samtools sort stuck during merging

Hi !

I got a new computer recently and had to re-install samtools (version 1.5) and a few other programs. Now when I try to sort a bam file, everything goes well (samtools creates all those little intermediate files) until the merging process :

[bam_sort_core] merging from 58 files...

Then it gets stuck. I get no error message but the output file (sorted.bam) remains empty even if I wait hours. When I monitor the activity of samtools, I see that it is reading a lot, but not writing. Any idea on what is going on ?

In case this is useful, I'm on MacOS 10.12, 8 Go, 4 cores and I tried two different settings for sorting :

samtools sort in.bam > sorted.bam              # 1st setting
samtools sort -@ 4 -m 1G in.bam > sorted.bam   # 2d setting

samtools sort bamtools next-gen

• 4,320 views • link

written 9.1 years ago by Carlo Yague

Have you tried explicitly specifying the output file using the -o argument?

• 0 views • link

written 9.1 years ago by WouterDeCoster

Ok, I just tried that (I had little hope) but IT WORKED ! Thank you ! But WTF is going on ? samtools sort used to work perfectly well with stdout...

• 0 views • link

written 9.1 years ago by Carlo Yague

I would argue it's a bug. Definitely given that the manual states:

The sorted output is written to standard output by default, or to the specified file (out.bam) when -o is used.

• 0 views • link

written 9.1 years ago by WouterDeCoster

0 answers

No answers yet.

More posts like this

Rna Seq Analysis Script
written 4.2 years ago by SomeOne •

Hello Everyone, Recently I had to perform RNA-Seq analysis on multiple datasets taken from NCBI-SRA. So I thought of making a GENERAL bash script where …
samtools sort not working when using multiple threads
written 4.5 years ago by bio_elle •

I'm trying to use the -@ option on samtools sort to speed up the sorting of a file using multiple threads. Using this line samtools …
Using featureCounts on paired-end reads aligned with HISAT2 resulting in 0 assigned fragments
written 5.9 years ago by turo.1 •

I am attempting to do an RNA-seq analysis with 3 SRA files, using HISAT2 to align and then featureCount to quantify transcripts. Organism is Arabidopsis …
Error: All columns in a tibble must be 1d or 2d objects:
written 6.5 years ago by yueli7

Hello, I got following error. I was trying to run the software zUMIs-zUMIs.0.0.6. Really appreciate any help and suggestion! Best, Yue $ zUMIs-zUMIs.0.0.6/zUMIs-master.sh -f barcoderead_HEK.1mio.fq.gz …
Tutorial: Piping With Samtools, Bwa And Bedtools
written 14.3 years ago by Ying W

In this tutorial I will introduce some concepts related to [unix piping][1]. Piping is a very useful feature to avoid creation of intermediate use once …
Best Way To Preprocess Barcoded Illumina Paired-End Data
written 14.5 years ago by Ying W

<p>I know this topic has come up <a href='http://biostar.stackexchange.com/questions/1675/filtering-paired-end-reads'>many</a> <a href='http://biostar.stackexchange.com/questions/8791/paired-end-sequence-preprocessing-effects-on-downstream-processes'>times</a> <a href='http://biostar.stackexchange.com/questions/3081/multiplexed-pair-end-sequences-barcode-sorting'>before</a> but I wanted to get feedback on what people are doing now …