ngmlr: Parse error at line

Good morning,

I’m having an issue with alignment and subsequent sorting of files. My pipeline is: sequencing with MinION (Nanopore), basecalling and demultiplexing with Guppy, alignment with NGMLR, sorting with samtools. I’m using the latest version of all software.

The command for NGMLR is: ngmlr -t 8 -r human_hg19_mod.fa -q file.fastq -o output.bam -x ont

With this, I get: Done (3591 reads mapped (7.32%), 45467 reads not mapped, 49449 lines written)(elapsed: 1m, 51 r/s)

Then I run: samtools sort output.bam > sorted.bam

and get: [W::sam_read1] Parse error at line 10440 samtools sort: truncated file. Aborting

So my questions are: why is NGMLR mapping only 7.32% of reads? What is the problem with samtools sort?

Thank you, Marco

About this issue

Original URL
State: open
Created 4 years ago
Comments: 19 (4 by maintainers)

Most upvoted comments

I face similar issue when running this tutorial https://github.com/fenderglass/jax-meta-tutorial minimap2 -ax map-hifi assembly_graph.fasta SRR13128014_1gb.fastq.gz -t 30 | samtools sort > graph_alignment.bam samtools index graph_alignment.bam

Hi @skr3178, this is a recent recurring issue with samtools installed from bioconda and conflicting with other libraries (ncurses, openssl, …). A fix is to use a non-conda copy of samtools installed on your server (works here for me)

splaisan on Nov 3, 2022

Hi wdecoster,

From NGMLR help: -o <string>, --output <string> Adds RG:Z:<string> to all alignments in SAM/BAM

So I’m guessing NGMLR can output a .bam file?

Also, I used the very sam epipeline a lot in the past and didn’t get any error. The parse error appeared only after upgrading to samtools 1.10. After going back to samtools 1.9 the error disappeared.

So I’m guessing samtools 1.10 doesn’t like the output from NGMLR?

marcotoffoli on Feb 3, 2020