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The meaning of the flag "ref_seq_choose_fail" #199

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IEkAdN opened this issue Oct 10, 2017 · 2 comments
Closed

The meaning of the flag "ref_seq_choose_fail" #199

IEkAdN opened this issue Oct 10, 2017 · 2 comments

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@IEkAdN
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IEkAdN commented Oct 10, 2017

Hello,

The document about the command flag describes the flag ref_seq_choose_fail as this is set to true if something went wrong when trying to find the closest reference sequence within a cluster. Could you please tell me what does something went wrong means? Does this indicate the case when the closest reference sequence does not belong to the cluster, which is described in the ARIBA paper?
@martinghunt
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It could happen for many reasons, including when the closest ref seq does not belong to the cluster. In that case, you should see 'Closest reference is XYZ and does not belong to cluster' in the log. Otherwise something else happened, eg there were no matches between the assembly and the reference for whatever reason (like a bad assembly with short contigs).

@IEkAdN
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IEkAdN commented Oct 11, 2017

Thank you for your quick response and detailed explanation.

@IEkAdN IEkAdN closed this as completed Oct 11, 2017
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@martinghunt @IEkAdN