Uncaught exception: Invalid_argument("combine: Different_list_size")

[Ge BoRo]

Hello,

pplacer is breaking with error "Fatal error: exception Invalid_argument("combine: Different_list_size")", after the following output:

Running pplacer v1.1.alpha19-0-g807f6f3 analysis on /scratch/beegfs/monthly/monthly/mls_2017/community_analysis11/Ref_tree/raxml/taxtastic/allreads.alignd_trimmed.fasta...
Found reference sequences in given alignment file. Using those for reference alignment.
found in reference alignment: 
[|R001; R002; R003; R004; R005; R006; R007; R010; R011; R012; R013; R014; 
R015; R016; R017; R018; R019; R020; R021; R022; R026; R030; R031; R032; 
R033; R034; R035; R037; R038; R039; R040; R041; R042; R043; R045; R052; 
R053; R055; R062; R069; R070; R072; R074; R079; R081; R083; R084; R086; 
R088; R093; R094; R098; R099; R100; R102; R103; R104; R106; R107; R108; 
R112; R113; R116; R117; R121; R122; R123; R124; R127; R129; R130; R137; 
R139; R140; R141; R142; R143; R144; R145; R149; R150; R151; R154; R156; 
R159; R161; R163; R167; R168; R170; R172; R173; R175; R176; R177; R178; 
R179; R180; R181; R182; R183; R184; R185; R186; R189; R200; R201; R202; 
R203; R204; R205; R207; R208; R210; R211; R213; R214; R215; R216; R217; 
R193; R194; R195; R218; R219; R220; R221; R222; R223; R224; R225; R226; 
R227; R228; R229; R230; R231; R232; R233; R235; R236; R237; R238; R239; 
R240; R241; R242; R243; R244; R249; R250; R252; R258; R259; R263; R264; 
R265; R266; R272; R276; R279; R280; R281; R282; R251; R245; R246; R247; 
R248; R283; R289; R291; R294; R295; R296; R297; R298; R302; R305; R308; 
R310; R311; R312; R314; R315; R316; R320; R321; R327; R328; R339; R340; 
R342; R346; R348; R349; R353; R354; R357; R363; R364; R365; R366; R372; 
R381; R383; R384; R386; R393; R394; R395; R396; R397; R398; R399; R400; 
R401; R404; R405; R406; R407; R410; R411; R412; R413; R414; R415; R416; 
R420; R423; R424; R425|]
emper freqs: {0.257694390376; 0.200676140438; 0.340177669803; 0.201451799382}
Pre-masking sequences... sequence length cut from 1142 to 314.
Determining figs... figs disabled.
Allocating memory for internal nodes... done.
nucleotide model
stat distn:
{0.257694390376; 0.200676140438; 0.340177669803; 0.201451799382}
site rates:
[|0.136953782645; 0.476751856235; 1.; 2.38629436112|]
Caching likelihood information on reference tree... done.
Pulling exponents... done.
Preparing the edges for baseball... done.

I have completely removed duplicates from the reference alignment using seqmagick, which seemed to be the problem in another post. 

Those are the sequence identifiers in my reference alignment as well.

Any idea why this could mean?

I am attaching my refpkg as well. 

Thanks in advance!

[Erick Matsen]

Haven't seen that before. Could you send on a minimal file of query sequences that makes an error?

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Frederick "Erick" Matsen, Associate Member
Fred Hutchinson Cancer Research Center
http://matsen.fredhutch.org/

[Ge BoRo]

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Frederick "Erick" Matsen, Associate Member
Fred Hutchinson Cancer Research Center
http://matsen.fredhutch.org/

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[Ge BoRo]

Here it is, only 1000 sequences and it fails with the same error.

Thanks!

[Erick Matsen]

There are some strange things with your files, e.g. that query file has "no comment" at the end of the reference sequences, and the number of "R" sequences in your query file differs from that of the fasta file in the refpkg. 

I haven't the time to really look into this, but if you clean things up and do some checks I bet you'll find the problem. 

Sorry for the uninformative error message.

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Frederick "Erick" Matsen, Associate Member
Fred Hutchinson Cancer Research Center
http://matsen.fredhutch.org/

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