get-reads-alt-unmap.sh get "[bwt_restore_sa] SA-BWT inconsistency: primary is not the same. Abort!"

[yubau1112]

Hi,

1.I used

NCBI Human Genome Resources Reference Genome Sequence https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/

GRCh38 GRCh38_latest_genomic.fna.gz fasta file ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.fna.gz

as BWA Reference Genome
instruction : bwa index ref.fa

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1188

than I used BWA to do sequence alignment (my HLA NGS data fastq is pair-end)
instruction : bwa mem ref.fa read1.fq read2.fq > aln-pe.sam

than used samtools to sort and Index

instruction :
samtools view -b -S aln-pe.sam > aln-pe.bam
samtools sort -m 4096M -o aln-pe.sorted.sam -@ 12 aln-pe.sam
samtools index aln-pe.sorted.sam

samtools --version
samtools 1.9
Using htslib 1.9
Copyright (C) 2018 Genome Research Ltd.

than used xHLA bin/get-reads-alt-unmap.sh to convert bam file, but I get results like follow messages:

[yubau@CNUH-i7 bin]$ get-reads-alt-unmap.sh aln-pe.sorted.bam aln-pe.sorted_xHLA_getreasds.sam
NCORE=12 MEM=187GB

sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018
LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)
sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018
LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)

[ ]Writing sorted chunks to temporary directory...
[=======================================================================================================================================]=========]
*****WARNING: Query M04622:111:000000000-G3CWM:1:1101:12467:2013 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.
*****WARNING: Query M04622:111:000000000-G3CWM:1:1101:13761:14426 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.
*****WARNING: Query M04622:111:000000000-G3CWM:1:1101:17424:18089 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.

[==============================================================================]
*****WARNING: Query M04622:111:000000000-G3CWM:1:2103:7820:5734 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.
*****WARNING: Query M04622:111:000000000-G3CWM:1:2103:9073:15589 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.
[bwt_restore_sa] SA-BWT inconsistency: primary is not the same. Abort!

sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018
LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)

/local_work/bin/xHLA/bin/get-reads-alt-unmap.sh: line 43: 46328 Aborted (core dumped) /local_work/bin/bwa-0.7.17/bwa mem -t $NCORE "$BIN/../data/chr6/hg38.chr6.fna" "${OUT}.1.fq" "${OUT}.2.fq"
46329 Done | /local_work/bin/samtools-1.9/samtools view -b -
46330 Done | /local_work/bin/xHLA/bin/sambamba sort -m $MEM -t $NCORE -o "${OUT}.full.bam" /dev/stdin

---

2. what is "[bwt_restore_sa] SA-BWT inconsistency: primary is not the same. Abort!" mean?

3.what is "*****WARNING: Query M04622:111:000000000-G3CWM:1:1101:12467:2013 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping." mean?

thanks for your time!

[tmhmxg59]

I think

[bwt_restore_sa] SA-BWT inconsistency: primary is not the same. Abort!

is your main issue. I think this is because you are missing .fna and/or proper bwa index.

[yubau1112]

I think

[bwt_restore_sa] SA-BWT inconsistency: primary is not the same. Abort!

is your main issue. I think this is because you are missing .fna and/or proper bwa index.

Hi, @tmhmxg59 thanks your reply
yes, I think so

/local_work/bin/bwa-0.7.17/bwa mem -t $NCORE "$BIN/../data/chr6/hg38.chr6.fna" "${OUT}.1.fq" "${OUT}.2.fq" | /local_work/bin/samtools-1.9/samtools view -b - | /local_work/bin/xHLA/bin/sambamba sort -m $MEM -t $NCORE -o "${OUT}.full.bam" /dev/stdin

$BIN/../data/chr6/hg38.chr6.fna

xHLA does not provide hg38.chr6.fna file

so this hg38.chr6.fna file require download by myself?

I used iGeome provided human chromosome 6 reference

https://support.illumina.com/sequencing/sequencing_software/igenome.html

ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/NCBI/GRCh38/Homo_sapiens_NCBI_GRCh38.tar.gz

And used bwa index human chromosome 6 reference

And then change get-reads-alt-unmap.sh file bwa reference path.

/local_work/bin/bwa-0.7.17/bwa mem -t $NCORE "/home/yubau/human_reference_genome/BWAIndex_CHR6/chr6.fa" "${OUT}.1.fq" "${OUT}.2.fq" | /local_work/bin/samtools-1.9/samtools view -b - | /local_work/bin/xHLA/bin/sambamba sort -m $MEM -t $NCORE -o "${OUT}.full.bam" /dev/stdin

Can work! results like the following message:

[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 20378 sequences (3058734 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 6867, 0, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (144, 184, 235)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 417)
[M::mem_pestat] mean and std.dev: (193.09, 68.00)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 508)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 20378 reads in 6.224 CPU sec, 0.528 real sec
[main] Version: 0.7.17-r1188
[main] CMD: /local_work/bin/bwa-0.7.17/bwa mem -t 12 /home/yubau/human_reference_genome/BWAIndex_CHR6/chr6.fa /home/yubau/HLA-B16_S14_BWAmem.sort.xHLA.bam.1.fq /home/yubau/HLA-B16_S14_BWAmem.sort.xHLA.bam.2.fq
[main] Real time: 1.187 sec; CPU: 6.462 sec

but still get WARNING like

*****WARNING: Query M04622:111:000000000-G3CWM:1:2103:7820:5734 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.

[tmhmxg59]

I get those warnings too. I'm not sure if they are significant or not. I tried resorting and removing unpaired reads (not sure if I was successful), but the warnings still appeared. It didn't seem to affect the outcome.

[AskPascal]

I got the [bwt_restore_sa] SA-BWT inconsistency: primary is not the same. Abort! error message too and figured out that my problem was that the docker container on https://hub.docker.com/r/humanlongevity/hla does not contain the full reference set for bwa, the file hg38.chr6.fna.bwt was truncated. Also the image contains an outdated version of the reads-alt-unmap.sh script.

Since I needed a singularity image for the cluster I am working at I converted the docker container to singularity and updated the two files in the process. Here is the singularity recipe I used:
xHLA.srecipe.txt