome fullTreeAnc211 /workDir/241-mammalian-2020v2_subset-45.hal \
	/workDir/cactus-update-input.txt --cactus-prepare-options '--alignCores 128' --outDir /workDir/cactus_out \
	--jobStore /scratch/dziedzie/jobStore --ancestorName AncMartes --topBranchLength 0.00059465

It results in the following output:

## generated by : /home/cactus/cactus_env/bin/cactus-update-prepare add branch --parentGenome fullTreeAnc212 --childGenome fullTreeAnc211 /workDir/241-mammalian-2020v2_subset-45.hal /workDir/cactus-update-input.txt --cactus-prepare-options '--alignCores 128' --outDir /workDir/cactus_out --jobStore /scratch/dziedzie/jobStore --ancestorName AncMartes --topBranchLength 0.00059465
## date : 2026-04-30 00:28:21.298971
## cactus commit : 00699c25d009c001b0c55c40de7651a25acce332
## wrapping : /home/cactus/cactus_env/bin/cactus-prepare /workDir/cactus_out/seq_file.in --outDir /workDir/cactus_out --outSeqFile /workDir/cactus_out/seq_file.out --jobStore /scratch/dziedzie/jobStore --alignCores 128 --outHal /workDir/cactus_out/fullTreeAnc212.hal


## Preprocessor
cactus-preprocess /scratch/dziedzie/jobStore/0 /workDir/cactus_out/seq_file.in /workDir/cactus_out/seq_file.out --inputNames Martes_caurina_humboldtensis | 2>&1 tee /workDir/cactus_out/logs/preprocess-Mellivora_capensis.log

## Alignment
### Round 0
cactus-blast /scratch/dziedzie/jobStore/1 /workDir/cactus_out/seq_file.out /workDir/cactus_out/AncMartes.paf.gz --root AncMartes   2>&1 | tee /workDir/cactus_out/logs/blast-AncMartes.log
cactus-align /scratch/dziedzie/jobStore/2 /workDir/cactus_out/seq_file.out /workDir/cactus_out/AncMartes.paf.gz /workDir/cactus_out/AncMartes.hal --root AncMartes  --maxCores 128 --consCores 128 2>&1 | tee /workDir/cactus_out/logs/align-AncMartes.log
cactus-hal2fasta /scratch/dziedzie/jobStore/3 /workDir/cactus_out/AncMartes.hal AncMartes /workDir/cactus_out/AncMartes.fa.gz   2>&1 | tee /workDir/cactus_out/logs/hal2fasta-AncMartes.log

### Round 1
cactus-blast /scratch/dziedzie/jobStore/4 /workDir/cactus_out/seq_file.out /workDir/cactus_out/fullTreeAnc212.paf.gz --root fullTreeAnc212   2>&1 | tee /workDir/cactus_out/logs/blast-fullTreeAnc212.log --includeRoot|cactus-blast /scratch/dziedzie/jobStore/4 /workDir/cactus_out/seq_file.out /workDir/cactus_out/fullTreeAnc212.paf.gz --root fullTreeAnc212   2>&1 | tee /workDir/cactus_out/logs/blast-fullTreeAnc212.log --includeRoot
cactus-align /scratch/dziedzie/jobStore/5 /workDir/cactus_out/seq_file.out /workDir/cactus_out/fullTreeAnc212.paf.gz /workDir/cactus_out/fullTreeAnc212.hal --root fullTreeAnc212  --maxCores 128 --consCores 128 2>&1 | tee /workDir/cactus_out/logs/align-fullTreeAnc212.log --includeRoot|cactus-align /scratch/dziedzie/jobStore/5 /workDir/cactus_out/seq_file.out /workDir/cactus_out/fullTreeAnc212.paf.gz /workDir/cactus_out/fullTreeAnc212.hal --root fullTreeAnc212  --maxCores 128 --consCores 128 2>&1 | tee /workDir/cactus_out/logs/align-fullTreeAnc212.log --includeRoot
|cactus-halAppendSubtrees /scratch/dziedzie/jobStore/7 /workDir/cactus_out/fullTreeAnc212.hal /workDir/cactus_out/AncMartes.hal /workDir/cactus_out/fullTreeAnc212.hal   2>&1 | tee /workDir/cactus_out/logs/halAppend-AncMartes.log

