Warning: Could not calculate ungapped Karlin-Altschul parameters

[ghost]

Hello,
I'm running some Vitaceae transcriptome data with Arabidopsis as ref, I got warning as below:
Warning: lcl|Query_10114 AT3G08520: Warning: Could not calculate ungapped Karlin-Altschul parameters du query sequence or its translation. Please verify the query sequence(s) and/or filtering options
...

Warning: lcl|Query_24489 AT2G40205: Warning: Could not calculate ungapped Karlin-Altschul parameters du query sequence or its translation. Please verify the query sequence(s) and/or filtering options

How to fix it?

Thanks!

Miao

[vivekkrish]

Hello Miao,

Please do not worry about this warning! This message should not affect the execution of the pipeline itself. This is merely a warning stating that some statistics could not be computed due to the choice of BLAST parameters and sequence type.

Is your pipeline failing to produce any results?

If yes, please share with us the exact command that you used (and also a sample of your input files) and we can help test things out.

Thank you!

cc @srikarchamala

[ghost]

Hi there, Thanks for your responding! I think it’s not a big deal now (Maybe I tried different ref genomes may reduce such warnings? What do you think?). Because I went back to the reference genome sequences with specific gen number (e.g., AT3G08520) of warinngs, then I realized that it came from reference sequence itself, containing a lot of Ns (marked Intron region). And therefore any of those gene number has warnings will NOT appear in the result files. I pasted my investigation here, hoping will bring calm and peace for new users ☺ [cactus@gator4 Resources]$ cd Athaliana/ #went to MarkerMiner source code file and check my reference genome folder (here is Athaliana) [cactus@gator4 Athaliana]$ ls ath_CDS_IntronMasked.fa proteome.ath.tfa_db.phr proteome.ath.tfa_db.psq proteome.ath.tfa proteome.ath.tfa_db.pin singleCopy_AT.txt [cactus@gator4 Athaliana]$ grep -A1 AT3G08520 ath_CDS_IntronMasked.fa #sequence number “AT3G08520” had warning, so check then sequences

AT3G08520

ATGAGAGCCAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGGAAGAAGAAGCGTATGAGGAGATTGAAGAGGAAGAGACGAAAGATGAGACAGCGATCTAAGTAG Cheers, Miao From: Vivek Krishnakumar [mailto:[email protected]] Sent: Monday, July 10, 2017 3:02 PM To: vivekkrish/markerminer-webapp Cc: Sun,Miao; Author Subject: Re: [vivekkrish/markerminer-webapp] Warning: Could not calculate ungapped Karlin-Altschul parameters (#1) Hello Miao, Please do not worry about this warning! This message should not affect the execution of the pipeline itself. This is merely a warning stating that some statistics could not be computed due to the choice of BLAST parameters and sequence type. Is your pipeline failing to produce any results? If yes, please share with us the exact command that you used (and also a sample of your input files) and we can help test things out. Thank you! cc @srikarchamala<https://github.com/srikarchamala> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#1 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AUT0uB6LsVibj3-5mQKZi4io3lvjASC_ks5sMnUKgaJpZM4OSLUx>.