Comments (3)
colinbrislawn
commented on August 19, 2024
Qiime is configured to uses swarm 1.2.19 followed by swarm_breaker.py. If qiime users are reporting this, the problem may be replicable in an older version of swarm.
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frederic-mahe
commented on August 19, 2024
I've tested the new version 1.2.21 and it works correctly on my computer (clustering results are unchanged). I've tried to compare the behavior of versions 1.2.20 and 1.2.21 on the oldest cluster nodes I could find (PowerEdge M605 Blade Server from 2009, AMD Opteron), but they both behave similarly, without any error messages. The next step is to ask the QIIME maintainers to point to a new release of swarm to see if it solves the SSE3 dependency problem reported by a few users.
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torognes
commented on August 19, 2024
We assume this is solved in version 1.2.21.
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Related Issues (20)
- Incorrect results with long sequences, very high gap penalties, and d>1 HOT 9
- Roadmap HOT 9
- table formats for making OTU table from swarm results HOT 2
- documentation: maximal input sequence length HOT 9
- Link to new swarm 3 paper HOT 3
- way too many clusters? HOT 7
- Issues with plotting: OTU not found HOT 3
- OTU table without abundance values HOT 6
- Compiling fails on Windows HOT 3
- maximal header length HOT 1
- uc file question HOT 7
- Invalid numeric argument for option -t or --threads HOT 8
- integer division might be one byte too small in some cases HOT 14
- Seeds not in same order as clusters in output files HOT 2
- Option to exclude seeds or clusters with low abundance HOT 1
- risk of silent 8-bit unsigned integer overflow in score matrix HOT 5
- fastidious boundary applies to the consolidated cluster mass? HOT 1
- Option to output cluster member ids/sequence id? HOT 3
- swarm terminates if any sequence in the input fasta file has an N HOT 2
- Refactor Bloom filter code
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