## Alignment update
halAddToBranch /workDir/241-mammalian-2020v2_subset-45.hal /workDir/cactus_out/AncMartes.hal /workDir/cactus_out/fullTreeAnc212.hal fullTreeAnc212 AncMartes fullTreeAnc211 Martes_caurina_humboldtensis 0.00059465 0.01545479 --hdf5InMemory 

## Alignment validation
halValidate --genome fullTreeAnc212 /workDir/241-mammalian-2020v2_subset-45.hal --hdf5InMemory
halValidate --genome AncMartes /workDir/241-mammalian-2020v2_subset-45.hal --hdf5InMemory
halValidate --genome fullTreeAnc211 /workDir/241-mammalian-2020v2_subset-45.hal --hdf5InMemory
halValidate --genome Martes_caurina_humboldtensis /workDir/241-mammalian-2020v2_subset-45.hal --hdf5InMemory

This has repeated text with the format 2>&1 | tee /workDir/cactus_out/logs/<filename>.log inserted into it and also appears to have repeated commands and erroneous pipes. I've edited it to the following but want to be sure this is the correct command as it should be run:

## Preprocessor
cactus-preprocess /scratch/dziedzie/jobStore/0 /workDir/cactus_out/seq_file.in /workDir/cactus_out/seq_file.out --inputNames Martes_caurina_humboldtensis

## Alignment
### Round 0
cactus-blast /scratch/dziedzie/jobStore/1 /workDir/cactus_out/seq_file.out /workDir/cactus_out/AncMartes.paf.gz --root AncMartes
cactus-align /scratch/dziedzie/jobStore/2 /workDir/cactus_out/seq_file.out /workDir/cactus_out/AncMartes.paf.gz /workDir/cactus_out/AncMartes.hal --root AncMartes  --maxCores 128 --consCores 128
cactus-hal2fasta /scratch/dziedzie/jobStore/3 /workDir/cactus_out/AncMartes.hal AncMartes /workDir/cactus_out/AncMartes.fa.gz

### Round 1
cactus-blast /scratch/dziedzie/jobStore/4 /workDir/cactus_out/seq_file.out /workDir/cactus_out/fullTreeAnc212.paf.gz --root fullTreeAnc212 --includeRoot
cactus-align /scratch/dziedzie/jobStore/5 /workDir/cactus_out/seq_file.out /workDir/cactus_out/fullTreeAnc212.paf.gz /workDir/cactus_out/fullTreeAnc212.hal --root fullTreeAnc212  --maxCores 128 --consCores 128 --includeRoot
cactus-halAppendSubtrees /scratch/dziedzie/jobStore/7 /workDir/cactus_out/fullTreeAnc212.hal /workDir/cactus_out/AncMartes.hal /workDir/cactus_out/fullTreeAnc212.hal

## Alignment update
halAddToBranch /workDir/241-mammalian-2020v2_subset-45.hal /workDir/cactus_out/AncMartes.hal /workDir/cactus_out/fullTreeAnc212.hal fullTreeAnc212 AncMartes fullTreeAnc211 Martes_caurina_humboldtensis 0.00059465 0.01545479 --hdf5InMemory 

## Alignment validation
halValidate --genome fullTreeAnc212 /workDir/241-mammalian-2020v2_subset-45.hal --hdf5InMemory
halValidate --genome AncMartes /workDir/241-mammalian-2020v2_subset-45.hal --hdf5InMemory
halValidate --genome fullTreeAnc211 /workDir/241-mammalian-2020v2_subset-45.hal --hdf5InMemory
halValidate --genome Martes_caurina_humboldtensis /workDir/241-mammalian-2020v2_subset-45.hal --hdf5InMemory

Many thanks! Cactus is absolutely invaluable!

Cheers,
Emily

[foreignsand]

These edited commands completed without errors and successfully added the M. caurina humboldtensis genome to the 45-species hal tree I extracted from the Zoonomia alignment. So that confirms the need to edit the output from cactus-update-prepare add branch.

Cheers,
Emily