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philres / ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
MIT License
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Error when converting sam file to bam #80

Closed Arfourie closed 4 years ago

Arfourie commented 4 years ago

Hi

I have seen others report a similar error, however their solutions have not helped me solve the problem. I did read mapping with ngmlr using my fasta genome file and mapping MinION reads to the genome, using the following command: ngmlr -t 4 --bam-fix -r Cmangi.fasta -q Cfim_Guppy.fastq -o CmanRef_CfimReads.sam -x ont After the run has completed I try to convert the file to bam using the following: samtools view -b -o CmanRef_CfimReads.bam CmanRef_CfimReads.sam. But I get the error: [W::sam_read1] Parse error at line 1914 [main_samview] truncated file. I am using samtools v 1.10. Is there a maximum read length that can be used or would this not be a problem? I also tried using another genome and other MinION sequence reads and I get the same error. If you could please provide any suggestions I would greatly appreciate it!

fritzsedlazeck commented 4 years ago

Sorry for the late reply. Can you make sure that NGMLR finished successfully ? Also (wont lead to this error) when you use samtools view you will need to add samtools view -hb to transfer the header over.

Thanks Fritz

Arfourie commented 4 years ago

Hi Fritz

Thank you, I managed to sort it out. The problem was the version of samtools, I had to revert to a previous version for samtools to convert the file from sam to bam successfully. Perhaps you could add a note to the users that they need to use samtools v1.9 and not a later version.

Kind regards Arista

On Thu, 11 Jun 2020 at 23:07, Fritz Sedlazeck notifications@github.com wrote:

Sorry for the late reply. Can you make sure that NGMLR finished successfully ? Also (wont lead to this error) when you use samtools view you will need to add samtools view -hb to transfer the header over.

Thanks Fritz

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fritzsedlazeck commented 4 years ago

Thanks for letting me know. Cheers Fritz