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No CIGAR result in one line of the output SAM #696

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luciaalvarez95 opened this issue Jan 12, 2021 · 4 comments
Open

No CIGAR result in one line of the output SAM #696

luciaalvarez95 opened this issue Jan 12, 2021 · 4 comments

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@luciaalvarez95
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Hello everyone,

I have used minimap2 to map nanopore reads to a genome assembly I want to improve. I used the following command:

minimap2 -ax map-ont ref.fa ont-reads.fq > aln.sam

Minimap2 works perfectly fine and ends with no error at all. However when I try to convert the sam file to a bam file, I can't because there is an error in line 1062685. Here is the line 1062685, it has no CIGAR results:

fdfaa6e3-ff51-4011-9391-2df5e44daff1 16 72697 3529726 60 14S201D18M2I7S * 0 0 AGTTACGTATTGC
The next line, the line 1062686 has CIGAR results:

a3000bed-6de4-425a-beb2-2c09ebf26d75 16 172 554179 60 21M1I22M1D11M2I10 * 0 0 ATTATCAGTCTTCT #'(''034%..)10?6?>=-;,&4447A- NM:i:2125 ms:i:52942 AS:i:52959 nn:i:10 tp:A:P cm:i:2990 s1:i:21512 s2:i:197 de:f:0.0492 rl:i:3723
I have no clue what is happening with that read, because it is mapped.

Many thanks for your help!

Lucía
@kullrich
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kullrich commented Feb 6, 2021

Here, more or less same problem.
I am using the wtdbg2.pl script to assemble 3G mouse genome, and samtools sort detects two problems:

  1. truncated read (missing "rl") tag on last column
  2. CIGAR length not equal to SEQUENCE length
    Command is:
    minimap2 -ax map-pb -t24 -r2k wtdbg2.raw.fa pacbio.fa
    Best regards
    Kristian

@lh3
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lh3 commented Feb 6, 2021

Do you have the sample sequences that trigger the issue?

@kullrich
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kullrich commented Feb 6, 2021

I will try to extract the lines and than the sequences, it is a rather large output file (60G)

@kullrich
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kullrich commented Feb 6, 2021

Hi, for me I could extract the sequences and repeat minimap2 on this smaller data set, now everything mapped correctly.
Maybe some issues with long multi-threaded runs or the input data which was produced with lordec pacbio polishing.
I will give feedback once resolved.

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@lh3 @kullrich @luciaalvarez95