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biocore / qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
GNU General Public License v2.0
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SUMACLUST is launched with 1 thread in multi-thread mode #2160

Closed stevendbrown closed 8 years ago

stevendbrown commented 8 years ago

using QIIME 1.9.1, i launch pick_open_reference_otus.py with -aO 12 but sumaclust is invoked with the -p 1 option, ignoring the 12 threads specified by the -aO 12.

command used to start pick_open_reference_otus.py:

pick_open_reference_otus.py -i /Vonnegut/20160624_16S/merge_chunk_1/combined_seqs.fna,[...],/Murakami/20160624_16S_combined/merge_chunk_8/combined_seqs.fna -o /Vonnegut/20160624_16S/merged_8_picked_12threads_sortmerna/ -r /home/sdbrown/Downloads/gg_13_8_otus/rep_set/99_otus.fasta -m sortmerna_sumaclust -aO 12

process observed in htop with the -p 1 switch indicating 1 thread to sumaclust:

sumaclust -f -l -O /Vonnegut/20160624_16S/merged_8_picked_12threads_sortmerna/1/step4_otus/failures_failures_otus.txt -t 0.97 -p 1 -R 1 /tmp/SumaClustExactMatchFilterEQdWwD.fasta

i tried running pick_open_reference_otus.py with --threads 12 in addition to -aO 12 but that script throws an error that --threads is not a supported argument. i haven't tried with pick_otus.py.

apologies if i've misunderstood something deeper or more profound about the software.

gregcaporaso commented 8 years ago

@stevendbrown, sorry for the slow reply on this. Can you please post this question to the QIIME Forum? We try to address these types of technical support questions there, as it's then easier for others to find answers when they have the same questions. We also don't generally monitor the issue tracker for support questions, hence the very delayed reply on this. Thank you!