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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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--restart did not fix failed job #1350

Closed scintilla9 closed 2 months ago

scintilla9 commented 2 months ago

Hi,

I'm using cactus to align few genomes, and I got error message "An invalid character was found in the first word of a fasta header". So I changed the header accordingly, in this case, from AADN05001177.1_Gallus_gallus_breed_Red_Jungle_fowl._inbred_line_UCD001_isolate_RJF_#256_Contig134.1._whole_genome_shotgun_sequence to AADN05001177.1_Gallus_gallus_breed_Red_Jungle_fowl._inbred_line_UCD001_isolate_RJF_256_Contig134.1._whole_genome_shotgun_sequence

However, when I run again with --restart the pipeline seems doesn't receive the change and still report that AADN05001177.1_Gallus_gallus_breed_Red_Jungle_fowl._inbred_line_UCD001_isolate_RJF_#256_Contig134.1._whole_genome_shotgun_sequence as invalid name.

I attach the log file below: stderr.log

This there any way that I can fix this issue? or I should restart the whole process from the beginning (I prefer not to, since the process have been run for about 3 weeks)?

Any suggestion is appreciated.

glennhickey commented 2 months ago

No. Changes to input data and even options (except a few Toil-specific ones) will not be taken into account with --restart. The good news is that it's failing at the very beginning of the pipeline, so you won't lose much rerunning from scratch.

scintilla9 commented 2 months ago

Ok, I got it. Now I start a new run. Thanks for clarifying.