Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • calctruequality in bbmap

    I'm trying to recalibrate Q scores of a NextSeq run using MiSeq contigs assembled with Tadpole. The commands I used to map the reads to the reference were as follows:

    >bbmap.sh in=concatABC.fastq.gz outm=mapped.sam ref=./Lpe09_06TdpAssemblies/contigs09_06.fa ignorequality maxindel=100 minratio=0.4 ambig=toss qahist=qahist_raw.txt qhist=qhist_raw.txt mhist=mhist_raw.txt

    The command I used to get the calibration matrices was:
    >calctruequality.sh in=mapped.sam

    I get the following output
    java -ea -Xmx57992m -Xms57992m -cp /home/me/bbmap/current/ jgi.CalcTrueQuality in=mapped.sam
    Executing jgi.CalcTrueQuality [in=mapped.sam]

    Exception in thread "Thread-2" Exception in thread "Thread-1" java.lang.AssertionError: TODO: Encountered a read with 'M' in cigar string but no MD tag and no ScafMap loaded.
    at stream.SamLine.toShortMatch(SamLine.java:1212)
    at stream.SamLine.toRead (SamLine.java:2015)
    at stream.SamLine.toRead (SamLine.java:1875)
    at stream.SamReadStreamer$ProcessThread.makeReads (SamReadStreamer.java:206)
    at stream.SamReadStreamer$ProcessThread.run (SamReadStreamer.java:135)
    java.lang.AssertionError: TODO: Encountered a read with 'M' in cigar string but no MD tag and no ScafMap loaded.
    at stream.SamLine.toShortMatch(SamLine.java:1212)
    at stream.SamLine.toRead (SamLine.java:2015)
    at stream.SamLine.toRead (SamLine.java:1875)
    at stream.SamReadStreamer$ProcessThread.makeReads (SamReadStreamer.java:206)
    at stream.SamReadStreamer$ProcessThread.run (SamReadStreamer.java:135)
    Exception in thread "Thread-3" java.lang.AssertionError: TODO: Encountered a read with 'M' in cigar string but no MD tag and no ScafMap loaded.
    at stream.SamLine.toShortMatch(SamLine.java:1212)
    at stream.SamLine.toRead (SamLine.java:2015)
    at stream.SamLine.toRead (SamLine.java:1875)
    at stream.SamReadStreamer$ProcessThread.makeReads (SamReadStreamer.java:206)
    at stream.SamReadStreamer$ProcessThread.run (SamReadStreamer.java:135)

    The program never quit so I don't know if it had stopped or was hanging but I let it sit there for over an hour. I didn't see /ref/qual/ files being generated. I'm not sure how to proceed. Since the mapped sam file was generated with bbmap using contigs from Tadpole, I'm not sure why there are Ms in the cigar strings. The infile I used for bbmap was made by first concatenating all Read1 from 3 libraries then all Read2 from 3 libraries then those two files concatenated.

Latest Articles

Collapse

  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM
  • seqadmin
    The Impact of AI in Genomic Medicine
    by seqadmin



    Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
    02-26-2024, 02:07 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-14-2024, 06:13 AM
0 responses
32 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-08-2024, 08:03 AM
0 responses
71 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-07-2024, 08:13 AM
0 responses
80 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-06-2024, 09:51 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X