(MaSuRCA v4.1.0) polca.sh failed with SAMtools error "[bam_header_read] EOF marker is absent. The input is probably truncated."

[wanyuac]

Hi,
I noted this issue when upgrading MaSuRCA from v4.0.5 to v4.1.0. The genome assembly that could be polished with the same Illumina paired-end reads using v4.0.5 could no longer be polished with v4.1.0. I used BWA v0.7.17, which was installed in /home/wan/bin/bwa.

System settings

• Ubuntu 22.04.3 LTS (GNU/Linux 6.2.0-35-generic x86_64)
• gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu1~22.04)

Command line:

/home/wan/bin/MaSuRCA-4.1.0/bin/polca.sh -a sample.fna -r "sample_1.fastq.gz sample_2.fastq.gz" -t 8 -m 8G

Error message in samtools.err:

[bam_header_read] EOF marker is absent. The input is probably truncated.

Messages from stdout:

/home/wan/bin/bwa/bwa
/home/wan/bin/MaSuRCA-4.1.0/bin/freebayes
/home/wan/bin/MaSuRCA-4.1.0/bin/samtools
[Sat 11 Nov 13:03:11 GMT 2023] Creating BWA index for /scratch/assembly/sample.fna
[Sat 11 Nov 13:03:14 GMT 2023] Aligning reads to /scratch/assembly/sample.fna
[Sat 11 Nov 13:03:29 GMT 2023] Sorting and indexing alignment file
[Sat 11 Nov 13:03:47 GMT 2023] Calling variants in sample.fna
Processing 1 scaffold(s) per batch

Files generated from the failed run:

sample.fna.alignSorted.bam
sample.fna.alignSorted.bam.bai
sample.fna.batches
sample.fna.bwa.amb
sample.fna.bwa.ann
sample.fna.bwa.bwt
sample.fna.bwa.pac
sample.fna.bwa.sa
sample.fna.fix/
    1.names
    2.names
    3.names
    4.names
    commands.sh
sample.fna.index.success
sample.fna.map.success
sample.fna.names
sample.fna.sort.success
sample.fna.unSorted.sam
sample.fna.vc/
    1.vcf (VCF header lines were generated but there was no variant detected)
    1.vc.success
    sample.vc.success
    batch.1
commands.sh
sample.fna.vcf.body.tmp
sample.fna.vcf.header1
sample.fna.vcf.header2
bwa.err
samtools.err

I could polish this genome with the same short reads, command, and BWA using MaSuRCA v4.0.5. So I would be much grateful if anyone would help me with this issue.