haystac database creation fails

[nicolaavogel]

Hi,

I installed haystac through conda like it was outlined on your GitHub, but when trying the example command (haystac database --mode build --query '"Yersinia"[Organism] AND "complete genome"[All Fields]' --output yersinia_example) of building a database the program crashes:

"[Wed Dec 21 10:53:23 2022] Job 6: The number of index chunks needed for the filtering alignment are being calculated. Downstream jobs will be updated after completion.

Not a conda environment: /home/haystac/cache/conda/a8748482f2d8c2ef49c84c3e2d1baa35 Not a conda environment: /home//haystac/cache/conda/a8748482f2d8c2ef49c84c3e2d1baa35 Not a conda environment: /home//haystac/cache/conda/a8748482f2d8c2ef49c84c3e2d1baa35 Not a conda environment: /home//haystac/cache/conda/a8748482f2d8c2ef49c84c3e2d1baa35 [Wed Dec 21 10:53:23 2022] Error in rule bowtie_index_accession: jobid: 43 output: /home/haystac/cache/ncbi/Yersinia_enterocolitica/NZ_HF571988.1.1.bt2l, /home/haystac/cache/ncbi/Yersinia_enterocolitica/NZ_HF571988.1.2.bt2l, /home/haystac/cache/ncbi/Yersinia_enterocolitica/NZ_HF571988.1.3.bt2l, /home/haystac/cache/ncbi/Yersinia_enterocolitica/NZ_HF571988.1.4.bt2l, /home/haystac/cache/ncbi/Yersinia_enterocolitica/NZ_HF571988.1.rev.1.bt2l, /home/haystac/cache/ncbi/Yersinia_enterocolitica/NZ_HF571988.1.rev.2.bt2l log: /home/haystac/cache/ncbi/Yersinia_enterocolitica/NZ_HF571988.1_index.log (check log file(s) for error message) conda-env: /home/haystac/cache/conda/a8748482f2d8c2ef49c84c3e2d1baa35 shell: bowtie2-build --large-index --threads 4 /home/haystac/cache/ncbi/Yersinia_enterocolitica/NZ_HF571988.1.fasta.gz /home/haystac/cache/ncbi/Yersinia_enterocolitica/NZ_HF571988.1 &> /home/haystac/cache/ncbi/Yersinia_enterocolitica/NZ_HF571988.1_index.log (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)"

Do you have any other ideas on how to fix this? Thank you for your help!

Best, Nicola

[antonisdim]

Hello Nicola,

Happy New Year and apologies for not getting back to you earlier ! Of course I am happy to help.

First I can see that a rule-specific Conda environment has not been built correctly, so I'll look into that for sure. Also would it be easy for you to share which Conda version you are using ? Finally I was wondering if you could post the error message that is printed in this file /home/haystac/cache/ncbi/Yersinia_enterocolitica/NZ_HF571988.1_index.log (I copied the path from the haystac log you posted above), that contains the actual reason the rule failed.

Thank you for your patience ! Antony

[nicolaavogel]

Hi Antony,

Happy new year to you, too! I should have closed this issue sooner. My apologies for that! I got everything to work two days before your answer. I am not 100% sure what the issue was, but when I created a new conda environment in a new directory, all the errors disappeared.

Anyways, thank you for your reply! All the best, Nicola